# 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb # **************************************************************************** DSSR: an Integrated Software Tool for Dissecting the Spatial Structure of RNA v1.9.9-2020feb06, by xiangjun@x3dna.org DSSR has been made possible by the NIH grant R01GM096889 (to X.J.Lu). It is being actively maintained and developed. As always, I greatly appreciate your feedback. Please report all DSSR-related issues on the 3DNA Forum (forum.x3dna.org). I strive to respond promptly to any questions posted there. DSSR is free of charge for NON-COMMERCIAL purposes, and it comes with ABSOLUTELY NO WARRANTY. **************************************************************************** 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-64bit -i=5k7c_clean_onechain_renumber_as_puzzle_srr.pdb Date and time: Thu Jun 29 19:07:18 2023 File name: 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb no. of DNA/RNA chains: 1 [A=58] no. of nucleotides: 58 no. of atoms: 1237 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 34 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.C1 A.G16 C-G WC 19-XIX cWW cW-W 2 A.G2 A.C15 G-C WC 19-XIX cWW cW-W 3 A.G2 A.U18 G+U -- n/a tSH tm+M 4 A.U3 A.A14 U-A WC 20-XX cWW cW-W 5 A.U3 A.A19 U+A -- n/a cSH cm+M 6 A.G4 A.C13 G-C WC 19-XIX cWW cW-W 7 A.G4 A.A21 G+A -- 10-X tSW tm+W 8 A.G5 A.C12 G-C WC 19-XIX cWW cW-W 9 A.G5 A.G24 G+G -- 04-IV tSS tm+m 10 A.U6 A.A39 U-A WC 20-XX cWW cW-W 11 A.U7 A.A38 U-A WC 20-XX cWW cW-W 12 A.A8 A.U37 A-U WC 20-XX cWW cW-W 13 A.G9 A.C36 G-C WC 19-XIX cWW cW-W 14 A.G10 A.C35 G-C WC 19-XIX cWW cW-W 15 A.G11 A.C34 G-C WC 19-XIX cWW cW-W 16 A.A14 A.A20 A-A -- n/a cSW cm-W 17 A.C15 A.A19 C-A -- n/a cSW cm-W 18 A.G16 A.U17 G-U Platform n/a cSW cm-W 19 A.U25 A.A62 U-A WC 20-XX cWW cW-W 20 A.U26 A.A61 U-A WC 20-XX cWW cW-W 21 A.G27 A.C60 G-C WC 19-XIX cWW cW-W 22 A.C28 A.G59 C-G WC 19-XIX cWW cW-W 23 A.U29 A.U58 U-U -- 16-XVI cWW cW-W 24 A.U30 A.A32 U-A -- n/a tSH tm-M 25 A.G33 A.G40 G-G -- n/a cW. cW-. 26 A.G33 A.C41 G-C WC 19-XIX cWW cW-W 27 A.G40 A.C41 G+C Platform n/a cSH cm+M 28 A.G40 A.G42 G+G -- n/a cSH cm+M 29 A.G42 A.G57 G-G -- n/a tHS tM-m 30 A.U43 A.G56 U-G -- n/a cWW cW-W 31 A.U43 A.G57 U-G -- n/a cWS cW-m 32 A.U44 A.A55 U-A WC 20-XX cWW cW-W 33 A.G45 A.C54 G-C WC 19-XIX cWW cW-W 34 A.A46 A.U53 A-U WC 20-XX cWW cW-W **************************************************************************** List of 7 multiplets 1 nts=3 CGU A.C1,A.G16,A.U17 2 nts=3 GCU A.G2,A.C15,A.U18 3 nts=3 UAA A.U3,A.A14,A.A20 4 nts=3* UCA A.U3,A.C15,A.A19 5 nts=3 GCA A.G4,A.C13,A.A21 6 nts=3 GCG A.G5,A.C12,A.G24 7 nts=3 GGC A.G33,A.G40,A.C41 **************************************************************************** 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[3] bps=17 strand-1 5'-CGUGGCCCUAACGUUGA-3' bp-type ||||||||||||..||| strand-2 3'-GCACCGGGAUUGGGACU-5' helix-form .AAAxAAAA.xx...A 1 A.C1 A.G16 C-G WC 19-XIX cWW cW-W 2 A.G2 A.C15 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A14 U-A WC 20-XX cWW cW-W 4 A.G4 A.C13 G-C WC 19-XIX cWW cW-W 5 A.G5 A.C12 G-C WC 19-XIX cWW cW-W 6 A.C34 A.G11 C-G WC 19-XIX cWW cW-W 7 A.C35 A.G10 C-G WC 19-XIX cWW cW-W 8 A.C36 A.G9 C-G WC 19-XIX cWW cW-W 9 A.U37 A.A8 U-A WC 20-XX cWW cW-W 10 A.A38 A.U7 A-U WC 20-XX cWW cW-W 11 A.A39 A.U6 A-U WC 20-XX cWW cW-W 12 A.C41 A.G33 C-G WC 19-XIX cWW cW-W 13 A.G42 A.G57 G-G -- n/a tHS tM-m 14 A.U43 A.G56 U-G -- n/a cWW cW-W 15 A.U44 A.A55 U-A WC 20-XX cWW cW-W 16 A.G45 A.C54 G-C WC 19-XIX cWW cW-W 17 A.A46 A.U53 A-U WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=6 strand-1 5'-UUGCUU-3' bp-type ||||.. strand-2 3'-AACGUA-5' helix-form ....x 1 A.U25 A.A62 U-A WC 20-XX cWW cW-W 2 A.U26 A.A61 U-A WC 20-XX cWW cW-W 3 A.G27 A.C60 G-C WC 19-XIX cWW cW-W 4 A.C28 A.G59 C-G WC 19-XIX cWW cW-W 5 A.U29 A.U58 U-U -- 16-XVI cWW cW-W 6 A.U30 A.A32 U-A -- n/a tSH tm-M **************************************************************************** List of 4 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=5 strand-1 5'-CGUGG-3' bp-type ||||| strand-2 3'-GCACC-5' helix-form .AAA 1 A.C1 A.G16 C-G WC 19-XIX cWW cW-W 2 A.G2 A.C15 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A14 U-A WC 20-XX cWW cW-W 4 A.G4 A.C13 G-C WC 19-XIX cWW cW-W 5 A.G5 A.C12 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=6 strand-1 5'-UUAGGG-3' bp-type |||||| strand-2 3'-AAUCCC-5' helix-form .AAAA 1 A.U6 A.A39 U-A WC 20-XX cWW cW-W 2 A.U7 A.A38 U-A WC 20-XX cWW cW-W 3 A.A8 A.U37 A-U WC 20-XX cWW cW-W 4 A.G9 A.C36 G-C WC 19-XIX cWW cW-W 5 A.G10 A.C35 G-C WC 19-XIX cWW cW-W 6 A.G11 A.C34 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=4 strand-1 5'-UUGC-3' bp-type |||| strand-2 3'-AACG-5' helix-form ... 1 A.U25 A.A62 U-A WC 20-XX cWW cW-W 2 A.U26 A.A61 U-A WC 20-XX cWW cW-W 3 A.G27 A.C60 G-C WC 19-XIX cWW cW-W 4 A.C28 A.G59 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=3 strand-1 5'-UGA-3' bp-type ||| strand-2 3'-ACU-5' helix-form .A 1 A.U44 A.A55 U-A WC 20-XX cWW cW-W 2 A.G45 A.C54 G-C WC 19-XIX cWW cW-W 3 A.A46 A.U53 A-U WC 20-XX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 A.G33 A.C41 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#4] **************************************************************************** List of 9 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 GC A.G5,A.C34 2 nts=2 GC A.G11,A.C12 3 nts=2 CU A.C28,A.U29 4 nts=2 AA A.A31,A.A32 5 nts=2 AU A.A46,A.U47 6 nts=3 UUG A.U30,A.U58,A.G59 7 nts=5 UCGUU A.U6,A.C41,A.G42,A.U43,A.U44 8 nts=5 AGGGA A.A39,A.G40,A.G57,A.G56,A.A55 9 nts=7 UUAAAAG A.U17,A.U18,A.A19,A.A20,A.A21,A.A23,A.G24 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 UUUA A.U7,A.U22,A.U25,A.A52 **************************************************************************** List of 3 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.C34 A.G24 2.90 2 phosphate OP2@A.A32 A.U30 2.89 3 sugar O4'@A.U58 A.A32 3.26 **************************************************************************** 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=8; [6]; linked by [#1] summary: [1] 6 [A.5 A.12] 5 nts=8 GUUAGGGC A.G5,A.U6,A.U7,A.A8,A.G9,A.G10,A.G11,A.C12 nts=6 UUAGGG A.U6,A.U7,A.A8,A.G9,A.G10,A.G11 2 hairpin loop: nts=24; [22]; linked by [#2] summary: [1] 22 [A.11 A.34] 6 nts=24 GCCACGUUAAAUAGUUGCUUAAGC A.G11,A.C12,A.C13,A.A14,A.C15,A.G16,A.U17,A.U18,A.A19,A.A20,A.A21,A.U22,A.A23,A.G24,A.U25,A.U26,A.G27,A.C28,A.U29,A.U30,A.A31,A.A32,A.G33,A.C34 nts=22 CCACGUUAAAUAGUUGCUUAAG A.C12,A.C13,A.A14,A.C15,A.G16,A.U17,A.U18,A.A19,A.A20,A.A21,A.U22,A.A23,A.G24,A.U25,A.U26,A.G27,A.C28,A.U29,A.U30,A.A31,A.A32,A.G33 3 hairpin loop: nts=9; [7]; linked by [#-1] summary: [1] 7 [A.33 A.41] 1 nts=9 GCCCUAAGC A.G33,A.C34,A.C35,A.C36,A.U37,A.A38,A.A39,A.G40,A.C41 nts=7 CCCUAAG A.C34,A.C35,A.C36,A.U37,A.A38,A.A39,A.G40 **************************************************************************** List of 2 junctions 1 3-way junction: nts=15; [4,2,3]; linked by [#3,#-1,#4] summary: [3] 4 2 3 [A.28 A.59 A.33 A.41 A.44 A.55] 4 1 3 nts=15 CUUAAGCGUUAGGUG A.C28,A.U29,A.U30,A.A31,A.A32,A.G33,A.C41,A.G42,A.U43,A.U44,A.A55,A.G56,A.G57,A.U58,A.G59 nts=4 UUAA A.U29,A.U30,A.A31,A.A32 nts=2 GU A.G42,A.U43 nts=3 GGU A.G56,A.G57,A.U58 2* 4-way junction: nts=9; [0,1,0,0]; linked by [#1,#2,#-1,#2] summary: [4] 0 1 0 0 [A.5 A.12 A.6 A.39 A.41 A.33 A.34 A.11] 5 6 1 6 nts=9 GUAGCGCGC A.G5,A.U6,A.A39,A.G40,A.C41,A.G33,A.C34,A.G11,A.C12 nts=0 nts=1 G A.G40 nts=0 nts=0 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=2* UA A.U47,A.A52 **************************************************************************** List of 1 kissing loop interaction 1 stem #2 between hairpin loops #1 and #3 **************************************************************************** List of 6 A-minor motifs (types I, II, or X) 1 type=X A|G-C A.A19|A.G2,A.C15 WC +A.G2 H-bonds[0]: "" -A.C15 H-bonds[2]: "N6(amino)-O2(carbonyl)[3.16],N1-O2'(hydroxyl)[2.87]" 2 type=X A|U-A A.A19|A.U3,A.A14 WC +A.U3 H-bonds[2]: "N7-O2'(hydroxyl)[2.97],N6(amino)-O2(carbonyl)[2.45]" -A.A14 H-bonds[0]: "" 3 type=X A|U-A A.A20|A.U3,A.A14 WC +A.U3 H-bonds[0]: "" -A.A14 H-bonds[2]: "N6(amino)-N3[2.97],N1-O2'(hydroxyl)[2.88]" 4 type=X A|G-C A.A21|A.G4,A.C13 WC +A.G4 H-bonds[2]: "N6(amino)-N3[3.55],N1-N2(amino)[3.30]" -A.C13 H-bonds[0]: "" 5 type=II A|G-C A.A23|A.G4,A.C13 WC +A.G4 H-bonds[0]: "" -A.C13 H-bonds[3]: "O2'(hydroxyl)-O3'[3.13],O2'(hydroxyl)-O2'(hydroxyl)[2.99],N3-O2'(hydroxyl)[2.81]" 6 type=X A|U-G A.A31|A.U43,A.G56 -- -A.U43 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.10]" +A.G56 H-bonds[0]: "" **************************************************************************** List of 1 ribose zipper 1 nts=4 CCAG A.C12,A.C13,A.A23,A.G24 **************************************************************************** List of 7 splayed-apart dinucleotides 1 A.G5 A.U6 angle=113 distance=14.6 ratio=0.83 2 A.A21 A.U22 angle=110 distance=15.7 ratio=0.82 3 A.U22 A.A23 angle=106 distance=15.6 ratio=0.80 4 A.G24 A.U25 angle=111 distance=14.3 ratio=0.83 5 A.G33 A.C34 angle=99 distance=13.6 ratio=0.76 6 A.A52 A.U53 angle=121 distance=16.7 ratio=0.87 7 A.G57 A.U58 angle=156 distance=19.3 ratio=0.98 ---------------------------------------------------------------- Summary of 6 splayed-apart units 1 nts=2 GU A.G5,A.U6 2 nts=3 AUA A.A21,A.U22,A.A23 3 nts=2 GU A.G24,A.U25 4 nts=2 GC A.G33,A.C34 5 nts=2 AU A.A52,A.U53 6 nts=2 GU A.G57,A.U58 **************************************************************************** This structure contains 1-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. **************************************************************************** List of 3 H-type pseudoknot loop segments 1 stem#1(hairpin#1) vs stem#2(hairpin#2) L1 groove=----- nts=0 2 stem#1(hairpin#1) vs stem#2(hairpin#2) L2 groove=----- nts=0 3 stem#1(hairpin#1) vs stem#2(hairpin#2) L3 groove=minor nts=17 UUAAAUAGUUGCUUAAG A.U17,A.U18,A.A19,A.A20,A.A21,A.U22,A.A23,A.G24,A.U25,A.U26,A.G27,A.C28,A.U29,A.U30,A.A31,A.A32,A.G33 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5k7c_clean_onechain_renumber_as_puzzle_srr nts=58 [whole] CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAU&AUCAGGUGCAA ((((([[[[[[)))))........((((....(]]]]]].)..(((.&.)))...)))) >5k7c_clean_onechain_renumber_as_puzzle_srr-A #1 nts=58 0.37(2.90) [chain] RNA[57]/1* CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAU&AUCAGGUGCAA ((((([[[[[[)))))........((((....(]]]]]].)..(((.&.)))...)))) **************************************************************************** Summary of structural features of 58 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.C1 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet 2 G ( A.G2 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 3 U ( A.U3 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 4 G ( A.G4 0.015 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 5 G ( A.G5 0.013 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,kissing-loop,splayed-apart 6 U [ A.U6 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,splayed-apart 7 U [ A.U7 0.024 pseudoknotted,anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 8 A [ A.A8 0.021 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 9 G [ A.G9 0.015 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 10 G [ A.G10 0.023 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 11 G [ A.G11 0.021 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 12 C ) A.C12 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,junction-loop,ribose-zipper,kissing-loop 13 C ) A.C13 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor,ribose-zipper 14 A ) A.A14 0.021 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor 15 C ) A.C15 0.013 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,hairpin-loop,A-minor 16 G ) A.G16 0.019 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet,hairpin-loop 17 U . A.U17 0.010 turn,syn,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop 18 U . A.U18 0.007 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop 19 A . A.A19 0.030 ~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,phosphate 20 A . A.A20 0.013 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor 21 A . A.A21 0.017 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,splayed-apart 22 U . A.U22 0.007 turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 23 A . A.A23 0.017 anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,splayed-apart 24 G . A.G24 0.010 anti,~C3'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,ribose-zipper,cap-acceptor,splayed-apart 25 U ( A.U25 0.015 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix-end,stem-end,hairpin-loop,splayed-apart 26 U ( A.U26 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,hairpin-loop 27 G ( A.G27 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,hairpin-loop 28 C ( A.C28 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,junction-loop 29 U . A.U29 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,junction-loop 30 U . A.U30 0.011 u-turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop,cap-acceptor 31 A . A.A31 0.013 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,junction-loop,A-minor 32 A . A.A32 0.035 u-turn,anti,~C3'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,junction-loop,cap-donor,cap-acceptor,phosphate 33 G ( A.G33 0.018 u-turn,anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,junction-loop,kissing-loop,phosphate,splayed-apart 34 C ] A.C34 0.019 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop,cap-donor,phosphate,splayed-apart 35 C ] A.C35 0.019 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 36 C ] A.C36 0.020 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 37 U ] A.U37 0.019 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 38 A ] A.A38 0.009 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,hairpin-loop,kissing-loop 39 A ] A.A39 0.024 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,junction-loop,kissing-loop 40 G . A.G40 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,multiplet,hairpin-loop,junction-loop,kissing-loop 41 C ) A.C41 0.021 anti,~C3'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,junction-loop,kissing-loop 42 G . A.G42 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 43 U . A.U43 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,A-minor 44 U ( A.U44 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 45 G ( A.G45 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 46 A ( A.A46 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 47 U . A.U47 0.015 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 48 A . A.A52 0.013 syn,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 49 U ) A.U53 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate,splayed-apart 50 C ) A.C54 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 51 A ) A.A55 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 52 G . A.G56 0.032 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,A-minor 53 G . A.G57 0.026 anti,non-canonical,non-pair-contact,helix,junction-loop,splayed-apart 54 U . A.U58 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop,cap-donor,splayed-apart 55 G ) A.G59 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,junction-loop 56 C ) A.C60 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 57 A ) A.A61 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 58 A ) A.A62 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 14 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-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 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-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 13 dssr-stacks.pdb -- an ensemble of stacks 14 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions DONE!