**************************************************************************** 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=5gun.pdb -o=5gun.out File name: 5gun.pdb no. of DNA/RNA chains: 6 [A=12,B=12,C=12,D=12,E=12,F=12] no. of nucleotides: 72 no. of atoms: 1522 no. of waters: 14 no. of metals: 8 [Co=8] **************************************************************************** List of 30 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG1 B.DC24 G-C WC 19-XIX cWW cW-W 2 A.DT2 B.DA23 T-A WC 20-XX cWW cW-W 3 A.DG3 B.DA22 G-A Sheared 11-XI tSH tm-M 4 A.DA5 B.DG20 A-G Sheared 11-XI tHS tM-m 5 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 6 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 7 A.DG8 B.DA17 G-A Sheared 11-XI tSH tm-M 8 A.DA10 B.DG15 A-G Sheared 11-XI tHS tM-m 9 A.DA11 B.DT14 A-T WC 20-XX cWW cW-W 10 A.DC12 B.DG13 C-G WC 19-XIX cWW cW-W 11 C.DG25 D.DC48 G-C WC 19-XIX cWW cW-W 12 C.DT26 D.DA47 T-A WC 20-XX cWW cW-W 13 C.DG27 D.DA46 G-A Sheared 11-XI tSH tm-M 14 C.DA29 D.DG44 A-G Sheared 11-XI tHS tM-m 15 C.DA30 D.DT43 A-T WC 20-XX cWW cW-W 16 C.DT31 D.DA42 T-A WC 20-XX cWW cW-W 17 C.DG32 D.DA41 G-A Sheared 11-XI tSH tm-M 18 C.DA34 D.DG39 A-G Sheared 11-XI tHS tM-m 19 C.DA35 D.DT38 A-T WC 20-XX cWW cW-W 20 C.DC36 D.DG37 C-G WC 19-XIX cWW cW-W 21 E.DG49 F.DC72 G-C WC 19-XIX cWW cW-W 22 E.DT50 F.DA71 T-A WC 20-XX cWW cW-W 23 E.DG51 F.DA70 G-A Sheared 11-XI tSH tm-M 24 E.DA53 F.DG68 A-G Sheared 11-XI tHS tM-m 25 E.DA54 F.DT67 A-T WC 20-XX cWW cW-W 26 E.DT55 F.DA66 T-A WC 20-XX cWW cW-W 27 E.DG56 F.DA65 G-A Sheared 11-XI tSH tm-M 28 E.DA58 F.DG63 A-G Sheared 11-XI tHS tM-m 29 E.DA59 F.DT62 A-T WC 20-XX cWW cW-W 30 E.DC60 F.DG61 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 8 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=3 strand-1 5'-GTG-3' bp-type ||. strand-2 3'-CAA-5' helix-form B. 1 A.DG1 B.DC24 G-C WC 19-XIX cWW cW-W 2 A.DT2 B.DA23 T-A WC 20-XX cWW cW-W 3 A.DG3 B.DA22 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#2[1] bps=4 strand-1 5'-AATG-3' bp-type .||. strand-2 3'-GTAA-5' helix-form .B. 1 A.DA5 B.DG20 A-G Sheared 11-XI tHS tM-m 2 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 3 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 4 A.DG8 B.DA17 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#3[1] bps=3 strand-1 5'-AAC-3' bp-type .|| strand-2 3'-GTG-5' helix-form .B 1 A.DA10 B.DG15 A-G Sheared 11-XI tHS tM-m 2 A.DA11 B.DT14 A-T WC 20-XX cWW cW-W 3 A.DC12 B.DG13 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[1] bps=4 strand-1 5'-AATG-3' bp-type .||. strand-2 3'-GTAA-5' helix-form .B. 1 C.DA29 D.DG44 A-G Sheared 11-XI tHS tM-m 2 C.DA30 D.DT43 A-T WC 20-XX cWW cW-W 3 C.DT31 D.DA42 T-A WC 20-XX cWW cW-W 4 C.DG32 D.DA41 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#5[1] bps=3 strand-1 5'-AAC-3' bp-type .|| strand-2 3'-GTG-5' helix-form .B 1 C.DA34 D.DG39 A-G Sheared 11-XI tHS tM-m 2 C.DA35 D.DT38 A-T WC 20-XX cWW cW-W 3 C.DC36 D.DG37 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#6[2] bps=6 strand-1 5'-AACGTG-3' bp-type .||||. strand-2 3'-GTGCAA-5' helix-form .Bx.. 1 D.DA46 C.DG27 A-G Sheared 11-XI tHS tM-m 2 D.DA47 C.DT26 A-T WC 20-XX cWW cW-W 3 D.DC48 C.DG25 C-G WC 19-XIX cWW cW-W 4 F.DG61 E.DC60 G-C WC 19-XIX cWW cW-W 5 F.DT62 E.DA59 T-A WC 20-XX cWW cW-W 6 F.DG63 E.DA58 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#7[1] bps=3 strand-1 5'-GTG-3' bp-type ||. strand-2 3'-CAA-5' helix-form .. 1 E.DG49 F.DC72 G-C WC 19-XIX cWW cW-W 2 E.DT50 F.DA71 T-A WC 20-XX cWW cW-W 3 E.DG51 F.DA70 G-A Sheared 11-XI tSH tm-M -------------------------------------------------------------------------- helix#8[1] bps=4 strand-1 5'-AATG-3' bp-type .||. strand-2 3'-GTAA-5' helix-form .B. 1 E.DA53 F.DG68 A-G Sheared 11-XI tHS tM-m 2 E.DA54 F.DT67 A-T WC 20-XX cWW cW-W 3 E.DT55 F.DA66 T-A WC 20-XX cWW cW-W 4 E.DG56 F.DA65 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'-GT-3' bp-type || strand-2 3'-CA-5' helix-form B 1 A.DG1 B.DC24 G-C WC 19-XIX cWW cW-W 2 A.DT2 B.DA23 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=2 strand-1 5'-AT-3' bp-type || strand-2 3'-TA-5' helix-form B 1 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 2 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#3] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-TG-5' helix-form B 1 A.DA11 B.DT14 A-T WC 20-XX cWW cW-W 2 A.DC12 B.DG13 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#6] bps=2 strand-1 5'-GT-3' bp-type || strand-2 3'-CA-5' helix-form B 1 C.DG25 D.DC48 G-C WC 19-XIX cWW cW-W 2 C.DT26 D.DA47 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#5[#4] bps=2 strand-1 5'-AT-3' bp-type || strand-2 3'-TA-5' helix-form B 1 C.DA30 D.DT43 A-T WC 20-XX cWW cW-W 2 C.DT31 D.DA42 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#6[#5] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-TG-5' helix-form B 1 C.DA35 D.DT38 A-T WC 20-XX cWW cW-W 2 C.DC36 D.DG37 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#7] bps=2 strand-1 5'-GT-3' bp-type || strand-2 3'-CA-5' helix-form . 1 E.DG49 F.DC72 G-C WC 19-XIX cWW cW-W 2 E.DT50 F.DA71 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#8[#8] bps=2 strand-1 5'-AT-3' bp-type || strand-2 3'-TA-5' helix-form B 1 E.DA54 F.DT67 A-T WC 20-XX cWW cW-W 2 E.DT55 F.DA66 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#9[#6] bps=2 strand-1 5'-AC-3' bp-type || strand-2 3'-TG-5' helix-form . 1 E.DA59 F.DT62 A-T WC 20-XX cWW cW-W 2 E.DC60 F.DG61 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#6 contains 2 stems: [#4,#9] **************************************************************************** List of 20 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 AA A.DA5,A.DA6 2 nts=2 AA A.DA10,A.DA11 3 nts=2 AA B.DA17,B.DA18 4 nts=2 AA B.DA22,B.DA23 5 nts=2 GC C.DG25,E.DC60 6 nts=2 AA C.DA29,C.DA30 7 nts=2 AA C.DA34,C.DA35 8 nts=2 AA D.DA41,D.DA42 9 nts=2 AA D.DA46,D.DA47 10 nts=2 CG D.DC48,F.DG61 11 nts=2 AA E.DA53,E.DA54 12 nts=2 AA E.DA58,E.DA59 13 nts=2 AA F.DA65,F.DA66 14 nts=2 AA F.DA70,F.DA71 15 nts=6 TGGGGT A.DT2,A.DG3,A.DG4,B.DG21,B.DG20,B.DT19 16 nts=6 TGGGGT A.DT7,A.DG8,A.DG9,B.DG16,B.DG15,B.DT14 17 nts=6 TGGGGT C.DT26,C.DG27,C.DG28,D.DG45,D.DG44,D.DT43 18 nts=6 TGGGGT C.DT31,C.DG32,C.DG33,D.DG40,D.DG39,D.DT38 19 nts=6 TGGGGT E.DT50,E.DG51,E.DG52,F.DG69,F.DG68,F.DT67 20 nts=6 TGGGGT E.DT55,E.DG56,E.DG57,F.DG64,F.DG63,F.DT62 **************************************************************************** List of 9 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@B.DG21 A.DA5 2.92 2 sugar O4'@B.DG16 A.DA10 3.06 3 sugar O4'@A.DG9 B.DA17 3.23 4 sugar O4'@A.DG4 B.DA22 3.11 5 sugar O4'@D.DG45 C.DA29 2.96 6 sugar O4'@C.DG33 D.DA41 3.27 7 sugar O4'@C.DG28 D.DA46 3.03 8 sugar O4'@F.DG64 E.DA58 3.23 9 sugar O4'@E.DG57 F.DA65 3.22 **************************************************************************** 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 internal loops 1 symmetric internal loop: nts=10; [3,3]; linked by [#1,#2] summary: [2] 3 3 [A.2 B.23 A.6 B.19] 2 2 nts=10 TGGAATGGAA A.DT2,A.DG3,A.DG4,A.DA5,A.DA6,B.DT19,B.DG20,B.DG21,B.DA22,B.DA23 nts=3 GGA A.DG3,A.DG4,A.DA5 nts=3 GGA B.DG20,B.DG21,B.DA22 2 symmetric internal loop: nts=10; [3,3]; linked by [#2,#3] summary: [2] 3 3 [A.7 B.18 A.11 B.14] 2 2 nts=10 TGGAATGGAA A.DT7,A.DG8,A.DG9,A.DA10,A.DA11,B.DT14,B.DG15,B.DG16,B.DA17,B.DA18 nts=3 GGA A.DG8,A.DG9,A.DA10 nts=3 GGA B.DG15,B.DG16,B.DA17 3 symmetric internal loop: nts=10; [3,3]; linked by [#4,#5] summary: [2] 3 3 [C.26 D.47 C.30 D.43] 2 2 nts=10 TGGAATGGAA C.DT26,C.DG27,C.DG28,C.DA29,C.DA30,D.DT43,D.DG44,D.DG45,D.DA46,D.DA47 nts=3 GGA C.DG27,C.DG28,C.DA29 nts=3 GGA D.DG44,D.DG45,D.DA46 4 symmetric internal loop: nts=10; [3,3]; linked by [#5,#6] summary: [2] 3 3 [C.31 D.42 C.35 D.38] 2 2 nts=10 TGGAATGGAA C.DT31,C.DG32,C.DG33,C.DA34,C.DA35,D.DT38,D.DG39,D.DG40,D.DA41,D.DA42 nts=3 GGA C.DG32,C.DG33,C.DA34 nts=3 GGA D.DG39,D.DG40,D.DA41 5 symmetric internal loop: nts=10; [3,3]; linked by [#7,#8] summary: [2] 3 3 [E.50 F.71 E.54 F.67] 2 2 nts=10 TGGAATGGAA E.DT50,E.DG51,E.DG52,E.DA53,E.DA54,F.DT67,F.DG68,F.DG69,F.DA70,F.DA71 nts=3 GGA E.DG51,E.DG52,E.DA53 nts=3 GGA F.DG68,F.DG69,F.DA70 6 symmetric internal loop: nts=10; [3,3]; linked by [#8,#9] summary: [2] 3 3 [E.55 F.66 E.59 F.62] 2 2 nts=10 TGGAATGGAA E.DT55,E.DG56,E.DG57,E.DA58,E.DA59,F.DT62,F.DG63,F.DG64,F.DA65,F.DA66 nts=3 GGA E.DG56,E.DG57,E.DA58 nts=3 GGA F.DG63,F.DG64,F.DA65 **************************************************************************** List of 7 A-minor motifs (types I, II, or X) 1 type=X A|A-T A.DA10|A.DA11,B.DT14 WC +A.DA11 H-bonds[0]: "" -B.DT14 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.70]" 2 type=X A|T-A B.DA17|A.DT7,B.DA18 WC -A.DT7 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.98]" +B.DA18 H-bonds[0]: "" 3 type=X A|A-T C.DA34|C.DA35,D.DT38 WC +C.DA35 H-bonds[0]: "" -D.DT38 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.83]" 4 type=X A|T-A D.DA46|C.DT26,D.DA47 WC -C.DT26 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.89]" +D.DA47 H-bonds[0]: "" 5 type=X A|A-T E.DA53|E.DA54,F.DT67 WC +E.DA54 H-bonds[0]: "" -F.DT67 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.84]" 6 type=X A|T-A F.DA65|E.DT55,F.DA66 WC -E.DT55 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.92]" +F.DA66 H-bonds[0]: "" 7 type=X A|T-A F.DA70|E.DT50,F.DA71 WC -E.DT50 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.91]" +F.DA71 H-bonds[0]: "" **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5gun nts=72 [whole] GTGGAATGGAAC>GGAATGGAAC>GGAATGGAAC>GGAATGGAAC>GGAATGGAAC>GGAATGGAAC ((...((...((&))...))...))&((...((...((&))...))...))&((...((...((&))...))...)) >5gun-A #1 nts=12 3.83(0.96) [chain] DNA GTGGAATGGAAC ((...((...(( >5gun-B #2 nts=12 3.81(1.03) [chain] DNA GTGGAATGGAAC ))...))...)) >5gun-C #3 nts=12 3.88(1.03) [chain] DNA GTGGAATGGAAC ((...((...(( >5gun-D #4 nts=12 3.99(1.17) [chain] DNA GTGGAATGGAAC ))...))...)) >5gun-E #5 nts=12 4.14(0.91) [chain] DNA GTGGAATGGAAC ((...((...(( >5gun-F #6 nts=12 4.15(0.89) [chain] DNA GTGGAATGGAAC ))...))...)) **************************************************************************** Summary of structural features of 72 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.DG1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 T ( A.DT2 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 3 G . A.DG3 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 4 G . A.DG4 0.003 anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor 5 A . A.DA5 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate 6 A ( A.DA6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 7 T ( A.DT7 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor,phosphate 8 G . A.DG8 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 9 G . A.DG9 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor 10 A . A.DA10 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,cap-acceptor,phosphate 11 A ( A.DA11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 12 C ( A.DC12 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 13 G ) B.DG13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 14 T ) B.DT14 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 15 G . B.DG15 0.005 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 16 G . B.DG16 0.005 anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor 17 A . B.DA17 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,cap-acceptor,phosphate 18 A ) B.DA18 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 19 T ) B.DT19 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 20 G . B.DG20 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 21 G . B.DG21 0.003 anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor,phosphate 22 A . B.DA22 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate 23 A ) B.DA23 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 24 C ) B.DC24 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 25 G ( C.DG25 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 26 T ( C.DT26 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor 27 G . C.DG27 0.003 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop 28 G . C.DG28 0.004 anti,~C2'-endo,BI,non-pair-contact,internal-loop,cap-donor 29 A . C.DA29 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor 30 A ( C.DA30 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 31 T ( C.DT31 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 32 G . C.DG32 0.004 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 33 G . C.DG33 0.004 anti,non-pair-contact,internal-loop,cap-donor 34 A . C.DA34 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor 35 A ( C.DA35 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 36 C ( C.DC36 0.002 anti,canonical,non-pair-contact,helix-end,stem-end 37 G ) D.DG37 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 38 T ) D.DT38 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 39 G . D.DG39 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 40 G . D.DG40 0.003 anti,non-pair-contact,internal-loop 41 A . D.DA41 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate 42 A ) D.DA42 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 43 T ) D.DT43 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop 44 G . D.DG44 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 45 G . D.DG45 0.004 anti,~C3'-endo,BI,non-pair-contact,internal-loop,cap-donor,phosphate 46 A . D.DA46 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,cap-acceptor,phosphate 47 A ) D.DA47 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,A-minor 48 C ) D.DC48 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 49 G ( E.DG49 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 50 T ( E.DT50 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 51 G . E.DG51 0.003 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-loop 52 G . E.DG52 0.003 anti,non-pair-contact,internal-loop 53 A . E.DA53 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor 54 A ( E.DA54 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 55 T ( E.DT55 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 56 G . E.DG56 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 57 G . E.DG57 0.005 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor 58 A . E.DA58 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop,cap-acceptor,phosphate 59 A ( E.DA59 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 60 C ( E.DC60 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 61 G ) F.DG61 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 62 T ) F.DT62 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 63 G . F.DG63 0.003 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 64 G . F.DG64 0.005 anti,BI,non-pair-contact,internal-loop,cap-donor 65 A . F.DA65 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor,cap-acceptor,phosphate 66 A ) F.DA66 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 67 T ) F.DT67 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 68 G . F.DG68 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 69 G . F.DG69 0.005 anti,~C2'-endo,non-pair-contact,internal-loop 70 A . F.DA70 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop,A-minor 71 A ) F.DA71 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,internal-loop,A-minor 72 C ) F.DC72 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** 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-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-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions