**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=6mih.pdb -o=6mih.out File name: 6mih.pdb no. of DNA/RNA chains: 2 [B=8,G=8] no. of nucleotides: 16 no. of atoms: 2522 no. of waters: 204 no. of metals: 0 **************************************************************************** List of 4 types of 4 modified nucleotides nt count list 1 1W5-c 1 G.1W5/12 2 1WA-g 1 B.1WA5 3 IGU-a 1 B.IGU7 4 JSP-t 1 G.JSP10 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DC1 G.DG16 C-G WC 19-XIX cWW cW-W 2 B.DT2 G.DA15 T-A WC 20-XX cWW cW-W 3 B.DT3 G.DA14 T-A WC 20-XX cWW cW-W 4 B.DA4 G.DT13 A-T WC 20-XX cWW cW-W 5 B.1WA5 G.1W5/12 g-c WC 19-XIX cWW cW-W 6 B.DC6 G.DG11 C-G WC 19-XIX cWW cW-W 7 B.IGU7 G.JSP10 a-t WC 20-XX cWW cW-W 8 B.DT8 G.DA9 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 helix Note: a helix is defined by base-stacking interactions, regardless of bp 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=8 strand-1 5'-CTTAgCaT-3' bp-type |||||||| strand-2 3'-GAATcGtA-5' helix-form BBBBBBB 1 B.DC1 G.DG16 C-G WC 19-XIX cWW cW-W 2 B.DT2 G.DA15 T-A WC 20-XX cWW cW-W 3 B.DT3 G.DA14 T-A WC 20-XX cWW cW-W 4 B.DA4 G.DT13 A-T WC 20-XX cWW cW-W 5 B.1WA5 G.1W5/12 g-c WC 19-XIX cWW cW-W 6 B.DC6 G.DG11 C-G WC 19-XIX cWW cW-W 7 B.IGU7 G.JSP10 a-t WC 20-XX cWW cW-W 8 B.DT8 G.DA9 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 stem Note: a stem is defined as a helix consisting of only 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=8 strand-1 5'-CTTAgCaT-3' bp-type |||||||| strand-2 3'-GAATcGtA-5' helix-form BBBBBBB 1 B.DC1 G.DG16 C-G WC 19-XIX cWW cW-W 2 B.DT2 G.DA15 T-A WC 20-XX cWW cW-W 3 B.DT3 G.DA14 T-A WC 20-XX cWW cW-W 4 B.DA4 G.DT13 A-T WC 20-XX cWW cW-W 5 B.1WA5 G.1W5/12 g-c WC 19-XIX cWW cW-W 6 B.DC6 G.DG11 C-G WC 19-XIX cWW cW-W 7 B.IGU7 G.JSP10 a-t WC 20-XX cWW cW-W 8 B.DT8 G.DA9 T-A WC 20-XX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6mih nts=16 [whole] CTTAgCaT&AtGcTAAG ((((((((&)))))))) >6mih-B #1 nts=8 3.58(0.28) [chain] DNA CTTAgCaT (((((((( >6mih-G #2 nts=8 3.30(0.28) [chain] DNA AtGcTAAG )))))))) **************************************************************************** Summary of structural features of 16 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 ( B.DC1 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 T ( B.DT2 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 T ( B.DT3 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 4 A ( B.DA4 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 g ( B.1WA5 0.049 modified,anti,~C2'-endo,canonical,non-pair-contact,helix,stem 6 C ( B.DC6 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 7 a ( B.IGU7 0.103 modified,anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 8 T ( B.DT8 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 9 A ) G.DA9 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 10 t ) G.JSP10 0.086 modified,anti,BI,canonical,non-pair-contact,helix,stem 11 G ) G.DG11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 c ) G.1W5/12 0.062 modified,anti,~C3'-endo,canonical,non-pair-contact,helix,stem 13 T ) G.DT13 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 A ) G.DA14 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 A ) G.DA15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 G ) G.DG16 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 7 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