**************************************************************************** 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=3p59.pdb -o=3p59.out File name: 3p59.pdb no. of DNA/RNA chains: 8 [A=15,B=10,C=15,D=10,E=15,F=10,G=13,H=10] no. of nucleotides: 98 no. of atoms: 2264 no. of waters: 118 no. of metals: 12 [Mg=2,Co=10] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5BU-u 4 A.5BU59,C.5BU59,E.5BU59,G.5BU59 **************************************************************************** List of 41 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.C46 D.G107 C-G WC 19-XIX cWW cW-W 2 A.C47 D.G106 C-G WC 19-XIX cWW cW-W 3 A.G48 D.C105 G-C WC 19-XIX cWW cW-W 4 A.G49 D.C104 G-C WC 19-XIX cWW cW-W 5 A.A50 B.U113 A-U WC 20-XX cWW cW-W 6 A.G51 B.C112 G-C WC 19-XIX cWW cW-W 7 A.G52 B.C111 G-C WC 19-XIX cWW cW-W 8 A.C58 B.G110 C-G WC 19-XIX cWW cW-W 9 A.5BU59 B.A109 u-A WC 20-XX cWW cW-W 10 A.G60 B.C108 G-C WC 19-XIX cWW cW-W 11 B.C104 G.G49 C-G WC 19-XIX cWW cW-W 12 B.C105 G.G48 C-G WC 19-XIX cWW cW-W 13 B.G106 G.C47 G-C WC 19-XIX cWW cW-W 14 B.G107 G.C46 G-C WC 19-XIX cWW cW-W 15 C.C46 F.G107 C-G WC 19-XIX cWW cW-W 16 C.C47 F.G106 C-G WC 19-XIX cWW cW-W 17 C.G48 F.C105 G-C WC 19-XIX cWW cW-W 18 C.G49 F.C104 G-C WC 19-XIX cWW cW-W 19 C.A50 D.U113 A-U WC 20-XX cWW cW-W 20 C.G51 D.C112 G-C WC 19-XIX cWW cW-W 21 C.G52 D.C111 G-C WC 19-XIX cWW cW-W 22 C.C58 D.G110 C-G ~Wobble -- cWW cW-W 23 C.G60 D.C108 G-C -- -- cHW cM-W 24 E.C46 H.G107 C-G WC 19-XIX cWW cW-W 25 E.C47 H.G106 C-G WC 19-XIX cWW cW-W 26 E.G48 H.C105 G-C WC 19-XIX cWW cW-W 27 E.G49 H.C104 G-C WC 19-XIX cWW cW-W 28 E.A50 F.U113 A-U WC 20-XX cWW cW-W 29 E.G51 F.C112 G-C WC 19-XIX cWW cW-W 30 E.C55 E.C58 C+C -- -- tWW tW+W 31 E.C55 F.G110 C-G -- -- tWH tW-M 32 E.A57 F.C111 A-C ~Wobble -- cWW cW-W 33 E.C58 F.G110 C-G WC 19-XIX cWW cW-W 34 E.5BU59 F.A109 u-A WC 20-XX cWW cW-W 35 E.G60 F.C108 G-C WC 19-XIX cWW cW-W 36 G.A50 H.U113 A-U WC 20-XX cWW cW-W 37 G.G51 H.C112 G-C WC 19-XIX cWW cW-W 38 G.G52 H.C111 G-C WC 19-XIX cWW cW-W 39 G.C58 H.G110 C-G WC 19-XIX cWW cW-W 40 G.5BU59 H.A109 u-A WC 20-XX cWW cW-W 41 G.G60 H.C108 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 multiplet 1 nts=3 CCG E.C55,E.C58,F.G110 **************************************************************************** List of 4 helices Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[3] bps=10 strand-1 5'-CuGCCGGAGG-3' bp-type |||||||||| strand-2 3'-GACGGCCUCC-5' helix-form ..xAAAx.A 1 A.C58 B.G110 C-G WC 19-XIX cWW cW-W 2 A.5BU59 B.A109 u-A WC 20-XX cWW cW-W 3 A.G60 B.C108 G-C WC 19-XIX cWW cW-W 4 G.C46 B.G107 C-G WC 19-XIX cWW cW-W 5 G.C47 B.G106 C-G WC 19-XIX cWW cW-W 6 G.G48 B.C105 G-C WC 19-XIX cWW cW-W 7 G.G49 B.C104 G-C WC 19-XIX cWW cW-W 8 G.A50 H.U113 A-U WC 20-XX cWW cW-W 9 G.G51 H.C112 G-C WC 19-XIX cWW cW-W 10 G.G52 H.C111 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[2] bps=8 strand-1 5'-CCUCCGGC-3' bp-type |||||||. strand-2 3'-GGAGGCCG-5' helix-form AAxAA.x 1 B.C111 A.G52 C-G WC 19-XIX cWW cW-W 2 B.C112 A.G51 C-G WC 19-XIX cWW cW-W 3 B.U113 A.A50 U-A WC 20-XX cWW cW-W 4 D.C104 A.G49 C-G WC 19-XIX cWW cW-W 5 D.C105 A.G48 C-G WC 19-XIX cWW cW-W 6 D.G106 A.C47 G-C WC 19-XIX cWW cW-W 7 D.G107 A.C46 G-C WC 19-XIX cWW cW-W 8 D.C108 C.G60 C-G -- -- cWH cW-M -------------------------------------------------------------------------- helix#3[3] bps=11 strand-1 5'-CCUCCGGCAGC-3' bp-type ||||||||||. strand-2 3'-GGAGGCCGuCA-5' helix-form AAxAAAx... 1 D.C111 C.G52 C-G WC 19-XIX cWW cW-W 2 D.C112 C.G51 C-G WC 19-XIX cWW cW-W 3 D.U113 C.A50 U-A WC 20-XX cWW cW-W 4 F.C104 C.G49 C-G WC 19-XIX cWW cW-W 5 F.C105 C.G48 C-G WC 19-XIX cWW cW-W 6 F.G106 C.C47 G-C WC 19-XIX cWW cW-W 7 F.G107 C.C46 G-C WC 19-XIX cWW cW-W 8 F.C108 E.G60 C-G WC 19-XIX cWW cW-W 9 F.A109 E.5BU59 A-u WC 20-XX cWW cW-W 10 F.G110 E.C58 G-C WC 19-XIX cWW cW-W 11 F.C111 E.A57 C-A ~Wobble -- cWW cW-W -------------------------------------------------------------------------- helix#4[3] bps=9 strand-1 5'-CUCCGGCAG-3' bp-type ||||||||| strand-2 3'-GAGGCCGuC-5' helix-form .x.A.x.. 1 F.C112 E.G51 C-G WC 19-XIX cWW cW-W 2 F.U113 E.A50 U-A WC 20-XX cWW cW-W 3 H.C104 E.G49 C-G WC 19-XIX cWW cW-W 4 H.C105 E.G48 C-G WC 19-XIX cWW cW-W 5 H.G106 E.C47 G-C WC 19-XIX cWW cW-W 6 H.G107 E.C46 G-C WC 19-XIX cWW cW-W 7 H.C108 G.G60 C-G WC 19-XIX cWW cW-W 8 H.A109 G.5BU59 A-u WC 20-XX cWW cW-W 9 H.G110 G.C58 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 11 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[#2] bps=4 strand-1 5'-CCGG-3' bp-type |||| strand-2 3'-GGCC-5' helix-form .AA 1 A.C46 D.G107 C-G WC 19-XIX cWW cW-W 2 A.C47 D.G106 C-G WC 19-XIX cWW cW-W 3 A.G48 D.C105 G-C WC 19-XIX cWW cW-W 4 A.G49 D.C104 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form AA 1 A.A50 B.U113 A-U WC 20-XX cWW cW-W 2 A.G51 B.C112 G-C WC 19-XIX cWW cW-W 3 A.G52 B.C111 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=3 strand-1 5'-CuG-3' bp-type ||| strand-2 3'-GAC-5' helix-form .. 1 A.C58 B.G110 C-G WC 19-XIX cWW cW-W 2 A.5BU59 B.A109 u-A WC 20-XX cWW cW-W 3 A.G60 B.C108 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=4 strand-1 5'-CCGG-3' bp-type |||| strand-2 3'-GGCC-5' helix-form AAA 1 B.C104 G.G49 C-G WC 19-XIX cWW cW-W 2 B.C105 G.G48 C-G WC 19-XIX cWW cW-W 3 B.G106 G.C47 G-C WC 19-XIX cWW cW-W 4 B.G107 G.C46 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#5[#3] bps=4 strand-1 5'-CCGG-3' bp-type |||| strand-2 3'-GGCC-5' helix-form AAA 1 C.C46 F.G107 C-G WC 19-XIX cWW cW-W 2 C.C47 F.G106 C-G WC 19-XIX cWW cW-W 3 C.G48 F.C105 G-C WC 19-XIX cWW cW-W 4 C.G49 F.C104 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#6[#3] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form AA 1 C.A50 D.U113 A-U WC 20-XX cWW cW-W 2 C.G51 D.C112 G-C WC 19-XIX cWW cW-W 3 C.G52 D.C111 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#4] bps=4 strand-1 5'-CCGG-3' bp-type |||| strand-2 3'-GGCC-5' helix-form .A. 1 E.C46 H.G107 C-G WC 19-XIX cWW cW-W 2 E.C47 H.G106 C-G WC 19-XIX cWW cW-W 3 E.G48 H.C105 G-C WC 19-XIX cWW cW-W 4 E.G49 H.C104 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#4] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-UC-5' helix-form . 1 E.A50 F.U113 A-U WC 20-XX cWW cW-W 2 E.G51 F.C112 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#3] bps=3 strand-1 5'-CuG-3' bp-type ||| strand-2 3'-GAC-5' helix-form .. 1 E.C58 F.G110 C-G WC 19-XIX cWW cW-W 2 E.5BU59 F.A109 u-A WC 20-XX cWW cW-W 3 E.G60 F.C108 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#10[#1] bps=3 strand-1 5'-AGG-3' bp-type ||| strand-2 3'-UCC-5' helix-form .A 1 G.A50 H.U113 A-U WC 20-XX cWW cW-W 2 G.G51 H.C112 G-C WC 19-XIX cWW cW-W 3 G.G52 H.C111 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#11[#4] bps=3 strand-1 5'-CuG-3' bp-type ||| strand-2 3'-GAC-5' helix-form .. 1 G.C58 H.G110 C-G WC 19-XIX cWW cW-W 2 G.5BU59 H.A109 u-A WC 20-XX cWW cW-W 3 G.G60 H.C108 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 4 coaxial stacks 1 Helix#1 contains 3 stems: [#3,#4,#10] 2 Helix#2 contains 2 stems: [#2,#1] 3 Helix#3 contains 3 stems: [#6,#5,#9] 4 Helix#4 contains 3 stems: [#8,#7,#11] **************************************************************************** List of 23 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 GA A.G49,A.A50 2 nts=2 GC A.G60,G.C46 3 nts=2 CU B.C104,H.U113 4 nts=2 GC B.G107,B.C108 5 nts=2 CG C.C46,E.G60 6 nts=2 GA C.G49,C.A50 7 nts=2 AC C.A57,C.C58 8 nts=2 UC D.U113,F.C104 9 nts=2 CG E.C46,G.G60 10 nts=2 GA E.G49,E.A50 11 nts=2 GC F.G107,F.C108 12 nts=2 GC F.G110,F.C111 13 nts=2 UC F.U113,H.C104 14 nts=2 GA G.G49,G.A50 15 nts=2 GC H.G107,H.C108 16 nts=3 UAC A.U56,A.A57,A.C58 17 nts=3 GAA C.G52,C.A53,C.A54 18 nts=3 GCA D.G107,D.C108,D.A109 19 nts=3 UAC E.U56,E.A57,E.C58 20 nts=4 CGuG A.C46,C.G60,C.5BU59,D.G110 21 nts=4 GAAC A.G52,A.A53,A.A54,A.C55 22 nts=4 GGAA E.G51,E.G52,E.A53,E.A54 23 nts=4 GAAC G.G52,G.A53,G.A54,G.C55 **************************************************************************** Nucleotides not involved in stacking interactions nts=7 CCCUCCC B.C105,B.C111,C.C55,C.U56,D.C104,E.C55,H.C111 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O2'@C.C55 C.A54 3.47 **************************************************************************** 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 1 bulge 1 bulge: nts=9; [5,0]; linked by [#2,#3] summary: [2] 5 0 [A.52 B.111 A.58 B.110] 3 3 nts=9 GAACUACGC A.G52,A.A53,A.A54,A.C55,A.U56,A.A57,A.C58,B.G110,B.C111 nts=5 AACUA A.A53,A.A54,A.C55,A.U56,A.A57 nts=0 **************************************************************************** List of 1 internal loop 1 asymmetric internal loop: nts=11; [6,1]; linked by [#8,#9] summary: [2] 6 1 [E.51 F.112 E.58 F.110] 2 3 nts=11 GGAACUACGCC E.G51,E.G52,E.A53,E.A54,E.C55,E.U56,E.A57,E.C58,F.G110,F.C111,F.C112 nts=6 GAACUA E.G52,E.A53,E.A54,E.C55,E.U56,E.A57 nts=1 C F.C111 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=8 AACUACuG C.A53,C.A54,C.C55,C.U56,C.A57,C.C58,C.5BU59,C.G60 2 nts=3 CAG D.C108,D.A109,D.G110 3 nts=3 AAC G.A53,G.A54,G.C55 **************************************************************************** List of 6 splayed-apart dinucleotides 1 A.C55 A.U56 angle=130 distance=15.7 ratio=0.91 2 B.G110 B.C111 angle=86 distance=13.1 ratio=0.69 3 C.C55 C.U56 angle=87 distance=13.0 ratio=0.69 4 D.G110 D.C111 angle=94 distance=13.8 ratio=0.74 5 E.A54 E.C55 angle=110 distance=15.2 ratio=0.82 6 H.G110 H.C111 angle=90 distance=13.3 ratio=0.71 ---------------------------------------------------------------- Summary of 6 splayed-apart units 1 nts=2 CU A.C55,A.U56 2 nts=2 GC B.G110,B.C111 3 nts=2 CU C.C55,C.U56 4 nts=2 GC D.G110,D.C111 5 nts=2 AC E.A54,E.C55 6 nts=2 GC H.G110,H.C111 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *2-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3p59 nts=98 [whole] CCGGAGGAACUACuG&CCGGCAGCCU&CCGGAGGAACUACuG&CCGGCAGCCU&CCGGAGGAACUACuG&CCGGCAGCCU&CCGGAGGAAC&CuG&CCGGCAGCCU (((((((.....(((&[[[[))))))&[[[[[[[........&))))...]]]&{{{{((......(((&]]]]))).))&]]]](((...&(((&}}}})))))) >3p59-A #1 nts=15 0.76(1.82) [chain] RNA CCGGAGGAACUACuG (((((((.....((( >3p59-B #2 nts=10 3.65(1.35) [chain] RNA CCGGCAGCCU [[[[)))))) >3p59-C #3 nts=15 0.48(1.95) [chain] RNA CCGGAGGAACUACuG [[[[[[[........ >3p59-D #4 nts=10 3.57(1.22) [chain] RNA CCGGCAGCCU ))))...]]] >3p59-E #5 nts=15 0.78(1.91) [chain] RNA CCGGAGGAACUACuG {{{{((......((( >3p59-F #6 nts=10 3.14(1.00) [chain] RNA CCGGCAGCCU ]]]]))).)) >3p59-G #7 nts=13 0.92(2.02) [chain] RNA* CCGGAGGAAC&CuG ]]]](((...&((( >3p59-H #8 nts=10 3.97(1.18) [chain] RNA CCGGCAGCCU }}}})))))) **************************************************************************** Summary of structural features of 98 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 C ( A.C46 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 2 C ( A.C47 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 G ( A.G48 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 G ( A.G49 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 5 A ( A.A50 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 6 G ( A.G51 0.034 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( A.G52 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,bulge 8 A . A.A53 0.017 anti,~C3'-endo,non-pair-contact,bulge 9 A . A.A54 0.014 anti,~C3'-endo,BI,non-pair-contact,bulge 10 C . A.C55 0.018 anti,~C3'-endo,BII,non-pair-contact,bulge,splayed-apart 11 U . A.U56 0.022 turn,anti,~C3'-endo,non-pair-contact,bulge,splayed-apart 12 A . A.A57 0.014 anti,~C3'-endo,BI,non-pair-contact,bulge 13 C ( A.C58 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,bulge 14 u ( A.5BU59 0.041 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 G ( A.G60 0.024 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 16 C [ B.C104 0.016 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 17 C [ B.C105 0.025 pseudoknotted,anti,~C3'-endo,BI,non-stack,canonical,helix,stem,coaxial-stack 18 G [ B.G106 0.031 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 G [ B.G107 0.019 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 20 C ) B.C108 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 21 A ) B.A109 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 G ) B.G110 0.026 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,bulge,phosphate,splayed-apart 23 C ) B.C111 0.008 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,bulge,splayed-apart 24 C ) B.C112 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 U ) B.U113 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 26 C [ C.C46 0.014 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 27 C [ C.C47 0.021 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 G [ C.G48 0.037 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 G [ C.G49 0.016 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 30 A [ C.A50 0.017 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 31 G [ C.G51 0.021 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 G [ C.G52 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 33 A . C.A53 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 34 A . C.A54 0.018 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor 35 C . C.C55 0.011 anti,~C3'-endo,BII,non-stack,non-pair-contact,ss-non-loop,cap-donor,splayed-apart 36 U . C.U56 0.005 anti,~C3'-endo,BI,non-stack,ss-non-loop,splayed-apart 37 A . C.A57 0.031 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 38 C . C.C58 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop 39 u . C.5BU59 0.054 modified,anti,~C3'-endo,non-pair-contact,ss-non-loop 40 G . C.G60 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,phosphate 41 C ) D.C104 0.022 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack 42 C ) D.C105 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 G ) D.G106 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 44 G ) D.G107 0.024 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 45 C . D.C108 0.007 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 46 A . D.A109 0.025 anti,~C3'-endo,non-pair-contact,ss-non-loop 47 G . D.G110 0.015 turn,anti,~C3'-endo,non-canonical,non-pair-contact,ss-non-loop,splayed-apart 48 C ] D.C111 0.014 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,splayed-apart 49 C ] D.C112 0.007 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 U ] D.U113 0.016 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 51 C { E.C46 0.012 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 52 C { E.C47 0.008 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 53 G { E.G48 0.021 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 54 G { E.G49 0.023 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 55 A ( E.A50 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 56 G ( E.G51 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 57 G . E.G52 0.032 anti,~C3'-endo,BI,non-pair-contact,internal-loop 58 A . E.A53 0.024 anti,~C3'-endo,BI,non-pair-contact,internal-loop 59 A . E.A54 0.020 anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 60 C . E.C55 0.004 anti,~C2'-endo,BII,non-stack,non-canonical,non-pair-contact,multiplet,internal-loop,phosphate,splayed-apart 61 U . E.U56 0.009 anti,~C3'-endo,BI,non-pair-contact,internal-loop 62 A . E.A57 0.023 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,internal-loop 63 C ( E.C58 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop 64 u ( E.5BU59 0.063 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 65 G ( E.G60 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 66 C ] F.C104 0.014 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 67 C ] F.C105 0.022 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 68 G ] F.G106 0.016 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 69 G ] F.G107 0.022 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 70 C ) F.C108 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 71 A ) F.A109 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 72 G ) F.G110 0.041 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,phosphate 73 C . F.C111 0.021 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,internal-loop 74 C ) F.C112 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 75 U ) F.U113 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 76 C ] G.C46 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 77 C ] G.C47 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 78 G ] G.G48 0.030 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 79 G ] G.G49 0.040 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 80 A ( G.A50 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 81 G ( G.G51 0.028 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 82 G ( G.G52 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 83 A . G.A53 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 84 A . G.A54 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 85 C . G.C55 0.010 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 86 C ( G.C58 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 87 u ( G.5BU59 0.044 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 88 G ( G.G60 0.023 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 89 C } H.C104 0.012 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 90 C } H.C105 0.018 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 91 G } H.G106 0.020 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 92 G } H.G107 0.018 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 93 C ) H.C108 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 94 A ) H.A109 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 95 G ) H.G110 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate,splayed-apart 96 C ) H.C111 0.014 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,splayed-apart 97 C ) H.C112 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 98 U ) H.U113 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack **************************************************************************** List of 13 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-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