**************************************************************************** File name: 1rsb.pdb no. of DNA/RNA chains: 4 [A=6,B=6,C=6,D=5] no. of nucleotides: 23 no. of atoms: 476 no. of waters: 34 no. of metals: 0 **************************************************************************** List of 10 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DA1 B.DT12 A+T Hoogsteen 23-XXIII cHW cM+W 2 A.DT2 B.DA11 T+A Hoogsteen 23-XXIII cWH cW+M 3 A.DA3 B.DT10 A+T Hoogsteen 23-XXIII cHW cM+W 4 A.DT4 B.DA9 T+A Hoogsteen 23-XXIII cWH cW+M 5 A.DA5 B.DT8 A+T Hoogsteen 23-XXIII cHW cM+W 6 A.DT6 B.DA7 T+A Hoogsteen 23-XXIII cWH cW+M 7 C.DA13 D.DT22 A+T Hoogsteen 23-XXIII cHW cM+W 8 C.DT14 D.DA21 T+A Hoogsteen 23-XXIII cWH cW+M 9 C.DA15 D.DT20 A+T Hoogsteen 23-XXIII cHW cM+W 10 C.DT16 D.DA19 T+A Hoogsteen 23-XXIII cWH cW+M **************************************************************************** List of 1 helix 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[0] bps=10 strand-1 5'-ATATATATAT-3' bp-type .......... strand-2 3'-TATATATATA-5' helix-form .....x... 1 B.DA7 A.DT6 A+T Hoogsteen 23-XXIII cHW cM+W 2 B.DT8 A.DA5 T+A Hoogsteen 23-XXIII cWH cW+M 3 B.DA9 A.DT4 A+T Hoogsteen 23-XXIII cHW cM+W 4 B.DT10 A.DA3 T+A Hoogsteen 23-XXIII cWH cW+M 5 B.DA11 A.DT2 A+T Hoogsteen 23-XXIII cHW cM+W 6 B.DT12 A.DA1 T+A Hoogsteen 23-XXIII cWH cW+M 7 C.DA13 D.DT22 A+T Hoogsteen 23-XXIII cHW cM+W 8 C.DT14 D.DA21 T+A Hoogsteen 23-XXIII cWH cW+M 9 C.DA15 D.DT20 A+T Hoogsteen 23-XXIII cHW cM+W 10 C.DT16 D.DA19 T+A Hoogsteen 23-XXIII cWH cW+M **************************************************************************** List of 2 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=10 TATATATATA A.DT6,A.DA5,A.DT4,A.DA3,A.DT2,A.DA1,D.DT22,D.DA21,D.DT20,D.DA19 2 nts=10 ATATATATAT B.DA7,B.DT8,B.DA9,B.DT10,B.DA11,B.DT12,C.DA13,C.DT14,C.DA15,C.DT16 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 AT C.DA17,C.DT18 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=6 ATATAT A.DA1,A.DT2,A.DA3,A.DT4,A.DA5,A.DT6 2 nts=6 ATATAT B.DA7,B.DT8,B.DA9,B.DT10,B.DA11,B.DT12 3 nts=6 ATATAT C.DA13,C.DT14,C.DA15,C.DT16,C.DA17,C.DT18 4 nts=5 ATATA D.DA19,D.DT20,D.DA21,D.DT22,D.DA23 **************************************************************************** List of 1 splayed-apart dinucleotide 1 C.DA17 C.DT18 angle=167 distance=18.6 ratio=0.99 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 AT C.DA17,C.DT18 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1rsb nts=23 [whole] ATATAT&ATATAT&ATATAT&ATATA ......&......&......&..... >1rsb-A #1 nts=6 3.18(0.14) [chain] DNA ATATAT ...... >1rsb-B #2 nts=6 3.49(0.14) [chain] DNA ATATAT ...... >1rsb-C #3 nts=6 0.77(1.18) [chain] DNA ATATAT ...... >1rsb-D #4 nts=5 2.97(0.11) [chain] DNA ATATA ..... **************************************************************************** Summary of structural features of 23 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 A . A.DA1 0.006 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 2 T . A.DT2 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 3 A . A.DA3 0.005 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 4 T . A.DT4 0.009 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 5 A . A.DA5 0.017 ~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 6 T . A.DT6 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 7 A . B.DA7 0.010 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 8 T . B.DT8 0.012 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 9 A . B.DA9 0.013 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 10 T . B.DT10 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 11 A . B.DA11 0.014 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 12 T . B.DT12 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 13 A . C.DA13 0.008 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 14 T . C.DT14 0.013 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 15 A . C.DA15 0.008 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 16 T . C.DT16 0.008 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop 17 A . C.DA17 0.008 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 18 T . C.DT18 0.011 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 19 A . D.DA19 0.008 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 20 T . D.DT20 0.009 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 21 A . D.DA21 0.011 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 22 T . D.DT22 0.012 anti,~C2'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 23 A . D.DA23 --- non-stack,ss-non-loop **************************************************************************** List of 12 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 3 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 4 dssr-2ndstrs.ct -- secondary structure in connectivity table format 5 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 6 dssr-torsions.txt -- backbone torsion angles and suite names 7 dssr-splays.pdb -- an ensemble of splayed-apart units 8 dssr-stacks.pdb -- an ensemble of base stacks 9 dssr-rotmat.txt -- position vector and rotation matrix 10 dssr-viewV.pdb -- vertical view of the principal moment of inertia 11 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 12 dssr-viewT.pdb -- top view of the principal moment of inertia