**************************************************************************** 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=4ynq.pdb -o=4ynq.out File name: 4ynq.pdb no. of DNA/RNA chains: 4 [E=21,F=20,G=21,H=21] no. of nucleotides: 83 no. of atoms: 8710 no. of waters: 39 no. of metals: 4 [Mg=4] **************************************************************************** List of 34 base pairs nt1 nt2 bp name Saenger LW DSSR 1 E.DG5 F.DC20 G-C WC 19-XIX cWW cW-W 2 E.DT6 F.DA19 T-A WC 20-XX cWW cW-W 3 E.DG7 F.DC18 G-C WC 19-XIX cWW cW-W 4 E.DC8 F.DG17 C-G WC 19-XIX cWW cW-W 5 E.DT9 F.DA16 T-A WC 20-XX cWW cW-W 6 E.DG10 F.DC15 G-C WC 19-XIX cWW cW-W 7 E.DA11 F.DT14 A-T WC 20-XX cWW cW-W 8 E.DC12 F.DG13 C-G WC 19-XIX cWW cW-W 9 E.DG13 F.DC12 G-C WC 19-XIX cWW cW-W 10 E.DT14 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DC15 F.DG10 C-G WC 19-XIX cWW cW-W 12 E.DA16 F.DT9 A-T WC 20-XX cWW cW-W 13 E.DG17 F.DC8 G-C WC 19-XIX cWW cW-W 14 E.DC18 F.DG7 C-G WC 19-XIX cWW cW-W 15 E.DA19 F.DT6 A-T WC 20-XX cWW cW-W 16 E.DC20 F.DG5 C-G WC 19-XIX cWW cW-W 17 E.DG21 F.DG5 G-G -- -- tWW tW-W 18 G.DG5 H.DC20 G-C WC 19-XIX cWW cW-W 19 G.DT6 H.DA19 T-A WC 20-XX cWW cW-W 20 G.DG7 H.DC18 G-C WC 19-XIX cWW cW-W 21 G.DC8 H.DG17 C-G WC 19-XIX cWW cW-W 22 G.DT9 H.DA16 T-A WC 20-XX cWW cW-W 23 G.DG10 H.DC15 G-C WC 19-XIX cWW cW-W 24 G.DA11 H.DT14 A-T WC 20-XX cWW cW-W 25 G.DC12 H.DG13 C-G WC 19-XIX cWW cW-W 26 G.DG13 H.DC12 G-C WC 19-XIX cWW cW-W 27 G.DT14 H.DA11 T-A WC 20-XX cWW cW-W 28 G.DC15 H.DG10 C-G WC 19-XIX cWW cW-W 29 G.DA16 H.DT9 A-T WC 20-XX cWW cW-W 30 G.DG17 H.DC8 G-C WC 19-XIX cWW cW-W 31 G.DC18 H.DG7 C-G WC 19-XIX cWW cW-W 32 G.DA19 H.DT6 A-T WC 20-XX cWW cW-W 33 G.DC20 H.DG5 C-G WC 19-XIX cWW cW-W 34 G.DG21 H.DG5 G-G -- -- tWW tW-W **************************************************************************** List of 2 multiplets 1 nts=3 CGG E.DC20,E.DG21,F.DG5 2 nts=3 CGG G.DC20,G.DG21,H.DG5 **************************************************************************** List of 2 helices 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=16 strand-1 5'-GTGCTGACGTCAGCAC-3' bp-type |||||||||||||||| strand-2 3'-CACGACTGCAGTCGTG-5' helix-form BBBBBBBBBBBBBB. 1 E.DG5 F.DC20 G-C WC 19-XIX cWW cW-W 2 E.DT6 F.DA19 T-A WC 20-XX cWW cW-W 3 E.DG7 F.DC18 G-C WC 19-XIX cWW cW-W 4 E.DC8 F.DG17 C-G WC 19-XIX cWW cW-W 5 E.DT9 F.DA16 T-A WC 20-XX cWW cW-W 6 E.DG10 F.DC15 G-C WC 19-XIX cWW cW-W 7 E.DA11 F.DT14 A-T WC 20-XX cWW cW-W 8 E.DC12 F.DG13 C-G WC 19-XIX cWW cW-W 9 E.DG13 F.DC12 G-C WC 19-XIX cWW cW-W 10 E.DT14 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DC15 F.DG10 C-G WC 19-XIX cWW cW-W 12 E.DA16 F.DT9 A-T WC 20-XX cWW cW-W 13 E.DG17 F.DC8 G-C WC 19-XIX cWW cW-W 14 E.DC18 F.DG7 C-G WC 19-XIX cWW cW-W 15 E.DA19 F.DT6 A-T WC 20-XX cWW cW-W 16 E.DC20 F.DG5 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=16 strand-1 5'-GTGCTGACGTCAGCAC-3' bp-type |||||||||||||||| strand-2 3'-CACGACTGCAGTCGTG-5' helix-form BB.BBBBBBBBBBB. 1 G.DG5 H.DC20 G-C WC 19-XIX cWW cW-W 2 G.DT6 H.DA19 T-A WC 20-XX cWW cW-W 3 G.DG7 H.DC18 G-C WC 19-XIX cWW cW-W 4 G.DC8 H.DG17 C-G WC 19-XIX cWW cW-W 5 G.DT9 H.DA16 T-A WC 20-XX cWW cW-W 6 G.DG10 H.DC15 G-C WC 19-XIX cWW cW-W 7 G.DA11 H.DT14 A-T WC 20-XX cWW cW-W 8 G.DC12 H.DG13 C-G WC 19-XIX cWW cW-W 9 G.DG13 H.DC12 G-C WC 19-XIX cWW cW-W 10 G.DT14 H.DA11 T-A WC 20-XX cWW cW-W 11 G.DC15 H.DG10 C-G WC 19-XIX cWW cW-W 12 G.DA16 H.DT9 A-T WC 20-XX cWW cW-W 13 G.DG17 H.DC8 G-C WC 19-XIX cWW cW-W 14 G.DC18 H.DG7 C-G WC 19-XIX cWW cW-W 15 G.DA19 H.DT6 A-T WC 20-XX cWW cW-W 16 G.DC20 H.DG5 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems 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=16 strand-1 5'-GTGCTGACGTCAGCAC-3' bp-type |||||||||||||||| strand-2 3'-CACGACTGCAGTCGTG-5' helix-form BBBBBBBBBBBBBB. 1 E.DG5 F.DC20 G-C WC 19-XIX cWW cW-W 2 E.DT6 F.DA19 T-A WC 20-XX cWW cW-W 3 E.DG7 F.DC18 G-C WC 19-XIX cWW cW-W 4 E.DC8 F.DG17 C-G WC 19-XIX cWW cW-W 5 E.DT9 F.DA16 T-A WC 20-XX cWW cW-W 6 E.DG10 F.DC15 G-C WC 19-XIX cWW cW-W 7 E.DA11 F.DT14 A-T WC 20-XX cWW cW-W 8 E.DC12 F.DG13 C-G WC 19-XIX cWW cW-W 9 E.DG13 F.DC12 G-C WC 19-XIX cWW cW-W 10 E.DT14 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DC15 F.DG10 C-G WC 19-XIX cWW cW-W 12 E.DA16 F.DT9 A-T WC 20-XX cWW cW-W 13 E.DG17 F.DC8 G-C WC 19-XIX cWW cW-W 14 E.DC18 F.DG7 C-G WC 19-XIX cWW cW-W 15 E.DA19 F.DT6 A-T WC 20-XX cWW cW-W 16 E.DC20 F.DG5 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=16 strand-1 5'-GTGCTGACGTCAGCAC-3' bp-type |||||||||||||||| strand-2 3'-CACGACTGCAGTCGTG-5' helix-form BB.BBBBBBBBBBB. 1 G.DG5 H.DC20 G-C WC 19-XIX cWW cW-W 2 G.DT6 H.DA19 T-A WC 20-XX cWW cW-W 3 G.DG7 H.DC18 G-C WC 19-XIX cWW cW-W 4 G.DC8 H.DG17 C-G WC 19-XIX cWW cW-W 5 G.DT9 H.DA16 T-A WC 20-XX cWW cW-W 6 G.DG10 H.DC15 G-C WC 19-XIX cWW cW-W 7 G.DA11 H.DT14 A-T WC 20-XX cWW cW-W 8 G.DC12 H.DG13 C-G WC 19-XIX cWW cW-W 9 G.DG13 H.DC12 G-C WC 19-XIX cWW cW-W 10 G.DT14 H.DA11 T-A WC 20-XX cWW cW-W 11 G.DC15 H.DG10 C-G WC 19-XIX cWW cW-W 12 G.DA16 H.DT9 A-T WC 20-XX cWW cW-W 13 G.DG17 H.DC8 G-C WC 19-XIX cWW cW-W 14 G.DC18 H.DG7 C-G WC 19-XIX cWW cW-W 15 G.DA19 H.DT6 A-T WC 20-XX cWW cW-W 16 G.DC20 H.DG5 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 6 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 CG E.DC4,E.DG5 2 nts=2 CG F.DC20,F.DG21 3 nts=2 CG G.DC4,G.DG5 4 nts=3 GAC E.DG21,E.DA22,E.DC23 5 nts=3 CGT H.DC20,H.DG21,H.DT101 6 nts=4 YCAG D.TYR129,G.DC23,G.DA22,G.DG21 **************************************************************************** Nucleotides not involved in stacking interactions nts=6 ACGACG F.DA22,F.DC23,F.DG24,H.DA22,H.DC23,H.DG24 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=1 C E.DC4 2 nts=4 GACG E.DG21,E.DA22,E.DC23,E.DG24 3 nts=4 GACG F.DG21,F.DA22,F.DC23,F.DG24 4 nts=1 C G.DC4 5 nts=4 GACG G.DG21,G.DA22,G.DC23,G.DG24 6 nts=5* GACGT H.DG21,H.DA22,H.DC23,H.DG24,H.DT101 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4ynq nts=83 [whole] CGTGCTGACGTCAGCACGACG>GCTGACGTCAGCACGACG&CGTGCTGACGTCAGCACGACG>GCTGACGTCAGCACGACG&T .((((((((((((((((....&))))))))))))))))....&.((((((((((((((((....&))))))))))))))))....&. >4ynq-E #1 nts=21 3.34(0.79) [chain] DNA CGTGCTGACGTCAGCACGACG .((((((((((((((((.... >4ynq-F #2 nts=20 3.70(1.12) [chain] DNA GTGCTGACGTCAGCACGACG )))))))))))))))).... >4ynq-G #3 nts=21 3.37(0.85) [chain] DNA CGTGCTGACGTCAGCACGACG .((((((((((((((((.... >4ynq-H #4 nts=21 0.86(2.20) [chain] DNA* GTGCTGACGTCAGCACGACG&T ))))))))))))))))....&. **************************************************************************** Summary of structural features of 83 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 . E.DC4 0.006 anti,BI,non-pair-contact,ss-non-loop 2 G ( E.DG5 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 3 T ( E.DT6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( E.DG7 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 C ( E.DC8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 T ( E.DT9 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 7 G ( E.DG10 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 8 A ( E.DA11 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 C ( E.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 G ( E.DG13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 T ( E.DT14 0.006 anti,BI,canonical,non-pair-contact,helix,stem 12 C ( E.DC15 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 13 A ( E.DA16 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 G ( E.DG17 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 C ( E.DC18 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 A ( E.DA19 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ( E.DC20 0.008 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,multiplet 18 G . E.DG21 0.006 anti,~C2'-endo,BI,non-canonical,non-pair-contact,multiplet,ss-non-loop 19 A . E.DA22 0.009 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 20 C . E.DC23 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 21 G . E.DG24 0.006 anti,~C3'-endo,ss-non-loop,phosphate 22 G ) F.DG5 0.004 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet 23 T ) F.DT6 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 G ) F.DG7 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 25 C ) F.DC8 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 T ) F.DT9 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 27 G ) F.DG10 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 A ) F.DA11 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 C ) F.DC12 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 30 G ) F.DG13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 T ) F.DT14 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 32 C ) F.DC15 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 33 A ) F.DA16 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 34 G ) F.DG17 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 35 C ) F.DC18 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 36 A ) F.DA19 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 37 C ) F.DC20 0.010 anti,canonical,non-pair-contact,helix-end,stem-end 38 G . F.DG21 0.008 anti,non-pair-contact,ss-non-loop 39 A . F.DA22 0.006 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop 40 C . F.DC23 0.007 anti,~C3'-endo,BI,non-stack,ss-non-loop 41 G . F.DG24 0.012 anti,~C3'-endo,non-stack,ss-non-loop 42 C . G.DC4 0.004 anti,BI,non-pair-contact,ss-non-loop 43 G ( G.DG5 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 44 T ( G.DT6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 45 G ( G.DG7 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 46 C ( G.DC8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 47 T ( G.DT9 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 48 G ( G.DG10 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 49 A ( G.DA11 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 50 C ( G.DC12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 51 G ( G.DG13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 52 T ( G.DT14 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 53 C ( G.DC15 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 54 A ( G.DA16 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 55 G ( G.DG17 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 56 C ( G.DC18 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 57 A ( G.DA19 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 58 C ( G.DC20 0.007 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,multiplet 59 G . G.DG21 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,multiplet,ss-non-loop 60 A . G.DA22 0.011 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 61 C . G.DC23 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 62 G . G.DG24 0.002 anti,~C3'-endo,ss-non-loop 63 G ) H.DG5 0.005 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,multiplet 64 T ) H.DT6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 65 G ) H.DG7 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 66 C ) H.DC8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 67 T ) H.DT9 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 68 G ) H.DG10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 69 A ) H.DA11 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 70 C ) H.DC12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 71 G ) H.DG13 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 72 T ) H.DT14 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 73 C ) H.DC15 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 74 A ) H.DA16 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 75 G ) H.DG17 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 76 C ) H.DC18 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 77 A ) H.DA19 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 78 C ) H.DC20 0.011 anti,canonical,non-pair-contact,helix-end,stem-end 79 G . H.DG21 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop 80 A . H.DA22 0.006 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop 81 C . H.DC23 0.005 anti,~C3'-endo,BI,non-stack,ss-non-loop 82 G . H.DG24 0.007 break,anti,~C3'-endo,non-stack,ss-non-loop 83 T . H.DT101 0.003 syn,~C2'-endo,non-pair-contact,ss-non-loop **************************************************************************** List of 9 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 9 dssr-stacks.pdb -- an ensemble of base stacks