**************************************************************************** File name: 3hvr.pdb no. of DNA/RNA chains: 4 [C=16,D=12,M=16,N=10] no. of nucleotides: 54 no. of atoms: 10637 no. of waters: 0 no. of metals: 6 [Mg=6] **************************************************************************** List of 22 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DG2 D.C18 G-C WC 19-XIX cWW cW-W 2 C.DA3 D.U17 A-U WC 20-XX cWW cW-W 3 C.DG4 D.C16 G-C WC 19-XIX cWW cW-W 4 C.DG5 D.C15 G-C WC 19-XIX cWW cW-W 5 C.DT6 D.A14 T-A WC 20-XX cWW cW-W 6 C.DA7 D.U13 A-U WC 20-XX cWW cW-W 7 C.DG8 D.C12 G-C WC 19-XIX cWW cW-W 8 C.DT9 D.A11 T-A WC 20-XX cWW cW-W 9 C.DA10 D.U10 A-U WC 20-XX cWW cW-W 10 C.DG11 D.C9 G-C WC 19-XIX cWW cW-W 11 C.DT13 D.C8 T-C -- -- cWW cW-W 12 M.DG2 N.C18 G-C WC 19-XIX cWW cW-W 13 M.DA3 N.U17 A-U WC 20-XX cWW cW-W 14 M.DG4 N.C16 G-C WC 19-XIX cWW cW-W 15 M.DG5 N.C15 G-C WC 19-XIX cWW cW-W 16 M.DT6 N.A14 T-A WC 20-XX cWW cW-W 17 M.DA7 N.U13 A-U WC 20-XX cWW cW-W 18 M.DG8 N.C12 G-C WC 19-XIX cWW cW-W 19 M.DT9 N.A11 T-A WC 20-XX cWW cW-W 20 M.DA10 N.U10 A-U WC 20-XX cWW cW-W 21 M.DG11 N.C9 G-C WC 19-XIX cWW cW-W 22 M.DG12 M.DT13 G+T Platform -- cSH cm+M **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[1] bps=11 strand-1 5'-GAGGTAGTAGT-3' bp-type ||||||||||. strand-2 3'-CUCCAUCAUCC-5' helix-form ..AA..A..x 1 C.DG2 D.C18 G-C WC 19-XIX cWW cW-W 2 C.DA3 D.U17 A-U WC 20-XX cWW cW-W 3 C.DG4 D.C16 G-C WC 19-XIX cWW cW-W 4 C.DG5 D.C15 G-C WC 19-XIX cWW cW-W 5 C.DT6 D.A14 T-A WC 20-XX cWW cW-W 6 C.DA7 D.U13 A-U WC 20-XX cWW cW-W 7 C.DG8 D.C12 G-C WC 19-XIX cWW cW-W 8 C.DT9 D.A11 T-A WC 20-XX cWW cW-W 9 C.DA10 D.U10 A-U WC 20-XX cWW cW-W 10 C.DG11 D.C9 G-C WC 19-XIX cWW cW-W 11 C.DT13 D.C8 T-C -- -- cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=11 strand-1 5'-GAGGTAGTAGG-3' bp-type ||||||||||. strand-2 3'-CUCCAUCAUCT-5' helix-form AAAA.A...x 1 M.DG2 N.C18 G-C WC 19-XIX cWW cW-W 2 M.DA3 N.U17 A-U WC 20-XX cWW cW-W 3 M.DG4 N.C16 G-C WC 19-XIX cWW cW-W 4 M.DG5 N.C15 G-C WC 19-XIX cWW cW-W 5 M.DT6 N.A14 T-A WC 20-XX cWW cW-W 6 M.DA7 N.U13 A-U WC 20-XX cWW cW-W 7 M.DG8 N.C12 G-C WC 19-XIX cWW cW-W 8 M.DT9 N.A11 T-A WC 20-XX cWW cW-W 9 M.DA10 N.U10 A-U WC 20-XX cWW cW-W 10 M.DG11 N.C9 G-C WC 19-XIX cWW cW-W 11 M.DG12 M.DT13 G+T Platform -- cSH cm+M **************************************************************************** List of 2 stems Note: A stem is defined as a helix consisting strictly of canonical WC/wobble pairs with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=10 strand-1 5'-GAGGTAGTAG-3' bp-type |||||||||| strand-2 3'-CUCCAUCAUC-5' helix-form ..AA..A.. 1 C.DG2 D.C18 G-C WC 19-XIX cWW cW-W 2 C.DA3 D.U17 A-U WC 20-XX cWW cW-W 3 C.DG4 D.C16 G-C WC 19-XIX cWW cW-W 4 C.DG5 D.C15 G-C WC 19-XIX cWW cW-W 5 C.DT6 D.A14 T-A WC 20-XX cWW cW-W 6 C.DA7 D.U13 A-U WC 20-XX cWW cW-W 7 C.DG8 D.C12 G-C WC 19-XIX cWW cW-W 8 C.DT9 D.A11 T-A WC 20-XX cWW cW-W 9 C.DA10 D.U10 A-U WC 20-XX cWW cW-W 10 C.DG11 D.C9 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=10 strand-1 5'-GAGGTAGTAG-3' bp-type |||||||||| strand-2 3'-CUCCAUCAUC-5' helix-form AAAA.A... 1 M.DG2 N.C18 G-C WC 19-XIX cWW cW-W 2 M.DA3 N.U17 A-U WC 20-XX cWW cW-W 3 M.DG4 N.C16 G-C WC 19-XIX cWW cW-W 4 M.DG5 N.C15 G-C WC 19-XIX cWW cW-W 5 M.DT6 N.A14 T-A WC 20-XX cWW cW-W 6 M.DA7 N.U13 A-U WC 20-XX cWW cW-W 7 M.DG8 N.C12 G-C WC 19-XIX cWW cW-W 8 M.DT9 N.A11 T-A WC 20-XX cWW cW-W 9 M.DA10 N.U10 A-U WC 20-XX cWW cW-W 10 M.DG11 N.C9 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 7 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 HC A.HIS445,D.C18 2 nts=2 HC B.HIS445,N.C18 3 nts=2 GG C.DG11,C.DG12 4 nts=2 GG M.DG11,M.DG12 5 nts=2 CC D.C8,D.C9 6 nts=3 TTG C.DT13,C.DT14,C.DG15 7 nts=3 TGT M.DT14,M.DG15,M.DT16 **************************************************************************** Nucleotides not involved in stacking interactions nts=6 TTTUCU C.DT1,C.DT16,M.DT13,D.U10,N.C9,N.U10 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=1 T C.DT1 2 nts=5 GTTGT C.DG12,C.DT13,C.DT14,C.DG15,C.DT16 3 nts=1 T M.DT1 4 nts=5 GTTGT M.DG12,M.DT13,M.DT14,M.DG15,M.DT16 5 nts=1 C D.C8 6 nts=1 G D.G19 **************************************************************************** List of 2 splayed-apart dinucleotides 1 C.DT1 C.DG2 angle=143 distance=18.3 ratio=0.95 2 M.DT1 M.DG2 angle=141 distance=17.7 ratio=0.94 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 TG C.DT1,C.DG2 2 nts=2 TG M.DT1,M.DG2 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3hvr nts=54 [whole] TGAGGTAGTAGGTTGT&TGAGGTAGTAGGTTGT&CCUACUACCUCG&CUACUACCUC .[[[[[[[[[[.....&.((((((((((.....&.]]]]]]]]]].&)))))))))) >3hvr-C #1 nts=16 2.82(1.48) [chain] DNA TGAGGTAGTAGGTTGT .[[[[[[[[[[..... >3hvr-M #2 nts=16 2.74(1.54) [chain] DNA TGAGGTAGTAGGTTGT .((((((((((..... >3hvr-D #3 nts=12 3.16(0.41) [chain] RNA[11]/1 CCUACUACCUCG .]]]]]]]]]]. >3hvr-N #4 nts=10 3.15(0.35) [chain] RNA CUACUACCUC )))))))))) **************************************************************************** Summary of structural features of 54 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 T . C.DT1 0.007 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 2 G [ C.DG2 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 3 A [ C.DA3 0.008 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 G [ C.DG4 0.007 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 G [ C.DG5 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 T [ C.DT6 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 A [ C.DA7 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 G [ C.DG8 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 T [ C.DT9 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 A [ C.DA10 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 G [ C.DG11 0.005 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 12 G . C.DG12 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop 13 T . C.DT13 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 14 T . C.DT14 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 15 G . C.DG15 0.019 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 16 T . C.DT16 0.007 anti,~C2'-endo,non-stack,ss-non-loop 17 T . M.DT1 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 18 G ( M.DG2 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 19 A ( M.DA3 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 G ( M.DG4 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 21 G ( M.DG5 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 22 T ( M.DT6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 23 A ( M.DA7 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 G ( M.DG8 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 T ( M.DT9 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 A ( M.DA10 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 27 G ( M.DG11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 28 G . M.DG12 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 29 T . M.DT13 0.004 anti,~C2'-endo,BI,non-stack,non-canonical,non-pair-contact,helix-end,ss-non-loop 30 T . M.DT14 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 31 G . M.DG15 0.019 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 32 T . M.DT16 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop 33 C . D.C8 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 34 C ] D.C9 0.016 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 35 U ] D.U10 0.009 pseudoknotted,anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,phosphate 36 A ] D.A11 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 37 C ] D.C12 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 38 U ] D.U13 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 39 A ] D.A14 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 40 C ] D.C15 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 41 C ] D.C16 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 42 U ] D.U17 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 43 C ] D.C18 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 44 G . D.G19 --- non-stack,ss-non-loop 45 C ) N.C9 0.008 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,phosphate 46 U ) N.U10 0.011 anti,~C3'-endo,BI,non-stack,canonical,helix,stem,phosphate 47 A ) N.A11 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 48 C ) N.C12 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 49 U ) N.U13 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 50 A ) N.A14 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 51 C ) N.C15 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 52 C ) N.C16 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 53 U ) N.U17 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 54 C ) N.C18 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 13 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks 10 dssr-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia