**************************************************************************** File name: 1k5f.pdb no. of DNA/RNA chains: 2 [A=11,B=11] no. of nucleotides: 22 no. of atoms: 713 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 ABS-a 1 A.ABS6 **************************************************************************** List of 11 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG22 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC21 G-C WC 19-XIX cWW cW-W 3 A.DG3 B.DC20 G-C WC 19-XIX cWW cW-W 4 A.DA4 B.DT19 A-T WC 20-XX cWW cW-W 5 A.DC5 B.DG18 C-G WC 19-XIX cWW cW-W 6 A.ABS6 B.DT17 a-T WC 20-XX cWW cW-W 7 A.DA7 B.DT16 A-T WC 20-XX cWW cW-W 8 A.DG8 B.DC15 G-C WC 19-XIX cWW cW-W 9 A.DA9 B.DT14 A-T WC 20-XX cWW cW-W 10 A.DA10 B.DT13 A-T WC 20-XX cWW cW-W 11 A.DG11 B.DC12 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=11 strand-1 5'-CGGACaAGAAG-3' bp-type ||||||||||| strand-2 3'-GCCTGTTCTTC-5' helix-form BBBBBBBBBB 1 A.DC1 B.DG22 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC21 G-C WC 19-XIX cWW cW-W 3 A.DG3 B.DC20 G-C WC 19-XIX cWW cW-W 4 A.DA4 B.DT19 A-T WC 20-XX cWW cW-W 5 A.DC5 B.DG18 C-G WC 19-XIX cWW cW-W 6 A.ABS6 B.DT17 a-T WC 20-XX cWW cW-W 7 A.DA7 B.DT16 A-T WC 20-XX cWW cW-W 8 A.DG8 B.DC15 G-C WC 19-XIX cWW cW-W 9 A.DA9 B.DT14 A-T WC 20-XX cWW cW-W 10 A.DA10 B.DT13 A-T WC 20-XX cWW cW-W 11 A.DG11 B.DC12 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=11 strand-1 5'-CGGACaAGAAG-3' bp-type ||||||||||| strand-2 3'-GCCTGTTCTTC-5' helix-form BBBBBBBBBB 1 A.DC1 B.DG22 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC21 G-C WC 19-XIX cWW cW-W 3 A.DG3 B.DC20 G-C WC 19-XIX cWW cW-W 4 A.DA4 B.DT19 A-T WC 20-XX cWW cW-W 5 A.DC5 B.DG18 C-G WC 19-XIX cWW cW-W 6 A.ABS6 B.DT17 a-T WC 20-XX cWW cW-W 7 A.DA7 B.DT16 A-T WC 20-XX cWW cW-W 8 A.DG8 B.DC15 G-C WC 19-XIX cWW cW-W 9 A.DA9 B.DT14 A-T WC 20-XX cWW cW-W 10 A.DA10 B.DT13 A-T WC 20-XX cWW cW-W 11 A.DG11 B.DC12 G-C WC 19-XIX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1k5f nts=22 [whole] CGGACaAGAAG&CTTCTTGTCCG (((((((((((&))))))))))) >1k5f-A #1 nts=11 2.97(0.36) [chain] DNA CGGACaAGAAG ((((((((((( >1k5f-B #2 nts=11 3.12(0.47) [chain] DNA CTTCTTGTCCG ))))))))))) **************************************************************************** Summary of structural features of 22 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 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( A.DG2 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( A.DG3 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 A ( A.DA4 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( A.DC5 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 a ( A.ABS6 0.023 modified,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 A ( A.DA7 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 G ( A.DG8 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 A ( A.DA9 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( A.DA10 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 G ( A.DG11 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 12 C ) B.DC12 0.009 anti,BI,canonical,non-pair-contact,helix-end,stem-end 13 T ) B.DT13 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 T ) B.DT14 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 C ) B.DC15 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 T ) B.DT16 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 T ) B.DT17 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 G ) B.DG18 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 T ) B.DT19 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 C ) B.DC20 0.009 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 0.019 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