**************************************************************************** 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=6pcm.pdb -o=6pcm.out File name: 6pcm.pdb no. of DNA/RNA chains: 2 [C=24,D=24] no. of nucleotides: 48 no. of atoms: 12445 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DA2 D.DT13 A-T WC 20-XX cWW cW-W 2 C.DG3 D.DC12 G-C WC 19-XIX cWW cW-W 3 C.DT4 D.DG11 T-G Wobble 28-XXVIII cWW cW-W 4 C.DG5 D.DA10 G-A Sheared 11-XI tSH tm-M 5 C.DA6 D.DG9 A-G Sheared 11-XI tHS tM-m 6 C.DG7 D.DC8 G-C WC 19-XIX cWW cW-W 7 C.DC8 D.DG7 C-G WC 19-XIX cWW cW-W 8 C.DG9 D.DA6 G-A Sheared 11-XI tSH tm-M 9 C.DA10 D.DG5 A-G Sheared 11-XI tHS tM-m 10 C.DG11 D.DT4 G-T Wobble 28-XXVIII cWW cW-W 11 C.DC12 D.DG3 C+G -- -- cWH cW+M 12 C.DT13 D.DA2 T+A -- -- cWH cW+M **************************************************************************** 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[2] bps=12 strand-1 5'-AGTGAGCGAGCT-3' bp-type |||..||..|.. strand-2 3'-TCGAGCGAGTGA-5' helix-form .....B..... 1 C.DA2 D.DT13 A-T WC 20-XX cWW cW-W 2 C.DG3 D.DC12 G-C WC 19-XIX cWW cW-W 3 C.DT4 D.DG11 T-G Wobble 28-XXVIII cWW cW-W 4 C.DG5 D.DA10 G-A Sheared 11-XI tSH tm-M 5 C.DA6 D.DG9 A-G Sheared 11-XI tHS tM-m 6 C.DG7 D.DC8 G-C WC 19-XIX cWW cW-W 7 C.DC8 D.DG7 C-G WC 19-XIX cWW cW-W 8 C.DG9 D.DA6 G-A Sheared 11-XI tSH tm-M 9 C.DA10 D.DG5 A-G Sheared 11-XI tHS tM-m 10 C.DG11 D.DT4 G-T Wobble 28-XXVIII cWW cW-W 11 C.DC12 D.DG3 C+G -- -- cWH cW+M 12 C.DT13 D.DA2 T+A -- -- cWH cW+M **************************************************************************** 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=3 strand-1 5'-AGT-3' bp-type ||| strand-2 3'-TCG-5' helix-form .. 1 C.DA2 D.DT13 A-T WC 20-XX cWW cW-W 2 C.DG3 D.DC12 G-C WC 19-XIX cWW cW-W 3 C.DT4 D.DG11 T-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form B 1 C.DG7 D.DC8 G-C WC 19-XIX cWW cW-W 2 C.DC8 D.DG7 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 C.DG11 D.DT4 G-T Wobble 28-XXVIII cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 15 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 YT A.TYR728,D.DT25 2 nts=2 YA A.TYR809,D.DA22 3 nts=2 WT B.TRP180,D.DT13 4 nts=2 YA B.TYR809,C.DA22 5 nts=3 FTC A.PHE725,D.DT24,D.DC23 6 nts=3 YGT A.TYR806,D.DG21,D.DT20 7 nts=3 YGT B.TYR806,C.DG21,C.DT20 8 nts=3 TYC C.DT14,A.TYR173,C.DC15 9 nts=4 TGGC C.DT4,C.DG5,D.DG9,D.DC8 10 nts=4 GAAG C.DG7,C.DA6,D.DA10,D.DG11 11 nts=5 RCGCT A.ARG165,C.DC16,C.DG17,C.DC18,C.DT19 12 nts=5 YTFTC B.TYR728,C.DT25,B.PHE725,C.DT24,C.DC23 13 nts=6 CGGTGA C.DC8,C.DG9,D.DG5,D.DT4,D.DG3,D.DA2 14 nts=7 WTCGAAG A.TRP180,C.DT13,C.DC12,C.DG11,C.DA10,D.DA6,D.DG7 15 nts=7 TYCCGCT D.DT14,B.TYR173,D.DC15,D.DC16,D.DG17,D.DC18,D.DT19 **************************************************************************** Note: for the various types of loops listed below, numbers within the first set of brackets are the number of loop nts, and numbers in the second set of brackets are the identities of the stems (positive number) or isolated WC/wobble pairs (negative numbers) to which they are linked. **************************************************************************** List of 2 internal loops 1 symmetric internal loop: nts=8; [2,2]; linked by [#1,#2] summary: [2] 2 2 [C.4 D.11 C.7 D.8] 3 2 nts=8 TGAGCGAG C.DT4,C.DG5,C.DA6,C.DG7,D.DC8,D.DG9,D.DA10,D.DG11 nts=2 GA C.DG5,C.DA6 nts=2 GA D.DG9,D.DA10 2 symmetric internal loop: nts=8; [2,2]; linked by [#2,#-1] summary: [2] 2 2 [C.8 D.7 C.11 D.4] 2 1 nts=8 CGAGTGAG C.DC8,C.DG9,C.DA10,C.DG11,D.DT4,D.DG5,D.DA6,D.DG7 nts=2 GA C.DG9,C.DA10 nts=2 GA D.DG5,D.DA6 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=14 CTTCCGCTTGACTT C.DC12,C.DT13,C.DT14,C.DC15,C.DC16,C.DG17,C.DC18,C.DT19,C.DT20,C.DG21,C.DA22,C.DC23,C.DT24,C.DT25 2 nts=2 AG D.DA2,D.DG3 3 nts=12 TCCGCTTGACTT D.DT14,D.DC15,D.DC16,D.DG17,D.DC18,D.DT19,D.DT20,D.DG21,D.DA22,D.DC23,D.DT24,D.DT25 **************************************************************************** List of 2 splayed-apart dinucleotides 1 C.DA22 C.DC23 angle=113 distance=14.0 ratio=0.84 2 D.DA22 D.DC23 angle=106 distance=15.3 ratio=0.80 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 AC C.DA22,C.DC23 2 nts=2 AC D.DA22,D.DC23 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6pcm nts=48 [whole] AGTGAGCGAGCTTCCGCTTGACTT&AGTGAGCGAGCTTCCGCTTGACTT (((..((..(..............&..)..))..)))............ >6pcm-C #1 nts=24 0.25(2.04) [chain] DNA AGTGAGCGAGCTTCCGCTTGACTT (((..((..(.............. >6pcm-D #2 nts=24 0.38(2.13) [chain] DNA AGTGAGCGAGCTTCCGCTTGACTT ..)..))..)))............ **************************************************************************** Summary of structural features of 48 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 ( C.DA2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( C.DG3 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 T ( C.DT4 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 4 G . C.DG5 0.004 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 5 A . C.DA6 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 6 G ( C.DG7 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 7 C ( C.DC8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 8 G . C.DG9 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 9 A . C.DA10 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 10 G ( C.DG11 0.004 anti,~C2'-endo,BI,isolated-canonical,non-pair-contact,helix,internal-loop 11 C . C.DC12 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 12 T . C.DT13 0.002 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 13 T . C.DT14 0.002 anti,~C2'-endo,BI,ss-non-loop,phosphate 14 C . C.DC15 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 15 C . C.DC16 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 16 G . C.DG17 0.004 anti,non-pair-contact,ss-non-loop,phosphate 17 C . C.DC18 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 18 T . C.DT19 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 19 T . C.DT20 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 20 G . C.DG21 0.005 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 21 A . C.DA22 0.003 anti,~C2'-endo,ss-non-loop,splayed-apart 22 C . C.DC23 0.004 ~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 23 T . C.DT24 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 24 T . C.DT25 0.002 anti,~C2'-endo,ss-non-loop,phosphate 25 A . D.DA2 0.003 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 26 G . D.DG3 0.006 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 27 T ) D.DT4 0.002 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,internal-loop 28 G . D.DG5 0.004 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 29 A . D.DA6 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 30 G ) D.DG7 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 31 C ) D.DC8 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 32 G . D.DG9 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 33 A . D.DA10 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 34 G ) D.DG11 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 35 C ) D.DC12 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 T ) D.DT13 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 37 T . D.DT14 0.002 anti,~C2'-endo,BI,ss-non-loop 38 C . D.DC15 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 39 C . D.DC16 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 40 G . D.DG17 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 41 C . D.DC18 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 42 T . D.DT19 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 43 T . D.DT20 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 44 G . D.DG21 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 45 A . D.DA22 0.003 syn,~C2'-endo,ss-non-loop,splayed-apart 46 C . D.DC23 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 47 T . D.DT24 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 48 T . D.DT25 0.002 anti,~C3'-endo,ss-non-loop,phosphate **************************************************************************** List of 10 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-iloops.pdb -- an ensemble of internal loops 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-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks