**************************************************************************** File name: 355d.pdb no. of DNA/RNA chains: 2 [A=12,B=12] no. of nucleotides: 24 no. of atoms: 660 no. of waters: 166 no. of metals: 1 [Mg=1] **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC23 G-C WC 19-XIX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC21 G-C WC 19-XIX cWW cW-W 5 A.DA5 B.DT20 A-T WC 20-XX cWW cW-W 6 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 7 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 8 A.DT8 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DG10 B.DC15 G-C WC 19-XIX cWW cW-W 11 A.DC11 B.DG14 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC13 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=12 strand-1 5'-CGCGAATTCGCG-3' bp-type |||||||||||| strand-2 3'-GCGCTTAAGCGC-5' helix-form BBBBBBBBBBB 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC23 G-C WC 19-XIX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC21 G-C WC 19-XIX cWW cW-W 5 A.DA5 B.DT20 A-T WC 20-XX cWW cW-W 6 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 7 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 8 A.DT8 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DG10 B.DC15 G-C WC 19-XIX cWW cW-W 11 A.DC11 B.DG14 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC13 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=12 strand-1 5'-CGCGAATTCGCG-3' bp-type |||||||||||| strand-2 3'-GCGCTTAAGCGC-5' helix-form BBBBBBBBBBB 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC23 G-C WC 19-XIX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DG4 B.DC21 G-C WC 19-XIX cWW cW-W 5 A.DA5 B.DT20 A-T WC 20-XX cWW cW-W 6 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 7 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 8 A.DT8 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DG10 B.DC15 G-C WC 19-XIX cWW cW-W 11 A.DC11 B.DG14 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC13 G-C WC 19-XIX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >355d nts=24 [whole] CGCGAATTCGCG&CGCGAATTCGCG ((((((((((((&)))))))))))) >355d-A #1 nts=12 3.21(0.51) [chain] DNA CGCGAATTCGCG (((((((((((( >355d-B #2 nts=12 3.37(0.50) [chain] DNA CGCGAATTCGCG )))))))))))) **************************************************************************** Summary of structural features of 24 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 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( A.DG2 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 3 C ( A.DC3 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( A.DG4 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 A ( A.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 A ( A.DA6 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 T ( A.DT7 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ( A.DT8 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 C ( A.DC9 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 G ( A.DG10 0.012 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 11 C ( A.DC11 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ( A.DG12 0.010 ~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 13 C ) B.DC13 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 14 G ) B.DG14 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 C ) B.DC15 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 G ) B.DG16 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 A ) B.DA17 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 A ) B.DA18 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 T ) B.DT19 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 T ) B.DT20 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ) B.DC21 0.010 anti,BI,canonical,non-pair-contact,helix,stem 22 G ) B.DG22 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 C ) B.DC23 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 24 G ) B.DG24 0.010 anti,~C3'-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