**************************************************************************** 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=6cvo.pdb -o=6cvo.out File name: 6cvo.pdb no. of DNA/RNA chains: 4 [D=22,E=6,G=22,H=6] no. of nucleotides: 58 no. of atoms: 8102 no. of waters: 404 no. of metals: 2 [Zn=2] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 AMP-a 2 A.AMP401,B.AMP401 **************************************************************************** List of 26 base pairs nt1 nt2 bp name Saenger LW DSSR 1 D.G1 G.DC16 G-C WC 19-XIX cWW cW-W 2 D.DT2 G.DA15 T-A WC 20-XX cWW cW-W 3 D.DT3 G.DA14 T-A WC 20-XX cWW cW-W 4 D.DC4 G.DG13 C-G WC 19-XIX cWW cW-W 5 D.DT5 G.DA12 T-A WC 20-XX cWW cW-W 6 D.DA6 G.DT11 A-T WC 20-XX cWW cW-W 7 D.DT7 G.DA10 T-A WC 20-XX cWW cW-W 8 D.DA8 G.DT9 A-T WC 20-XX cWW cW-W 9 D.DT9 G.DA8 T-A WC 20-XX cWW cW-W 10 D.DA10 G.DT7 A-T WC 20-XX cWW cW-W 11 D.DT11 G.DA6 T-A WC 20-XX cWW cW-W 12 D.DA12 G.DT5 A-T WC 20-XX cWW cW-W 13 D.DG13 G.DC4 G-C WC 19-XIX cWW cW-W 14 D.DA14 G.DT3 A-T WC 20-XX cWW cW-W 15 D.DA15 G.DT2 A-T WC 20-XX cWW cW-W 16 D.DG17 H.DC6 G-C WC 19-XIX cWW cW-W 17 D.DC18 H.DG5 C-G WC 19-XIX cWW cW-W 18 D.DT19 H.DA4 T-A WC 20-XX cWW cW-W 19 D.DG20 H.DC3 G-C WC 19-XIX cWW cW-W 20 D.DT21 H.DA2 T-A WC 20-XX cWW cW-W 21 D.DT22 H.DA1 T-A WC 20-XX cWW cW-W 22 G.DC18 E.DG5 C-G WC 19-XIX cWW cW-W 23 G.DT19 E.DA4 T-A WC 20-XX cWW cW-W 24 G.DG20 E.DC3 G-C WC 19-XIX cWW cW-W 25 G.DT21 E.DA2 T-A WC 20-XX cWW cW-W 26 G.DT22 E.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 3 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=15 strand-1 5'-GTTCTATATATAGAA-3' bp-type ||||||||||||||| strand-2 3'-CAAGATATATATCTT-5' helix-form .BBBBBBBBBBBBB 1 D.G1 G.DC16 G-C WC 19-XIX cWW cW-W 2 D.DT2 G.DA15 T-A WC 20-XX cWW cW-W 3 D.DT3 G.DA14 T-A WC 20-XX cWW cW-W 4 D.DC4 G.DG13 C-G WC 19-XIX cWW cW-W 5 D.DT5 G.DA12 T-A WC 20-XX cWW cW-W 6 D.DA6 G.DT11 A-T WC 20-XX cWW cW-W 7 D.DT7 G.DA10 T-A WC 20-XX cWW cW-W 8 D.DA8 G.DT9 A-T WC 20-XX cWW cW-W 9 D.DT9 G.DA8 T-A WC 20-XX cWW cW-W 10 D.DA10 G.DT7 A-T WC 20-XX cWW cW-W 11 D.DT11 G.DA6 T-A WC 20-XX cWW cW-W 12 D.DA12 G.DT5 A-T WC 20-XX cWW cW-W 13 D.DG13 G.DC4 G-C WC 19-XIX cWW cW-W 14 D.DA14 G.DT3 A-T WC 20-XX cWW cW-W 15 D.DA15 G.DT2 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=6 strand-1 5'-GCTGTT-3' bp-type |||||| strand-2 3'-CGACAA-5' helix-form BBBBB 1 D.DG17 H.DC6 G-C WC 19-XIX cWW cW-W 2 D.DC18 H.DG5 C-G WC 19-XIX cWW cW-W 3 D.DT19 H.DA4 T-A WC 20-XX cWW cW-W 4 D.DG20 H.DC3 G-C WC 19-XIX cWW cW-W 5 D.DT21 H.DA2 T-A WC 20-XX cWW cW-W 6 D.DT22 H.DA1 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=5 strand-1 5'-CTGTT-3' bp-type ||||| strand-2 3'-GACAA-5' helix-form B.BB 1 G.DC18 E.DG5 C-G WC 19-XIX cWW cW-W 2 G.DT19 E.DA4 T-A WC 20-XX cWW cW-W 3 G.DG20 E.DC3 G-C WC 19-XIX cWW cW-W 4 G.DT21 E.DA2 T-A WC 20-XX cWW cW-W 5 G.DT22 E.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 3 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=15 strand-1 5'-GTTCTATATATAGAA-3' bp-type ||||||||||||||| strand-2 3'-CAAGATATATATCTT-5' helix-form .BBBBBBBBBBBBB 1 D.G1 G.DC16 G-C WC 19-XIX cWW cW-W 2 D.DT2 G.DA15 T-A WC 20-XX cWW cW-W 3 D.DT3 G.DA14 T-A WC 20-XX cWW cW-W 4 D.DC4 G.DG13 C-G WC 19-XIX cWW cW-W 5 D.DT5 G.DA12 T-A WC 20-XX cWW cW-W 6 D.DA6 G.DT11 A-T WC 20-XX cWW cW-W 7 D.DT7 G.DA10 T-A WC 20-XX cWW cW-W 8 D.DA8 G.DT9 A-T WC 20-XX cWW cW-W 9 D.DT9 G.DA8 T-A WC 20-XX cWW cW-W 10 D.DA10 G.DT7 A-T WC 20-XX cWW cW-W 11 D.DT11 G.DA6 T-A WC 20-XX cWW cW-W 12 D.DA12 G.DT5 A-T WC 20-XX cWW cW-W 13 D.DG13 G.DC4 G-C WC 19-XIX cWW cW-W 14 D.DA14 G.DT3 A-T WC 20-XX cWW cW-W 15 D.DA15 G.DT2 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=6 strand-1 5'-GCTGTT-3' bp-type |||||| strand-2 3'-CGACAA-5' helix-form BBBBB 1 D.DG17 H.DC6 G-C WC 19-XIX cWW cW-W 2 D.DC18 H.DG5 C-G WC 19-XIX cWW cW-W 3 D.DT19 H.DA4 T-A WC 20-XX cWW cW-W 4 D.DG20 H.DC3 G-C WC 19-XIX cWW cW-W 5 D.DT21 H.DA2 T-A WC 20-XX cWW cW-W 6 D.DT22 H.DA1 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#3] bps=5 strand-1 5'-CTGTT-3' bp-type ||||| strand-2 3'-GACAA-5' helix-form B.BB 1 G.DC18 E.DG5 C-G WC 19-XIX cWW cW-W 2 G.DT19 E.DA4 T-A WC 20-XX cWW cW-W 3 G.DG20 E.DC3 G-C WC 19-XIX cWW cW-W 4 G.DT21 E.DA2 T-A WC 20-XX cWW cW-W 5 G.DT22 E.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 3 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 WG A.TRP167,D.G1 2 nts=2 GC G.DG17,G.DC18 3 nts=3 WGT B.TRP167,G.G1,G.DT2 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 CC D.DC16,E.DC6 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=1 C D.DC16 2 nts=1 G G.G1 3 nts=1 G G.DG17 4 nts=1 C E.DC6 5 nts=1 a A.AMP401 6 nts=1 a B.AMP401 **************************************************************************** List of 3 splayed-apart dinucleotides 1 D.DA15 D.DC16 angle=100 distance=15.0 ratio=0.77 2 D.DC16 D.DG17 angle=127 distance=17.6 ratio=0.90 3 E.DG5 E.DC6 angle=102 distance=15.1 ratio=0.78 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 ACG D.DA15,D.DC16,D.DG17 2 nts=2 GC E.DG5,E.DC6 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6cvo nts=58 [whole] GTTCTATATATAGAACGCTGTT>TCTATATATAGAACGCTGTT&AACAGC&AACAGC&a&a (((((((((((((((.[[[[[[&.))))))))))))))).(((((&))))).&]]]]]]&.&. >6cvo-D #1 nts=22 2.92(0.85) [chain] DNA[21]/1 GTTCTATATATAGAACGCTGTT (((((((((((((((.[[[[[[ >6cvo-G #2 nts=22 3.26(0.77) [chain] DNA[21]/1 GTTCTATATATAGAACGCTGTT .))))))))))))))).((((( >6cvo-E #3 nts=6 3.93(0.26) [chain] DNA AACAGC ))))). >6cvo-H #4 nts=6 3.22(0.15) [chain] DNA AACAGC ]]]]]] **************************************************************************** Summary of structural features of 58 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 G ( D.G1 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 2 T ( D.DT2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 3 T ( D.DT3 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 C ( D.DC4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 T ( D.DT5 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 A ( D.DA6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 T ( D.DT7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 A ( D.DA8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 T ( D.DT9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( D.DA10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 T ( D.DT11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 A ( D.DA12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 G ( D.DG13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 A ( D.DA14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 A ( D.DA15 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 16 C . D.DC16 0.002 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 17 G [ D.DG17 0.005 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 18 C [ D.DC18 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 T [ D.DT19 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 G [ D.DG20 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 T [ D.DT21 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T [ D.DT22 0.002 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 23 G . G.G1 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 24 T ) G.DT2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 25 T ) G.DT3 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 C ) G.DC4 0.002 anti,BI,canonical,non-pair-contact,helix,stem 27 T ) G.DT5 0.003 anti,BI,canonical,non-pair-contact,helix,stem 28 A ) G.DA6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 T ) G.DT7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 A ) G.DA8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 T ) G.DT9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 32 A ) G.DA10 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 33 T ) G.DT11 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 34 A ) G.DA12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 35 G ) G.DG13 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 36 A ) G.DA14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 37 A ) G.DA15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 38 C ) G.DC16 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end 39 G . G.DG17 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 40 C ( G.DC18 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 41 T ( G.DT19 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 42 G ( G.DG20 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 43 T ( G.DT21 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 44 T ( G.DT22 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 45 A ) E.DA1 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 46 A ) E.DA2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 47 C ) E.DC3 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 48 A ) E.DA4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 49 G ) E.DG5 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 50 C . E.DC6 0.002 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 51 A ] H.DA1 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 52 A ] H.DA2 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 53 C ] H.DC3 0.002 pseudoknotted,anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 54 A ] H.DA4 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 55 G ] H.DG5 0.003 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 56 C ] H.DC6 0.002 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 57 a . A.AMP401 0.016 modified,anti,~C2'-endo,ss-non-loop,phosphate 58 a . B.AMP401 0.015 modified,anti,~C2'-endo,ss-non-loop,phosphate **************************************************************************** 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