**************************************************************************** File name: 1oct.pdb no. of DNA/RNA chains: 2 [A=15,B=15] no. of nucleotides: 30 no. of atoms: 1670 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 14 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG202 B.DC230 G-C WC 19-XIX cWW cW-W 2 A.DT203 B.DA229 T-A WC 20-XX cWW cW-W 3 A.DA204 B.DT228 A-T WC 20-XX cWW cW-W 4 A.DT205 B.DA227 T-A WC 20-XX cWW cW-W 5 A.DG206 B.DC226 G-C WC 19-XIX cWW cW-W 6 A.DC207 B.DG225 C-G WC 19-XIX cWW cW-W 7 A.DA208 B.DT224 A-T WC 20-XX cWW cW-W 8 A.DA209 B.DT223 A-T WC 20-XX cWW cW-W 9 A.DA210 B.DT222 A-T WC 20-XX cWW cW-W 10 A.DT211 B.DA221 T-A WC 20-XX cWW cW-W 11 A.DA212 B.DT220 A-T WC 20-XX cWW cW-W 12 A.DA213 B.DT219 A-T WC 20-XX cWW cW-W 13 A.DG214 B.DC218 G-C WC 19-XIX cWW cW-W 14 A.DG215 B.DC217 G-C WC 19-XIX 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=14 strand-1 5'-GTATGCAAATAAGG-3' bp-type |||||||||||||| strand-2 3'-CATACGTTTATTCC-5' helix-form BBBBBBBBBBBBB 1 A.DG202 B.DC230 G-C WC 19-XIX cWW cW-W 2 A.DT203 B.DA229 T-A WC 20-XX cWW cW-W 3 A.DA204 B.DT228 A-T WC 20-XX cWW cW-W 4 A.DT205 B.DA227 T-A WC 20-XX cWW cW-W 5 A.DG206 B.DC226 G-C WC 19-XIX cWW cW-W 6 A.DC207 B.DG225 C-G WC 19-XIX cWW cW-W 7 A.DA208 B.DT224 A-T WC 20-XX cWW cW-W 8 A.DA209 B.DT223 A-T WC 20-XX cWW cW-W 9 A.DA210 B.DT222 A-T WC 20-XX cWW cW-W 10 A.DT211 B.DA221 T-A WC 20-XX cWW cW-W 11 A.DA212 B.DT220 A-T WC 20-XX cWW cW-W 12 A.DA213 B.DT219 A-T WC 20-XX cWW cW-W 13 A.DG214 B.DC218 G-C WC 19-XIX cWW cW-W 14 A.DG215 B.DC217 G-C WC 19-XIX 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=14 strand-1 5'-GTATGCAAATAAGG-3' bp-type |||||||||||||| strand-2 3'-CATACGTTTATTCC-5' helix-form BBBBBBBBBBBBB 1 A.DG202 B.DC230 G-C WC 19-XIX cWW cW-W 2 A.DT203 B.DA229 T-A WC 20-XX cWW cW-W 3 A.DA204 B.DT228 A-T WC 20-XX cWW cW-W 4 A.DT205 B.DA227 T-A WC 20-XX cWW cW-W 5 A.DG206 B.DC226 G-C WC 19-XIX cWW cW-W 6 A.DC207 B.DG225 C-G WC 19-XIX cWW cW-W 7 A.DA208 B.DT224 A-T WC 20-XX cWW cW-W 8 A.DA209 B.DT223 A-T WC 20-XX cWW cW-W 9 A.DA210 B.DT222 A-T WC 20-XX cWW cW-W 10 A.DT211 B.DA221 T-A WC 20-XX cWW cW-W 11 A.DA212 B.DT220 A-T WC 20-XX cWW cW-W 12 A.DA213 B.DT219 A-T WC 20-XX cWW cW-W 13 A.DG214 B.DC218 G-C WC 19-XIX cWW cW-W 14 A.DG215 B.DC217 G-C WC 19-XIX cWW cW-W **************************************************************************** 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=2 TG A.DT201,A.DG202 2 nts=2 AC B.DA216,B.DC217 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 T A.DT201 2 nts=1 A B.DA216 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1oct nts=30 [whole] TGTATGCAAATAAGG&ACCTTATTTGCATAC .((((((((((((((&.)))))))))))))) >1oct-A #1 nts=15 3.37(0.56) [chain] DNA TGTATGCAAATAAGG .(((((((((((((( >1oct-B #2 nts=15 3.30(0.69) [chain] DNA ACCTTATTTGCATAC .)))))))))))))) **************************************************************************** Summary of structural features of 30 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 . A.DT201 0.014 anti,~C2'-endo,non-pair-contact,ss-non-loop 2 G ( A.DG202 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 3 T ( A.DT203 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 A ( A.DA204 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( A.DT205 0.024 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 6 G ( A.DG206 0.030 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( A.DC207 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 A ( A.DA208 0.024 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 9 A ( A.DA209 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( A.DA210 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 T ( A.DT211 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 A ( A.DA212 0.032 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 A ( A.DA213 0.039 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 G ( A.DG214 0.014 anti,canonical,non-pair-contact,helix,stem 15 G ( A.DG215 0.027 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 16 A . B.DA216 0.025 anti,~C3'-endo,non-pair-contact,ss-non-loop 17 C ) B.DC217 0.023 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 18 C ) B.DC218 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 T ) B.DT219 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 T ) B.DT220 0.031 anti,BI,canonical,non-pair-contact,helix,stem 21 A ) B.DA221 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ) B.DT222 0.030 anti,BI,canonical,non-pair-contact,helix,stem 23 T ) B.DT223 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 T ) B.DT224 0.017 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) B.DG225 0.028 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 26 C ) B.DC226 0.019 anti,BI,canonical,non-pair-contact,helix,stem 27 A ) B.DA227 0.029 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 T ) B.DT228 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 29 A ) B.DA229 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 C ) B.DC230 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 12 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-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