**************************************************************************** File name: 5ink.pdb no. of DNA/RNA chains: 2 [C=9,D=9] no. of nucleotides: 18 no. of atoms: 4800 no. of waters: 441 no. of metals: 2 [Mg=2] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 3DR-? 2 C.3DR1,D.3DR1 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DC2 D.DG9 C-G WC 19-XIX cWW cW-W 2 C.DG3 D.DC8 G-C WC 19-XIX cWW cW-W 3 C.DA4 D.DT7 A-T WC 20-XX cWW cW-W 4 C.DA5 D.DT6 A-T WC 20-XX cWW cW-W 5 C.DT6 D.DA5 T-A WC 20-XX cWW cW-W 6 C.DT7 D.DA4 T-A WC 20-XX cWW cW-W 7 C.DC8 D.DG3 C-G WC 19-XIX cWW cW-W 8 C.DG9 D.DC2 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=8 strand-1 5'-CGAATTCG-3' bp-type |||||||| strand-2 3'-GCTTAAGC-5' helix-form BBBBBBB 1 C.DC2 D.DG9 C-G WC 19-XIX cWW cW-W 2 C.DG3 D.DC8 G-C WC 19-XIX cWW cW-W 3 C.DA4 D.DT7 A-T WC 20-XX cWW cW-W 4 C.DA5 D.DT6 A-T WC 20-XX cWW cW-W 5 C.DT6 D.DA5 T-A WC 20-XX cWW cW-W 6 C.DT7 D.DA4 T-A WC 20-XX cWW cW-W 7 C.DC8 D.DG3 C-G WC 19-XIX cWW cW-W 8 C.DG9 D.DC2 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=8 strand-1 5'-CGAATTCG-3' bp-type |||||||| strand-2 3'-GCTTAAGC-5' helix-form BBBBBBB 1 C.DC2 D.DG9 C-G WC 19-XIX cWW cW-W 2 C.DG3 D.DC8 G-C WC 19-XIX cWW cW-W 3 C.DA4 D.DT7 A-T WC 20-XX cWW cW-W 4 C.DA5 D.DT6 A-T WC 20-XX cWW cW-W 5 C.DT6 D.DA5 T-A WC 20-XX cWW cW-W 6 C.DT7 D.DA4 T-A WC 20-XX cWW cW-W 7 C.DC8 D.DG3 C-G WC 19-XIX cWW cW-W 8 C.DG9 D.DC2 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 ? C.3DR1 2 nts=1 ? D.3DR1 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5ink nts=18 [whole] ?CGAATTCG&?CGAATTCG .((((((((&.)))))))) >5ink-C #1 nts=9 3.08(0.68) [chain] DNA ?CGAATTCG .(((((((( >5ink-D #2 nts=9 3.17(0.69) [chain] DNA ?CGAATTCG .)))))))) **************************************************************************** Summary of structural features of 18 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 ? . C.3DR1 --- modified,~C2'-endo,BII,non-stack,ss-non-loop,phosphate 2 C ( C.DC2 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 3 G ( C.DG3 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 4 A ( C.DA4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( C.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 T ( C.DT6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 T ( C.DT7 0.002 anti,canonical,non-pair-contact,helix,stem 8 C ( C.DC8 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 G ( C.DG9 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 10 ? . D.3DR1 --- modified,~C2'-endo,non-stack,ss-non-loop,phosphate 11 C ) D.DC2 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 12 G ) D.DG3 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 13 A ) D.DA4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 A ) D.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 T ) D.DT6 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 T ) D.DT7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ) D.DC8 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 18 G ) D.DG9 0.005 anti,~C2'-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