**************************************************************************** File name: 1ehz.pdb no. of DNA/RNA chains: 1 [A=76] no. of nucleotides: 76 no. of atoms: 1821 no. of waters: 160 no. of metals: 9 [Mg=6,Mn=3] **************************************************************************** List of 11 types of 14 modified nucleotides nt count list 1 1MA-a 1 A.1MA58 2 2MG-g 1 A.2MG10 3 5MC-c 2 A.5MC40,A.5MC49 4 5MU-t 1 A.5MU54 5 7MG-g 1 A.7MG46 6 H2U-u 2 A.H2U16,A.H2U17 7 M2G-g 1 A.M2G26 8 OMC-c 1 A.OMC32 9 OMG-g 1 A.OMG34 10 PSU-P 2 A.PSU39,A.PSU55 11 YYG-g 1 A.YYG37 **************************************************************************** List of 34 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 A.C72 G-C WC 19-XIX cWW cW-W 2 A.C2 A.G71 C-G WC 19-XIX cWW cW-W 3 A.G3 A.C70 G-C WC 19-XIX cWW cW-W 4 A.G4 A.U69 G-U Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U68 A-U WC 20-XX cWW cW-W 6 A.U6 A.A67 U-A WC 20-XX cWW cW-W 7 A.U7 A.A66 U-A WC 20-XX cWW cW-W 8 A.U8 A.A14 U-A rHoogsteen 24-XXIV tWH tW-M 9 A.U8 A.A21 U+A -- -- tSW tm+W 10 A.A9 A.A23 A+A -- 02-II tHH tM+M 11 A.2MG10 A.C25 g-C WC 19-XIX cWW cW-W 12 A.2MG10 A.G45 g+G -- -- cHS cM+m 13 A.C11 A.G24 C-G WC 19-XIX cWW cW-W 14 A.U12 A.A23 U-A WC 20-XX cWW cW-W 15 A.C13 A.G22 C-G WC 19-XIX cWW cW-W 16 A.G15 A.C48 G+C rWC 22-XXII tWW tW+W 17 A.H2U16 A.U59 u+U -- -- tSW tm+W 18 A.G18 A.PSU55 G+P -- -- tWS tW+m 19 A.G19 A.C56 G-C WC 19-XIX cWW cW-W 20 A.G22 A.7MG46 G-g -- 07-VII tHW tM-W 21 A.M2G26 A.A44 g-A Imino 08-VIII cWW cW-W 22 A.C27 A.G43 C-G WC 19-XIX cWW cW-W 23 A.C28 A.G42 C-G WC 19-XIX cWW cW-W 24 A.A29 A.U41 A-U WC 20-XX cWW cW-W 25 A.G30 A.5MC40 G-c WC 19-XIX cWW cW-W 26 A.A31 A.PSU39 A-P -- -- cWW cW-W 27 A.OMC32 A.A38 c-A -- -- c.W c.-W 28 A.U33 A.A36 U-A -- -- tSH tm-M 29 A.5MC49 A.G65 c-G WC 19-XIX cWW cW-W 30 A.U50 A.A64 U-A WC 20-XX cWW cW-W 31 A.G51 A.C63 G-C WC 19-XIX cWW cW-W 32 A.U52 A.A62 U-A WC 20-XX cWW cW-W 33 A.G53 A.C61 G-C WC 19-XIX cWW cW-W 34 A.5MU54 A.1MA58 t-a rHoogsteen 24-XXIV tWH tW-M **************************************************************************** List of 4 multiplets 1 nts=3 UAA A.U8,A.A14,A.A21 2 nts=3 AUA A.A9,A.U12,A.A23 3 nts=3 gCG A.2MG10,A.C25,A.G45 4 nts=3 CGg A.C13,A.G22,A.7MG46 **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair 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[2] bps=15 strand-1 5'-GCGGAUUcUGUGtPC-3' bp-type ||||||||||||..| strand-2 3'-CGCUUAAGACACaGG-5' helix-form AA....xAAAAxx. 1 A.G1 A.C72 G-C WC 19-XIX cWW cW-W 2 A.C2 A.G71 C-G WC 19-XIX cWW cW-W 3 A.G3 A.C70 G-C WC 19-XIX cWW cW-W 4 A.G4 A.U69 G-U Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U68 A-U WC 20-XX cWW cW-W 6 A.U6 A.A67 U-A WC 20-XX cWW cW-W 7 A.U7 A.A66 U-A WC 20-XX cWW cW-W 8 A.5MC49 A.G65 c-G WC 19-XIX cWW cW-W 9 A.U50 A.A64 U-A WC 20-XX cWW cW-W 10 A.G51 A.C63 G-C WC 19-XIX cWW cW-W 11 A.U52 A.A62 U-A WC 20-XX cWW cW-W 12 A.G53 A.C61 G-C WC 19-XIX cWW cW-W 13 A.5MU54 A.1MA58 t-a rHoogsteen 24-XXIV tWH tW-M 14 A.PSU55 A.G18 P+G -- -- tSW tm+W 15 A.C56 A.G19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[2] bps=15 strand-1 5'-AAPcUGGAgCUCAGu-3' bp-type ...||||.||||... strand-2 3'-UcAGACCgCGAGUCU-5' helix-form x..AAAAxAA.xxx 1 A.A36 A.U33 A-U -- -- tHS tM-m 2 A.A38 A.OMC32 A-c -- -- cW. cW-. 3 A.PSU39 A.A31 P-A -- -- cWW cW-W 4 A.5MC40 A.G30 c-G WC 19-XIX cWW cW-W 5 A.U41 A.A29 U-A WC 20-XX cWW cW-W 6 A.G42 A.C28 G-C WC 19-XIX cWW cW-W 7 A.G43 A.C27 G-C WC 19-XIX cWW cW-W 8 A.A44 A.M2G26 A-g Imino 08-VIII cWW cW-W 9 A.2MG10 A.C25 g-C WC 19-XIX cWW cW-W 10 A.C11 A.G24 C-G WC 19-XIX cWW cW-W 11 A.U12 A.A23 U-A WC 20-XX cWW cW-W 12 A.C13 A.G22 C-G WC 19-XIX cWW cW-W 13 A.A14 A.U8 A-U rHoogsteen 24-XXIV tHW tM-W 14 A.G15 A.C48 G+C rWC 22-XXII tWW tW+W 15 A.H2U16 A.U59 u+U -- -- tSW tm+W **************************************************************************** List of 4 stems Note: A stem is defined as a helix consisting strictly of 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=7 strand-1 5'-GCGGAUU-3' bp-type ||||||| strand-2 3'-CGCUUAA-5' helix-form AA.... 1 A.G1 A.C72 G-C WC 19-XIX cWW cW-W 2 A.C2 A.G71 C-G WC 19-XIX cWW cW-W 3 A.G3 A.C70 G-C WC 19-XIX cWW cW-W 4 A.G4 A.U69 G-U Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U68 A-U WC 20-XX cWW cW-W 6 A.U6 A.A67 U-A WC 20-XX cWW cW-W 7 A.U7 A.A66 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=4 strand-1 5'-gCUC-3' bp-type |||| strand-2 3'-CGAG-5' helix-form AA. 1 A.2MG10 A.C25 g-C WC 19-XIX cWW cW-W 2 A.C11 A.G24 C-G WC 19-XIX cWW cW-W 3 A.U12 A.A23 U-A WC 20-XX cWW cW-W 4 A.C13 A.G22 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=4 strand-1 5'-CCAG-3' bp-type |||| strand-2 3'-GGUc-5' helix-form AAA 1 A.C27 A.G43 C-G WC 19-XIX cWW cW-W 2 A.C28 A.G42 C-G WC 19-XIX cWW cW-W 3 A.A29 A.U41 A-U WC 20-XX cWW cW-W 4 A.G30 A.5MC40 G-c WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#1] bps=5 strand-1 5'-cUGUG-3' bp-type ||||| strand-2 3'-GACAC-5' helix-form AAAA 1 A.5MC49 A.G65 c-G WC 19-XIX cWW cW-W 2 A.U50 A.A64 U-A WC 20-XX cWW cW-W 3 A.G51 A.C63 G-C WC 19-XIX cWW cW-W 4 A.U52 A.A62 U-A WC 20-XX cWW cW-W 5 A.G53 A.C61 G-C WC 19-XIX 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.G19 A.C56 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 coaxial stacks 1 Helix#1 contains 2 stems: [#1,#4] 2 Helix#2 contains 2 stems: [#3,#2] **************************************************************************** List of 11 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 Uc A.U7,A.5MC49 2 nts=2 UC A.U8,A.C13 3 nts=2 GA A.G65,A.A66 4 nts=3 CgC A.C25,A.M2G26,A.C27 5 nts=3 gAC A.7MG46,A.A21,A.C48 6 nts=3 GtP A.G53,A.5MU54,A.PSU55 7 nts=4 GACC A.G1,A.A73,A.C74,A.C75 8 nts=4 GAcU A.G30,A.A31,A.OMC32,A.U33 9 nts=5 GGGaC A.G19,A.G57,A.G18,A.1MA58,A.C61 10 nts=7 gAAgAPc A.OMG34,A.A35,A.A36,A.YYG37,A.A38,A.PSU39,A.5MC40 11 nts=9 GAGAGAGUC A.G43,A.A44,A.G45,A.A9,A.G22,A.A14,A.G15,A.U59,A.C60 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 uGUA A.H2U17,A.G20,A.U47,A.A76 **************************************************************************** List of 4 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.H2U16 A.H2U16 2.59 2 phosphate OP2@A.A35 A.U33 2.85 3 sugar O4'@A.U59 A.C48 3.10 4 phosphate OP2@A.G57 A.PSU55 2.90 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 3 hairpin loops 1 hairpin loop: nts=10; [8]; linked by [#2] summary: [1] 8 [A.13 A.22] 4 nts=10 CAGuuGGGAG A.C13,A.A14,A.G15,A.H2U16,A.H2U17,A.G18,A.G19,A.G20,A.A21,A.G22 nts=8 AGuuGGGA A.A14,A.G15,A.H2U16,A.H2U17,A.G18,A.G19,A.G20,A.A21 2 hairpin loop: nts=11; [9]; linked by [#3] summary: [1] 9 [A.30 A.40] 4 nts=11 GAcUgAAgAPc A.G30,A.A31,A.OMC32,A.U33,A.OMG34,A.A35,A.A36,A.YYG37,A.A38,A.PSU39,A.5MC40 nts=9 AcUgAAgAP A.A31,A.OMC32,A.U33,A.OMG34,A.A35,A.A36,A.YYG37,A.A38,A.PSU39 3 hairpin loop: nts=9; [7]; linked by [#4] summary: [1] 7 [A.53 A.61] 5 nts=9 GtPCGaUCC A.G53,A.5MU54,A.PSU55,A.C56,A.G57,A.1MA58,A.U59,A.C60,A.C61 nts=7 tPCGaUC A.5MU54,A.PSU55,A.C56,A.G57,A.1MA58,A.U59,A.C60 **************************************************************************** List of 1 junction 1 4-way junction: nts=16; [2,1,5,0]; linked by [#1,#2,#3,#4] summary: [4] 2 1 5 0 [A.7 A.66 A.10 A.25 A.27 A.43 A.49 A.65] 7 4 4 5 nts=16 UUAgCgCGAGgUCcGA A.U7,A.U8,A.A9,A.2MG10,A.C25,A.M2G26,A.C27,A.G43,A.A44,A.G45,A.7MG46,A.U47,A.C48,A.5MC49,A.G65,A.A66 nts=2 UA A.U8,A.A9 nts=1 g A.M2G26 nts=5 AGgUC A.A44,A.G45,A.7MG46,A.U47,A.C48 nts=0 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=4 ACCA A.A73,A.C74,A.C75,A.A76 **************************************************************************** List of 1 kissing loop interaction 1 isolated-pair #-1 between hairpin loops #1 and #3 **************************************************************************** List of 9 splayed-apart dinucleotides 1 A.U7 A.U8 angle=127 distance=17.2 ratio=0.90 2 A.H2U16 A.H2U17 angle=146 distance=19.5 ratio=0.96 3 A.H2U17 A.G18 angle=106 distance=15.8 ratio=0.80 4 A.G19 A.G20 angle=130 distance=16.8 ratio=0.91 5 A.7MG46 A.U47 angle=139 distance=19.0 ratio=0.94 6 A.U47 A.C48 angle=157 distance=19.7 ratio=0.98 7 A.C48 A.5MC49 angle=148 distance=17.5 ratio=0.96 8 A.C60 A.C61 angle=91 distance=13.8 ratio=0.71 9 A.C75 A.A76 angle=160 distance=18.7 ratio=0.98 ---------------------------------------------------------------- Summary of 6 splayed-apart units 1 nts=2 UU A.U7,A.U8 2 nts=3 uuG A.H2U16,A.H2U17,A.G18 3 nts=2 GG A.G19,A.G20 4 nts=4 gUCc A.7MG46,A.U47,A.C48,A.5MC49 5 nts=2 CC A.C60,A.C61 6 nts=2 CA A.C75,A.A76 **************************************************************************** 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. **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1ehz nts=76 [whole] GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAPcUGGAGgUCcUGUGtPCGaUCCACAGAAUUCGCACCA (((((((..((((.....[..)))).((((.........)))).....(((((..]....)))))))))))).... >1ehz-A #1 nts=76 0.09(2.86) [chain] RNA GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAPcUGGAGgUCcUGUGtPCGaUCCACAGAAUUCGCACCA (((((((..((((.....[..)))).((((.........)))).....(((((..]....)))))))))))).... **************************************************************************** Summary of structural features of 76 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 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 C ( A.C2 0.006 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,coaxial-stack 4 G ( A.G4 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 A ( A.A5 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 U ( A.U6 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 U ( A.U7 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 8 U . A.U8 0.016 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,splayed-apart 9 A . A.A9 0.032 ~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,phosphate 10 g ( A.2MG10 0.018 modified,turn,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 11 C ( A.C11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 U ( A.U12 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 13 C ( A.C13 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 14 A . A.A14 0.025 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,kissing-loop,phosphate 15 G . A.G15 0.021 anti,~C3'-endo,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop 16 u . A.H2U16 0.188 modified,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,cap-donor,cap-acceptor,phosphate,splayed-apart 17 u . A.H2U17 0.201 modified,turn,anti,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,splayed-apart 18 G . A.G18 0.028 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate,splayed-apart 19 G [ A.G19 0.026 pseudoknotted,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,phosphate,splayed-apart 20 G . A.G20 0.018 ~C3'-endo,non-stack,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 21 A . A.A21 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,kissing-loop,phosphate 22 G ) A.G22 0.017 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,hairpin-loop,kissing-loop 23 A ) A.A23 0.030 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,phosphate 24 G ) A.G24 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 C ) A.C25 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,junction-loop 26 g . A.M2G26 0.013 modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 27 C ( A.C27 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 28 C ( A.C28 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 A ( A.A29 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 G ( A.G30 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 31 A . A.A31 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 32 c . A.OMC32 0.008 modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 33 U . A.U33 0.014 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 34 g . A.OMG34 0.021 modified,turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 35 A . A.A35 0.006 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 36 A . A.A36 0.015 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 37 g . A.YYG37 0.015 modified,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 38 A . A.A38 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 39 P . A.PSU39 0.004 modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop 40 c ) A.5MC40 0.005 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 41 U ) A.U41 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 G ) A.G42 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 G ) A.G43 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 44 A . A.A44 0.015 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,junction-loop 45 G . A.G45 0.026 anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,junction-loop 46 g . A.7MG46 0.022 modified,~C2'-endo,non-canonical,non-pair-contact,multiplet,junction-loop,splayed-apart 47 U . A.U47 0.007 turn,anti,~C2'-endo,non-stack,non-pair-contact,junction-loop,splayed-apart 48 C . A.C48 0.015 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix,junction-loop,cap-acceptor,phosphate,splayed-apart 49 c ( A.5MC49 0.020 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate,splayed-apart 50 U ( A.U50 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 51 G ( A.G51 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 52 U ( A.U52 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 53 G ( A.G53 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop 54 t . A.5MU54 0.010 modified,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop 55 P . A.PSU55 0.024 modified,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,cap-acceptor 56 C ] A.C56 0.014 pseudoknotted,turn,u-turn,anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop 57 G . A.G57 0.017 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,kissing-loop,cap-donor,phosphate 58 a . A.1MA58 0.012 modified,u-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,hairpin-loop,kissing-loop,phosphate 59 U . A.U59 0.029 turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,kissing-loop,cap-donor 60 C . A.C60 0.016 anti,~C2'-endo,non-pair-contact,hairpin-loop,kissing-loop,phosphate,splayed-apart 61 C ) A.C61 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,kissing-loop,splayed-apart 62 A ) A.A62 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 63 C ) A.C63 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 64 A ) A.A64 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 65 G ) A.G65 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 66 A ) A.A66 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 67 A ) A.A67 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 68 U ) A.U68 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 69 U ) A.U69 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 70 C ) A.C70 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 71 G ) A.G71 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 72 C ) A.C72 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 73 A . A.A73 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 74 C . A.C74 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 75 C . A.C75 0.007 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 76 A . A.A76 0.010 ~C2'-endo,non-stack,ss-non-loop,splayed-apart **************************************************************************** List of 17 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-stacks.pdb -- an ensemble of base stacks 13 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 14 dssr-rotmat.txt -- position vector and rotation matrix 15 dssr-viewV.pdb -- vertical view of the principal moment of inertia 16 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 17 dssr-viewT.pdb -- top view of the principal moment of inertia