**************************************************************************** File name: 224d.pdb no. of DNA/RNA chains: 2 [A=6,B=6] no. of nucleotides: 12 no. of atoms: 429 no. of waters: 77 no. of metals: 0 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DT1 B.DA12 T-A WC 20-XX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DA3 B.DT10 A-T WC 20-XX cWW cW-W 4 A.DT4 B.DA9 T-A WC 20-XX 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'-TGATCA-3' bp-type |||||| strand-2 3'-ACTAGT-5' helix-form .BBB. 1 A.DT1 B.DA12 T-A WC 20-XX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DA3 B.DT10 A-T WC 20-XX cWW cW-W 4 A.DT4 B.DA9 T-A WC 20-XX 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'-TGATCA-3' bp-type |||||| strand-2 3'-ACTAGT-5' helix-form .BBB. 1 A.DT1 B.DA12 T-A WC 20-XX cWW cW-W 2 A.DG2 B.DC11 G-C WC 19-XIX cWW cW-W 3 A.DA3 B.DT10 A-T WC 20-XX cWW cW-W 4 A.DT4 B.DA9 T-A WC 20-XX 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=4 TATA A.DT1,A.DA6,B.DT7,B.DA12 **************************************************************************** List of 8 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other O12@A.NGM14 A.DT1 3.23 2 other O12@A.NGM14 A.DG2 3.28 3 other O4@B.NGM13 A.DC5 3.02 4 other O6@B.NGM13 A.DA6 3.14 5 other O12@B.NGM13 B.DT7 3.29 6 other O12@B.NGM13 B.DG8 3.22 7 other O4@A.NGM14 B.DC11 2.97 8 other O6@A.NGM14 B.DA12 3.10 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >224d nts=12 [whole] TGATCA&TGATCA ((((((&)))))) >224d-A #1 nts=6 4.26(0.44) [chain] DNA TGATCA (((((( >224d-B #2 nts=6 4.41(0.44) [chain] DNA TGATCA )))))) **************************************************************************** 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 T ( A.DT1 0.022 anti,~C3'-endo,BI,non-stack,canonical,helix-end,stem-end,cap-acceptor 2 G ( A.DG2 0.030 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 3 A ( A.DA3 0.028 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( A.DT4 0.025 anti,BI,canonical,non-pair-contact,helix,stem 5 C ( A.DC5 0.028 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,cap-acceptor 6 A ( A.DA6 0.042 anti,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor 7 T ) B.DT7 0.024 anti,non-stack,canonical,helix-end,stem-end,cap-acceptor 8 G ) B.DG8 0.033 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 9 A ) B.DA9 0.027 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 T ) B.DT10 0.026 anti,BI,canonical,non-pair-contact,helix,stem 11 C ) B.DC11 0.021 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,cap-acceptor 12 A ) B.DA12 0.029 anti,~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