**************************************************************************** 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=7re3.pdb -o=7re3.out File name: 7re3.pdb no. of DNA/RNA chains: 4 [P=34,Q=34,T=37,U=37] no. of nucleotides: 148 no. of atoms: 43154 no. of waters: 0 no. of metals: 26 [Mg=6,Al=4,Zn=16] **************************************************************************** List of 1 type of 6 modified nucleotides nt count list 1 ADP-a 6 A.ADP2003,E.ADP704,F.ADP1003,G.ADP2003,K.ADP704,L.ADP1003 **************************************************************************** List of 68 base pairs nt1 nt2 bp name Saenger LW DSSR 1 P.G2 T.C54 G-C WC 19-XIX cWW cW-W 2 P.C3 T.G53 C-G WC 19-XIX cWW cW-W 3 P.G4 T.C52 G-C WC 19-XIX cWW cW-W 4 P.U5 T.A51 U-A WC 20-XX cWW cW-W 5 P.A6 T.U50 A-U WC 20-XX cWW cW-W 6 P.G7 T.C49 G-C WC 19-XIX cWW cW-W 7 P.C8 T.G48 C-G WC 19-XIX cWW cW-W 8 P.A9 T.U47 A-U WC 20-XX cWW cW-W 9 P.U10 T.A46 U-A WC 20-XX cWW cW-W 10 P.G11 T.C45 G-C WC 19-XIX cWW cW-W 11 P.C12 T.G44 C-G WC 19-XIX cWW cW-W 12 P.U13 T.A43 U-A WC 20-XX cWW cW-W 13 P.A14 T.U42 A-U WC 20-XX cWW cW-W 14 P.C15 T.G41 C-G WC 19-XIX cWW cW-W 15 P.G16 T.C40 G-C WC 19-XIX cWW cW-W 16 P.U17 T.A39 U-A WC 20-XX cWW cW-W 17 P.C18 T.G38 C-G WC 19-XIX cWW cW-W 18 P.A19 T.U37 A-U WC 20-XX cWW cW-W 19 P.U20 T.A36 U-A WC 20-XX cWW cW-W 20 P.U21 T.A35 U-A WC 20-XX cWW cW-W 21 P.C22 T.G34 C-G WC 19-XIX cWW cW-W 22 P.U23 T.A33 U-A WC 20-XX cWW cW-W 23 P.C24 T.G32 C-G WC 19-XIX cWW cW-W 24 P.C25 T.G31 C-G WC 19-XIX cWW cW-W 25 P.U26 T.A30 U-A WC 20-XX cWW cW-W 26 P.A27 T.U29 A-U WC 20-XX cWW cW-W 27 P.A28 T.U28 A-U WC 20-XX cWW cW-W 28 P.G29 T.C27 G-C WC 19-XIX cWW cW-W 29 P.A30 T.U26 A-U WC 20-XX cWW cW-W 30 P.A31 T.U25 A-U WC 20-XX cWW cW-W 31 P.G32 T.C24 G-C WC 19-XIX cWW cW-W 32 P.C33 T.G23 C-G WC 19-XIX cWW cW-W 33 P.U34 T.A22 U-A WC 20-XX cWW cW-W 34 P.A35 T.U21 A-U WC 20-XX cWW cW-W 35 Q.G2 U.C54 G-C WC 19-XIX cWW cW-W 36 Q.C3 U.G53 C-G WC 19-XIX cWW cW-W 37 Q.G4 U.C52 G-C WC 19-XIX cWW cW-W 38 Q.U5 U.A51 U-A WC 20-XX cWW cW-W 39 Q.A6 U.U50 A-U WC 20-XX cWW cW-W 40 Q.G7 U.C49 G-C WC 19-XIX cWW cW-W 41 Q.C8 U.G48 C-G WC 19-XIX cWW cW-W 42 Q.A9 U.U47 A-U WC 20-XX cWW cW-W 43 Q.U10 U.A46 U-A WC 20-XX cWW cW-W 44 Q.G11 U.C45 G-C WC 19-XIX cWW cW-W 45 Q.C12 U.G44 C-G WC 19-XIX cWW cW-W 46 Q.U13 U.A43 U-A WC 20-XX cWW cW-W 47 Q.A14 U.U42 A-U WC 20-XX cWW cW-W 48 Q.C15 U.G41 C-G WC 19-XIX cWW cW-W 49 Q.G16 U.C40 G-C WC 19-XIX cWW cW-W 50 Q.U17 U.A39 U-A WC 20-XX cWW cW-W 51 Q.C18 U.G38 C-G WC 19-XIX cWW cW-W 52 Q.A19 U.U37 A-U WC 20-XX cWW cW-W 53 Q.U20 U.A36 U-A WC 20-XX cWW cW-W 54 Q.U21 U.A35 U-A WC 20-XX cWW cW-W 55 Q.C22 U.G34 C-G WC 19-XIX cWW cW-W 56 Q.U23 U.A33 U-A WC 20-XX cWW cW-W 57 Q.C24 U.G32 C-G WC 19-XIX cWW cW-W 58 Q.C25 U.G31 C-G WC 19-XIX cWW cW-W 59 Q.U26 U.A30 U-A WC 20-XX cWW cW-W 60 Q.A27 U.U29 A-U WC 20-XX cWW cW-W 61 Q.A28 U.U28 A-U WC 20-XX cWW cW-W 62 Q.G29 U.C27 G-C WC 19-XIX cWW cW-W 63 Q.A30 U.U26 A-U WC 20-XX cWW cW-W 64 Q.A31 U.U25 A-U WC 20-XX cWW cW-W 65 Q.G32 U.C24 G-C WC 19-XIX cWW cW-W 66 Q.C33 U.G23 C-G WC 19-XIX cWW cW-W 67 Q.U34 U.A22 U-A WC 20-XX cWW cW-W 68 Q.A35 U.U21 A-U WC 20-XX cWW cW-W **************************************************************************** List of 2 helices Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[1] bps=34 strand-1 5'-GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA-3' bp-type |||||||||||||||||||||||||||||||||| strand-2 3'-CGCAUCGUACGAUGCAGUAAGAGGAUUCUUCGAU-5' helix-form .AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 P.G2 T.C54 G-C WC 19-XIX cWW cW-W 2 P.C3 T.G53 C-G WC 19-XIX cWW cW-W 3 P.G4 T.C52 G-C WC 19-XIX cWW cW-W 4 P.U5 T.A51 U-A WC 20-XX cWW cW-W 5 P.A6 T.U50 A-U WC 20-XX cWW cW-W 6 P.G7 T.C49 G-C WC 19-XIX cWW cW-W 7 P.C8 T.G48 C-G WC 19-XIX cWW cW-W 8 P.A9 T.U47 A-U WC 20-XX cWW cW-W 9 P.U10 T.A46 U-A WC 20-XX cWW cW-W 10 P.G11 T.C45 G-C WC 19-XIX cWW cW-W 11 P.C12 T.G44 C-G WC 19-XIX cWW cW-W 12 P.U13 T.A43 U-A WC 20-XX cWW cW-W 13 P.A14 T.U42 A-U WC 20-XX cWW cW-W 14 P.C15 T.G41 C-G WC 19-XIX cWW cW-W 15 P.G16 T.C40 G-C WC 19-XIX cWW cW-W 16 P.U17 T.A39 U-A WC 20-XX cWW cW-W 17 P.C18 T.G38 C-G WC 19-XIX cWW cW-W 18 P.A19 T.U37 A-U WC 20-XX cWW cW-W 19 P.U20 T.A36 U-A WC 20-XX cWW cW-W 20 P.U21 T.A35 U-A WC 20-XX cWW cW-W 21 P.C22 T.G34 C-G WC 19-XIX cWW cW-W 22 P.U23 T.A33 U-A WC 20-XX cWW cW-W 23 P.C24 T.G32 C-G WC 19-XIX cWW cW-W 24 P.C25 T.G31 C-G WC 19-XIX cWW cW-W 25 P.U26 T.A30 U-A WC 20-XX cWW cW-W 26 P.A27 T.U29 A-U WC 20-XX cWW cW-W 27 P.A28 T.U28 A-U WC 20-XX cWW cW-W 28 P.G29 T.C27 G-C WC 19-XIX cWW cW-W 29 P.A30 T.U26 A-U WC 20-XX cWW cW-W 30 P.A31 T.U25 A-U WC 20-XX cWW cW-W 31 P.G32 T.C24 G-C WC 19-XIX cWW cW-W 32 P.C33 T.G23 C-G WC 19-XIX cWW cW-W 33 P.U34 T.A22 U-A WC 20-XX cWW cW-W 34 P.A35 T.U21 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=34 strand-1 5'-GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA-3' bp-type |||||||||||||||||||||||||||||||||| strand-2 3'-CGCAUCGUACGAUGCAGUAAGAGGAUUCUUCGAU-5' helix-form .AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 Q.G2 U.C54 G-C WC 19-XIX cWW cW-W 2 Q.C3 U.G53 C-G WC 19-XIX cWW cW-W 3 Q.G4 U.C52 G-C WC 19-XIX cWW cW-W 4 Q.U5 U.A51 U-A WC 20-XX cWW cW-W 5 Q.A6 U.U50 A-U WC 20-XX cWW cW-W 6 Q.G7 U.C49 G-C WC 19-XIX cWW cW-W 7 Q.C8 U.G48 C-G WC 19-XIX cWW cW-W 8 Q.A9 U.U47 A-U WC 20-XX cWW cW-W 9 Q.U10 U.A46 U-A WC 20-XX cWW cW-W 10 Q.G11 U.C45 G-C WC 19-XIX cWW cW-W 11 Q.C12 U.G44 C-G WC 19-XIX cWW cW-W 12 Q.U13 U.A43 U-A WC 20-XX cWW cW-W 13 Q.A14 U.U42 A-U WC 20-XX cWW cW-W 14 Q.C15 U.G41 C-G WC 19-XIX cWW cW-W 15 Q.G16 U.C40 G-C WC 19-XIX cWW cW-W 16 Q.U17 U.A39 U-A WC 20-XX cWW cW-W 17 Q.C18 U.G38 C-G WC 19-XIX cWW cW-W 18 Q.A19 U.U37 A-U WC 20-XX cWW cW-W 19 Q.U20 U.A36 U-A WC 20-XX cWW cW-W 20 Q.U21 U.A35 U-A WC 20-XX cWW cW-W 21 Q.C22 U.G34 C-G WC 19-XIX cWW cW-W 22 Q.U23 U.A33 U-A WC 20-XX cWW cW-W 23 Q.C24 U.G32 C-G WC 19-XIX cWW cW-W 24 Q.C25 U.G31 C-G WC 19-XIX cWW cW-W 25 Q.U26 U.A30 U-A WC 20-XX cWW cW-W 26 Q.A27 U.U29 A-U WC 20-XX cWW cW-W 27 Q.A28 U.U28 A-U WC 20-XX cWW cW-W 28 Q.G29 U.C27 G-C WC 19-XIX cWW cW-W 29 Q.A30 U.U26 A-U WC 20-XX cWW cW-W 30 Q.A31 U.U25 A-U WC 20-XX cWW cW-W 31 Q.G32 U.C24 G-C WC 19-XIX cWW cW-W 32 Q.C33 U.G23 C-G WC 19-XIX cWW cW-W 33 Q.U34 U.A22 U-A WC 20-XX cWW cW-W 34 Q.A35 U.U21 A-U WC 20-XX cWW cW-W **************************************************************************** List of 2 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=34 strand-1 5'-GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA-3' bp-type |||||||||||||||||||||||||||||||||| strand-2 3'-CGCAUCGUACGAUGCAGUAAGAGGAUUCUUCGAU-5' helix-form .AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 P.G2 T.C54 G-C WC 19-XIX cWW cW-W 2 P.C3 T.G53 C-G WC 19-XIX cWW cW-W 3 P.G4 T.C52 G-C WC 19-XIX cWW cW-W 4 P.U5 T.A51 U-A WC 20-XX cWW cW-W 5 P.A6 T.U50 A-U WC 20-XX cWW cW-W 6 P.G7 T.C49 G-C WC 19-XIX cWW cW-W 7 P.C8 T.G48 C-G WC 19-XIX cWW cW-W 8 P.A9 T.U47 A-U WC 20-XX cWW cW-W 9 P.U10 T.A46 U-A WC 20-XX cWW cW-W 10 P.G11 T.C45 G-C WC 19-XIX cWW cW-W 11 P.C12 T.G44 C-G WC 19-XIX cWW cW-W 12 P.U13 T.A43 U-A WC 20-XX cWW cW-W 13 P.A14 T.U42 A-U WC 20-XX cWW cW-W 14 P.C15 T.G41 C-G WC 19-XIX cWW cW-W 15 P.G16 T.C40 G-C WC 19-XIX cWW cW-W 16 P.U17 T.A39 U-A WC 20-XX cWW cW-W 17 P.C18 T.G38 C-G WC 19-XIX cWW cW-W 18 P.A19 T.U37 A-U WC 20-XX cWW cW-W 19 P.U20 T.A36 U-A WC 20-XX cWW cW-W 20 P.U21 T.A35 U-A WC 20-XX cWW cW-W 21 P.C22 T.G34 C-G WC 19-XIX cWW cW-W 22 P.U23 T.A33 U-A WC 20-XX cWW cW-W 23 P.C24 T.G32 C-G WC 19-XIX cWW cW-W 24 P.C25 T.G31 C-G WC 19-XIX cWW cW-W 25 P.U26 T.A30 U-A WC 20-XX cWW cW-W 26 P.A27 T.U29 A-U WC 20-XX cWW cW-W 27 P.A28 T.U28 A-U WC 20-XX cWW cW-W 28 P.G29 T.C27 G-C WC 19-XIX cWW cW-W 29 P.A30 T.U26 A-U WC 20-XX cWW cW-W 30 P.A31 T.U25 A-U WC 20-XX cWW cW-W 31 P.G32 T.C24 G-C WC 19-XIX cWW cW-W 32 P.C33 T.G23 C-G WC 19-XIX cWW cW-W 33 P.U34 T.A22 U-A WC 20-XX cWW cW-W 34 P.A35 T.U21 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=34 strand-1 5'-GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA-3' bp-type |||||||||||||||||||||||||||||||||| strand-2 3'-CGCAUCGUACGAUGCAGUAAGAGGAUUCUUCGAU-5' helix-form .AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 Q.G2 U.C54 G-C WC 19-XIX cWW cW-W 2 Q.C3 U.G53 C-G WC 19-XIX cWW cW-W 3 Q.G4 U.C52 G-C WC 19-XIX cWW cW-W 4 Q.U5 U.A51 U-A WC 20-XX cWW cW-W 5 Q.A6 U.U50 A-U WC 20-XX cWW cW-W 6 Q.G7 U.C49 G-C WC 19-XIX cWW cW-W 7 Q.C8 U.G48 C-G WC 19-XIX cWW cW-W 8 Q.A9 U.U47 A-U WC 20-XX cWW cW-W 9 Q.U10 U.A46 U-A WC 20-XX cWW cW-W 10 Q.G11 U.C45 G-C WC 19-XIX cWW cW-W 11 Q.C12 U.G44 C-G WC 19-XIX cWW cW-W 12 Q.U13 U.A43 U-A WC 20-XX cWW cW-W 13 Q.A14 U.U42 A-U WC 20-XX cWW cW-W 14 Q.C15 U.G41 C-G WC 19-XIX cWW cW-W 15 Q.G16 U.C40 G-C WC 19-XIX cWW cW-W 16 Q.U17 U.A39 U-A WC 20-XX cWW cW-W 17 Q.C18 U.G38 C-G WC 19-XIX cWW cW-W 18 Q.A19 U.U37 A-U WC 20-XX cWW cW-W 19 Q.U20 U.A36 U-A WC 20-XX cWW cW-W 20 Q.U21 U.A35 U-A WC 20-XX cWW cW-W 21 Q.C22 U.G34 C-G WC 19-XIX cWW cW-W 22 Q.U23 U.A33 U-A WC 20-XX cWW cW-W 23 Q.C24 U.G32 C-G WC 19-XIX cWW cW-W 24 Q.C25 U.G31 C-G WC 19-XIX cWW cW-W 25 Q.U26 U.A30 U-A WC 20-XX cWW cW-W 26 Q.A27 U.U29 A-U WC 20-XX cWW cW-W 27 Q.A28 U.U28 A-U WC 20-XX cWW cW-W 28 Q.G29 U.C27 G-C WC 19-XIX cWW cW-W 29 Q.A30 U.U26 A-U WC 20-XX cWW cW-W 30 Q.A31 U.U25 A-U WC 20-XX cWW cW-W 31 Q.G32 U.C24 G-C WC 19-XIX cWW cW-W 32 Q.C33 U.G23 C-G WC 19-XIX cWW cW-W 33 Q.U34 U.A22 U-A WC 20-XX cWW cW-W 34 Q.A35 U.U21 A-U WC 20-XX cWW cW-W **************************************************************************** List of 6 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 Ha A.HIS75,A.ADP2003 2 nts=2 Ha E.HIS290,E.ADP704 3 nts=2 AU T.A20,T.U21 4 nts=2 Ha G.HIS75,G.ADP2003 5 nts=2 Ha K.HIS290,K.ADP704 6 nts=2 AU U.A20,U.U21 **************************************************************************** Nucleotides not involved in stacking interactions nts=6 CUACUA P.C18,T.U18,T.A19,Q.C18,U.U18,U.A19 **************************************************************************** List of 8 non-loop single-stranded segments 1 nts=3 UAA T.U18,T.A19,T.A20 2 nts=3 UAA U.U18,U.A19,U.A20 3 nts=1 a A.ADP2003 4 nts=1 a E.ADP704 5 nts=1 a F.ADP1003 6 nts=1 a G.ADP2003 7 nts=1 a K.ADP704 8 nts=1 a L.ADP1003 **************************************************************************** List of 2 splayed-apart dinucleotides 1 T.A19 T.A20 angle=118 distance=15.2 ratio=0.86 2 U.A19 U.A20 angle=118 distance=15.2 ratio=0.86 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 AA T.A19,T.A20 2 nts=2 AA U.A19,U.A20 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7re3 nts=148 [whole] GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA&UAAUAGCUUCUUAGGAGAAUGACGUAGCAUGCUACGC&GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA&UAAUAGCUUCUUAGGAGAAUGACGUAGCAUGCUACGC&a&a&a&a&a&a ((((((((((((((((((((((((((((((((((&...))))))))))))))))))))))))))))))))))&((((((((((((((((((((((((((((((((((&...))))))))))))))))))))))))))))))))))&.&.&.&.&.&. >7re3-P #1 nts=34 2.71(0.29) [chain] RNA GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA (((((((((((((((((((((((((((((((((( >7re3-T #2 nts=37 2.75(0.49) [chain] RNA UAAUAGCUUCUUAGGAGAAUGACGUAGCAUGCUACGC ...)))))))))))))))))))))))))))))))))) >7re3-Q #3 nts=34 2.71(0.29) [chain] RNA GCGUAGCAUGCUACGUCAUUCUCCUAAGAAGCUA (((((((((((((((((((((((((((((((((( >7re3-U #4 nts=37 2.75(0.49) [chain] RNA UAAUAGCUUCUUAGGAGAAUGACGUAGCAUGCUACGC ...)))))))))))))))))))))))))))))))))) **************************************************************************** Summary of structural features of 148 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 ( P.G2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( P.C3 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( P.G4 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 U ( P.U5 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( P.A6 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 6 G ( P.G7 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( P.C8 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 A ( P.A9 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 U ( P.U10 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 10 G ( P.G11 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 11 C ( P.C12 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 12 U ( P.U13 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 13 A ( P.A14 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 14 C ( P.C15 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ( P.G16 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 U ( P.U17 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ( P.C18 0.004 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem 18 A ( P.A19 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 19 U ( P.U20 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 20 U ( P.U21 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ( P.C22 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 22 U ( P.U23 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 23 C ( P.C24 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 24 C ( P.C25 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 U ( P.U26 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 26 A ( P.A27 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 27 A ( P.A28 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 28 G ( P.G29 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 29 A ( P.A30 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 30 A ( P.A31 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 31 G ( P.G32 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 32 C ( P.C33 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 33 U ( P.U34 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 34 A ( P.A35 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 35 U . T.U18 0.003 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop 36 A . T.A19 0.003 anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 37 A . T.A20 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 38 U ) T.U21 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 39 A ) T.A22 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 40 G ) T.G23 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 41 C ) T.C24 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 42 U ) T.U25 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 43 U ) T.U26 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 44 C ) T.C27 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 45 U ) T.U28 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 46 U ) T.U29 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 47 A ) T.A30 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 48 G ) T.G31 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 49 G ) T.G32 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 50 A ) T.A33 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 51 G ) T.G34 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 52 A ) T.A35 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 53 A ) T.A36 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 54 U ) T.U37 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 55 G ) T.G38 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 56 A ) T.A39 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 57 C ) T.C40 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 58 G ) T.G41 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 59 U ) T.U42 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 60 A ) T.A43 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 61 G ) T.G44 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 62 C ) T.C45 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 63 A ) T.A46 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 64 U ) T.U47 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 65 G ) T.G48 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 66 C ) T.C49 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 67 U ) T.U50 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 68 A ) T.A51 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 69 C ) T.C52 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 70 G ) T.G53 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 71 C ) T.C54 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 72 G ( Q.G2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 73 C ( Q.C3 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 74 G ( Q.G4 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 75 U ( Q.U5 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 76 A ( Q.A6 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 77 G ( Q.G7 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 78 C ( Q.C8 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 79 A ( Q.A9 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 80 U ( Q.U10 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 81 G ( Q.G11 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 82 C ( Q.C12 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 83 U ( Q.U13 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 84 A ( Q.A14 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 85 C ( Q.C15 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 86 G ( Q.G16 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 87 U ( Q.U17 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 88 C ( Q.C18 0.004 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem 89 A ( Q.A19 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 90 U ( Q.U20 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 91 U ( Q.U21 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 92 C ( Q.C22 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 93 U ( Q.U23 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 94 C ( Q.C24 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 95 C ( Q.C25 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 96 U ( Q.U26 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 97 A ( Q.A27 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 98 A ( Q.A28 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 99 G ( Q.G29 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 100 A ( Q.A30 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 101 A ( Q.A31 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 102 G ( Q.G32 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 103 C ( Q.C33 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 104 U ( Q.U34 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 105 A ( Q.A35 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 106 U . U.U18 0.003 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop 107 A . U.A19 0.003 anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 108 A . U.A20 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 109 U ) U.U21 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 110 A ) U.A22 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 111 G ) U.G23 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 112 C ) U.C24 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 113 U ) U.U25 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 114 U ) U.U26 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 115 C ) U.C27 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 116 U ) U.U28 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 117 U ) U.U29 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 118 A ) U.A30 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 119 G ) U.G31 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 120 G ) U.G32 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 121 A ) U.A33 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 122 G ) U.G34 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 123 A ) U.A35 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 124 A ) U.A36 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 125 U ) U.U37 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 126 G ) U.G38 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 127 A ) U.A39 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 128 C ) U.C40 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 129 G ) U.G41 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 130 U ) U.U42 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 131 A ) U.A43 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 132 G ) U.G44 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 133 C ) U.C45 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 134 A ) U.A46 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 135 U ) U.U47 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 136 G ) U.G48 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 137 C ) U.C49 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 138 U ) U.U50 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 139 A ) U.A51 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 140 C ) U.C52 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 141 G ) U.G53 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 142 C ) U.C54 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 143 a . A.ADP2003 0.061 modified,anti,ss-non-loop 144 a . E.ADP704 0.061 modified,anti,ss-non-loop 145 a . F.ADP1003 0.062 modified,anti,ss-non-loop 146 a . G.ADP2003 0.061 modified,anti,ss-non-loop 147 a . K.ADP704 0.061 modified,anti,ss-non-loop 148 a . L.ADP1003 0.062 modified,anti,ss-non-loop **************************************************************************** List of 9 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-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks