**************************************************************************** File name: 5jw0.pdb no. of DNA/RNA chains: 2 [A=10,B=10] no. of nucleotides: 20 no. of atoms: 759 no. of waters: 10 no. of metals: 6 [Zn=6] **************************************************************************** List of 10 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DA4 B.DT7 A-T WC 20-XX cWW cW-W 2 A.DG5 B.DC6 G-C WC 19-XIX cWW cW-W 3 A.DG6 B.DC5 G-C WC 19-XIX cWW cW-W 4 A.DG7 B.DC4 G-C WC 19-XIX cWW cW-W 5 A.DT8 B.DA3 T-A WC 20-XX cWW cW-W 6 A.DA9 B.DT2 A-T WC 20-XX cWW cW-W 7 A.DC10 B.DG1 C-G WC 19-XIX cWW cW-W 8 A.DC11 B.DG0 C-G WC 19-XIX cWW cW-W 9 A.DC12 B.DG-1 C-G WC 19-XIX cWW cW-W 10 A.DT13 B.DA-2 T-A WC 20-XX cWW cW-W **************************************************************************** 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[1] bps=10 strand-1 5'-AGGGTACCCT-3' bp-type |||||||||| strand-2 3'-TCCCATGGGA-5' helix-form ....B.... 1 A.DA4 B.DT7 A-T WC 20-XX cWW cW-W 2 A.DG5 B.DC6 G-C WC 19-XIX cWW cW-W 3 A.DG6 B.DC5 G-C WC 19-XIX cWW cW-W 4 A.DG7 B.DC4 G-C WC 19-XIX cWW cW-W 5 A.DT8 B.DA3 T-A WC 20-XX cWW cW-W 6 A.DA9 B.DT2 A-T WC 20-XX cWW cW-W 7 A.DC10 B.DG1 C-G WC 19-XIX cWW cW-W 8 A.DC11 B.DG0 C-G WC 19-XIX cWW cW-W 9 A.DC12 B.DG-1 C-G WC 19-XIX cWW cW-W 10 A.DT13 B.DA-2 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 stem 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'-AGGGTACCCT-3' bp-type |||||||||| strand-2 3'-TCCCATGGGA-5' helix-form ....B.... 1 A.DA4 B.DT7 A-T WC 20-XX cWW cW-W 2 A.DG5 B.DC6 G-C WC 19-XIX cWW cW-W 3 A.DG6 B.DC5 G-C WC 19-XIX cWW cW-W 4 A.DG7 B.DC4 G-C WC 19-XIX cWW cW-W 5 A.DT8 B.DA3 T-A WC 20-XX cWW cW-W 6 A.DA9 B.DT2 A-T WC 20-XX cWW cW-W 7 A.DC10 B.DG1 C-G WC 19-XIX cWW cW-W 8 A.DC11 B.DG0 C-G WC 19-XIX cWW cW-W 9 A.DC12 B.DG-1 C-G WC 19-XIX cWW cW-W 10 A.DT13 B.DA-2 T-A WC 20-XX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5jw0 nts=20 [whole] AGGGTACCCT&AGGGTACCCT ((((((((((&)))))))))) >5jw0-A #1 nts=10 3.45(0.30) [chain] DNA AGGGTACCCT (((((((((( >5jw0-B #2 nts=10 2.97(0.53) [chain] DNA AGGGTACCCT )))))))))) **************************************************************************** Summary of structural features of 20 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.DA4 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( A.DG5 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( A.DG6 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( A.DG7 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 T ( A.DT8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 A ( A.DA9 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( A.DC10 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 C ( A.DC11 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 C ( A.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 T ( A.DT13 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 11 A ) B.DA-2 0.011 anti,BI,canonical,non-pair-contact,helix-end,stem-end 12 G ) B.DG-1 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 13 G ) B.DG0 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 14 G ) B.DG1 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 15 T ) B.DT2 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 A ) B.DA3 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ) B.DC4 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ) B.DC5 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 C ) B.DC6 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 20 T ) B.DT7 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 11 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-rotmat.txt -- position vector and rotation matrix 9 dssr-viewV.pdb -- vertical view of the principal moment of inertia 10 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 11 dssr-viewT.pdb -- top view of the principal moment of inertia