**************************************************************************** File name: 1x2o.pdb no. of DNA/RNA chains: 2 [A=12,B=12] no. of nucleotides: 24 no. of atoms: 760 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG1 B.DC24 G-C WC 19-XIX cWW cW-W 2 A.DA2 B.DT23 A-T WC 20-XX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DT4 B.DA21 T-A WC 20-XX cWW cW-W 5 A.DG5 B.DC20 G-C WC 19-XIX cWW cW-W 6 A.DT6 B.DA19 T-A WC 20-XX cWW cW-W 7 A.DA7 B.DT18 A-T WC 20-XX cWW cW-W 8 A.DC8 B.DG17 C-G WC 19-XIX cWW cW-W 9 A.DA9 B.DT16 A-T WC 20-XX cWW cW-W 10 A.DG10 B.DC15 G-C WC 19-XIX cWW cW-W 11 A.DT11 B.DA14 T-A WC 20-XX cWW cW-W 12 A.DC12 B.DG13 C-G 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'-GACTGTACAGTC-3' bp-type |||||||||||| strand-2 3'-CTGACATGTCAG-5' helix-form .B.......B. 1 A.DG1 B.DC24 G-C WC 19-XIX cWW cW-W 2 A.DA2 B.DT23 A-T WC 20-XX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DT4 B.DA21 T-A WC 20-XX cWW cW-W 5 A.DG5 B.DC20 G-C WC 19-XIX cWW cW-W 6 A.DT6 B.DA19 T-A WC 20-XX cWW cW-W 7 A.DA7 B.DT18 A-T WC 20-XX cWW cW-W 8 A.DC8 B.DG17 C-G WC 19-XIX cWW cW-W 9 A.DA9 B.DT16 A-T WC 20-XX cWW cW-W 10 A.DG10 B.DC15 G-C WC 19-XIX cWW cW-W 11 A.DT11 B.DA14 T-A WC 20-XX cWW cW-W 12 A.DC12 B.DG13 C-G 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'-GACTGTACAGTC-3' bp-type |||||||||||| strand-2 3'-CTGACATGTCAG-5' helix-form .B.......B. 1 A.DG1 B.DC24 G-C WC 19-XIX cWW cW-W 2 A.DA2 B.DT23 A-T WC 20-XX cWW cW-W 3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W 4 A.DT4 B.DA21 T-A WC 20-XX cWW cW-W 5 A.DG5 B.DC20 G-C WC 19-XIX cWW cW-W 6 A.DT6 B.DA19 T-A WC 20-XX cWW cW-W 7 A.DA7 B.DT18 A-T WC 20-XX cWW cW-W 8 A.DC8 B.DG17 C-G WC 19-XIX cWW cW-W 9 A.DA9 B.DT16 A-T WC 20-XX cWW cW-W 10 A.DG10 B.DC15 G-C WC 19-XIX cWW cW-W 11 A.DT11 B.DA14 T-A WC 20-XX cWW cW-W 12 A.DC12 B.DG13 C-G WC 19-XIX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1x2o nts=24 [whole] GACTGTACAGTC&GACTGTACAGTC ((((((((((((&)))))))))))) >1x2o-A #1 nts=12 3.21(0.07) [chain] DNA GACTGTACAGTC (((((((((((( >1x2o-B #2 nts=12 3.21(0.06) [chain] DNA GACTGTACAGTC )))))))))))) **************************************************************************** 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 G ( A.DG1 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( A.DA2 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 C ( A.DC3 0.001 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( A.DT4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 G ( A.DG5 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 T ( A.DT6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 A ( A.DA7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 C ( A.DC8 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 A ( A.DA9 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 G ( A.DG10 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 T ( A.DT11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 C ( A.DC12 0.001 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 13 G ) B.DG13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 14 A ) B.DA14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 C ) B.DC15 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 T ) B.DT16 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 G ) B.DG17 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 T ) B.DT18 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 A ) B.DA19 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 C ) B.DC20 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ) B.DA21 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 G ) B.DG22 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 T ) B.DT23 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 C ) B.DC24 0.002 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