**************************************************************************** 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=1i2y.pdb -o=1i2y.out File name: 1i2y.pdb no. of DNA/RNA chains: 6 [A=11,B=11,C=11,D=11,E=11,F=11] no. of nucleotides: 66 no. of atoms: 1728 no. of waters: 334 no. of metals: 0 **************************************************************************** List of 30 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 B.U31 G-U Wobble 28-XXVIII cWW cW-W 2 A.C2 B.G30 C-G WC 19-XIX cWW cW-W 3 A.G3 B.C29 G-C WC 19-XIX cWW cW-W 4 A.DA4 B.DT27 A-T WC 20-XX cWW cW-W 5 A.DT5 B.DA26 T-A WC 20-XX cWW cW-W 6 A.DA6 B.DT25 A-T WC 20-XX cWW cW-W 7 A.DT7 B.DA24 T-A WC 20-XX cWW cW-W 8 A.C9 B.G23 C-G WC 19-XIX cWW cW-W 9 A.G10 B.C22 G-C WC 19-XIX cWW cW-W 10 A.U11 B.G21 U-G Wobble 28-XXVIII cWW cW-W 11 C.G101 D.U131 G-U Wobble 28-XXVIII cWW cW-W 12 C.C102 D.G130 C-G WC 19-XIX cWW cW-W 13 C.G103 D.C129 G-C WC 19-XIX cWW cW-W 14 C.DA104 D.DT127 A-T WC 20-XX cWW cW-W 15 C.DT105 D.DA126 T-A WC 20-XX cWW cW-W 16 C.DA106 D.DT125 A-T WC 20-XX cWW cW-W 17 C.DT107 D.DA124 T-A WC 20-XX cWW cW-W 18 C.C109 D.G123 C-G WC 19-XIX cWW cW-W 19 C.G110 D.C122 G-C WC 19-XIX cWW cW-W 20 C.U111 D.G121 U-G Wobble 28-XXVIII cWW cW-W 21 E.G201 F.U231 G-U Wobble 28-XXVIII cWW cW-W 22 E.C202 F.G230 C-G WC 19-XIX cWW cW-W 23 E.G203 F.C229 G-C WC 19-XIX cWW cW-W 24 E.DA204 F.DT227 A-T WC 20-XX cWW cW-W 25 E.DT205 F.DA226 T-A WC 20-XX cWW cW-W 26 E.DA206 F.DT225 A-T WC 20-XX cWW cW-W 27 E.DT207 F.DA224 T-A WC 20-XX cWW cW-W 28 E.C209 F.G223 C-G WC 19-XIX cWW cW-W 29 E.G210 F.C222 G-C WC 19-XIX cWW cW-W 30 E.U211 F.G221 U-G Wobble 28-XXVIII cWW cW-W **************************************************************************** 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[9] bps=30 strand-1 5'-GCGATATCGUGCGATATCGUGCGATATCGU-3' bp-type |||||||||||||||||||||||||||||| strand-2 3'-UGCTATAGCGUGCTATAGCGUGCTATAGCG-5' helix-form .AxBB.x..x.Ax.B.xA.x.Ax.B.x.. 1 D.G121 C.U111 G-U Wobble 28-XXVIII cWW cW-W 2 D.C122 C.G110 C-G WC 19-XIX cWW cW-W 3 D.G123 C.C109 G-C WC 19-XIX cWW cW-W 4 D.DA124 C.DT107 A-T WC 20-XX cWW cW-W 5 D.DT125 C.DA106 T-A WC 20-XX cWW cW-W 6 D.DA126 C.DT105 A-T WC 20-XX cWW cW-W 7 D.DT127 C.DA104 T-A WC 20-XX cWW cW-W 8 D.C129 C.G103 C-G WC 19-XIX cWW cW-W 9 D.G130 C.C102 G-C WC 19-XIX cWW cW-W 10 D.U131 C.G101 U-G Wobble 28-XXVIII cWW cW-W 11 A.G1 B.U31 G-U Wobble 28-XXVIII cWW cW-W 12 A.C2 B.G30 C-G WC 19-XIX cWW cW-W 13 A.G3 B.C29 G-C WC 19-XIX cWW cW-W 14 A.DA4 B.DT27 A-T WC 20-XX cWW cW-W 15 A.DT5 B.DA26 T-A WC 20-XX cWW cW-W 16 A.DA6 B.DT25 A-T WC 20-XX cWW cW-W 17 A.DT7 B.DA24 T-A WC 20-XX cWW cW-W 18 A.C9 B.G23 C-G WC 19-XIX cWW cW-W 19 A.G10 B.C22 G-C WC 19-XIX cWW cW-W 20 A.U11 B.G21 U-G Wobble 28-XXVIII cWW cW-W 21 E.G201 F.U231 G-U Wobble 28-XXVIII cWW cW-W 22 E.C202 F.G230 C-G WC 19-XIX cWW cW-W 23 E.G203 F.C229 G-C WC 19-XIX cWW cW-W 24 E.DA204 F.DT227 A-T WC 20-XX cWW cW-W 25 E.DT205 F.DA226 T-A WC 20-XX cWW cW-W 26 E.DA206 F.DT225 A-T WC 20-XX cWW cW-W 27 E.DT207 F.DA224 T-A WC 20-XX cWW cW-W 28 E.C209 F.G223 C-G WC 19-XIX cWW cW-W 29 E.G210 F.C222 G-C WC 19-XIX cWW cW-W 30 E.U211 F.G221 U-G Wobble 28-XXVIII cWW cW-W **************************************************************************** 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=3 strand-1 5'-GCG-3' bp-type ||| strand-2 3'-UGC-5' helix-form .A 1 A.G1 B.U31 G-U Wobble 28-XXVIII cWW cW-W 2 A.C2 B.G30 C-G WC 19-XIX cWW cW-W 3 A.G3 B.C29 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=4 strand-1 5'-ATAT-3' bp-type |||| strand-2 3'-TATA-5' helix-form .B. 1 A.DA4 B.DT27 A-T WC 20-XX cWW cW-W 2 A.DT5 B.DA26 T-A WC 20-XX cWW cW-W 3 A.DA6 B.DT25 A-T WC 20-XX cWW cW-W 4 A.DT7 B.DA24 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=3 strand-1 5'-CGU-3' bp-type ||| strand-2 3'-GCG-5' helix-form A. 1 A.C9 B.G23 C-G WC 19-XIX cWW cW-W 2 A.G10 B.C22 G-C WC 19-XIX cWW cW-W 3 A.U11 B.G21 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=3 strand-1 5'-GCG-3' bp-type ||| strand-2 3'-UGC-5' helix-form .. 1 C.G101 D.U131 G-U Wobble 28-XXVIII cWW cW-W 2 C.C102 D.G130 C-G WC 19-XIX cWW cW-W 3 C.G103 D.C129 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#1] bps=4 strand-1 5'-ATAT-3' bp-type |||| strand-2 3'-TATA-5' helix-form .BB 1 C.DA104 D.DT127 A-T WC 20-XX cWW cW-W 2 C.DT105 D.DA126 T-A WC 20-XX cWW cW-W 3 C.DA106 D.DT125 A-T WC 20-XX cWW cW-W 4 C.DT107 D.DA124 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#6[#1] bps=3 strand-1 5'-CGU-3' bp-type ||| strand-2 3'-GCG-5' helix-form A. 1 C.C109 D.G123 C-G WC 19-XIX cWW cW-W 2 C.G110 D.C122 G-C WC 19-XIX cWW cW-W 3 C.U111 D.G121 U-G Wobble 28-XXVIII cWW cW-W -------------------------------------------------------------------------- stem#7[#1] bps=3 strand-1 5'-GCG-3' bp-type ||| strand-2 3'-UGC-5' helix-form .A 1 E.G201 F.U231 G-U Wobble 28-XXVIII cWW cW-W 2 E.C202 F.G230 C-G WC 19-XIX cWW cW-W 3 E.G203 F.C229 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#1] bps=4 strand-1 5'-ATAT-3' bp-type |||| strand-2 3'-TATA-5' helix-form .B. 1 E.DA204 F.DT227 A-T WC 20-XX cWW cW-W 2 E.DT205 F.DA226 T-A WC 20-XX cWW cW-W 3 E.DA206 F.DT225 A-T WC 20-XX cWW cW-W 4 E.DT207 F.DA224 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#9[#1] bps=3 strand-1 5'-CGU-3' bp-type ||| strand-2 3'-GCG-5' helix-form .. 1 E.C209 F.G223 C-G WC 19-XIX cWW cW-W 2 E.G210 F.C222 G-C WC 19-XIX cWW cW-W 3 E.U211 F.G221 U-G Wobble 28-XXVIII cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 9 stems: [#6,#5,#4,#1,#2,#3,#7,#8,#9] **************************************************************************** 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 GG A.G1,C.G101 2 nts=2 GA A.G3,A.DA4 3 nts=2 GG B.G21,E.G201 4 nts=2 GA B.G23,B.DA24 5 nts=2 TC B.DT27,B.C29 6 nts=2 GA C.G103,C.DA104 7 nts=2 TC C.DT107,C.C109 8 nts=2 GA D.G123,D.DA124 9 nts=2 GA E.G203,E.DA204 10 nts=2 TC E.DT207,E.C209 11 nts=2 GA F.G223,F.DA224 12 nts=2 TC F.DT227,F.C229 **************************************************************************** Nucleotides not involved in stacking interactions nts=8 ACAAACAA A.A8,A.C9,B.A28,C.A108,D.A128,D.C129,E.A208,F.A228 **************************************************************************** List of 5 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@E.G201 A.U11 2.93 2 sugar O4'@C.G101 B.U31 2.99 3 sugar O4'@A.G1 D.U131 2.93 4 sugar O4'@E.C209 E.DT207 3.39 5 sugar O4'@B.G21 F.U231 2.98 **************************************************************************** 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 6 bulges 1 bulge: nts=5; [0,1]; linked by [#1,#2] summary: [2] 0 1 [A.3 B.29 A.4 B.27] 3 4 nts=5 GATAC A.G3,A.DA4,B.DT27,B.A28,B.C29 nts=0 nts=1 A B.A28 2 bulge: nts=5; [1,0]; linked by [#2,#3] summary: [2] 1 0 [A.7 B.24 A.9 B.23] 4 3 nts=5 TACGA A.DT7,A.A8,A.C9,B.G23,B.DA24 nts=1 A A.A8 nts=0 3 bulge: nts=5; [0,1]; linked by [#4,#5] summary: [2] 0 1 [C.103 D.129 C.104 D.127] 3 4 nts=5 GATAC C.G103,C.DA104,D.DT127,D.A128,D.C129 nts=0 nts=1 A D.A128 4 bulge: nts=5; [1,0]; linked by [#5,#6] summary: [2] 1 0 [C.107 D.124 C.109 D.123] 4 3 nts=5 TACGA C.DT107,C.A108,C.C109,D.G123,D.DA124 nts=1 A C.A108 nts=0 5 bulge: nts=5; [0,1]; linked by [#7,#8] summary: [2] 0 1 [E.203 F.229 E.204 F.227] 3 4 nts=5 GATAC E.G203,E.DA204,F.DT227,F.A228,F.C229 nts=0 nts=1 A F.A228 6 bulge: nts=5; [1,0]; linked by [#8,#9] summary: [2] 1 0 [E.207 F.224 E.209 F.223] 4 3 nts=5 TACGA E.DT207,E.A208,E.C209,F.G223,F.DA224 nts=1 A E.A208 nts=0 **************************************************************************** List of 12 splayed-apart dinucleotides 1 A.DT7 A.A8 angle=139 distance=17.8 ratio=0.94 2 A.A8 A.C9 angle=126 distance=17.9 ratio=0.89 3 B.DT27 B.A28 angle=127 distance=18.2 ratio=0.90 4 B.A28 B.C29 angle=132 distance=19.4 ratio=0.91 5 C.DT107 C.A108 angle=113 distance=16.9 ratio=0.84 6 C.A108 C.C109 angle=112 distance=17.6 ratio=0.83 7 D.DT127 D.A128 angle=160 distance=18.6 ratio=0.98 8 D.A128 D.C129 angle=137 distance=18.4 ratio=0.93 9 E.DT207 E.A208 angle=113 distance=17.0 ratio=0.83 10 E.A208 E.C209 angle=113 distance=17.9 ratio=0.83 11 F.DT227 F.A228 angle=105 distance=16.4 ratio=0.79 12 F.A228 F.C229 angle=137 distance=17.1 ratio=0.93 ---------------------------------------------------------------- Summary of 6 splayed-apart units 1 nts=3 TAC A.DT7,A.A8,A.C9 2 nts=3 TAC B.DT27,B.A28,B.C29 3 nts=3 TAC C.DT107,C.A108,C.C109 4 nts=3 TAC D.DT127,D.A128,D.C129 5 nts=3 TAC E.DT207,E.A208,E.C209 6 nts=3 TAC F.DT227,F.A228,F.C229 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1i2y nts=66 [whole] GCGATATACGU&GCGATATACGU&GCGATATACGU&GCGATATACGU&GCGATATACGU&GCGATATACGU (((((((.(((&))))))).)))&(((((((.(((&))))))).)))&(((((((.(((&))))))).))) >1i2y-A #1 nts=11 2.55(0.75) [chain] DNA[4]/RNA[7] GCGATATACGU (((((((.((( >1i2y-B #2 nts=11 2.05(1.11) [chain] DNA[4]/RNA[7] GCGATATACGU ))))))).))) >1i2y-C #3 nts=11 2.34(1.12) [chain] DNA[4]/RNA[7] GCGATATACGU (((((((.((( >1i2y-D #4 nts=11 2.20(1.17) [chain] DNA[4]/RNA[7] GCGATATACGU ))))))).))) >1i2y-E #5 nts=11 1.95(1.32) [chain] DNA[4]/RNA[7] GCGATATACGU (((((((.((( >1i2y-F #6 nts=11 1.48(1.78) [chain] DNA[4]/RNA[7] GCGATATACGU ))))))).))) **************************************************************************** Summary of structural features of 66 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.G1 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-donor 2 C ( A.C2 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 G ( A.G3 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 4 A ( A.DA4 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 5 T ( A.DT5 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 A ( A.DA6 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 T ( A.DT7 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 8 A . A.A8 0.009 turn,anti,~C2'-endo,non-stack,bulge,splayed-apart 9 C ( A.C9 0.010 anti,~C3'-endo,BI,non-stack,canonical,helix,stem-end,coaxial-stack,bulge,splayed-apart 10 G ( A.G10 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 U ( A.U11 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor 12 G ) B.G21 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-donor 13 C ) B.C22 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 G ) B.G23 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 15 A ) B.DA24 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 16 T ) B.DT25 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 A ) B.DA26 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 T ) B.DT27 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 19 A . B.A28 0.014 turn,anti,~C2'-endo,non-stack,bulge,splayed-apart 20 C ) B.C29 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 21 G ) B.G30 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 U ) B.U31 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor 23 G ( C.G101 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-donor 24 C ( C.C102 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ( C.G103 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 26 A ( C.DA104 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 27 T ( C.DT105 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 A ( C.DA106 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 T ( C.DT107 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 30 A . C.A108 0.004 turn,anti,~C2'-endo,non-stack,bulge,splayed-apart 31 C ( C.C109 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 32 G ( C.G110 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 33 U ( C.U111 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 34 G ) D.G121 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 35 C ) D.C122 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 G ) D.G123 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 37 A ) D.DA124 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 38 T ) D.DT125 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 A ) D.DA126 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 T ) D.DT127 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 41 A . D.A128 0.019 turn,anti,~C2'-endo,non-stack,bulge,splayed-apart 42 C ) D.C129 0.006 anti,~C3'-endo,BI,non-stack,canonical,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 43 G ) D.G130 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 44 U ) D.U131 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor 45 G ( E.G201 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-donor 46 C ( E.C202 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 47 G ( E.G203 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 48 A ( E.DA204 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 49 T ( E.DT205 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 A ( E.DA206 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 51 T ( E.DT207 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,cap-acceptor,splayed-apart 52 A . E.A208 0.019 turn,anti,non-stack,bulge,splayed-apart 53 C ( E.C209 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,cap-donor,splayed-apart 54 G ( E.G210 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 55 U ( E.U211 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 56 G ) F.G221 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 57 C ) F.C222 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 58 G ) F.G223 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 59 A ) F.DA224 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 60 T ) F.DT225 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 61 A ) F.DA226 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 62 T ) F.DT227 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 63 A . F.A228 0.006 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,splayed-apart 64 C ) F.C229 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 65 G ) F.G230 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 66 U ) F.U231 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor **************************************************************************** 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