**************************************************************************** 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=5w66.pdb -o=5w66.out File name: 5w66.pdb no. of DNA/RNA chains: 3 [R=6,S=45,T=54] no. of nucleotides: 105 no. of atoms: 48857 no. of waters: 0 no. of metals: 6 [Zn=6] **************************************************************************** List of 49 base pairs nt1 nt2 bp name Saenger LW DSSR 1 R.A1 T.DA20 A-A -- -- cWW cW-W 2 R.A1 T.DT21 A-T WC 20-XX cWW cW-W 3 R.U2 T.DA20 U-A -- -- cWW cW-W 4 R.G3 T.DC19 G-C WC 19-XIX cWW cW-W 5 R.C4 T.DG18 C-G WC 19-XIX cWW cW-W 6 R.G5 T.DC17 G-C WC 19-XIX cWW cW-W 7 R.A6 T.DT16 A-T WC 20-XX cWW cW-W 8 S.DA2 T.DT52 A+T -- -- cHW cM+W 9 S.DG4 T.DC51 G-C WC 19-XIX cWW cW-W 10 S.DT5 T.DA50 T-A WC 20-XX cWW cW-W 11 S.DG6 T.DC49 G-C -- -- c.W c.-W 12 S.DA9 T.DT46 A-T WC 20-XX cWW cW-W 13 S.DG10 T.DC45 G-C WC 19-XIX cWW cW-W 14 S.DG11 T.DC44 G-C WC 19-XIX cWW cW-W 15 S.DA12 T.DT43 A-T WC 20-XX cWW cW-W 16 S.DA13 T.DT42 A-T WC 20-XX cWW cW-W 17 S.DA14 T.DT41 A-T WC 20-XX cWW cW-W 18 S.DA15 T.DT40 A-T WC 20-XX cWW cW-W 19 S.DG16 T.DC39 G-C WC 19-XIX cWW cW-W 20 S.DT17 T.DA38 T-A WC 20-XX cWW cW-W 21 S.DA18 T.DT37 A-T WC 20-XX cWW cW-W 22 S.DG19 T.DA35 G-A -- -- cWW cW-W 23 S.DG19 T.DC36 G-C WC 19-XIX cWW cW-W 24 S.DT20 T.DA35 T-A WC 20-XX cWW cW-W 25 S.DT21 T.DA34 T-A WC 20-XX cWW cW-W 26 S.DG22 T.DC33 G-C WC 19-XIX cWW cW-W 27 S.DG23 T.DC32 G-C WC 19-XIX cWW cW-W 28 S.DG24 T.DC31 G-C WC 19-XIX cWW cW-W 29 S.DT25 T.DT30 T-T -- -- cWW cW-W 30 S.DT26 T.DC29 T-C -- -- cWW cW-W 31 S.DT27 T.DC28 T-C -- -- cWW cW-W 32 S.DT28 T.DT26 T-T -- -- tHW tM-W 33 S.DT28 T.DA27 T-A -- -- cWW cW-W 34 S.DT40 S.DG42 T-G -- -- cHH cM-M 35 S.DG42 T.DC13 G-C WC 19-XIX cWW cW-W 36 S.DC43 T.DG12 C-G -- -- cWW cW-W 37 S.DC43 T.DC13 C-C -- -- cWW cW-W 38 S.DA44 T.DT11 A-T WC 20-XX cWW cW-W 39 S.DG45 T.DC10 G-C WC 19-XIX cWW cW-W 40 S.DT46 T.DA9 T-A WC 20-XX cWW cW-W 41 S.DT47 T.DA8 T-A WC 20-XX cWW cW-W 42 S.DG48 T.DC7 G-C WC 19-XIX cWW cW-W 43 S.DA49 T.DT6 A-T -- -- cWW cW-W 44 S.DA50 T.DT5 A-T WC 20-XX cWW cW-W 45 S.DG51 T.DC4 G-C WC 19-XIX cWW cW-W 46 S.DG51 T.DT5 G-T -- -- cWW cW-W 47 S.DA52 T.DT3 A-T WC 20-XX cWW cW-W 48 S.DC53 T.DG2 C-G WC 19-XIX cWW cW-W 49 S.DA54 T.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 2 multiplets 1 nts=3* TTA S.DT28,T.DT26,T.DA27 2 nts=3* TGC S.DT40,S.DG42,T.DC13 **************************************************************************** List of 4 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=6 strand-1 5'-AUGCGA-3' bp-type |.|||| strand-2 3'-TACGCT-5' helix-form ..... 1 R.A1 T.DT21 A-T WC 20-XX cWW cW-W 2 R.U2 T.DA20 U-A -- -- cWW cW-W 3 R.G3 T.DC19 G-C WC 19-XIX cWW cW-W 4 R.C4 T.DG18 C-G WC 19-XIX cWW cW-W 5 R.G5 T.DC17 G-C WC 19-XIX cWW cW-W 6 R.A6 T.DT16 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=4 strand-1 5'-AGTG-3' bp-type .||. strand-2 3'-TCAC-5' helix-form x.. 1 S.DA2 T.DT52 A+T -- -- cHW cM+W 2 S.DG4 T.DC51 G-C WC 19-XIX cWW cW-W 3 S.DT5 T.DA50 T-A WC 20-XX cWW cW-W 4 S.DG6 T.DC49 G-C -- -- c.W c.-W -------------------------------------------------------------------------- helix#3[1] bps=20 strand-1 5'-AGGAAAAGTAGTTGGGTTTT-3' bp-type ||||||||||||||||.... strand-2 3'-TCCTTTTCATCAACCCTCCA-5' helix-form B....BBBB...BB..... 1 S.DA9 T.DT46 A-T WC 20-XX cWW cW-W 2 S.DG10 T.DC45 G-C WC 19-XIX cWW cW-W 3 S.DG11 T.DC44 G-C WC 19-XIX cWW cW-W 4 S.DA12 T.DT43 A-T WC 20-XX cWW cW-W 5 S.DA13 T.DT42 A-T WC 20-XX cWW cW-W 6 S.DA14 T.DT41 A-T WC 20-XX cWW cW-W 7 S.DA15 T.DT40 A-T WC 20-XX cWW cW-W 8 S.DG16 T.DC39 G-C WC 19-XIX cWW cW-W 9 S.DT17 T.DA38 T-A WC 20-XX cWW cW-W 10 S.DA18 T.DT37 A-T WC 20-XX cWW cW-W 11 S.DG19 T.DC36 G-C WC 19-XIX cWW cW-W 12 S.DT20 T.DA35 T-A WC 20-XX cWW cW-W 13 S.DT21 T.DA34 T-A WC 20-XX cWW cW-W 14 S.DG22 T.DC33 G-C WC 19-XIX cWW cW-W 15 S.DG23 T.DC32 G-C WC 19-XIX cWW cW-W 16 S.DG24 T.DC31 G-C WC 19-XIX cWW cW-W 17 S.DT25 T.DT30 T-T -- -- cWW cW-W 18 S.DT26 T.DC29 T-C -- -- cWW cW-W 19 S.DT27 T.DC28 T-C -- -- cWW cW-W 20 S.DT28 T.DA27 T-A -- -- cWW cW-W -------------------------------------------------------------------------- helix#4[2] bps=13 strand-1 5'-GCAGTTGAAGACA-3' bp-type |.|||||.||||| strand-2 3'-CGTCAACTTCTGT-5' helix-form ....BB...... 1 S.DG42 T.DC13 G-C WC 19-XIX cWW cW-W 2 S.DC43 T.DG12 C-G -- -- cWW cW-W 3 S.DA44 T.DT11 A-T WC 20-XX cWW cW-W 4 S.DG45 T.DC10 G-C WC 19-XIX cWW cW-W 5 S.DT46 T.DA9 T-A WC 20-XX cWW cW-W 6 S.DT47 T.DA8 T-A WC 20-XX cWW cW-W 7 S.DG48 T.DC7 G-C WC 19-XIX cWW cW-W 8 S.DA49 T.DT6 A-T -- -- cWW cW-W 9 S.DA50 T.DT5 A-T WC 20-XX cWW cW-W 10 S.DG51 T.DC4 G-C WC 19-XIX cWW cW-W 11 S.DA52 T.DT3 A-T WC 20-XX cWW cW-W 12 S.DC53 T.DG2 C-G WC 19-XIX cWW cW-W 13 S.DA54 T.DT1 A-T WC 20-XX 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=4 strand-1 5'-GCGA-3' bp-type |||| strand-2 3'-CGCT-5' helix-form ... 1 R.G3 T.DC19 G-C WC 19-XIX cWW cW-W 2 R.C4 T.DG18 C-G WC 19-XIX cWW cW-W 3 R.G5 T.DC17 G-C WC 19-XIX cWW cW-W 4 R.A6 T.DT16 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=2 strand-1 5'-GT-3' bp-type || strand-2 3'-CA-5' helix-form . 1 S.DG4 T.DC51 G-C WC 19-XIX cWW cW-W 2 S.DT5 T.DA50 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#3] bps=16 strand-1 5'-AGGAAAAGTAGTTGGG-3' bp-type |||||||||||||||| strand-2 3'-TCCTTTTCATCAACCC-5' helix-form B....BBBB...BB. 1 S.DA9 T.DT46 A-T WC 20-XX cWW cW-W 2 S.DG10 T.DC45 G-C WC 19-XIX cWW cW-W 3 S.DG11 T.DC44 G-C WC 19-XIX cWW cW-W 4 S.DA12 T.DT43 A-T WC 20-XX cWW cW-W 5 S.DA13 T.DT42 A-T WC 20-XX cWW cW-W 6 S.DA14 T.DT41 A-T WC 20-XX cWW cW-W 7 S.DA15 T.DT40 A-T WC 20-XX cWW cW-W 8 S.DG16 T.DC39 G-C WC 19-XIX cWW cW-W 9 S.DT17 T.DA38 T-A WC 20-XX cWW cW-W 10 S.DA18 T.DT37 A-T WC 20-XX cWW cW-W 11 S.DG19 T.DC36 G-C WC 19-XIX cWW cW-W 12 S.DT20 T.DA35 T-A WC 20-XX cWW cW-W 13 S.DT21 T.DA34 T-A WC 20-XX cWW cW-W 14 S.DG22 T.DC33 G-C WC 19-XIX cWW cW-W 15 S.DG23 T.DC32 G-C WC 19-XIX cWW cW-W 16 S.DG24 T.DC31 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#4] bps=5 strand-1 5'-AGTTG-3' bp-type ||||| strand-2 3'-TCAAC-5' helix-form ..BB 1 S.DA44 T.DT11 A-T WC 20-XX cWW cW-W 2 S.DG45 T.DC10 G-C WC 19-XIX cWW cW-W 3 S.DT46 T.DA9 T-A WC 20-XX cWW cW-W 4 S.DT47 T.DA8 T-A WC 20-XX cWW cW-W 5 S.DG48 T.DC7 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#4] bps=5 strand-1 5'-AGACA-3' bp-type ||||| strand-2 3'-TCTGT-5' helix-form .... 1 S.DA50 T.DT5 A-T WC 20-XX cWW cW-W 2 S.DG51 T.DC4 G-C WC 19-XIX cWW cW-W 3 S.DA52 T.DT3 A-T WC 20-XX cWW cW-W 4 S.DC53 T.DG2 C-G WC 19-XIX cWW cW-W 5 S.DA54 T.DT1 A-T WC 20-XX 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 R.A1 T.DT21 A-T WC 20-XX cWW cW-W [#4] -2 S.DG42 T.DC13 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#4 contains 2 stems: [#4,#5] **************************************************************************** List of 17 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 FT B.PHE508,S.DT39 2 nts=2 CA S.DC1,S.DA2 3 nts=2 AG S.DA3,S.DG4 4 nts=2 GA S.DG8,S.DA9 5 nts=2 TT S.DT40,S.DT41 6 nts=2 GC S.DG42,S.DC43 7 nts=2 GA S.DG48,S.DA49 8 nts=2 TT T.DT5,T.DT6 9 nts=2 TT T.DT15,T.DT16 10 nts=3 AUG R.A1,R.U2,R.G3 11 nts=3 TGT S.DT5,S.DG6,S.DT7 12 nts=3 TGC T.DT11,T.DG12,T.DC13 13 nts=3 ACA T.DA48,T.DC49,T.DA50 14 nts=4 ACCT T.DA27,T.DC28,T.DC29,T.DT30 15 nts=4 CTTG T.DC51,T.DT52,T.DT53,T.DG54 16 nts=6 GTTTTT S.DG24,S.DT25,S.DT26,S.DT27,S.DT28,S.DT29 17 nts=6 CATGAA T.DC19,T.DA20,T.DT21,T.DG22,T.DA23,T.DA24 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 TGTC T.DT14,T.DG25,T.DT26,T.DC47 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@S.DT28 S.DT29 2.94 **************************************************************************** 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 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#-1,#1] summary: [2] 1 1 [R.1 T.21 R.3 T.19] 1 4 nts=6 AUGCAT R.A1,R.U2,R.G3,T.DC19,T.DA20,T.DT21 nts=1 U R.U2 nts=1 A T.DA20 2 symmetric internal loop: nts=6; [1,1]; linked by [#-2,#4] summary: [2] 1 1 [S.42 T.13 S.44 T.11] 1 5 nts=6 GCATGC S.DG42,S.DC43,S.DA44,T.DT11,T.DG12,T.DC13 nts=1 C S.DC43 nts=1 G T.DG12 3 symmetric internal loop: nts=6; [1,1]; linked by [#4,#5] summary: [2] 1 1 [S.48 T.7 S.50 T.5] 5 5 nts=6 GAATTC S.DG48,S.DA49,S.DA50,T.DT5,T.DT6,T.DC7 nts=1 A S.DA49 nts=1 T T.DT6 4 symmetric internal loop: nts=10; [3,3]; linked by [#2,#3] summary: [2] 3 3 [S.5 T.50 S.9 T.46] 2 16 nts=10 TGTGATCACA S.DT5,S.DG6,S.DT7,S.DG8,S.DA9,T.DT46,T.DC47,T.DA48,T.DC49,T.DA50 nts=3 GTG S.DG6,S.DT7,S.DG8 nts=3 CAC T.DC47,T.DA48,T.DC49 **************************************************************************** List of 5 non-loop single-stranded segments 1 nts=3 CAA S.DC1,S.DA2,S.DA3 2 nts=8* TTTTTTTT S.DT25,S.DT26,S.DT27,S.DT28,S.DT29,S.DT39,S.DT40,S.DT41 3 nts=2 TT T.DT14,T.DT15 4 nts=9 GAAGTACCT T.DG22,T.DA23,T.DA24,T.DG25,T.DT26,T.DA27,T.DC28,T.DC29,T.DT30 5 nts=3 TTG T.DT52,T.DT53,T.DG54 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DT14 T.DT15 angle=158 distance=17.4 ratio=0.98 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 TT T.DT14,T.DT15 **************************************************************************** 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 >5w66 nts=105 [whole] AUGCGA&CAAGTGTGAGGAAAAGTAGTTGGGTTTTT&TTTGCAGTTGAAGACA&TGTCTTCAACTGCTTTCGCATGAAGTACCTCCCAACTACTTTTCCTCACACTTG [.[[[[&...((...((((((((((((((((.....&...(.(((((.(((((&))))).))))).)..]]]].].........))))))))))))))))...))... >5w66-R #1 nts=6 3.22(0.28) [chain] RNA AUGCGA [.[[[[ >5w66-S #2 nts=45 2.80(1.85) [chain] DNA* CAAGTGTGAGGAAAAGTAGTTGGGTTTTT&TTTGCAGTTGAAGACA ...((...((((((((((((((((.....&...(.(((((.((((( >5w66-T #3 nts=54 2.98(1.47) [chain] DNA TGTCTTCAACTGCTTTCGCATGAAGTACCTCCCAACTACTTTTCCTCACACTTG ))))).))))).)..]]]].].........))))))))))))))))...))... **************************************************************************** Summary of structural features of 105 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 [ R.A1 0.015 pseudoknotted,anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix-end,internal-loop 2 U . R.U2 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 3 G [ R.G3 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 4 C [ R.C4 0.009 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem,phosphate 5 G [ R.G5 0.033 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 A [ R.A6 0.009 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 7 C . S.DC1 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 8 A . S.DA2 0.005 syn,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 9 A . S.DA3 0.009 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 10 G ( S.DG4 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end 11 T ( S.DT5 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 12 G . S.DG6 0.008 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 13 T . S.DT7 0.006 anti,~C2'-endo,BII,non-pair-contact,internal-loop 14 G . S.DG8 0.011 anti,~C2'-endo,BI,non-pair-contact,internal-loop 15 A ( S.DA9 0.009 anti,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 16 G ( S.DG10 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 17 G ( S.DG11 0.014 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 18 A ( S.DA12 0.008 anti,BI,canonical,non-pair-contact,helix,stem 19 A ( S.DA13 0.013 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 20 A ( S.DA14 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ( S.DA15 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 G ( S.DG16 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 T ( S.DT17 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 A ( S.DA18 0.014 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ( S.DG19 0.013 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 26 T ( S.DT20 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 T ( S.DT21 0.017 anti,BI,canonical,non-pair-contact,helix,stem 28 G ( S.DG22 0.008 anti,BI,canonical,non-pair-contact,helix,stem 29 G ( S.DG23 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 G ( S.DG24 0.020 anti,canonical,non-pair-contact,helix,stem-end 31 T . S.DT25 0.033 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 32 T . S.DT26 0.000 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 33 T . S.DT27 0.000 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 34 T . S.DT28 0.001 ~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,cap-donor 35 T . S.DT29 0.010 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-acceptor 36 T . S.DT39 0.001 anti,~C3'-endo,ss-non-loop 37 T . S.DT40 0.015 syn,~C2'-endo,non-canonical,non-pair-contact,multiplet,ss-non-loop,phosphate 38 T . S.DT41 0.010 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 39 G ( S.DG42 0.008 anti,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 40 C . S.DC43 0.033 anti,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 41 A ( S.DA44 0.014 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 42 G ( S.DG45 0.012 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 T ( S.DT46 0.010 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 44 T ( S.DT47 0.008 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 45 G ( S.DG48 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 46 A . S.DA49 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 47 A ( S.DA50 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 48 G ( S.DG51 0.012 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 49 A ( S.DA52 0.014 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 C ( S.DC53 0.016 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 51 A ( S.DA54 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 52 T ) T.DT1 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 53 G ) T.DG2 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 54 T ) T.DT3 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 55 C ) T.DC4 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 56 T ) T.DT5 0.019 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 57 T . T.DT6 0.017 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 58 C ) T.DC7 0.024 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 59 A ) T.DA8 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 A ) T.DA9 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 61 C ) T.DC10 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 62 T ) T.DT11 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 63 G . T.DG12 0.021 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 64 C ) T.DC13 0.016 anti,~C2'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop 65 T . T.DT14 0.010 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 66 T . T.DT15 0.008 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 67 T ] T.DT16 0.024 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 68 C ] T.DC17 0.021 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem 69 G ] T.DG18 0.025 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem,phosphate 70 C ] T.DC19 0.017 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 71 A . T.DA20 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 72 T ] T.DT21 0.008 pseudoknotted,anti,BI,isolated-canonical,non-pair-contact,helix-end,internal-loop,phosphate 73 G . T.DG22 0.007 anti,BI,non-pair-contact,ss-non-loop,phosphate 74 A . T.DA23 0.010 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 75 A . T.DA24 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 76 G . T.DG25 0.009 anti,~C2'-endo,non-stack,ss-non-loop 77 T . T.DT26 0.008 anti,~C2'-endo,non-stack,non-canonical,multiplet,ss-non-loop 78 A . T.DA27 0.009 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop 79 C . T.DC28 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 80 C . T.DC29 0.010 anti,BI,non-canonical,non-pair-contact,helix,ss-non-loop,phosphate 81 T . T.DT30 0.022 anti,BII,non-canonical,non-pair-contact,helix,ss-non-loop 82 C ) T.DC31 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end 83 C ) T.DC32 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 84 C ) T.DC33 0.006 anti,BI,canonical,non-pair-contact,helix,stem 85 A ) T.DA34 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 86 A ) T.DA35 0.017 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem 87 C ) T.DC36 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 88 T ) T.DT37 0.010 anti,BI,canonical,non-pair-contact,helix,stem 89 A ) T.DA38 0.011 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 90 C ) T.DC39 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 91 T ) T.DT40 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 92 T ) T.DT41 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 93 T ) T.DT42 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 94 T ) T.DT43 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 95 C ) T.DC44 0.006 anti,BI,canonical,non-pair-contact,helix,stem 96 C ) T.DC45 0.006 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 97 T ) T.DT46 0.018 anti,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 98 C . T.DC47 0.010 anti,~C2'-endo,BI,non-stack,non-pair-contact,internal-loop,phosphate 99 A . T.DA48 0.019 anti,~C3'-endo,BI,non-pair-contact,internal-loop 100 C . T.DC49 0.013 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 101 A ) T.DA50 0.008 anti,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 102 C ) T.DC51 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end 103 T . T.DT52 0.009 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 104 T . T.DT53 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 105 G . T.DG54 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop **************************************************************************** List of 12 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-iloops.pdb -- an ensemble of internal loops 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks 12 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions