**************************************************************************** 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=6x6d.pdb -o=6x6d.out File name: 6x6d.pdb no. of DNA/RNA chains: 2 [C=18,D=18] no. of nucleotides: 36 no. of atoms: 2997 no. of waters: 13 no. of metals: 4 [Zn=4] **************************************************************************** List of 17 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DC2 D.DG18 C-G WC 19-XIX cWW cW-W 2 C.DA3 D.DT17 A-T WC 20-XX cWW cW-W 3 C.DG4 D.DC16 G-C WC 19-XIX cWW cW-W 4 C.DA5 D.DT15 A-T WC 20-XX cWW cW-W 5 C.DA6 D.DT14 A-T WC 20-XX cWW cW-W 6 C.DC7 D.DG13 C-G WC 19-XIX cWW cW-W 7 C.DG8 D.DC12 G-C WC 19-XIX cWW cW-W 8 C.DG9 D.DC11 G-C WC 19-XIX cWW cW-W 9 C.DA10 D.DT10 A-T WC 20-XX cWW cW-W 10 C.DG11 D.DC9 G-C WC 19-XIX cWW cW-W 11 C.DC12 D.DG8 C-G WC 19-XIX cWW cW-W 12 C.DG13 D.DC7 G-C WC 19-XIX cWW cW-W 13 C.DT14 D.DA6 T-A WC 20-XX cWW cW-W 14 C.DT15 D.DA5 T-A WC 20-XX cWW cW-W 15 C.DC16 D.DG4 C-G WC 19-XIX cWW cW-W 16 C.DT17 D.DA3 T-A WC 20-XX cWW cW-W 17 C.DG18 D.DC2 G-C WC 19-XIX 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=17 strand-1 5'-CAGAACGGAGCGTTCTG-3' bp-type ||||||||||||||||| strand-2 3'-GTCTTGCCTCGCAAGAC-5' helix-form BBBBBBBBBBBBBBBB 1 C.DC2 D.DG18 C-G WC 19-XIX cWW cW-W 2 C.DA3 D.DT17 A-T WC 20-XX cWW cW-W 3 C.DG4 D.DC16 G-C WC 19-XIX cWW cW-W 4 C.DA5 D.DT15 A-T WC 20-XX cWW cW-W 5 C.DA6 D.DT14 A-T WC 20-XX cWW cW-W 6 C.DC7 D.DG13 C-G WC 19-XIX cWW cW-W 7 C.DG8 D.DC12 G-C WC 19-XIX cWW cW-W 8 C.DG9 D.DC11 G-C WC 19-XIX cWW cW-W 9 C.DA10 D.DT10 A-T WC 20-XX cWW cW-W 10 C.DG11 D.DC9 G-C WC 19-XIX cWW cW-W 11 C.DC12 D.DG8 C-G WC 19-XIX cWW cW-W 12 C.DG13 D.DC7 G-C WC 19-XIX cWW cW-W 13 C.DT14 D.DA6 T-A WC 20-XX cWW cW-W 14 C.DT15 D.DA5 T-A WC 20-XX cWW cW-W 15 C.DC16 D.DG4 C-G WC 19-XIX cWW cW-W 16 C.DT17 D.DA3 T-A WC 20-XX cWW cW-W 17 C.DG18 D.DC2 G-C WC 19-XIX 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=17 strand-1 5'-CAGAACGGAGCGTTCTG-3' bp-type ||||||||||||||||| strand-2 3'-GTCTTGCCTCGCAAGAC-5' helix-form BBBBBBBBBBBBBBBB 1 C.DC2 D.DG18 C-G WC 19-XIX cWW cW-W 2 C.DA3 D.DT17 A-T WC 20-XX cWW cW-W 3 C.DG4 D.DC16 G-C WC 19-XIX cWW cW-W 4 C.DA5 D.DT15 A-T WC 20-XX cWW cW-W 5 C.DA6 D.DT14 A-T WC 20-XX cWW cW-W 6 C.DC7 D.DG13 C-G WC 19-XIX cWW cW-W 7 C.DG8 D.DC12 G-C WC 19-XIX cWW cW-W 8 C.DG9 D.DC11 G-C WC 19-XIX cWW cW-W 9 C.DA10 D.DT10 A-T WC 20-XX cWW cW-W 10 C.DG11 D.DC9 G-C WC 19-XIX cWW cW-W 11 C.DC12 D.DG8 C-G WC 19-XIX cWW cW-W 12 C.DG13 D.DC7 G-C WC 19-XIX cWW cW-W 13 C.DT14 D.DA6 T-A WC 20-XX cWW cW-W 14 C.DT15 D.DA5 T-A WC 20-XX cWW cW-W 15 C.DC16 D.DG4 C-G WC 19-XIX cWW cW-W 16 C.DT17 D.DA3 T-A WC 20-XX cWW cW-W 17 C.DG18 D.DC2 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 base stack Note: a stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 CC C.DC1,C.DC2 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T D.DT1 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 C C.DC1 2 nts=1 T D.DT1 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6x6d nts=36 [whole] CCAGAACGGAGCGTTCTG&TCAGAACGCTCCGTTCTG .(((((((((((((((((&.))))))))))))))))) >6x6d-C #1 nts=18 3.41(0.30) [chain] DNA CCAGAACGGAGCGTTCTG .((((((((((((((((( >6x6d-D #2 nts=18 3.42(0.59) [chain] DNA TCAGAACGCTCCGTTCTG .))))))))))))))))) **************************************************************************** Summary of structural features of 36 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 . C.DC1 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 C ( C.DC2 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 3 A ( C.DA3 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 4 G ( C.DG4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 A ( C.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 A ( C.DA6 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 7 C ( C.DC7 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 8 G ( C.DG8 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 9 G ( C.DG9 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( C.DA10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 G ( C.DG11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 C ( C.DC12 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 G ( C.DG13 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 14 T ( C.DT14 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 T ( C.DT15 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( C.DC16 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 17 T ( C.DT17 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 18 G ( C.DG18 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 19 T . D.DT1 0.002 anti,~C2'-endo,BI,non-stack,non-pair-contact,ss-non-loop 20 C ) D.DC2 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 21 A ) D.DA3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 22 G ) D.DG4 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 23 A ) D.DA5 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 A ) D.DA6 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 25 C ) D.DC7 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 26 G ) D.DG8 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 27 C ) D.DC9 0.003 anti,BI,canonical,non-pair-contact,helix,stem 28 T ) D.DT10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 C ) D.DC11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 C ) D.DC12 0.003 anti,BI,canonical,non-pair-contact,helix,stem 31 G ) D.DG13 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 32 T ) D.DT14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 33 T ) D.DT15 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 34 C ) D.DC16 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 35 T ) D.DT17 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 36 G ) D.DG18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 8 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-stacks.pdb -- an ensemble of base stacks