**************************************************************************** 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=4a04.pdb -o=4a04.out File name: 4a04.pdb no. of DNA/RNA chains: 2 [D=23,E=24] no. of nucleotides: 47 no. of atoms: 4062 no. of waters: 66 no. of metals: 0 **************************************************************************** List of 22 base pairs nt1 nt2 bp name Saenger LW DSSR 1 D.DA2 E.DT23 A-T WC 20-XX cWW cW-W 2 D.DT3 E.DA22 T-A WC 20-XX cWW cW-W 3 D.DT4 E.DA21 T-A WC 20-XX cWW cW-W 4 D.DT5 E.DA20 T-A WC 20-XX cWW cW-W 5 D.DC6 E.DG19 C-G WC 19-XIX cWW cW-W 6 D.DA7 E.DT18 A-T WC 20-XX cWW cW-W 7 D.DC8 E.DG17 C-G WC 19-XIX cWW cW-W 8 D.DA9 E.DT16 A-T WC 20-XX cWW cW-W 9 D.DC10 E.DG15 C-G WC 19-XIX cWW cW-W 10 D.DC11 E.DG14 C-G WC 19-XIX cWW cW-W 11 D.DT12 E.DA13 T-A WC 20-XX cWW cW-W 12 D.DA13 E.DT12 A-T WC 20-XX cWW cW-W 13 D.DG14 E.DC11 G-C WC 19-XIX cWW cW-W 14 D.DG15 E.DC10 G-C WC 19-XIX cWW cW-W 15 D.DT16 E.DA9 T-A WC 20-XX cWW cW-W 16 D.DG17 E.DC8 G-C WC 19-XIX cWW cW-W 17 D.DT18 E.DA7 T-A WC 20-XX cWW cW-W 18 D.DG19 E.DC6 G-C WC 19-XIX cWW cW-W 19 D.DA20 E.DT5 A-T WC 20-XX cWW cW-W 20 D.DA21 E.DT4 A-T WC 20-XX cWW cW-W 21 D.DA22 E.DT3 A-T WC 20-XX cWW cW-W 22 D.DT23 E.DA2 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=22 strand-1 5'-ATTTCACACCTAGGTGTGAAAT-3' bp-type |||||||||||||||||||||| strand-2 3'-TAAAGTGTGGATCCACACTTTA-5' helix-form BBBBBBB.BB.BB.BBBBBBB 1 D.DA2 E.DT23 A-T WC 20-XX cWW cW-W 2 D.DT3 E.DA22 T-A WC 20-XX cWW cW-W 3 D.DT4 E.DA21 T-A WC 20-XX cWW cW-W 4 D.DT5 E.DA20 T-A WC 20-XX cWW cW-W 5 D.DC6 E.DG19 C-G WC 19-XIX cWW cW-W 6 D.DA7 E.DT18 A-T WC 20-XX cWW cW-W 7 D.DC8 E.DG17 C-G WC 19-XIX cWW cW-W 8 D.DA9 E.DT16 A-T WC 20-XX cWW cW-W 9 D.DC10 E.DG15 C-G WC 19-XIX cWW cW-W 10 D.DC11 E.DG14 C-G WC 19-XIX cWW cW-W 11 D.DT12 E.DA13 T-A WC 20-XX cWW cW-W 12 D.DA13 E.DT12 A-T WC 20-XX cWW cW-W 13 D.DG14 E.DC11 G-C WC 19-XIX cWW cW-W 14 D.DG15 E.DC10 G-C WC 19-XIX cWW cW-W 15 D.DT16 E.DA9 T-A WC 20-XX cWW cW-W 16 D.DG17 E.DC8 G-C WC 19-XIX cWW cW-W 17 D.DT18 E.DA7 T-A WC 20-XX cWW cW-W 18 D.DG19 E.DC6 G-C WC 19-XIX cWW cW-W 19 D.DA20 E.DT5 A-T WC 20-XX cWW cW-W 20 D.DA21 E.DT4 A-T WC 20-XX cWW cW-W 21 D.DA22 E.DT3 A-T WC 20-XX cWW cW-W 22 D.DT23 E.DA2 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=22 strand-1 5'-ATTTCACACCTAGGTGTGAAAT-3' bp-type |||||||||||||||||||||| strand-2 3'-TAAAGTGTGGATCCACACTTTA-5' helix-form BBBBBBB.BB.BB.BBBBBBB 1 D.DA2 E.DT23 A-T WC 20-XX cWW cW-W 2 D.DT3 E.DA22 T-A WC 20-XX cWW cW-W 3 D.DT4 E.DA21 T-A WC 20-XX cWW cW-W 4 D.DT5 E.DA20 T-A WC 20-XX cWW cW-W 5 D.DC6 E.DG19 C-G WC 19-XIX cWW cW-W 6 D.DA7 E.DT18 A-T WC 20-XX cWW cW-W 7 D.DC8 E.DG17 C-G WC 19-XIX cWW cW-W 8 D.DA9 E.DT16 A-T WC 20-XX cWW cW-W 9 D.DC10 E.DG15 C-G WC 19-XIX cWW cW-W 10 D.DC11 E.DG14 C-G WC 19-XIX cWW cW-W 11 D.DT12 E.DA13 T-A WC 20-XX cWW cW-W 12 D.DA13 E.DT12 A-T WC 20-XX cWW cW-W 13 D.DG14 E.DC11 G-C WC 19-XIX cWW cW-W 14 D.DG15 E.DC10 G-C WC 19-XIX cWW cW-W 15 D.DT16 E.DA9 T-A WC 20-XX cWW cW-W 16 D.DG17 E.DC8 G-C WC 19-XIX cWW cW-W 17 D.DT18 E.DA7 T-A WC 20-XX cWW cW-W 18 D.DG19 E.DC6 G-C WC 19-XIX cWW cW-W 19 D.DA20 E.DT5 A-T WC 20-XX cWW cW-W 20 D.DA21 E.DT4 A-T WC 20-XX cWW cW-W 21 D.DA22 E.DT3 A-T WC 20-XX cWW cW-W 22 D.DT23 E.DA2 T-A WC 20-XX cWW cW-W **************************************************************************** List of 2 base stacks 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 AA D.DA1,D.DA2 2 nts=2 AA E.DA1,E.DA2 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T E.DT24 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=1 A D.DA1 2 nts=1 A E.DA1 3 nts=1 T E.DT24 **************************************************************************** List of 1 splayed-apart dinucleotide 1 E.DT23 E.DT24 angle=107 distance=15.1 ratio=0.81 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 TT E.DT23,E.DT24 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4a04 nts=47 [whole] AATTTCACACCTAGGTGTGAAAT&AATTTCACACCTAGGTGTGAAATT .((((((((((((((((((((((&.)))))))))))))))))))))). >4a04-D #1 nts=23 3.28(0.49) [chain] DNA AATTTCACACCTAGGTGTGAAAT .(((((((((((((((((((((( >4a04-E #2 nts=24 3.27(0.51) [chain] DNA AATTTCACACCTAGGTGTGAAATT .)))))))))))))))))))))). **************************************************************************** Summary of structural features of 47 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 A . D.DA1 0.013 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 A ( D.DA2 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 3 T ( D.DT3 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( D.DT4 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( D.DT5 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 C ( D.DC6 0.011 anti,BI,canonical,non-pair-contact,helix,stem 7 A ( D.DA7 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 C ( D.DC8 0.014 anti,BI,canonical,non-pair-contact,helix,stem 9 A ( D.DA9 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( D.DC10 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 C ( D.DC11 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 12 T ( D.DT12 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 A ( D.DA13 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 G ( D.DG14 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 15 G ( D.DG15 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 T ( D.DT16 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 17 G ( D.DG17 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 T ( D.DT18 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 G ( D.DG19 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 20 A ( D.DA20 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ( D.DA21 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 A ( D.DA22 0.015 anti,canonical,non-pair-contact,helix,stem 23 T ( D.DT23 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 24 A . E.DA1 0.017 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop 25 A ) E.DA2 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 26 T ) E.DT3 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 T ) E.DT4 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 28 T ) E.DT5 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 C ) E.DC6 0.011 anti,BI,canonical,non-pair-contact,helix,stem 30 A ) E.DA7 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 C ) E.DC8 0.010 anti,BI,canonical,non-pair-contact,helix,stem 32 A ) E.DA9 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 33 C ) E.DC10 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 34 C ) E.DC11 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 35 T ) E.DT12 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 36 A ) E.DA13 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 37 G ) E.DG14 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 38 G ) E.DG15 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 39 T ) E.DT16 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 40 G ) E.DG17 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 41 T ) E.DT18 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 42 G ) E.DG19 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 43 A ) E.DA20 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 44 A ) E.DA21 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 45 A ) E.DA22 0.012 anti,canonical,non-pair-contact,helix,stem 46 T ) E.DT23 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 47 T . E.DT24 0.013 anti,non-stack,ss-non-loop,splayed-apart **************************************************************************** List of 9 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-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks