**************************************************************************** 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=1dct.pdb -o=1dct.out File name: 1dct.pdb no. of DNA/RNA chains: 4 [F=18,G=16,M=18,N=17] no. of nucleotides: 69 no. of atoms: 6908 no. of waters: 0 no. of metals: 2 [Ca=2] **************************************************************************** List of 2 types of 4 modified nucleotides nt count list 1 5CM-c 2 M.5CM11,N.5CM11 2 C49-c 2 F.C49/10,G.C49/10 **************************************************************************** List of 31 base pairs nt1 nt2 bp name Saenger LW DSSR 1 F.DC2 M.DG18 C-G WC 19-XIX cWW cW-W 2 F.DC3 M.DG17 C-G WC 19-XIX cWW cW-W 3 F.DA4 M.DT16 A-T WC 20-XX cWW cW-W 4 F.DG5 M.DC15 G-C WC 19-XIX cWW cW-W 5 F.DC6 M.DG14 C-G WC 19-XIX cWW cW-W 6 F.DA7 M.DT13 A-T WC 20-XX cWW cW-W 7 F.DG8 M.DC12 G-C WC 19-XIX cWW cW-W 8 F.DG9 M.5CM11 G-c WC 19-XIX cWW cW-W 9 F.DC11 M.DG10 C-G WC 19-XIX cWW cW-W 10 F.DA12 M.DT8 A-T WC 20-XX cWW cW-W 11 F.DC13 M.DG7 C-G WC 19-XIX cWW cW-W 12 F.DC14 M.DG6 C-G WC 19-XIX cWW cW-W 13 F.DA15 M.DT5 A-T WC 20-XX cWW cW-W 14 F.DG16 M.DC4 G-C WC 19-XIX cWW cW-W 15 F.DT17 M.DA3 T-A WC 20-XX cWW cW-W 16 F.DG18 M.DC2 G-C WC 19-XIX cWW cW-W 17 G.DC3 N.DG17 C-G WC 19-XIX cWW cW-W 18 G.DA4 N.DT16 A-T WC 20-XX cWW cW-W 19 G.DG5 N.DC15 G-C WC 19-XIX cWW cW-W 20 G.DC6 N.DG14 C-G WC 19-XIX cWW cW-W 21 G.DA7 N.DT13 A-T WC 20-XX cWW cW-W 22 G.DG8 N.DC12 G-C WC 19-XIX cWW cW-W 23 G.DG9 N.5CM11 G-c WC 19-XIX cWW cW-W 24 G.DC11 N.DG10 C-G WC 19-XIX cWW cW-W 25 G.DA12 N.DT8 A-T WC 20-XX cWW cW-W 26 G.DC13 N.DG7 C-G WC 19-XIX cWW cW-W 27 G.DC14 N.DG6 C-G WC 19-XIX cWW cW-W 28 G.DA15 N.DT5 A-T WC 20-XX cWW cW-W 29 G.DG16 N.DC4 G-C WC 19-XIX cWW cW-W 30 G.DT17 N.DA3 T-A WC 20-XX cWW cW-W 31 G.DG18 N.DC2 G-C WC 19-XIX cWW cW-W **************************************************************************** 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[2] bps=16 strand-1 5'-CCAGCAGGCACCAGTG-3' bp-type |||||||||||||||| strand-2 3'-GGTCGTCcGTGGTCAC-5' helix-form B..B.BBxx..BBBB 1 F.DC2 M.DG18 C-G WC 19-XIX cWW cW-W 2 F.DC3 M.DG17 C-G WC 19-XIX cWW cW-W 3 F.DA4 M.DT16 A-T WC 20-XX cWW cW-W 4 F.DG5 M.DC15 G-C WC 19-XIX cWW cW-W 5 F.DC6 M.DG14 C-G WC 19-XIX cWW cW-W 6 F.DA7 M.DT13 A-T WC 20-XX cWW cW-W 7 F.DG8 M.DC12 G-C WC 19-XIX cWW cW-W 8 F.DG9 M.5CM11 G-c WC 19-XIX cWW cW-W 9 F.DC11 M.DG10 C-G WC 19-XIX cWW cW-W 10 F.DA12 M.DT8 A-T WC 20-XX cWW cW-W 11 F.DC13 M.DG7 C-G WC 19-XIX cWW cW-W 12 F.DC14 M.DG6 C-G WC 19-XIX cWW cW-W 13 F.DA15 M.DT5 A-T WC 20-XX cWW cW-W 14 F.DG16 M.DC4 G-C WC 19-XIX cWW cW-W 15 F.DT17 M.DA3 T-A WC 20-XX cWW cW-W 16 F.DG18 M.DC2 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[2] bps=15 strand-1 5'-CAGCAGGCACCAGTG-3' bp-type ||||||||||||||| strand-2 3'-GTCGTCcGTGGTCAC-5' helix-form BBB.BBxxB.BBBB 1 G.DC3 N.DG17 C-G WC 19-XIX cWW cW-W 2 G.DA4 N.DT16 A-T WC 20-XX cWW cW-W 3 G.DG5 N.DC15 G-C WC 19-XIX cWW cW-W 4 G.DC6 N.DG14 C-G WC 19-XIX cWW cW-W 5 G.DA7 N.DT13 A-T WC 20-XX cWW cW-W 6 G.DG8 N.DC12 G-C WC 19-XIX cWW cW-W 7 G.DG9 N.5CM11 G-c WC 19-XIX cWW cW-W 8 G.DC11 N.DG10 C-G WC 19-XIX cWW cW-W 9 G.DA12 N.DT8 A-T WC 20-XX cWW cW-W 10 G.DC13 N.DG7 C-G WC 19-XIX cWW cW-W 11 G.DC14 N.DG6 C-G WC 19-XIX cWW cW-W 12 G.DA15 N.DT5 A-T WC 20-XX cWW cW-W 13 G.DG16 N.DC4 G-C WC 19-XIX cWW cW-W 14 G.DT17 N.DA3 T-A WC 20-XX cWW cW-W 15 G.DG18 N.DC2 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 4 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=8 strand-1 5'-CCAGCAGG-3' bp-type |||||||| strand-2 3'-GGTCGTCc-5' helix-form B..B.BB 1 F.DC2 M.DG18 C-G WC 19-XIX cWW cW-W 2 F.DC3 M.DG17 C-G WC 19-XIX cWW cW-W 3 F.DA4 M.DT16 A-T WC 20-XX cWW cW-W 4 F.DG5 M.DC15 G-C WC 19-XIX cWW cW-W 5 F.DC6 M.DG14 C-G WC 19-XIX cWW cW-W 6 F.DA7 M.DT13 A-T WC 20-XX cWW cW-W 7 F.DG8 M.DC12 G-C WC 19-XIX cWW cW-W 8 F.DG9 M.5CM11 G-c WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=7 strand-1 5'-ACCAGTG-3' bp-type ||||||| strand-2 3'-TGGTCAC-5' helix-form ..BBBB 1 F.DA12 M.DT8 A-T WC 20-XX cWW cW-W 2 F.DC13 M.DG7 C-G WC 19-XIX cWW cW-W 3 F.DC14 M.DG6 C-G WC 19-XIX cWW cW-W 4 F.DA15 M.DT5 A-T WC 20-XX cWW cW-W 5 F.DG16 M.DC4 G-C WC 19-XIX cWW cW-W 6 F.DT17 M.DA3 T-A WC 20-XX cWW cW-W 7 F.DG18 M.DC2 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=7 strand-1 5'-CAGCAGG-3' bp-type ||||||| strand-2 3'-GTCGTCc-5' helix-form BBB.BB 1 G.DC3 N.DG17 C-G WC 19-XIX cWW cW-W 2 G.DA4 N.DT16 A-T WC 20-XX cWW cW-W 3 G.DG5 N.DC15 G-C WC 19-XIX cWW cW-W 4 G.DC6 N.DG14 C-G WC 19-XIX cWW cW-W 5 G.DA7 N.DT13 A-T WC 20-XX cWW cW-W 6 G.DG8 N.DC12 G-C WC 19-XIX cWW cW-W 7 G.DG9 N.5CM11 G-c WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#2] bps=7 strand-1 5'-ACCAGTG-3' bp-type ||||||| strand-2 3'-TGGTCAC-5' helix-form B.BBBB 1 G.DA12 N.DT8 A-T WC 20-XX cWW cW-W 2 G.DC13 N.DG7 C-G WC 19-XIX cWW cW-W 3 G.DC14 N.DG6 C-G WC 19-XIX cWW cW-W 4 G.DA15 N.DT5 A-T WC 20-XX cWW cW-W 5 G.DG16 N.DC4 G-C WC 19-XIX cWW cW-W 6 G.DT17 N.DA3 T-A WC 20-XX cWW cW-W 7 G.DG18 N.DC2 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 isolated WC/wobble pairs Note: isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 F.DC11 M.DG10 C-G WC 19-XIX cWW cW-W [#2] -2 G.DC11 N.DG10 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 coaxial stacks 1 Helix#1 contains 2 stems: [#1,#2] 2 Helix#2 contains 2 stems: [#3,#4] **************************************************************************** List of 12 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 AC F.DA1,F.DC2 2 nts=2 GD F.DG18,B.ASP84 3 nts=2 TY M.DT1,B.TYR30 4 nts=2 CR M.DC2,B.ARG81 5 nts=2 TR M.DT8,A.ARG243 6 nts=2 cN G.C49/10,B.ASN110 7 nts=2 GD G.DG18,A.ASP84 8 nts=2 TY N.DT1,A.TYR30 9 nts=2 CR N.DC2,A.ARG81 10 nts=2 TR N.DT8,B.ARG243 11 nts=3 AGG F.DA12,M.DG9,M.DG10 12 nts=3 AGG G.DA12,N.DG9,N.DG10 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@M.DG17 M.DG17 2.59 **************************************************************************** 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 4 bulges 1 bulge: nts=5; [1,0]; linked by [#1,#-1] summary: [2] 1 0 [F.9 M.11 F.11 M.10] 8 1 nts=5 GcCGc F.DG9,F.C49/10,F.DC11,M.DG10,M.5CM11 nts=1 c F.C49/10 nts=0 2 bulge: nts=5; [0,1]; linked by [#-1,#2] summary: [2] 0 1 [F.11 M.10 F.12 M.8] 1 7 nts=5 CATGG F.DC11,F.DA12,M.DT8,M.DG9,M.DG10 nts=0 nts=1 G M.DG9 3 bulge: nts=5; [1,0]; linked by [#3,#-2] summary: [2] 1 0 [G.9 N.11 G.11 N.10] 7 1 nts=5 GcCGc G.DG9,G.C49/10,G.DC11,N.DG10,N.5CM11 nts=1 c G.C49/10 nts=0 4 bulge: nts=5; [0,1]; linked by [#-2,#4] summary: [2] 0 1 [G.11 N.10 G.12 N.8] 1 7 nts=5 CATGG G.DC11,G.DA12,N.DT8,N.DG9,N.DG10 nts=0 nts=1 G N.DG9 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=1 A F.DA1 2 nts=1 T M.DT1 3 nts=1 T N.DT1 **************************************************************************** List of 6 splayed-apart dinucleotides 1 F.DG9 F.C49/10 angle=169 distance=19.0 ratio=1.00 2 F.C49/10 F.DC11 angle=149 distance=19.5 ratio=0.96 3 M.DT1 M.DC2 angle=113 distance=17.5 ratio=0.83 4 G.DG9 G.C49/10 angle=169 distance=19.0 ratio=1.00 5 G.C49/10 G.DC11 angle=148 distance=19.5 ratio=0.96 6 N.DT1 N.DC2 angle=113 distance=17.5 ratio=0.83 ---------------------------------------------------------------- Summary of 4 splayed-apart units 1 nts=3 GcC F.DG9,F.C49/10,F.DC11 2 nts=2 TC M.DT1,M.DC2 3 nts=3 GcC G.DG9,G.C49/10,G.DC11 4 nts=2 TC N.DT1,N.DC2 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1dct nts=69 [whole] ACCAGCAGGcCACCAGTG&TCACTGGTGGcCTGCTGG&CAGCAGGcCACCAGTG&TCACTGGTGGcCTGCTG .((((((((.((((((((&.))))))).)))))))))&(((((((.((((((((&.))))))).)))))))) >1dct-F #1 nts=18 3.65(0.79) [chain] DNA ACCAGCAGGcCACCAGTG .((((((((.(((((((( >1dct-M #2 nts=18 3.50(0.91) [chain] DNA TCACTGGTGGcCTGCTGG .))))))).))))))))) >1dct-G #3 nts=16 3.35(0.81) [chain] DNA CAGCAGGcCACCAGTG (((((((.(((((((( >1dct-N #4 nts=17 3.47(0.92) [chain] DNA TCACTGGTGGcCTGCTG .))))))).)))))))) **************************************************************************** Summary of structural features of 69 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 . F.DA1 0.033 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 C ( F.DC2 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 3 C ( F.DC3 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 4 A ( F.DA4 0.024 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 5 G ( F.DG5 0.029 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 C ( F.DC6 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 A ( F.DA7 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 G ( F.DG8 0.021 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 9 G ( F.DG9 0.024 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 10 c . F.C49/10 0.106 modified,turn,~C3'-endo,bulge,phosphate,splayed-apart 11 C ( F.DC11 0.017 anti,~C2'-endo,BI,isolated-canonical,helix,bulge,phosphate,splayed-apart 12 A ( F.DA12 0.028 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 13 C ( F.DC13 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 14 C ( F.DC14 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 A ( F.DA15 0.021 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 16 G ( F.DG16 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 T ( F.DT17 0.030 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 G ( F.DG18 0.022 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 19 T . M.DT1 0.033 syn,~C2'-endo,ss-non-loop,splayed-apart 20 C ) M.DC2 0.017 anti,~C2'-endo,BI,canonical,helix-end,stem-end,coaxial-stack,splayed-apart 21 A ) M.DA3 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 C ) M.DC4 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 T ) M.DT5 0.033 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 24 G ) M.DG6 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ) M.DG7 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 T ) M.DT8 0.026 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 27 G . M.DG9 0.023 anti,BI,non-pair-contact,bulge 28 G ) M.DG10 0.030 anti,~C2'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge 29 c ) M.5CM11 0.019 modified,anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 30 C ) M.DC12 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 T ) M.DT13 0.029 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 G ) M.DG14 0.032 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 33 C ) M.DC15 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 34 T ) M.DT16 0.028 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 35 G ) M.DG17 0.035 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor,cap-acceptor,phosphate 36 G ) M.DG18 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 37 C ( G.DC3 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 38 A ( G.DA4 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 G ( G.DG5 0.027 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 40 C ( G.DC6 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 41 A ( G.DA7 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 G ( G.DG8 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 43 G ( G.DG9 0.029 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 44 c . G.C49/10 0.096 modified,turn,~C3'-endo,bulge,phosphate,splayed-apart 45 C ( G.DC11 0.016 anti,~C2'-endo,BI,isolated-canonical,helix,bulge,phosphate,splayed-apart 46 A ( G.DA12 0.027 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 47 C ( G.DC13 0.019 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 48 C ( G.DC14 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 49 A ( G.DA15 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 G ( G.DG16 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 51 T ( G.DT17 0.029 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 52 G ( G.DG18 0.025 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 53 T . N.DT1 0.035 syn,~C2'-endo,ss-non-loop,splayed-apart 54 C ) N.DC2 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,splayed-apart 55 A ) N.DA3 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 56 C ) N.DC4 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 57 T ) N.DT5 0.030 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 58 G ) N.DG6 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 59 G ) N.DG7 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 T ) N.DT8 0.026 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 61 G . N.DG9 0.020 anti,BI,non-pair-contact,bulge 62 G ) N.DG10 0.024 anti,~C2'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,phosphate 63 c ) N.5CM11 0.019 modified,anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 64 C ) N.DC12 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 65 T ) N.DT13 0.027 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 66 G ) N.DG14 0.036 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 67 C ) N.DC15 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 68 T ) N.DT16 0.026 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 69 G ) N.DG17 0.019 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 11 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-bulges.pdb -- an ensemble of bulges 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 11 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions