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"vert_dist": 3.289 }, { "index": 59, "type": "sugar", "atom": "///A/846/O4'", "nt": "///A/845", "vert_dist": 3.050 }, { "index": 60, "type": "sugar", "atom": "///A/868/O4'", "nt": "///A/873", "vert_dist": 3.310 }, { "index": 61, "type": "sugar", "atom": "///A/22/O2'", "nt": "///A/885", "vert_dist": 3.282 }, { "index": 62, "type": "sugar", "atom": "///A/23/O4'", "nt": "///A/913", "vert_dist": 3.341 }, { "index": 63, "type": "sugar", "atom": "///A/916/O4'", "nt": "///A/915", "vert_dist": 3.189 }, { "index": 64, "type": "sugar", "atom": "///A/922/O2'", "nt": "///A/923", "vert_dist": 2.915 }, { "index": 65, "type": "sugar", "atom": "///A/15/O4'", "nt": "///A/1397", "vert_dist": 2.811 }, { "index": 66, "type": "phosphate", "atom": "///A/1503/OP1", "nt": "///A/1503", "vert_dist": 3.395 }, { "index": 67, "type": "sugar", "atom": "///A/1505/O2'", "nt": "///A/1506", "vert_dist": 3.050 } ], "num_hairpins": 22, "hairpins": [ { "index": 1, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ 1 ], "summary": "[1] 11 [A.11 A.23] 3", "num_nts": 13, "nts_short": "GUUUGAUCAUGGC", "nts_long": "///A/11,///A/12,///A/13,///A/14,///A/15,///A/16,///A/17,///A/18,///A/19,///A/20,///A/21,///A/22,///A/23", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "UUUGAUCAUGG", "nts_long": "///A/12,///A/13,///A/14,///A/15,///A/16,///A/17,///A/18,///A/19,///A/20,///A/21,///A/22" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 13 ], "summary": "[1] 4 [A.82 A.87] 6", "num_nts": 6, "nts_short": "GCUUGC", "nts_long": "///A/82,///A/83,///A/84,///A/85,///A/86,///A/87", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUUG", "nts_long": "///A/83,///A/84,///A/85,///A/86" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ -3 ], "summary": "[1] 4 [A.158 A.163] 1", "num_nts": 6, "nts_short": "GGAAAC", "nts_long": "///A/158,///A/159,///A/160,///A/161,///A/162,///A/163", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/159,///A/160,///A/161,///A/162" } ] }, { "index": 4, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 20 ], "summary": "[1] 4 [A.186 A.191] 3", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///A/186,///A/187,///A/188,///A/189,///A/190,///A/191", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/187,///A/188,///A/189,///A/190" } ] }, { "index": 5, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 22 ], "summary": "[1] 4 [A.207 A.212] 2", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///A/207,///A/208,///A/209,///A/210,///A/211,///A/212", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///A/208,///A/209,///A/210,///A/211" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 25 ], "summary": "[1] 7 [A.259 A.267] 8", "num_nts": 9, "nts_short": "GGUAACGGC", "nts_long": "///A/259,///A/260,///A/261,///A/262,///A/263,///A/264,///A/265,///A/266,///A/267", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUAACGG", "nts_long": "///A/260,///A/261,///A/262,///A/263,///A/264,///A/265,///A/266" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 27 ], "summary": "[1] 4 [A.296 A.301] 4", "num_nts": 6, "nts_short": "UGAGAG", "nts_long": "///A/296,///A/297,///A/298,///A/299,///A/300,///A/301", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAGA", "nts_long": "///A/297,///A/298,///A/299,///A/300" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 12 ], "stem_indices": [ 28 ], "summary": "[1] 12 [A.320 A.333] 5", "num_nts": 14, "nts_short": "AACUGAGACACGGU", "nts_long": "///A/320,///A/321,///A/322,///A/323,///A/324,///A/325,///A/326,///A/327,///A/328,///A/329,///A/330,///A/331,///A/332,///A/333", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 12, "nts_short": "ACUGAGACACGG", "nts_long": "///A/321,///A/322,///A/323,///A/324,///A/325,///A/326,///A/327,///A/328,///A/329,///A/330,///A/331,///A/332" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 29 ], "summary": "[1] 4 [A.342 A.347] 4", "num_nts": 6, "nts_short": "CUACGG", "nts_long": "///A/342,///A/343,///A/344,///A/345,///A/346,///A/347", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UACG", "nts_long": "///A/343,///A/344,///A/345,///A/346" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 31 ], "summary": "[1] 4 [A.379 A.384] 4", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///A/379,///A/380,///A/381,///A/382,///A/383,///A/384", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/380,///A/381,///A/382,///A/383" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 33 ], "summary": "[1] 4 [A.419 A.424] 4", "num_nts": 6, "nts_short": "CUUCGG", "nts_long": "///A/419,///A/420,///A/421,///A/422,///A/423,///A/424", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///A/420,///A/421,///A/422,///A/423" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ -10 ], "summary": "[1] 7 [A.462 A.470] 1", "num_nts": 9, "nts_short": "GUUAAUACC", "nts_long": "///A/462,///A/463,///A/464,///A/465,///A/466,///A/467,///A/468,///A/469,///A/470", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UUAAUAC", "nts_long": "///A/463,///A/464,///A/465,///A/466,///A/467,///A/468,///A/469" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 16 ], "stem_indices": [ 38 ], "summary": "[1] 16 [A.507 A.524] 3", "num_nts": 18, "nts_short": "CUAACUCCGUGCCAGCAG", "nts_long": "///A/507,///A/508,///A/509,///A/510,///A/511,///A/512,///A/513,///A/514,///A/515,///A/516,///A/517,///A/518,///A/519,///A/520,///A/521,///A/522,///A/523,///A/524", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 16, "nts_short": "UAACUCCGUGCCAGCA", "nts_long": "///A/508,///A/509,///A/510,///A/511,///A/512,///A/513,///A/514,///A/515,///A/516,///A/517,///A/518,///A/519,///A/520,///A/521,///A/522,///A/523" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 40 ], "summary": "[1] 4 [A.522 A.527] 2", "num_nts": 6, "nts_short": "CAGCCG", "nts_long": "///A/522,///A/523,///A/524,///A/525,///A/526,///A/527", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGCC", "nts_long": "///A/523,///A/524,///A/525,///A/526" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 48 ], "summary": "[1] 5 [A.617 A.623] 6", "num_nts": 7, "nts_short": "GCUCAAC", "nts_long": "///A/617,///A/618,///A/619,///A/620,///A/621,///A/622,///A/623", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CUCAA", "nts_long": "///A/618,///A/619,///A/620,///A/621,///A/622" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 53 ], "summary": "[1] 8 [A.689 A.698] 2", "num_nts": 10, "nts_short": "CGGUGAAAUG", "nts_long": "///A/689,///A/690,///A/691,///A/692,///A/693,///A/694,///A/695,///A/696,///A/697,///A/698", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GGUGAAAU", "nts_long": "///A/690,///A/691,///A/692,///A/693,///A/694,///A/695,///A/696,///A/697" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 54 ], "summary": "[1] 4 [A.726 A.731] 2", "num_nts": 6, "nts_short": "CGAAGG", "nts_long": "///A/726,///A/727,///A/728,///A/729,///A/730,///A/731", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAG", "nts_long": "///A/727,///A/728,///A/729,///A/730" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 56 ], "summary": "[1] 9 [A.786 A.796] 4", "num_nts": 11, "nts_short": "GAUUAGAUACC", "nts_long": "///A/786,///A/787,///A/788,///A/789,///A/790,///A/791,///A/792,///A/793,///A/794,///A/795,///A/796", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AUUAGAUAC", "nts_long": "///A/787,///A/788,///A/789,///A/790,///A/791,///A/792,///A/793,///A/794,///A/795" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 59 ], "summary": "[1] 5 [A.840 A.846] 3", "num_nts": 7, "nts_short": "CCUUGAG", "nts_long": "///A/840,///A/841,///A/842,///A/843,///A/844,///A/845,///A/846", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "CUUGA", "nts_long": "///A/841,///A/842,///A/843,///A/844,///A/845" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 60 ], "summary": "[1] 4 [A.862 A.867] 2", "num_nts": 6, "nts_short": "CUAACG", "nts_long": "///A/862,///A/863,///A/864,///A/865,///A/866,///A/867", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UAAC", "nts_long": "///A/863,///A/864,///A/865,///A/866" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 62 ], "summary": "[1] 4 [A.897 A.902] 4", "num_nts": 6, "nts_short": "CGCAAG", "nts_long": "///A/897,///A/898,///A/899,///A/900,///A/901,///A/902", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/898,///A/899,///A/900,///A/901" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 65 ], "summary": "[1] 4 [A.1515 A.1520] 9", "num_nts": 6, "nts_short": "GGGAAC", "nts_long": "///A/1515,///A/1516,///A/1517,///A/1518,///A/1519,///A/1520", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGAA", "nts_long": "///A/1516,///A/1517,///A/1518,///A/1519" } ] } ], 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"///A/388" } ] }, { "index": 6, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -8, -9 ], "summary": "[2] 0 1 [A.459 A.473 A.460 A.471] 1 1", "num_nts": 5, "nts_short": "AAUUU", "nts_long": "///A/459,///A/460,///A/471,///A/472,///A/473", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///A/472" } ] }, { "index": 7, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -9, -10 ], "summary": "[2] 1 0 [A.460 A.471 A.462 A.470] 1 1", "num_nts": 5, "nts_short": "AAGCU", "nts_long": "///A/460,///A/461,///A/462,///A/470,///A/471", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/461" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 8, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 45, 46 ], "summary": "[2] 1 0 [A.594 A.645 A.596 A.644] 7 2", "num_nts": 5, "nts_short": "UAAUG", "nts_long": "///A/594,///A/595,///A/596,///A/644,///A/645", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/595" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 9, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ 49, 50 ], "summary": "[2] 0 1 [A.658 A.748 A.659 A.746] 4 4", "num_nts": 5, "nts_short": "CUAAG", "nts_long": "///A/658,///A/659,///A/746,///A/747,///A/748", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/747" } ] }, { "index": 10, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 52, -14 ], "summary": "[2] 1 0 [A.681 A.709 A.683 A.708] 4 1", "num_nts": 5, "nts_short": "AGGCU", "nts_long": "///A/681,///A/682,///A/683,///A/708,///A/709", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/682" }, { "index": 2, "num_nts": 0, 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A.178 A.146 A.176] 1 2", "num_nts": 6, "nts_short": "GGGCGC", "nts_long": "///A/144,///A/145,///A/146,///A/176,///A/177,///A/178", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/145" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/177" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 19, -3 ], "summary": "[2] 1 1 [A.156 A.165 A.158 A.163] 4 1", "num_nts": 6, "nts_short": "CUGCGG", "nts_long": "///A/156,///A/157,///A/158,///A/163,///A/164,///A/165", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/157" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/164" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -7, 36 ], "summary": "[2] 1 1 [A.453 A.479 A.455 A.477] 1 3", "num_nts": 6, "nts_short": "GGGCAU", "nts_long": "///A/453,///A/454,///A/455,///A/477,///A/478,///A/479", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/454" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/478" } ] }, { "index": 4, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 36, -8 ], "summary": "[2] 1 1 [A.457 A.475 A.459 A.473] 3 1", "num_nts": 6, "nts_short": "GUAUGC", "nts_long": "///A/457,///A/458,///A/459,///A/473,///A/474,///A/475", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///A/458" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/474" } ] }, { "index": 5, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 10, 11 ], "summary": "[2] 1 2 [A.67 A.102 A.69 A.99] 2 2", "num_nts": 7, "nts_short": "CGGCGAG", "nts_long": "///A/67,///A/68,///A/69,///A/99,///A/100,///A/101,///A/102", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/68" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/100,///A/101" } ] }, { "index": 6, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ 12, 13 ], "summary": "[2] 1 2 [A.75 A.95 A.77 A.92] 3 6", "num_nts": 7, "nts_short": "GGAUUGC", "nts_long": "///A/75,///A/76,///A/77,///A/92,///A/93,///A/94,///A/95", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/76" }, { "index": 2, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/93,///A/94" } ] }, { "index": 7, "type": "asymmetric internal loop", "bridging_nts": [ 2, 1 ], "stem_indices": [ 15, 16 ], "summary": "[2] 2 1 [A.128 A.233 A.131 A.231] 7 2", "num_nts": 7, "nts_short": "GAAAUGC", "nts_long": "///A/128,///A/129,///A/130,///A/131,///A/231,///A/232,///A/233", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/129,///A/130" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/232" } ] }, { "index": 8, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 58, 59 ], "summary": "[2] 2 2 [A.835 A.851 A.838 A.848] 7 3", "num_nts": 8, "nts_short": "UGUGCGUG", "nts_long": "///A/835,///A/836,///A/837,///A/838,///A/848,///A/849,///A/850,///A/851", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/836,///A/837" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/849,///A/850" } ] }, { "index": 9, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ -1, 7 ], "summary": "[2] 4 1 [A.47 A.361 A.52 A.359] 1 3", "num_nts": 9, "nts_short": "CCUAACGGG", "nts_long": "///A/47,///A/48,///A/49,///A/50,///A/51,///A/52,///A/359,///A/360,///A/361", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///A/48,///A/49,///A/50,///A/51" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///A/360" } ] }, { "index": 10, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 16, 17 ], "summary": "[2] 3 2 [A.132 A.230 A.136 A.227] 2 7", "num_nts": 9, "nts_short": "CUGCCGAUG", "nts_long": "///A/132,///A/133,///A/134,///A/135,///A/136,///A/227,///A/228,///A/229,///A/230", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGC", "nts_long": "///A/133,///A/134,///A/135" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/228,///A/229" } ] }, { "index": 11, "type": "asymmetric internal loop", "bridging_nts": [ 1, 4 ], "stem_indices": [ 34, 35 ], "summary": "[2] 1 4 [A.440 A.497 A.442 A.492] 2 5", "num_nts": 9, "nts_short": "CAGCAGAAG", "nts_long": "///A/440,///A/441,///A/442,///A/492,///A/493,///A/494,///A/495,///A/496,///A/497", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/441" }, { "index": 2, "num_nts": 4, "nts_short": "AGAA", "nts_long": "///A/493,///A/494,///A/495,///A/496" } ] }, { "index": 12, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ -6, -7 ], "summary": "[2] 2 3 [A.450 A.483 A.453 A.479] 1 1", "num_nts": 9, "nts_short": "GAAGUUGAC", "nts_long": "///A/450,///A/451,///A/452,///A/453,///A/479,///A/480,///A/481,///A/482,///A/483", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/451,///A/452" }, { "index": 2, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/480,///A/481,///A/482" } ] }, { "index": 13, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ 50, 51 ], "summary": "[2] 3 2 [A.662 A.743 A.666 A.740] 4 5", "num_nts": 9, "nts_short": "UAGAGUGGA", "nts_long": "///A/662,///A/663,///A/664,///A/665,///A/666,///A/740,///A/741,///A/742,///A/743", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AGA", "nts_long": "///A/663,///A/664,///A/665" }, { "index": 2, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/741,///A/742" } ] }, { "index": 14, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 43, 44 ], "summary": "[2] 3 3 [A.580 A.761 A.584 A.757] 4 3", "num_nts": 10, "nts_short": "CGCAGUCAGG", "nts_long": "///A/580,///A/581,///A/582,///A/583,///A/584,///A/757,///A/758,///A/759,///A/760,///A/761", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GCA", "nts_long": "///A/581,///A/582,///A/583" }, { "index": 2, "num_nts": 3, "nts_short": "CAG", "nts_long": "///A/758,///A/759,///A/760" } ] }, { "index": 15, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ 35, -6 ], "summary": "[2] 3 4 [A.446 A.488 A.450 A.483] 5 1", "num_nts": 11, "nts_short": "GGAGGCGUUAC", "nts_long": "///A/446,///A/447,///A/448,///A/449,///A/450,///A/483,///A/484,///A/485,///A/486,///A/487,///A/488", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAG", "nts_long": "///A/447,///A/448,///A/449" }, { "index": 2, "num_nts": 4, "nts_short": "GUUA", "nts_long": "///A/484,///A/485,///A/486,///A/487" } ] }, { "index": 16, "type": "symmetric internal loop", "bridging_nts": [ 4, 4 ], "stem_indices": [ -13, 52 ], "summary": "[2] 4 4 [A.673 A.717 A.678 A.712] 1 4", "num_nts": 12, "nts_short": "AGAAUUAGGAAU", "nts_long": "///A/673,///A/674,///A/675,///A/676,///A/677,///A/678,///A/712,///A/713,///A/714,///A/715,///A/716,///A/717", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAU", "nts_long": "///A/674,///A/675,///A/676,///A/677" }, { "index": 2, "num_nts": 4, "nts_short": "GGAA", "nts_long": "///A/713,///A/714,///A/715,///A/716" } ] }, { "index": 17, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ -15, 53 ], "summary": "[2] 3 6 [A.684 A.706 A.688 A.699] 1 2", "num_nts": 13, "nts_short": "UGUAGCGUAGAGA", "nts_long": "///A/684,///A/685,///A/686,///A/687,///A/688,///A/699,///A/700,///A/701,///A/702,///A/703,///A/704,///A/705,///A/706", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GUA", "nts_long": "///A/685,///A/686,///A/687" }, { "index": 2, "num_nts": 6, "nts_short": "GUAGAG", "nts_long": "///A/700,///A/701,///A/702,///A/703,///A/704,///A/705" } ] }, { "index": 18, "type": "asymmetric internal loop", "bridging_nts": [ 4, 6 ], "stem_indices": [ 23, 24 ], "summary": "[2] 4 6 [A.242 A.284 A.247 A.277] 3 3 k-turn:normal", "num_nts": 14, "nts_short": "GAUUAGCGACGAUC", "nts_long": "///A/242,///A/243,///A/244,///A/245,///A/246,///A/247,///A/277,///A/278,///A/279,///A/280,///A/281,///A/282,///A/283,///A/284", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUUA", "nts_long": "///A/243,///A/244,///A/245,///A/246" }, { "index": 2, "num_nts": 6, "nts_short": "GACGAU", "nts_long": "///A/278,///A/279,///A/280,///A/281,///A/282,///A/283" } ] }, { "index": 19, "type": "asymmetric internal loop", "bridging_nts": [ 6, 4 ], "stem_indices": [ 47, 48 ], "summary": "[2] 6 4 [A.605 A.633 A.612 A.628] 8 6", "num_nts": 14, "nts_short": "UGAAAUCCGAACUG", "nts_long": "///A/605,///A/606,///A/607,///A/608,///A/609,///A/610,///A/611,///A/612,///A/628,///A/629,///A/630,///A/631,///A/632,///A/633", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAAAUC", "nts_long": "///A/606,///A/607,///A/608,///A/609,///A/610,///A/611" }, { "index": 2, "num_nts": 4, "nts_short": "AACU", "nts_long": "///A/629,///A/630,///A/631,///A/632" } ] }, { "index": 20, "type": "asymmetric internal loop", "bridging_nts": [ 6, 4 ], "stem_indices": [ 61, 62 ], "summary": "[2] 6 4 [A.887 A.910 A.894 A.905] 3 4", "num_nts": 14, "nts_short": "GGAGUACGUAAAAC", "nts_long": "///A/887,///A/888,///A/889,///A/890,///A/891,///A/892,///A/893,///A/894,///A/905,///A/906,///A/907,///A/908,///A/909,///A/910", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAGUAC", "nts_long": "///A/888,///A/889,///A/890,///A/891,///A/892,///A/893" }, { "index": 2, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///A/906,///A/907,///A/908,///A/909" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ 63, 64 ], "summary": "[2] 5 5 [A.922 A.1395 A.928 A.1389] 2 2", "num_nts": 14, "nts_short": "GACGGGGCUUGUAC", "nts_long": "///A/922,///A/923,///A/924,///A/925,///A/926,///A/927,///A/928,///A/1389,///A/1390,///A/1391,///A/1392,///A/1393,///A/1394,///A/1395", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "ACGGG", "nts_long": "///A/923,///A/924,///A/925,///A/926,///A/927" }, { "index": 2, "num_nts": 5, "nts_short": "UUGUA", "nts_long": "///A/1390,///A/1391,///A/1392,///A/1393,///A/1394" } ] }, { "index": 22, "type": "asymmetric internal loop", "bridging_nts": [ 5, 6 ], "stem_indices": [ 18, 19 ], "summary": "[2] 5 6 [A.147 A.175 A.153 A.168] 2 4", "num_nts": 15, "nts_short": "GGAUAACGCUAAUAC", "nts_long": "///A/147,///A/148,///A/149,///A/150,///A/151,///A/152,///A/153,///A/168,///A/169,///A/170,///A/171,///A/172,///A/173,///A/174,///A/175", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUAA", "nts_long": "///A/148,///A/149,///A/150,///A/151,///A/152" }, { "index": 2, "num_nts": 6, "nts_short": "CUAAUA", "nts_long": "///A/169,///A/170,///A/171,///A/172,///A/173,///A/174" } ] }, { "index": 23, "type": "asymmetric internal loop", "bridging_nts": [ 6, 5 ], "stem_indices": [ 32, 33 ], "summary": "[2] 6 5 [A.409 A.433 A.416 A.427] 4 4 k-turn:undecided", "num_nts": 15, "nts_short": "UGAAGAAGUGUAAAG", "nts_long": "///A/409,///A/410,///A/411,///A/412,///A/413,///A/414,///A/415,///A/416,///A/427,///A/428,///A/429,///A/430,///A/431,///A/432,///A/433", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAAGAA", "nts_long": "///A/410,///A/411,///A/412,///A/413,///A/414,///A/415" }, { "index": 2, "num_nts": 5, "nts_short": "GUAAA", "nts_long": "///A/428,///A/429,///A/430,///A/431,///A/432" } ] }, { "index": 24, "type": "asymmetric internal loop", "bridging_nts": [ 5, 7 ], "stem_indices": [ 39, 40 ], "summary": "[2] 5 7 [A.515 A.536 A.521 A.528] 5 2 k-turn:normal", "num_nts": 16, "nts_short": "GUGCCAGCGGUAAUAC", "nts_long": "///A/515,///A/516,///A/517,///A/518,///A/519,///A/520,///A/521,///A/528,///A/529,///A/530,///A/531,///A/532,///A/533,///A/534,///A/535,///A/536", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGCCA", "nts_long": "///A/516,///A/517,///A/518,///A/519,///A/520" }, { "index": 2, "num_nts": 7, "nts_short": "GGUAAUA", "nts_long": "///A/529,///A/530,///A/531,///A/532,///A/533,///A/534,///A/535" } ] }, { "index": 25, "type": "asymmetric internal loop", "bridging_nts": [ 8, 5 ], "stem_indices": [ 55, 56 ], "summary": "[2] 8 5 [A.774 A.805 A.783 A.799] 6 4", "num_nts": 17, "nts_short": "GGGAGCAAACGGUAGUC", "nts_long": "///A/774,///A/775,///A/776,///A/777,///A/778,///A/779,///A/780,///A/781,///A/782,///A/783,///A/799,///A/800,///A/801,///A/802,///A/803,///A/804,///A/805", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GGAGCAAA", "nts_long": "///A/775,///A/776,///A/777,///A/778,///A/779,///A/780,///A/781,///A/782" }, { "index": 2, "num_nts": 5, "nts_short": "GUAGU", "nts_long": "///A/800,///A/801,///A/802,///A/803,///A/804" } ] } ], "num_junctions": 10, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 1, 2, 0 ], "stem_indices": [ 44, 45, -12 ], "summary": "[3] 1 2 0 [A.586 A.755 A.588 A.651 A.654 A.754] 3 7 1", "num_nts": 9, "nts_short": "CGGCUUGCG", "nts_long": "///A/586,///A/587,///A/588,///A/651,///A/652,///A/653,///A/654,///A/754,///A/755", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/587" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/652,///A/653" }, { "index": 3, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 0, 5, 1 ], "stem_indices": [ 6, -1, -4 ], "summary": "[3] 0 5 1 [A.46 A.395 A.47 A.361 A.367 A.393] 2 1 1", "num_nts": 12, "nts_short": "GCGGAAUAUAGC", "nts_long": "///A/46,///A/47,///A/361,///A/362,///A/363,///A/364,///A/365,///A/366,///A/367,///A/393,///A/394,///A/395", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 5, "nts_short": "GAAUA", "nts_long": "///A/362,///A/363,///A/364,///A/365,///A/366" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///A/394" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 2, 3, 5 ], "stem_indices": [ 57, 58, 60 ], "summary": "[3] 2 3 5 [A.826 A.874 A.829 A.857 A.861 A.868] 6 7 2", "num_nts": 16, "nts_short": "CUUGCGGAGCGUUAAG", "nts_long": "///A/826,///A/827,///A/828,///A/829,///A/857,///A/858,///A/859,///A/860,///A/861,///A/868,///A/869,///A/870,///A/871,///A/872,///A/873,///A/874", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/827,///A/828" }, { "index": 2, "num_nts": 3, "nts_short": "GGA", "nts_long": "///A/858,///A/859,///A/860" }, { "index": 3, "num_nts": 5, "nts_short": "GUUAA", "nts_long": "///A/869,///A/870,///A/871,///A/872,///A/873" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 2, 7, 3 ], "stem_indices": [ 51, -13, 54 ], "summary": "[3] 2 7 3 [A.670 A.736 A.673 A.717 A.725 A.732] 5 1 2", "num_nts": 18, "nts_short": "GGUAUACCGGUGGCGGCC", "nts_long": "///A/670,///A/671,///A/672,///A/673,///A/717,///A/718,///A/719,///A/720,///A/721,///A/722,///A/723,///A/724,///A/725,///A/732,///A/733,///A/734,///A/735,///A/736", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/671,///A/672" }, { "index": 2, "num_nts": 7, "nts_short": "ACCGGUG", "nts_long": "///A/718,///A/719,///A/720,///A/721,///A/722,///A/723,///A/724" }, { "index": 3, "num_nts": 3, "nts_short": "GGC", "nts_long": "///A/733,///A/734,///A/735" } ] }, { "index": 5, "type": "4-way junction", "bridging_nts": [ 6, 0, 2, 0 ], "stem_indices": [ 14, 15, 23, 26 ], "summary": "[4] 6 0 2 0 [A.115 A.312 A.122 A.239 A.240 A.286 A.289 A.311] 3 7 3 4", "num_nts": 16, "nts_short": "GAGUAAUGUGCUAGCC", "nts_long": "///A/115,///A/116,///A/117,///A/118,///A/119,///A/120,///A/121,///A/122,///A/239,///A/240,///A/286,///A/287,///A/288,///A/289,///A/311,///A/312", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "AGUAAU", "nts_long": "///A/116,///A/117,///A/118,///A/119,///A/120,///A/121" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/287,///A/288" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 6, "type": "4-way junction", "bridging_nts": [ 1, 5, 4, 1 ], "stem_indices": [ 17, -2, 20, 21 ], "summary": "[4] 1 5 4 1 [A.142 A.221 A.144 A.178 A.184 A.193 A.198 A.219] 7 1 3 6", "num_nts": 19, "nts_short": "GAGCAUAACGCCAAAGUGC", "nts_long": "///A/142,///A/143,///A/144,///A/178,///A/179,///A/180,///A/181,///A/182,///A/183,///A/184,///A/193,///A/194,///A/195,///A/196,///A/197,///A/198,///A/219,///A/220,///A/221", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/143" }, { "index": 2, "num_nts": 5, "nts_short": "AUAAC", "nts_long": "///A/179,///A/180,///A/181,///A/182,///A/183" }, { "index": 3, "num_nts": 4, "nts_short": "CAAA", "nts_long": "///A/194,///A/195,///A/196,///A/197" }, { "index": 4, "num_nts": 1, "nts_short": "G", "nts_long": "///A/220" } ] }, { "index": 7, "type": "5-way junction", "bridging_nts": [ 0, 0, 1, 3, 0 ], "stem_indices": [ 37, 38, 40, 38, 39 ], "summary": "[5] 0 0 1 3 0 [A.504 A.541 A.505 A.526 A.527 A.522 A.524 A.507 A.511 A.540] 5 3 2 3 5", "is_repeated": true, "num_nts": 14, "nts_short": "CGCGCAGCUAACGG", "nts_long": "///A/504,///A/505,///A/526,///A/527,///A/522,///A/523,///A/524,///A/507,///A/508,///A/509,///A/510,///A/511,///A/540,///A/541", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/523" }, { "index": 4, "num_nts": 3, "nts_short": "UAA", "nts_long": "///A/508,///A/509,///A/510" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 8, "type": "5-way junction", "bridging_nts": [ 0, 0, 2, 3, 0 ], "stem_indices": [ 41, 42, 60, 42, -11 ], "summary": "[5] 0 0 2 3 0 [A.569 A.881 A.570 A.866 A.867 A.862 A.865 A.571 A.575 A.880] 3 2 2 2 1", "is_repeated": true, "num_nts": 15, "nts_short": "CGCGCUAAUAAAGCG", "nts_long": "///A/569,///A/570,///A/866,///A/867,///A/862,///A/863,///A/864,///A/865,///A/571,///A/572,///A/573,///A/574,///A/575,///A/880,///A/881", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/863,///A/864" }, { "index": 4, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/572,///A/573,///A/574" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 9, "type": "5-way junction", "bridging_nts": [ 2, 2, 2, 1, 2 ], "stem_indices": [ 4, 5, 32, 34, 37 ], "summary": "[5] 2 2 2 1 2 [A.36 A.548 A.39 A.403 A.406 A.436 A.439 A.498 A.500 A.545] 5 6 4 2 5", "num_nts": 19, "nts_short": "CUGGCGUGCUUUAAGCAAG", "nts_long": "///A/36,///A/37,///A/38,///A/39,///A/403,///A/404,///A/405,///A/406,///A/436,///A/437,///A/438,///A/439,///A/498,///A/499,///A/500,///A/545,///A/546,///A/547,///A/548", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/37,///A/38" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/404,///A/405" }, { "index": 3, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/437,///A/438" }, { "index": 4, "num_nts": 1, "nts_short": "A", "nts_long": "///A/499" }, { "index": 5, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/546,///A/547" } ] }, { "index": 10, "type": "5-way junction", "bridging_nts": [ 2, 6, 1, 1, 3 ], "stem_indices": [ 8, 9, 14, 28, 29 ], "summary": "[5] 2 6 1 1 3 [A.58 A.354 A.61 A.106 A.113 A.314 A.316 A.337 A.339 A.350] 3 3 3 5 4", "num_nts": 23, "nts_short": "CAAGCGGACGGGCACGACGGCAG", "nts_long": "///A/58,///A/59,///A/60,///A/61,///A/106,///A/107,///A/108,///A/109,///A/110,///A/111,///A/112,///A/113,///A/314,///A/315,///A/316,///A/337,///A/338,///A/339,///A/350,///A/351,///A/352,///A/353,///A/354", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/59,///A/60" }, { "index": 2, "num_nts": 6, "nts_short": "GGACGG", "nts_long": "///A/107,///A/108,///A/109,///A/110,///A/111,///A/112" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///A/315" }, { "index": 4, "num_nts": 1, "nts_short": "A", "nts_long": "///A/338" }, { "index": 5, "num_nts": 3, "nts_short": "GCA", "nts_long": "///A/351,///A/352,///A/353" } ] } ], "num_ssSegments": 12, "ssSegments": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/7,///A/8" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///A/26" }, { "index": 3, "num_nts": 10, "nts_short": "GGAAUUACUG", "nts_long": "///A/557,///A/558,///A/559,///A/560,///A/561,///A/562,///A/563,///A/564,///A/565,///A/566" }, { "index": 4, "num_nts": 1, "nts_short": "C", "nts_long": "///A/576" }, { "index": 5, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///A/765,///A/766,///A/767,///A/768" }, { "index": 6, "num_nts": 6, "nts_short": "CGUAAA", "nts_long": "///A/811,///A/812,///A/813,///A/814,///A/815,///A/816" }, { "index": 7, "num_nts": 3, "nts_short": "GAU", "nts_long": "///A/818,///A/819,///A/820" }, { "index": 8, "num_nts": 1, "nts_short": "U", "nts_long": "///A/884" }, { "index": 9, "num_nts": 3, "nts_short": "AAA", "nts_long": "///A/913,///A/914,///A/915" }, { "index": 10, "num_nts": 2, "nts_short": "AU", "nts_long": "///A/919,///A/920" }, { "index": 11, "is_broken": true, "num_nts": 7, "nts_short": "CCAAGGU", "nts_long": "///A/1397,///A/1501,///A/1502,///A/1503,///A/1504,///A/1505,///A/1506" }, { "index": 12, "num_nts": 1, "nts_short": "G", "nts_long": "///A/1530" } ], "num_Aminors": 43, "Aminors": [ { "index": 1, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/51 vs ///A/113,///A/314", "A_nt1": { "desc": "///A/51 vs ///A/113", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/51 vs ///A/314", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.88]" } }, { "index": 2, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/51 vs ///A/114,///A/313", "A_nt1": { "desc": "///A/51 vs ///A/114", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7-O2'(hydroxyl)[2.49],N6(amino)-O2(carbonyl)[2.90]" }, "A_nt2": { "desc": "///A/51 vs ///A/313", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 3, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/55 vs ///A/54,///A/357", "A_nt1": { "desc": "///A/55 vs ///A/54", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/55 vs ///A/357", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "N7-N2(amino)[2.89],N6(amino)-O2'(hydroxyl)[3.14],N6(amino)-N3[3.19]" } }, { "index": 4, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/71 vs ///A/69,///A/99", "A_nt1": { "desc": "///A/71 vs ///A/69", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/71 vs ///A/99", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.63],N1-O2'(hydroxyl)[2.49]" } }, { "index": 5, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/71 vs ///A/70,///A/98", "A_nt1": { "desc": "///A/71 vs ///A/70", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7*O4'[3.14],N6(amino)-O2(carbonyl)[2.79]" }, "A_nt2": { "desc": "///A/71 vs ///A/98", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 6, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/72 vs ///A/70,///A/98", "A_nt1": { "desc": "///A/72 vs ///A/70", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/72 vs ///A/98", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.78],N1-O2'(hydroxyl)[3.51]" } }, { "index": 7, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/116 vs ///A/114,///A/313", "A_nt1": { "desc": "///A/116 vs ///A/114", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/116 vs ///A/313", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.88],N1-O2'(hydroxyl)[2.83]" } }, { "index": 8, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/130 vs ///A/128,///A/233", "A_nt1": { "desc": "///A/130 vs ///A/128", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/130 vs ///A/233", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.23],N6(amino)-O2(carbonyl)[3.25],N1-O2'(hydroxyl)[2.55]" } }, { "index": 9, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/151 vs ///A/67,///A/102", "A_nt1": { "desc": "///A/151 vs ///A/67", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/151 vs ///A/102", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.11],N3-O2'(hydroxyl)[3.00]" } }, { "index": 10, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/160 vs ///A/342,///A/347", "A_nt1": { "desc": "///A/160 vs ///A/342", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/160 vs ///A/347", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.78],N1-N2(amino)[2.98]" } }, { "index": 11, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/161 vs ///A/342,///A/347", "A_nt1": { "desc": "///A/161 vs ///A/342", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/161 vs ///A/347", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.04],N1-O2'(hydroxyl)[2.39]" } }, { "index": 12, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/171 vs ///A/67,///A/102", "A_nt1": { "desc": "///A/171 vs ///A/67", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.18],O2'(hydroxyl)-O2'(hydroxyl)[2.82],N3-O2'(hydroxyl)[2.75]" }, "A_nt2": { "desc": "///A/171 vs ///A/102", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 13, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///A/172 vs ///A/66,///A/103", "A_nt1": { "desc": "///A/172 vs ///A/66", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.20]" }, "A_nt2": { "desc": "///A/172 vs ///A/103", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.01]" } }, { "index": 14, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/195 vs ///A/141,///A/222", "A_nt1": { "desc": "///A/195 vs ///A/141", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/195 vs ///A/222", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.88]" } }, { "index": 15, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/196 vs ///A/142,///A/221", "A_nt1": { "desc": "///A/196 vs ///A/142", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.55],N3-N2(amino)[3.14]" }, "A_nt2": { "desc": "///A/196 vs ///A/221", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.64]" } }, { "index": 16, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/205 vs ///A/203,///A/214", "A_nt1": { "desc": "///A/205 vs ///A/203", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/205 vs ///A/214", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.78]" } }, { "index": 17, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///A/262 vs ///A/131,///A/231", "A_nt1": { "desc": "///A/262 vs ///A/131", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.20],O2'(hydroxyl)-O2'(hydroxyl)[2.82],N3-O2'(hydroxyl)[2.56]" }, "A_nt2": { "desc": "///A/262 vs ///A/231", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 18, "type": "X", "desc_short": "A vs A-G (--)", "desc_long": "///A/263 vs ///A/129,///A/232", "A_nt1": { "desc": "///A/263 vs ///A/129", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/263 vs ///A/232", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.12],N3-N2(amino)[3.28]" } }, { "index": 19, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/282 vs ///A/247,///A/277", "A_nt1": { "desc": "///A/282 vs ///A/247", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.72],N3-N2(amino)[3.27]" }, "A_nt2": { "desc": "///A/282 vs ///A/277", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.05]" } }, { "index": 20, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///A/373 vs ///A/370,///A/391", "A_nt1": { "desc": "///A/373 vs ///A/370", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/373 vs ///A/391", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.04],N1-O2'(hydroxyl)[2.73]" } }, { "index": 21, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/373 vs ///A/371,///A/390", "A_nt1": { "desc": "///A/373 vs ///A/371", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7-O2'(hydroxyl)[2.77],N6(amino)-N3[3.29]" }, "A_nt2": { "desc": "///A/373 vs ///A/390", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 22, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///A/374 vs ///A/371,///A/390", "A_nt1": { "desc": "///A/374 vs ///A/371", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/374 vs ///A/390", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.95],N1-O2'(hydroxyl)[2.81]" } }, { "index": 23, "type": "II", "desc_short": "A vs A-U (WC)", "desc_long": "///A/509 vs ///A/502,///A/543", "A_nt1": { "desc": "///A/509 vs ///A/502", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/509 vs ///A/543", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.15],N3-O2'(hydroxyl)[2.26]" } }, { "index": 24, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/510 vs ///A/503,///A/542", "A_nt1": { "desc": "///A/510 vs ///A/503", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.57]" }, "A_nt2": { "desc": "///A/510 vs ///A/542", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.73],N3-N2(amino)[3.24]" } }, { "index": 25, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/535 vs ///A/522,///A/527", "A_nt1": { "desc": "///A/535 vs ///A/522", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/535 vs ///A/527", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.29],N1-O2'(hydroxyl)[2.40]" } }, { "index": 26, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///A/572 vs ///A/19,///A/916", "A_nt1": { "desc": "///A/572 vs ///A/19", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.32]" }, "A_nt2": { "desc": "///A/572 vs ///A/916", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.18]" } }, { "index": 27, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/573 vs ///A/567,///A/883", "A_nt1": { "desc": "///A/573 vs ///A/567", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/573 vs ///A/883", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.52]" } }, { "index": 28, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/574 vs ///A/568,///A/882", "A_nt1": { "desc": "///A/574 vs ///A/568", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.31],N3-N2(amino)[3.09]" }, "A_nt2": { "desc": "///A/574 vs ///A/882", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.27],O2'(hydroxyl)-O2(carbonyl)[3.15]" } }, { "index": 29, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/607 vs ///A/291,///A/309", "A_nt1": { "desc": "///A/607 vs ///A/291", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/607 vs ///A/309", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.20],N1-O2'(hydroxyl)[2.42]" } }, { "index": 30, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/608 vs ///A/292,///A/308", "A_nt1": { "desc": "///A/608 vs ///A/292", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.82],N6(amino)-N3[2.88],N1-N2(amino)[3.06]" }, "A_nt2": { "desc": "///A/608 vs ///A/308", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 31, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///A/621 vs ///A/41,///A/401", "A_nt1": { "desc": "///A/621 vs ///A/41", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/621 vs ///A/401", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.13],O2'(hydroxyl)-O2'(hydroxyl)[3.03],N3-O2'(hydroxyl)[2.43]" } }, { "index": 32, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///A/622 vs ///A/42,///A/400", "A_nt1": { "desc": "///A/622 vs ///A/42", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.73],N3-N2(amino)[3.51]" }, "A_nt2": { "desc": "///A/622 vs ///A/400", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.13]" } }, { "index": 33, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///A/642 vs ///A/598,///A/640", "A_nt1": { "desc": "///A/642 vs ///A/598", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.85]" }, "A_nt2": { "desc": "///A/642 vs ///A/640", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 34, "type": "X", "desc_short": "A vs A-C (--)", "desc_long": "///A/694 vs ///A/787,///A/796", "A_nt1": { "desc": "///A/694 vs ///A/787", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.56]" }, "A_nt2": { "desc": "///A/694 vs ///A/796", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 35, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/696 vs ///A/785,///A/797", "A_nt1": { "desc": "///A/696 vs ///A/785", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/696 vs ///A/797", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.84],N1-O2'(hydroxyl)[3.02]" } }, { "index": 36, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///A/728 vs ///A/578,///A/763", "A_nt1": { "desc": "///A/728 vs ///A/578", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.22]" }, "A_nt2": { "desc": "///A/728 vs ///A/763", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 37, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/729 vs ///A/577,///A/764", "A_nt1": { "desc": "///A/729 vs ///A/577", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.23],N3-N2(amino)[3.28]" }, "A_nt2": { "desc": "///A/729 vs ///A/764", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.28]" } }, { "index": 38, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/766 vs ///A/1511,///A/1524", "A_nt1": { "desc": "///A/766 vs ///A/1511", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.83]" }, "A_nt2": { "desc": "///A/766 vs ///A/1524", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 39, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/767 vs ///A/1511,///A/1524", "A_nt1": { "desc": "///A/767 vs ///A/1511", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[2.63]" }, "A_nt2": { "desc": "///A/767 vs ///A/1524", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[2.85],O2'(hydroxyl)-O2'(hydroxyl)[2.84],O2'(hydroxyl)-O2(carbonyl)[2.24]" } }, { "index": 40, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/864 vs ///A/18,///A/917", "A_nt1": { "desc": "///A/864 vs ///A/18", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.54]" }, "A_nt2": { "desc": "///A/864 vs ///A/917", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.12],N3-N2(amino)[2.95]" } }, { "index": 41, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///A/873 vs ///A/862,///A/867", "A_nt1": { "desc": "///A/873 vs ///A/862", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/873 vs ///A/867", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.19],N1-O2'(hydroxyl)[2.21]" } }, { "index": 42, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/914 vs ///A/885,///A/912", "A_nt1": { "desc": "///A/914 vs ///A/885", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.45],N3-N2(amino)[3.24]" }, "A_nt2": { "desc": "///A/914 vs ///A/912", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 43, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///A/1519 vs ///A/1515,///A/1520", "A_nt1": { "desc": "///A/1519 vs ///A/1515", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///A/1519 vs ///A/1520", "face_type": "+", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-OP2[2.55],O2'(hydroxyl)-O5'[2.64],O2'(hydroxyl)-O4'[3.19]" } } ], "num_riboseZippers": 12, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "ACAA", "nts_long": "///A/66,///A/67,///A/171,///A/172" }, { "index": 2, "num_nts": 4, "nts_short": "GGAG", "nts_long": "///A/112,///A/113,///A/353,///A/354" }, { "index": 3, "num_nts": 4, "nts_short": "UGCA", "nts_long": "///A/125,///A/126,///A/634,///A/635" }, { "index": 4, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///A/130,///A/131,///A/262,///A/263" }, { "index": 5, "num_nts": 4, "nts_short": "AACC", "nts_long": "///A/195,///A/196,///A/221,///A/222" }, { "index": 6, "num_nts": 4, "nts_short": "CCAA", "nts_long": "///A/400,///A/401,///A/621,///A/622" }, { "index": 7, "num_nts": 4, "nts_short": "AAGU", "nts_long": "///A/509,///A/510,///A/542,///A/543" }, { "index": 8, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///A/577,///A/578,///A/728,///A/729" }, { "index": 9, "num_nts": 4, "nts_short": "GUCC", "nts_long": "///A/691,///A/692,///A/796,///A/797" }, { "index": 10, "num_nts": 4, "nts_short": "AUGG", "nts_long": "///A/696,///A/697,///A/785,///A/786" }, { "index": 11, "num_nts": 4, "nts_short": "AACG", "nts_long": "///A/766,///A/767,///A/1524,///A/1525" }, { "index": 12, "num_nts": 4, "nts_short": "UACG", "nts_long": "///A/813,///A/814,///A/1510,///A/1511" } ], "num_Kturns": 3, "Kturns": [ { "index": 1, "type": "Normal k-turn", "iloop_index": 18, "bounding_stems": [ 24, 23 ], "Cstem_index": 24, "NCstem_index": 23, "Cstem_pair": "C-G (///A/277,///A/247) WC", "NCstem_pair": "C-G (///A/284,///A/242) WC", "GA_pair": "G-A (///A/281,///A/246) Sheared", "bending_angle": 60.376, "strand1": { "num_nts": 12, "nts_short": "GGCGACGAUCCC", "nts_long": "///A/275,///A/276,///A/277,///A/278,///A/279,///A/280,///A/281,///A/282,///A/283,///A/284,///A/285,///A/286" }, "strand2": { "num_nts": 10, "nts_short": "GGGAUUAGCU", "nts_long": "///A/240,///A/241,///A/242,///A/243,///A/244,///A/245,///A/246,///A/247,///A/248,///A/249" } }, { "index": 2, "type": "Normal k-turn", "iloop_index": 24, "bounding_stems": [ 40, 39 ], "Cstem_index": 40, "NCstem_index": 39, "Cstem_pair": "C-G (///A/528,///A/521) WC", "NCstem_pair": "C-G (///A/536,///A/515) WC", "GA_pair": "G-A (///A/529,///A/520) Sheared", "bending_angle": 36.656, "strand1": { "num_nts": 14, "nts_short": "GCGGUAAUACGGAG", "nts_long": "///A/527,///A/528,///A/529,///A/530,///A/531,///A/532,///A/533,///A/534,///A/535,///A/536,///A/537,///A/538,///A/539,///A/540" }, "strand2": { "num_nts": 12, "nts_short": "CUCCGUGCCAGC", "nts_long": "///A/511,///A/512,///A/513,///A/514,///A/515,///A/516,///A/517,///A/518,///A/519,///A/520,///A/521,///A/522" } }, { "index": 3, "type": "Undecided case", "iloop_index": 23, "bounding_stems": [ 32, 33 ], "Cstem_index": 32, "NCstem_index": 33, "Cstem_pair": "U-G (///A/409,///A/433) Wobble", "NCstem_pair": "G-U (///A/416,///A/427) Wobble", "GA_pair": "G-A (///A/410,///A/432) Sheared", "bending_angle": 55.749, "strand1": { "num_nts": 14, "nts_short": "GUAUGAAGAAGGCC", "nts_long": "///A/406,///A/407,///A/408,///A/409,///A/410,///A/411,///A/412,///A/413,///A/414,///A/415,///A/416,///A/417,///A/418,///A/419" }, "strand2": { "num_nts": 13, "nts_short": "GGUUGUAAAGUAC", "nts_long": "///A/424,///A/425,///A/426,///A/427,///A/428,///A/429,///A/430,///A/431,///A/432,///A/433,///A/434,///A/435,///A/436" } } ], "num_splayUnits": 69, "splayUnits": [ { "index": 1, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/8,///A/9" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/13,///A/14" }, { "index": 3, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/30,///A/31,///A/32" }, { "index": 4, "num_nts": 4, "nts_short": "GCCU", "nts_long": "///A/46,///A/47,///A/48,///A/49" }, { "index": 5, "num_nts": 3, "nts_short": "AAC", "nts_long": "///A/50,///A/51,///A/52" }, { "index": 6, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/59,///A/60" }, { "index": 7, "num_nts": 3, "nts_short": "GAA", "nts_long": "///A/64,///A/65,///A/66" }, { "index": 8, "num_nts": 3, "nts_short": "AUG", "nts_long": "///A/120,///A/121,///A/122" }, { "index": 9, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/133,///A/134" }, { "index": 10, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/143,///A/144" }, { "index": 11, "num_nts": 3, "nts_short": "AUA", "nts_long": "///A/172,///A/173,///A/174" }, { "index": 12, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/196,///A/197" }, { "index": 13, "num_nts": 2, "nts_short": "UU", "nts_long": "///A/208,///A/209" }, { "index": 14, "num_nts": 3, "nts_short": "AUU", "nts_long": "///A/243,///A/244,///A/245" }, { "index": 15, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/250,///A/251" }, { "index": 16, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/265,///A/266" }, { "index": 17, "num_nts": 3, "nts_short": "ACG", "nts_long": "///A/279,///A/280,///A/281" }, { "index": 18, "num_nts": 2, "nts_short": "GA", "nts_long": "///A/305,///A/306" }, { "index": 19, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/315,///A/316" }, { "index": 20, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/329,///A/330" }, { "index": 21, "num_nts": 2, "nts_short": "GG", "nts_long": "///A/331,///A/332" }, { "index": 22, "num_nts": 3, "nts_short": "UAC", "nts_long": "///A/343,///A/344,///A/345" }, { "index": 23, "num_nts": 4, "nts_short": "GCAG", "nts_long": "///A/351,///A/352,///A/353,///A/354" }, { "index": 24, "num_nts": 2, "nts_short": "UA", "nts_long": "///A/365,///A/366" }, { "index": 25, "num_nts": 3, "nts_short": "UUG", "nts_long": "///A/367,///A/368,///A/369" }, { "index": 26, "num_nts": 3, "nts_short": "UGA", "nts_long": "///A/387,///A/388,///A/389" }, { "index": 27, "num_nts": 3, "nts_short": "CAU", "nts_long": "///A/396,///A/397,///A/398" }, { "index": 28, "num_nts": 2, "nts_short": "UG", "nts_long": "///A/405,///A/406" }, { "index": 29, "num_nts": 3, "nts_short": "AGA", "nts_long": "///A/412,///A/413,///A/414" }, { "index": 30, "num_nts": 3, "nts_short": "UUC", "nts_long": "///A/420,///A/421,///A/422" }, { "index": 31, "num_nts": 3, "nts_short": "AAG", "nts_long": "///A/460,///A/461,///A/462" }, { "index": 32, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/465,///A/466" }, { "index": 33, "num_nts": 3, "nts_short": "GUU", "nts_long": "///A/484,///A/485,///A/486" }, { "index": 34, "num_nts": 2, "nts_short": "AA", "nts_long": "///A/498,///A/499" }, { "index": 35, "num_nts": 2, "nts_short": "CG", "nts_long": "///A/504,///A/505" }, { "index": 36, "num_nts": 2, "nts_short": "AG", "nts_long": "///A/523,///A/524" }, { "index": 37, "num_nts": 2, "nts_short": "GU", "nts_long": "///A/530,///A/531" }, { "index": 38, "num_nts": 3, "nts_short": "AAU", "nts_long": "///A/532,///A/533,///A/534" }, { "index": 39, "num_nts": 2, "nts_short": "AC", "nts_long": "///A/535,///A/536" }, { "index": 40, 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3.035, "atom1_id": "///A/1526/O2'", "atom2_id": "///A/1527/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 3077, "atom1_serNum": 28816, "atom2_serNum": 28832, "donAcc_type": "acceptable", "distance": 3.522, "atom1_id": "///A/1527/O2'", "atom2_id": "///A/1528/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 3078, "atom1_serNum": 28836, "atom2_serNum": 28848, "donAcc_type": "acceptable", "distance": 2.340, "atom1_id": "///A/1528/O2'", "atom2_id": "///A/1529/OP2", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 3079, "atom1_serNum": 28840, "atom2_serNum": 28856, "donAcc_type": "acceptable", "distance": 3.536, "atom1_id": "///A/1528/O2", "atom2_id": "///A/1529/O2'", "atom_pair": "O:O", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "7oi0", "num_aaChains": 10, "aaChains": "D=205,F=100,H=129,K=95,L=123,O=88,P=82,Q=80,R=50,T=85", "num_naChains": 1, "naChains": "A=963", "num_atoms": 29255, "num_waters": 374, "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 21, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-multiplets.pdb", "desc": "an ensemble of multiplets" }, { "index": 3, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 4, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 5, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 6, "name": "dssr-bulges.pdb", "desc": "an ensemble of bulges" }, { "index": 7, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 8, "name": "dssr-junctions.pdb", "desc": "an ensemble of junctions (multi-branch)" }, { "index": 9, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 10, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 11, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 12, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 13, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 14, "name": "dssr-Aminors.pdb", "desc": "an ensemble of A minor motifs (types I and II)" }, { "index": 15, "name": "dssr-Kturns.pdb", "desc": "an ensemble of kink-turn motifs" }, { "index": 16, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 17, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 18, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 19, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 20, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 21, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }