**************************************************************************** File name: 4bzt.pdb no. of DNA/RNA chains: 2 [A=7,B=6] no. of nucleotides: 12 no. of atoms: 460 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DA1 B.DT12 A-T WC 20-XX cWW cW-W 2 A.DT2 B.DA11 T-A WC 20-XX cWW cW-W 3 A.DG3 B.DC10 G-C WC 19-XIX cWW cW-W 4 A.DC4 B.DG9 C-G WC 19-XIX cWW cW-W 5 A.DA5 B.DT8 A-T WC 20-XX cWW cW-W 6 A.DT6 B.DA7 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=6 strand-1 5'-ATGCAT-3' bp-type |||||| strand-2 3'-TACGTA-5' helix-form ..B.. 1 A.DA1 B.DT12 A-T WC 20-XX cWW cW-W 2 A.DT2 B.DA11 T-A WC 20-XX cWW cW-W 3 A.DG3 B.DC10 G-C WC 19-XIX cWW cW-W 4 A.DC4 B.DG9 C-G WC 19-XIX cWW cW-W 5 A.DA5 B.DT8 A-T WC 20-XX cWW cW-W 6 A.DT6 B.DA7 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=6 strand-1 5'-ATGCAT-3' bp-type |||||| strand-2 3'-TACGTA-5' helix-form ..B.. 1 A.DA1 B.DT12 A-T WC 20-XX cWW cW-W 2 A.DT2 B.DA11 T-A WC 20-XX cWW cW-W 3 A.DG3 B.DC10 G-C WC 19-XIX cWW cW-W 4 A.DC4 B.DG9 C-G WC 19-XIX cWW cW-W 5 A.DA5 B.DT8 A-T WC 20-XX cWW cW-W 6 A.DT6 B.DA7 T-A WC 20-XX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4bzt nts=12 [whole] ATGCAT&ATGCAT ((((((&)))))) >4bzt-A #1 nts=6 3.96(0.31) [chain] DNA* ATGCAT (((((( >4bzt-B #2 nts=6 3.75(0.96) [chain] DNA ATGCAT )))))) **************************************************************************** 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 A ( A.DA1 0.034 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 T ( A.DT2 0.028 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( A.DG3 0.037 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem 4 C ( A.DC4 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 5 A ( A.DA5 0.039 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 T ( A.DT6 0.029 anti,canonical,non-pair-contact,helix-end,stem-end 7 A ) B.DA7 0.034 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 8 T ) B.DT8 0.035 anti,BI,canonical,non-pair-contact,helix,stem 9 G ) B.DG9 0.036 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem 10 C ) B.DC10 0.018 anti,BI,canonical,non-pair-contact,helix,stem 11 A ) B.DA11 0.027 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 T ) B.DT12 0.029 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