**************************************************************************** File name: 1xa2.pdb no. of DNA/RNA chains: 2 [A=6,B=6] no. of nucleotides: 12 no. of atoms: 292 no. of waters: 45 no. of metals: 1 [Co=1] **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DC3 B.DG10 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC9 G-C WC 19-XIX cWW cW-W 5 A.DC5 B.DG8 C-G WC 19-XIX cWW cW-W 6 A.DA6 B.DT7 A-T 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=6 strand-1 5'-CGCGCA-3' bp-type |||||| strand-2 3'-GCGCGT-5' helix-form Z.ZZZ 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DC3 B.DG10 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC9 G-C WC 19-XIX cWW cW-W 5 A.DC5 B.DG8 C-G WC 19-XIX cWW cW-W 6 A.DA6 B.DT7 A-T 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=6 strand-1 5'-CGCGCA-3' bp-type |||||| strand-2 3'-GCGCGT-5' helix-form Z.ZZZ 1 A.DC1 B.DG12 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DC3 B.DG10 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC9 G-C WC 19-XIX cWW cW-W 5 A.DC5 B.DG8 C-G WC 19-XIX cWW cW-W 6 A.DA6 B.DT7 A-T WC 20-XX cWW cW-W **************************************************************************** Nucleotides not involved in stacking interactions nts=2 AG A.DA6,B.DG12 **************************************************************************** List of 6 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.DC1 A.DG2 2.79 2 sugar O4'@A.DC3 A.DG4 2.86 3 sugar O4'@A.DC5 A.DA6 2.89 4 sugar O4'@B.DT7 B.DG8 2.82 5 sugar O4'@B.DC9 B.DG10 2.96 6 sugar O4'@B.DC11 B.DG12 2.92 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1xa2 nts=12 [whole] CGCGCA&TGCGCG ((((((&)))))) >1xa2-A #1 nts=6 3.74(0.20) [chain] DNA CGCGCA (((((( >1xa2-B #2 nts=6 3.69(0.15) [chain] DNA TGCGCG )))))) **************************************************************************** Summary of structural features of 12 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 ( A.DC1 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,cap-donor 2 G ( A.DG2 0.039 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 3 C ( A.DC3 0.024 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor,phosphate 4 G ( A.DG4 0.027 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 5 C ( A.DC5 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 6 A ( A.DA6 0.034 syn,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor 7 T ) B.DT7 0.021 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,cap-donor 8 G ) B.DG8 0.020 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 9 C ) B.DC9 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 10 G ) B.DG10 0.020 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 11 C ) B.DC11 0.038 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 12 G ) B.DG12 0.022 syn,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor **************************************************************************** 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-atom2bases.pdb -- an ensemble of atom-base stacking interactions 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