**************************************************************************** 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=7dn3.pdb -o=7dn3.out File name: 7dn3.pdb no. of DNA/RNA chains: 3 [R=6,X=16,Y=23] no. of nucleotides: 45 no. of atoms: 36856 no. of waters: 0 no. of metals: 11 [Mg=1,Fe=4,Zn=6] **************************************************************************** List of 21 base pairs nt1 nt2 bp name Saenger LW DSSR 1 X.DT27 Y.DA16 T-A -- -- cWW cW-W 2 X.DC28 Y.DG15 C-G WC 19-XIX cWW cW-W 3 X.DG29 Y.DC14 G-C WC 19-XIX cWW cW-W 4 X.DT30 Y.DA13 T+A -- -- cWH cW+M 5 X.DC31 Y.DG12 C-G WC 19-XIX cWW cW-W 6 X.DT32 Y.DA11 T-A WC 20-XX cWW cW-W 7 X.DG33 Y.DC10 G-C WC 19-XIX cWW cW-W 8 X.DA34 Y.DT9 A+T -- -- cHW cM+W 9 X.DT35 Y.DA8 T-A WC 20-XX cWW cW-W 10 X.DC36 Y.DG7 C-G WC 19-XIX cWW cW-W 11 X.DT37 Y.DA6 T-A WC 20-XX cWW cW-W 12 X.DG39 Y.DC4 G-C WC 19-XIX cWW cW-W 13 X.DG40 Y.DC3 G-C WC 19-XIX cWW cW-W 14 X.DA41 Y.DT2 A-T WC 20-XX cWW cW-W 15 X.DA42 Y.DT1 A-T WC 20-XX cWW cW-W 16 Y.DA18 R.U9 A-U WC 20-XX cWW cW-W 17 Y.DT19 R.A8 T-A WC 20-XX cWW cW-W 18 Y.DC20 R.G7 C-G WC 19-XIX cWW cW-W 19 Y.DG21 R.C6 G-C WC 19-XIX cWW cW-W 20 Y.DG22 R.C5 G-C WC 19-XIX cWW cW-W 21 Y.DG23 R.C4 G-C WC 19-XIX 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[3] bps=11 strand-1 5'-TCGTCTGATCT-3' bp-type .||.|||.||| strand-2 3'-AGCAGACTAGA-5' helix-form .......... 1 X.DT27 Y.DA16 T-A -- -- cWW cW-W 2 X.DC28 Y.DG15 C-G WC 19-XIX cWW cW-W 3 X.DG29 Y.DC14 G-C WC 19-XIX cWW cW-W 4 X.DT30 Y.DA13 T+A -- -- cWH cW+M 5 X.DC31 Y.DG12 C-G WC 19-XIX cWW cW-W 6 X.DT32 Y.DA11 T-A WC 20-XX cWW cW-W 7 X.DG33 Y.DC10 G-C WC 19-XIX cWW cW-W 8 X.DA34 Y.DT9 A+T -- -- cHW cM+W 9 X.DT35 Y.DA8 T-A WC 20-XX cWW cW-W 10 X.DC36 Y.DG7 C-G WC 19-XIX cWW cW-W 11 X.DT37 Y.DA6 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=4 strand-1 5'-GGAA-3' bp-type |||| strand-2 3'-CCTT-5' helix-form ... 1 X.DG39 Y.DC4 G-C WC 19-XIX cWW cW-W 2 X.DG40 Y.DC3 G-C WC 19-XIX cWW cW-W 3 X.DA41 Y.DT2 A-T WC 20-XX cWW cW-W 4 X.DA42 Y.DT1 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=6 strand-1 5'-ATCGGG-3' bp-type |||||| strand-2 3'-UAGCCC-5' helix-form ..... 1 Y.DA18 R.U9 A-U WC 20-XX cWW cW-W 2 Y.DT19 R.A8 T-A WC 20-XX cWW cW-W 3 Y.DC20 R.G7 C-G WC 19-XIX cWW cW-W 4 Y.DG21 R.C6 G-C WC 19-XIX cWW cW-W 5 Y.DG22 R.C5 G-C WC 19-XIX cWW cW-W 6 Y.DG23 R.C4 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 5 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=2 strand-1 5'-CG-3' bp-type || strand-2 3'-GC-5' helix-form . 1 X.DC28 Y.DG15 C-G WC 19-XIX cWW cW-W 2 X.DG29 Y.DC14 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=3 strand-1 5'-CTG-3' bp-type ||| strand-2 3'-GAC-5' helix-form .. 1 X.DC31 Y.DG12 C-G WC 19-XIX cWW cW-W 2 X.DT32 Y.DA11 T-A WC 20-XX cWW cW-W 3 X.DG33 Y.DC10 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=3 strand-1 5'-TCT-3' bp-type ||| strand-2 3'-AGA-5' helix-form .. 1 X.DT35 Y.DA8 T-A WC 20-XX cWW cW-W 2 X.DC36 Y.DG7 C-G WC 19-XIX cWW cW-W 3 X.DT37 Y.DA6 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#4[#2] bps=4 strand-1 5'-GGAA-3' bp-type |||| strand-2 3'-CCTT-5' helix-form ... 1 X.DG39 Y.DC4 G-C WC 19-XIX cWW cW-W 2 X.DG40 Y.DC3 G-C WC 19-XIX cWW cW-W 3 X.DA41 Y.DT2 A-T WC 20-XX cWW cW-W 4 X.DA42 Y.DT1 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#5[#3] bps=6 strand-1 5'-ATCGGG-3' bp-type |||||| strand-2 3'-UAGCCC-5' helix-form ..... 1 Y.DA18 R.U9 A-U WC 20-XX cWW cW-W 2 Y.DT19 R.A8 T-A WC 20-XX cWW cW-W 3 Y.DC20 R.G7 C-G WC 19-XIX cWW cW-W 4 Y.DG21 R.C6 G-C WC 19-XIX cWW cW-W 5 Y.DG22 R.C5 G-C WC 19-XIX cWW cW-W 6 Y.DG23 R.C4 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** List of 9 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 TC X.DT27,X.DC28 2 nts=2 GA Y.DG12,Y.DA13 3 nts=2 GA Y.DG15,Y.DA16 4 nts=2 GA Y.DG17,Y.DA18 5 nts=3 GTC X.DG29,X.DT30,X.DC31 6 nts=3 GAT X.DG33,X.DA34,X.DT35 7 nts=3 TCG X.DT37,X.DC38,X.DG39 8 nts=3 CGA Y.DC4,Y.DG5,Y.DA6 9 nts=3 ATC Y.DA8,Y.DT9,Y.DC10 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 A X.DA42 **************************************************************************** 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 3 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [X.29 Y.14 X.31 Y.12] 2 3 nts=6 GTCGAC X.DG29,X.DT30,X.DC31,Y.DG12,Y.DA13,Y.DC14 nts=1 T X.DT30 nts=1 A Y.DA13 2 symmetric internal loop: nts=6; [1,1]; linked by [#2,#3] summary: [2] 1 1 [X.33 Y.10 X.35 Y.8] 3 3 nts=6 GATATC X.DG33,X.DA34,X.DT35,Y.DA8,Y.DT9,Y.DC10 nts=1 A X.DA34 nts=1 T Y.DT9 3 symmetric internal loop: nts=6; [1,1]; linked by [#3,#4] summary: [2] 1 1 [X.37 Y.6 X.39 Y.4] 3 4 nts=6 TCGCGA X.DT37,X.DC38,X.DG39,Y.DC4,Y.DG5,Y.DA6 nts=1 C X.DC38 nts=1 G Y.DG5 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 T X.DT27 2 nts=2 AG Y.DA16,Y.DG17 **************************************************************************** List of 1 splayed-apart dinucleotide 1 Y.DA16 Y.DG17 angle=136 distance=17.9 ratio=0.93 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 AG Y.DA16,Y.DG17 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7dn3 nts=45 [whole] TCGTCTGATCTCGGAA&TTCCGAGATCAGACGAGATCGGG&CCCGAU .((.(((.(((.((((&)))).))).))).))..((((((&)))))) >7dn3-X #1 nts=16 3.54(0.72) [chain] DNA TCGTCTGATCTCGGAA .((.(((.(((.(((( >7dn3-Y #2 nts=23 3.43(1.17) [chain] DNA TTCCGAGATCAGACGAGATCGGG )))).))).))).))..(((((( >7dn3-R #3 nts=6 3.61(0.17) [chain] RNA CCCGAU )))))) **************************************************************************** Summary of structural features of 45 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 T . X.DT27 0.004 anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,ss-non-loop 2 C ( X.DC28 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 3 G ( X.DG29 0.003 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 4 T . X.DT30 0.002 anti,BI,non-canonical,non-pair-contact,helix,internal-loop 5 C ( X.DC31 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 6 T ( X.DT32 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( X.DG33 0.017 anti,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 8 A . X.DA34 0.010 ~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 9 T ( X.DT35 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 10 C ( X.DC36 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 T ( X.DT37 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 12 C . X.DC38 0.008 anti,~C2'-endo,non-pair-contact,internal-loop 13 G ( X.DG39 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 14 G ( X.DG40 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 15 A ( X.DA41 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 16 A ( X.DA42 0.001 anti,~C2'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end 17 T ) Y.DT1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 18 T ) Y.DT2 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 C ) Y.DC3 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 20 C ) Y.DC4 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 21 G . Y.DG5 0.008 anti,~C2'-endo,BI,non-pair-contact,internal-loop 22 A ) Y.DA6 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop,phosphate 23 G ) Y.DG7 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 A ) Y.DA8 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 25 T . Y.DT9 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 26 C ) Y.DC10 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 27 A ) Y.DA11 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 28 G ) Y.DG12 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 29 A . Y.DA13 0.012 syn,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 30 C ) Y.DC14 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 31 G ) Y.DG15 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 32 A . Y.DA16 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate,splayed-apart 33 G . Y.DG17 0.002 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 34 A ( Y.DA18 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 35 T ( Y.DT19 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 36 C ( Y.DC20 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 37 G ( Y.DG21 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 38 G ( Y.DG22 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 39 G ( Y.DG23 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 40 C ) R.C4 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 41 C ) R.C5 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 42 C ) R.C6 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 43 G ) R.G7 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 44 A ) R.A8 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 45 U ) R.U9 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,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