**************************************************************************** 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=6vvj.pdb -o=6vvj.out File name: 6vvj.pdb no. of DNA/RNA chains: 1 [A=130] no. of nucleotides: 130 no. of atoms: 4179 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 M7G-g 1 A.M7G2 **************************************************************************** List of 59 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.M7G2 A.C56 g-C WC 19-XIX cWW cW-W 2 A.G3 A.C55 G-C WC 19-XIX cWW cW-W 3 A.U4 A.A54 U-A WC 20-XX cWW cW-W 4 A.C5 A.A54 C-A ~Wobble -- cWW cW-W 5 A.U6 A.A53 U-A WC 20-XX cWW cW-W 6 A.C7 A.G52 C-G WC 19-XIX cWW cW-W 7 A.C9 A.G51 C-G WC 19-XIX cWW cW-W 8 A.U10 A.A50 U-A WC 20-XX cWW cW-W 9 A.U11 A.A49 U-A WC 20-XX cWW cW-W 10 A.G12 A.C48 G-C WC 19-XIX cWW cW-W 11 A.U13 A.G47 U-G Wobble 28-XXVIII cWW cW-W 12 A.U14 A.A46 U-A WC 20-XX cWW cW-W 13 A.A15 A.U45 A-U WC 20-XX cWW cW-W 14 A.G16 A.C44 G-C WC 19-XIX cWW cW-W 15 A.C18 A.G43 C-G WC 19-XIX cWW cW-W 16 A.C19 A.G42 C-G WC 19-XIX cWW cW-W 17 A.A20 A.U41 A-U WC 20-XX cWW cW-W 18 A.G21 A.C40 G-C WC 19-XIX cWW cW-W 19 A.G22 A.U39 G-U Wobble 28-XXVIII cWW cW-W 20 A.G25 A.C38 G-C WC 19-XIX cWW cW-W 21 A.A26 A.U37 A-U WC 20-XX cWW cW-W 22 A.G27 A.C36 G-C WC 19-XIX cWW cW-W 23 A.C28 A.G35 C-G WC 19-XIX cWW cW-W 24 A.C29 A.A34 C-A ~Wobble -- cWW cW-W 25 A.C30 A.G33 C-G WC 19-XIX cWW cW-W 26 A.C57 A.G103 C-G WC 19-XIX cWW cW-W 27 A.A58 A.U102 A-U WC 20-XX cWW cW-W 28 A.C59 A.G101 C-G WC 19-XIX cWW cW-W 29 A.U60 A.A100 U-A WC 20-XX cWW cW-W 30 A.G61 A.C99 G-C WC 19-XIX cWW cW-W 31 A.C62 A.G98 C-G WC 19-XIX cWW cW-W 32 A.U63 A.A97 U-A WC 20-XX cWW cW-W 33 A.U64 A.A96 U-A WC 20-XX cWW cW-W 34 A.A65 A.C95 A-C ~Wobble -- cWW cW-W 35 A.A66 A.U94 A-U WC 20-XX cWW cW-W 36 A.G67 A.C93 G-C WC 19-XIX cWW cW-W 37 A.C68 A.G91 C-G WC 19-XIX cWW cW-W 38 A.C69 A.G89 C-G WC 19-XIX cWW cW-W 39 A.U70 A.A88 U-A WC 20-XX cWW cW-W 40 A.C71 A.G87 C-G WC 19-XIX cWW cW-W 41 A.A72 A.U86 A-U WC 20-XX cWW cW-W 42 A.A73 A.U85 A-U WC 20-XX cWW cW-W 43 A.U74 A.C84 U-C -- 18-XVIII cWW cW-W 44 A.A75 A.C83 A-C ~Wobble -- cWW cW-W 45 A.A76 A.G82 A-G Imino 08-VIII cWW cW-W 46 A.A77 A.U81 A-U WC 20-XX cWW cW-W 47 A.U104 A.G359 U-G Wobble 28-XXVIII cWW cW-W 48 A.G105 A.C358 G-C WC 19-XIX cWW cW-W 49 A.U106 A.G357 U-G Wobble 28-XXVIII cWW cW-W 50 A.G107 A.U356 G-U Wobble 28-XXVIII cWW cW-W 51 A.C108 A.G355 C-G WC 19-XIX cWW cW-W 52 A.C109 A.G354 C-G WC 19-XIX cWW cW-W 53 A.C110 A.G353 C-G WC 19-XIX cWW cW-W 54 A.A111 A.U352 A-U WC 20-XX cWW cW-W 55 A.U112 A.A351 U-A WC 20-XX cWW cW-W 56 A.C113 A.G350 C-G WC 19-XIX cWW cW-W 57 A.U114 A.A349 U-A WC 20-XX cWW cW-W 58 A.C115 A.G120 C-G WC 19-XIX cWW cW-W 59 A.G116 A.A119 G-A Sheared 11-XI tSH tm-M **************************************************************************** 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[8] bps=45 strand-1 5'-GAGCUCUCUGGCUAGCAAGGAACCCACUGCUUAAGCCUCAAUAAA-3' bp-type |.||||||||||||||||||||||||||||||.||||||||...| strand-2 3'-CCCGAGGGACCGAUUGUUCCUUGgGUGACGAACUCGGAGUUCCGU-5' helix-form .AAAAx.AAAxAA..AAAxAxAxxAAAAAAAAAAxxAAAA...A 1 A.G33 A.C30 G-C WC 19-XIX cWW cW-W 2 A.A34 A.C29 A-C ~Wobble -- cWW cW-W 3 A.G35 A.C28 G-C WC 19-XIX cWW cW-W 4 A.C36 A.G27 C-G WC 19-XIX cWW cW-W 5 A.U37 A.A26 U-A WC 20-XX cWW cW-W 6 A.C38 A.G25 C-G WC 19-XIX cWW cW-W 7 A.U39 A.G22 U-G Wobble 28-XXVIII cWW cW-W 8 A.C40 A.G21 C-G WC 19-XIX cWW cW-W 9 A.U41 A.A20 U-A WC 20-XX cWW cW-W 10 A.G42 A.C19 G-C WC 19-XIX cWW cW-W 11 A.G43 A.C18 G-C WC 19-XIX cWW cW-W 12 A.C44 A.G16 C-G WC 19-XIX cWW cW-W 13 A.U45 A.A15 U-A WC 20-XX cWW cW-W 14 A.A46 A.U14 A-U WC 20-XX cWW cW-W 15 A.G47 A.U13 G-U Wobble 28-XXVIII cWW cW-W 16 A.C48 A.G12 C-G WC 19-XIX cWW cW-W 17 A.A49 A.U11 A-U WC 20-XX cWW cW-W 18 A.A50 A.U10 A-U WC 20-XX cWW cW-W 19 A.G51 A.C9 G-C WC 19-XIX cWW cW-W 20 A.G52 A.C7 G-C WC 19-XIX cWW cW-W 21 A.A53 A.U6 A-U WC 20-XX cWW cW-W 22 A.A54 A.U4 A-U WC 20-XX cWW cW-W 23 A.C55 A.G3 C-G WC 19-XIX cWW cW-W 24 A.C56 A.M7G2 C-g WC 19-XIX cWW cW-W 25 A.C57 A.G103 C-G WC 19-XIX cWW cW-W 26 A.A58 A.U102 A-U WC 20-XX cWW cW-W 27 A.C59 A.G101 C-G WC 19-XIX cWW cW-W 28 A.U60 A.A100 U-A WC 20-XX cWW cW-W 29 A.G61 A.C99 G-C WC 19-XIX cWW cW-W 30 A.C62 A.G98 C-G WC 19-XIX cWW cW-W 31 A.U63 A.A97 U-A WC 20-XX cWW cW-W 32 A.U64 A.A96 U-A WC 20-XX cWW cW-W 33 A.A65 A.C95 A-C ~Wobble -- cWW cW-W 34 A.A66 A.U94 A-U WC 20-XX cWW cW-W 35 A.G67 A.C93 G-C WC 19-XIX cWW cW-W 36 A.C68 A.G91 C-G WC 19-XIX cWW cW-W 37 A.C69 A.G89 C-G WC 19-XIX cWW cW-W 38 A.U70 A.A88 U-A WC 20-XX cWW cW-W 39 A.C71 A.G87 C-G WC 19-XIX cWW cW-W 40 A.A72 A.U86 A-U WC 20-XX cWW cW-W 41 A.A73 A.U85 A-U WC 20-XX cWW cW-W 42 A.U74 A.C84 U-C -- 18-XVIII cWW cW-W 43 A.A75 A.C83 A-C ~Wobble -- cWW cW-W 44 A.A76 A.G82 A-G Imino 08-VIII cWW cW-W 45 A.A77 A.U81 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=13 strand-1 5'-UGUGCCCAUCUCG-3' bp-type ||||||||||||. strand-2 3'-GCGUGGGUAGAGA-5' helix-form .A..AAAAAAA. 1 A.U104 A.G359 U-G Wobble 28-XXVIII cWW cW-W 2 A.G105 A.C358 G-C WC 19-XIX cWW cW-W 3 A.U106 A.G357 U-G Wobble 28-XXVIII cWW cW-W 4 A.G107 A.U356 G-U Wobble 28-XXVIII cWW cW-W 5 A.C108 A.G355 C-G WC 19-XIX cWW cW-W 6 A.C109 A.G354 C-G WC 19-XIX cWW cW-W 7 A.C110 A.G353 C-G WC 19-XIX cWW cW-W 8 A.A111 A.U352 A-U WC 20-XX cWW cW-W 9 A.U112 A.A351 U-A WC 20-XX cWW cW-W 10 A.C113 A.G350 C-G WC 19-XIX cWW cW-W 11 A.U114 A.A349 U-A WC 20-XX cWW cW-W 12 A.C115 A.G120 C-G WC 19-XIX cWW cW-W 13 A.G116 A.A119 G-A Sheared 11-XI tSH tm-M **************************************************************************** List of 9 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'-GU-3' bp-type || strand-2 3'-CA-5' helix-form A 1 A.G3 A.C55 G-C WC 19-XIX cWW cW-W 2 A.U4 A.A54 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-UC-3' bp-type || strand-2 3'-AG-5' helix-form A 1 A.U6 A.A53 U-A WC 20-XX cWW cW-W 2 A.C7 A.G52 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=8 strand-1 5'-CUUGUUAG-3' bp-type |||||||| strand-2 3'-GAACGAUC-5' helix-form AAA..AA 1 A.C9 A.G51 C-G WC 19-XIX cWW cW-W 2 A.U10 A.A50 U-A WC 20-XX cWW cW-W 3 A.U11 A.A49 U-A WC 20-XX cWW cW-W 4 A.G12 A.C48 G-C WC 19-XIX cWW cW-W 5 A.U13 A.G47 U-G Wobble 28-XXVIII cWW cW-W 6 A.U14 A.A46 U-A WC 20-XX cWW cW-W 7 A.A15 A.U45 A-U WC 20-XX cWW cW-W 8 A.G16 A.C44 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=5 strand-1 5'-CCAGG-3' bp-type ||||| strand-2 3'-GGUCU-5' helix-form AAA. 1 A.C18 A.G43 C-G WC 19-XIX cWW cW-W 2 A.C19 A.G42 C-G WC 19-XIX cWW cW-W 3 A.A20 A.U41 A-U WC 20-XX cWW cW-W 4 A.G21 A.C40 G-C WC 19-XIX cWW cW-W 5 A.G22 A.U39 G-U Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#5[#1] bps=4 strand-1 5'-GAGC-3' bp-type |||| strand-2 3'-CUCG-5' helix-form AAA 1 A.G25 A.C38 G-C WC 19-XIX cWW cW-W 2 A.A26 A.U37 A-U WC 20-XX cWW cW-W 3 A.G27 A.C36 G-C WC 19-XIX cWW cW-W 4 A.C28 A.G35 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#6[#1] bps=8 strand-1 5'-CACUGCUU-3' bp-type |||||||| strand-2 3'-GUGACGAA-5' helix-form AAAAAAA 1 A.C57 A.G103 C-G WC 19-XIX cWW cW-W 2 A.A58 A.U102 A-U WC 20-XX cWW cW-W 3 A.C59 A.G101 C-G WC 19-XIX cWW cW-W 4 A.U60 A.A100 U-A WC 20-XX cWW cW-W 5 A.G61 A.C99 G-C WC 19-XIX cWW cW-W 6 A.C62 A.G98 C-G WC 19-XIX cWW cW-W 7 A.U63 A.A97 U-A WC 20-XX cWW cW-W 8 A.U64 A.A96 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#7[#1] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-UC-5' helix-form A 1 A.A66 A.U94 A-U WC 20-XX cWW cW-W 2 A.G67 A.C93 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#1] bps=5 strand-1 5'-CUCAA-3' bp-type ||||| strand-2 3'-GAGUU-5' helix-form AAAA 1 A.C69 A.G89 C-G WC 19-XIX cWW cW-W 2 A.U70 A.A88 U-A WC 20-XX cWW cW-W 3 A.C71 A.G87 C-G WC 19-XIX cWW cW-W 4 A.A72 A.U86 A-U WC 20-XX cWW cW-W 5 A.A73 A.U85 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#9[#2] bps=12 strand-1 5'-UGUGCCCAUCUC-3' bp-type |||||||||||| strand-2 3'-GCGUGGGUAGAG-5' helix-form .A..AAAAAAA 1 A.U104 A.G359 U-G Wobble 28-XXVIII cWW cW-W 2 A.G105 A.C358 G-C WC 19-XIX cWW cW-W 3 A.U106 A.G357 U-G Wobble 28-XXVIII cWW cW-W 4 A.G107 A.U356 G-U Wobble 28-XXVIII cWW cW-W 5 A.C108 A.G355 C-G WC 19-XIX cWW cW-W 6 A.C109 A.G354 C-G WC 19-XIX cWW cW-W 7 A.C110 A.G353 C-G WC 19-XIX cWW cW-W 8 A.A111 A.U352 A-U WC 20-XX cWW cW-W 9 A.U112 A.A351 U-A WC 20-XX cWW cW-W 10 A.C113 A.G350 C-G WC 19-XIX cWW cW-W 11 A.U114 A.A349 U-A WC 20-XX cWW cW-W 12 A.C115 A.G120 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 4 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 A.M7G2 A.C56 g-C WC 19-XIX cWW cW-W [#1] -2 A.C30 A.G33 C-G WC 19-XIX cWW cW-W [#1] -3 A.C68 A.G91 C-G WC 19-XIX cWW cW-W [#1] -4 A.A77 A.U81 A-U WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 8 stems: [#5,#4,#3,#2,#1,#6,#7,#8] **************************************************************************** List of 22 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 GG A.G31,A.G32 2 nts=2 GC A.G43,A.C44 3 nts=2 GG A.G51,A.G52 4 nts=2 AA A.A53,A.A54 5 nts=2 AU A.A73,A.U74 6 nts=2 CU A.C84,A.U85 7 nts=2 UC A.U94,A.C95 8 nts=2 GG A.G116,A.G120 9 nts=3 GgG A.G3,A.M7G2,A.G103 10 nts=3 UCU A.U4,A.C5,A.U6 11 nts=3 CUC A.C7,A.U8,A.C9 12 nts=3 GAC A.G16,A.A17,A.C18 13 nts=3 CCC A.C28,A.C29,A.C30 14 nts=3 GAG A.G33,A.A34,A.G35 15 nts=3 CCC A.C55,A.C56,A.C57 16 nts=3 AAA A.A66,A.A65,A.A96 17 nts=3 GCC A.G67,A.C68,A.C69 18 nts=3 UGC A.U81,A.G82,A.C83 19 nts=3 AGA A.A117,A.G118,A.A119 20 nts=4 GUCG A.G22,A.U23,A.C24,A.G25 21 nts=4 AAAG A.A75,A.A76,A.A77,A.G78 22 nts=4 GUGC A.G89,A.U90,A.G91,A.C93 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 CUC A.C79,A.U80,A.C92 **************************************************************************** List of 3 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.G32 A.G33 3.02 2 phosphate OP2@A.G118 A.G116 3.05 3 sugar O4'@A.G120 A.A119 3.27 **************************************************************************** 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 hairpin loops 1 hairpin loop: nts=4; [2]; linked by [#-2] summary: [1] 2 [A.30 A.33] 1 nts=4 CGGG A.C30,A.G31,A.G32,A.G33 nts=2 GG A.G31,A.G32 2 hairpin loop: nts=5; [3]; linked by [#-4] summary: [1] 3 [A.77 A.81] 1 nts=5 AGCUU A.A77,A.G78,A.C79,A.U80,A.U81 nts=3 GCU A.G78,A.C79,A.U80 3 hairpin loop: nts=6; [4]; linked by [#9] summary: [1] 4 [A.115 A.120] 12 nts=6 CGAGAG A.C115,A.G116,A.A117,A.G118,A.A119,A.G120 nts=4 GAGA A.G116,A.A117,A.G118,A.A119 **************************************************************************** List of 6 bulges 1 bulge: nts=5; [1,0]; linked by [#1,#2] summary: [2] 1 0 [A.4 A.54 A.6 A.53] 2 2 nts=5 UCUAA A.U4,A.C5,A.U6,A.A53,A.A54 nts=1 C A.C5 nts=0 2 bulge: nts=5; [1,0]; linked by [#2,#3] summary: [2] 1 0 [A.7 A.52 A.9 A.51] 2 8 nts=5 CUCGG A.C7,A.U8,A.C9,A.G51,A.G52 nts=1 U A.U8 nts=0 3 bulge: nts=5; [1,0]; linked by [#3,#4] summary: [2] 1 0 [A.16 A.44 A.18 A.43] 8 5 nts=5 GACGC A.G16,A.A17,A.C18,A.G43,A.C44 nts=1 A A.A17 nts=0 4 bulge: nts=5; [0,1]; linked by [#7,#-3] summary: [2] 0 1 [A.67 A.93 A.68 A.91] 2 1 nts=5 GCGCC A.G67,A.C68,A.G91,A.C92,A.C93 nts=0 nts=1 C A.C92 5 bulge: nts=5; [0,1]; linked by [#-3,#8] summary: [2] 0 1 [A.68 A.91 A.69 A.89] 1 5 nts=5 CCGUG A.C68,A.C69,A.G89,A.U90,A.G91 nts=0 nts=1 U A.U90 6 bulge: nts=6; [2,0]; linked by [#4,#5] summary: [2] 2 0 [A.22 A.39 A.25 A.38] 5 4 nts=6 GUCGCU A.G22,A.U23,A.C24,A.G25,A.C38,A.U39 nts=2 UC A.U23,A.C24 nts=0 **************************************************************************** List of 3 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#5,#-2] summary: [2] 1 1 [A.28 A.35 A.30 A.33] 4 1 nts=6 CCCGAG A.C28,A.C29,A.C30,A.G33,A.A34,A.G35 nts=1 C A.C29 nts=1 A A.A34 2 symmetric internal loop: nts=6; [1,1]; linked by [#6,#7] summary: [2] 1 1 [A.64 A.96 A.66 A.94] 8 2 nts=6 UAAUCA A.U64,A.A65,A.A66,A.U94,A.C95,A.A96 nts=1 A A.A65 nts=1 C A.C95 3 symmetric internal loop: nts=10; [3,3]; linked by [#8,#-4] summary: [2] 3 3 [A.73 A.85 A.77 A.81] 5 1 nts=10 AUAAAUGCCU A.A73,A.U74,A.A75,A.A76,A.A77,A.U81,A.G82,A.C83,A.C84,A.U85 nts=3 UAA A.U74,A.A75,A.A76 nts=3 GCC A.G82,A.C83,A.C84 **************************************************************************** List of 4 splayed-apart dinucleotides 1 A.G78 A.C79 angle=122 distance=15.6 ratio=0.87 2 A.U80 A.U81 angle=112 distance=16.0 ratio=0.83 3 A.G91 A.C92 angle=90 distance=15.4 ratio=0.71 4 A.C92 A.C93 angle=88 distance=13.4 ratio=0.70 ---------------------------------------------------------------- Summary of 3 splayed-apart units 1 nts=2 GC A.G78,A.C79 2 nts=2 UU A.U80,A.U81 3 nts=3 GCC A.G91,A.C92,A.C93 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6vvj nts=130 [whole] g&GUCUCUCUUGUUAGACCAGGUCGAGCCCGGGAGCUCUCUGGCUAGCAAGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCCUCAAGCAGUGUGUGCCCAUCUCGAGAGAGAUGGGUGCG (&((.((.((((((((.(((((..((((.(..).))))))))))))))))))))))((((((((.((((((((...(...)...))))).).)).))))))))((((((((((((....)))))))))))) >6vvj-A #1 nts=130 0.06(2.93) [chain] RNA* g&GUCUCUCUUGUUAGACCAGGUCGAGCCCGGGAGCUCUCUGGCUAGCAAGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCCUCAAGCAGUGUGUGCCCAUCUCGAGAGAGAUGGGUGCG (&((.((.((((((((.(((((..((((.(..).))))))))))))))))))))))((((((((.((((((((...(...)...))))).).)).))))))))((((((((((((....)))))))))))) **************************************************************************** Summary of structural features of 130 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 ( A.M7G2 0.049 modified,break,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix 2 G ( A.G3 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 3 U ( A.U4 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 4 C . A.C5 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,bulge 5 U ( A.U6 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 6 C ( A.C7 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 7 U . A.U8 0.025 anti,~C3'-endo,BI,non-pair-contact,bulge 8 C ( A.C9 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 9 U ( A.U10 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 U ( A.U11 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 G ( A.G12 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 U ( A.U13 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 U ( A.U14 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 A ( A.A15 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 G ( A.G16 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 16 A . A.A17 0.027 anti,~C3'-endo,BI,non-pair-contact,bulge 17 C ( A.C18 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 18 C ( A.C19 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 A ( A.A20 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 G ( A.G21 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 G ( A.G22 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 22 U . A.U23 0.026 anti,~C3'-endo,non-pair-contact,bulge 23 C . A.C24 0.014 anti,~C3'-endo,BI,non-pair-contact,bulge 24 G ( A.G25 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 25 A ( A.A26 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 G ( A.G27 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 C ( A.C28 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 28 C . A.C29 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 29 C ( A.C30 0.016 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,internal-loop 30 G . A.G31 0.023 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 31 G . A.G32 0.022 anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 32 G ) A.G33 0.019 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,internal-loop,cap-acceptor,phosphate 33 A . A.A34 0.031 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 34 G ) A.G35 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 35 C ) A.C36 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 U ) A.U37 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 37 C ) A.C38 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 38 U ) A.U39 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 39 C ) A.C40 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 U ) A.U41 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 41 G ) A.G42 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 G ) A.G43 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 43 C ) A.C44 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 44 U ) A.U45 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 45 A ) A.A46 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 46 G ) A.G47 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 47 C ) A.C48 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 48 A ) A.A49 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 49 A ) A.A50 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 G ) A.G51 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 51 G ) A.G52 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 52 A ) A.A53 0.035 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 53 A ) A.A54 0.028 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 54 C ) A.C55 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 55 C ) A.C56 0.016 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix 56 C ( A.C57 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 57 A ( A.A58 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 58 C ( A.C59 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 59 U ( A.U60 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 G ( A.G61 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 61 C ( A.C62 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 62 U ( A.U63 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 63 U ( A.U64 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 64 A . A.A65 0.030 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 65 A ( A.A66 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 66 G ( A.G67 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 67 C ( A.C68 0.015 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge 68 C ( A.C69 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 69 U ( A.U70 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 70 C ( A.C71 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 71 A ( A.A72 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 72 A ( A.A73 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 73 U . A.U74 0.027 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 74 A . A.A75 0.028 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 75 A . A.A76 0.027 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 76 A ( A.A77 0.031 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,internal-loop 77 G . A.G78 0.023 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 78 C . A.C79 0.013 anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 79 U . A.U80 0.025 turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 80 U ) A.U81 0.026 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,internal-loop,phosphate,splayed-apart 81 G . A.G82 0.021 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 82 C . A.C83 0.014 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 83 C . A.C84 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 84 U ) A.U85 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 85 U ) A.U86 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 86 G ) A.G87 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 87 A ) A.A88 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 88 G ) A.G89 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 89 U . A.U90 0.024 anti,~C3'-endo,BI,non-pair-contact,bulge 90 G ) A.G91 0.022 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix,bulge,splayed-apart 91 C . A.C92 0.013 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,splayed-apart 92 C ) A.C93 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 93 U ) A.U94 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 94 C . A.C95 0.013 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 95 A ) A.A96 0.032 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 96 A ) A.A97 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 97 G ) A.G98 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 98 C ) A.C99 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 99 A ) A.A100 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 100 G ) A.G101 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 101 U ) A.U102 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 102 G ) A.G103 0.026 turn,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 103 U ( A.U104 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 104 G ( A.G105 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 105 U ( A.U106 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 106 G ( A.G107 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 107 C ( A.C108 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 108 C ( A.C109 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 109 C ( A.C110 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 110 A ( A.A111 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 111 U ( A.U112 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 112 C ( A.C113 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 113 U ( A.U114 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 114 C ( A.C115 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 115 G . A.G116 0.021 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 116 A . A.A117 0.028 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 117 G . A.G118 0.021 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 118 A . A.A119 0.028 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate 119 G ) A.G120 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-donor 120 A ) A.A349 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 121 G ) A.G350 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 122 A ) A.A351 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 123 U ) A.U352 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 124 G ) A.G353 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 125 G ) A.G354 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 126 G ) A.G355 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 127 U ) A.U356 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 128 G ) A.G357 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 129 C ) A.C358 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 130 G ) A.G359 0.022 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 13 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-hairpins.pdb -- an ensemble of hairpin loops 5 dssr-bulges.pdb -- an ensemble of bulges 6 dssr-iloops.pdb -- an ensemble of internal loops 7 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 8 dssr-2ndstrs.ct -- secondary structure in connectivity table format 9 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 10 dssr-torsions.txt -- backbone torsion angles and suite names 11 dssr-splays.pdb -- an ensemble of splayed-apart units 12 dssr-stacks.pdb -- an ensemble of base stacks 13 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions