**************************************************************************** File name: 2hoj.pdb no. of DNA/RNA chains: 1 [A=79] no. of nucleotides: 79 no. of atoms: 1723 no. of waters: 22 no. of metals: 14 [Mg=2,Mn=12] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 A23-a 1 A.A23/91 **************************************************************************** List of 38 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G9 A.C90 G-C WC 19-XIX cWW cW-W 2 A.C10 A.G89 C-G WC 19-XIX cWW cW-W 3 A.G11 A.C88 G-C WC 19-XIX cWW cW-W 4 A.A12 A.U87 A-U WC 20-XX cWW cW-W 5 A.C13 A.G86 C-G WC 19-XIX cWW cW-W 6 A.U14 A.A85 U-A WC 20-XX cWW cW-W 7 A.C15 A.G51 C-G WC 19-XIX cWW cW-W 8 A.G16 A.C50 G-C WC 19-XIX cWW cW-W 9 A.G16 A.A84 G-A -- -- cSS cm-m 10 A.G17 A.C49 G-C WC 19-XIX cWW cW-W 11 A.G17 A.A56 G+A Linker -- tSS tm+m 12 A.G18 A.C48 G-C WC 19-XIX cWW cW-W 13 A.G19 A.G42 G+G -- 04-IV tSS tm+m 14 A.G19 A.A47 G-A Imino 08-VIII cWW cW-W 15 A.U20 A.A45 U-A WC 20-XX cWW cW-W 16 A.G21 A.C38 G-C WC 19-XIX cWW cW-W 17 A.G21 A.U71 G-U -- -- cSS cm-m 18 A.C22 A.G37 C-G WC 19-XIX cWW cW-W 19 A.C23 A.G36 C-G WC 19-XIX cWW cW-W 20 A.C24 A.A35 C-A -- -- c.W c.-W 21 A.U25 A.G36 U-G -- -- tHS tM-m 22 A.G33 A.A34 G-A Platform -- cHH cM-M 23 A.G37 A.A69 G+A -- 10-X .SW .m+W 24 A.U39 A.A43 U-A rHoogsteen 24-XXIV tWH tW-M 25 A.A41 A.C48 A-C -- -- cSS cm-m 26 A.C50 A.A84 C+A -- -- tSW tm+W 27 A.A53 A.A84 A+A -- 02-II tHH tM+M 28 A.A56 A.G83 A-G Sheared 11-XI tHS tM-m 29 A.C57 A.G82 C-G WC 19-XIX cWW cW-W 30 A.C58 A.G81 C-G WC 19-XIX cWW cW-W 31 A.U59 A.A80 U-A WC 20-XX cWW cW-W 32 A.G60 A.G78 G+G Metal 06-VI cWH cW+M 33 A.A61 A.C77 A+C -- -- tW. tW+. 34 A.C63 A.G76 C-G WC 19-XIX cWW cW-W 35 A.U64 A.A75 U-A WC 20-XX cWW cW-W 36 A.G65 A.C74 G-C WC 19-XIX cWW cW-W 37 A.G66 A.C73 G-C WC 19-XIX cWW cW-W 38 A.A67 A.U71 A-U -- -- tWH tW-M **************************************************************************** List of 7 multiplets 1 nts=3 GAC A.G18,A.A41,A.C48 2 nts=3 GGA A.G19,A.G42,A.A47 3 nts=3 CGA A.C22,A.G37,A.A69 4 nts=3 CUG A.C23,A.U25,A.G36 5 nts=4 GCAA A.G16,A.C50,A.A53,A.A84 6 nts=4 GCAG A.G17,A.C49,A.A56,A.G83 7 nts=4 GCAU A.G21,A.C38,A.A67,A.U71 **************************************************************************** List of 3 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=12 strand-1 5'-GCGACUCGGGGU-3' bp-type ||||||||||.| strand-2 3'-CGCUGAGCCCAA-5' helix-form AAAA.xA.AAx 1 A.G9 A.C90 G-C WC 19-XIX cWW cW-W 2 A.C10 A.G89 C-G WC 19-XIX cWW cW-W 3 A.G11 A.C88 G-C WC 19-XIX cWW cW-W 4 A.A12 A.U87 A-U WC 20-XX cWW cW-W 5 A.C13 A.G86 C-G WC 19-XIX cWW cW-W 6 A.U14 A.A85 U-A WC 20-XX cWW cW-W 7 A.C15 A.G51 C-G WC 19-XIX cWW cW-W 8 A.G16 A.C50 G-C WC 19-XIX cWW cW-W 9 A.G17 A.C49 G-C WC 19-XIX cWW cW-W 10 A.G18 A.C48 G-C WC 19-XIX cWW cW-W 11 A.G19 A.A47 G-A Imino 08-VIII cWW cW-W 12 A.U20 A.A45 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=6 strand-1 5'-AAGGCU-3' bp-type ..|||. strand-2 3'-GCCCGA-5' helix-form x.AAx 1 A.A34 A.G33 A-G Platform -- cHH cM-M 2 A.A35 A.C24 A-C -- -- cW. cW-. 3 A.G36 A.C23 G-C WC 19-XIX cWW cW-W 4 A.G37 A.C22 G-C WC 19-XIX cWW cW-W 5 A.C38 A.G21 C-G WC 19-XIX cWW cW-W 6 A.U39 A.A43 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#3[2] bps=12 strand-1 5'-AACCUGACUGGA-3' bp-type ..|||..||||. strand-2 3'-AGGGAGCGACCU-5' helix-form x.AAx.xAAAx 1 A.A53 A.A84 A+A -- 02-II tHH tM+M 2 A.A56 A.G83 A-G Sheared 11-XI tHS tM-m 3 A.C57 A.G82 C-G WC 19-XIX cWW cW-W 4 A.C58 A.G81 C-G WC 19-XIX cWW cW-W 5 A.U59 A.A80 U-A WC 20-XX cWW cW-W 6 A.G60 A.G78 G+G Metal 06-VI cWH cW+M 7 A.A61 A.C77 A+C -- -- tW. tW+. 8 A.C63 A.G76 C-G WC 19-XIX cWW cW-W 9 A.U64 A.A75 U-A WC 20-XX cWW cW-W 10 A.G65 A.C74 G-C WC 19-XIX cWW cW-W 11 A.G66 A.C73 G-C WC 19-XIX cWW cW-W 12 A.A67 A.U71 A-U -- -- tWH tW-M **************************************************************************** List of 5 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=6 strand-1 5'-GCGACU-3' bp-type |||||| strand-2 3'-CGCUGA-5' helix-form AAAA. 1 A.G9 A.C90 G-C WC 19-XIX cWW cW-W 2 A.C10 A.G89 C-G WC 19-XIX cWW cW-W 3 A.G11 A.C88 G-C WC 19-XIX cWW cW-W 4 A.A12 A.U87 A-U WC 20-XX cWW cW-W 5 A.C13 A.G86 C-G WC 19-XIX cWW cW-W 6 A.U14 A.A85 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=4 strand-1 5'-CGGG-3' bp-type |||| strand-2 3'-GCCC-5' helix-form A.A 1 A.C15 A.G51 C-G WC 19-XIX cWW cW-W 2 A.G16 A.C50 G-C WC 19-XIX cWW cW-W 3 A.G17 A.C49 G-C WC 19-XIX cWW cW-W 4 A.G18 A.C48 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=3 strand-1 5'-GCC-3' bp-type ||| strand-2 3'-CGG-5' helix-form A. 1 A.G21 A.C38 G-C WC 19-XIX cWW cW-W 2 A.C22 A.G37 C-G WC 19-XIX cWW cW-W 3 A.C23 A.G36 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#3] bps=3 strand-1 5'-CCU-3' bp-type ||| strand-2 3'-GGA-5' helix-form AA 1 A.C57 A.G82 C-G WC 19-XIX cWW cW-W 2 A.C58 A.G81 C-G WC 19-XIX cWW cW-W 3 A.U59 A.A80 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#5[#3] bps=4 strand-1 5'-CUGG-3' bp-type |||| strand-2 3'-GACC-5' helix-form AAA 1 A.C63 A.G76 C-G WC 19-XIX cWW cW-W 2 A.U64 A.A75 U-A WC 20-XX cWW cW-W 3 A.G65 A.C74 G-C WC 19-XIX cWW cW-W 4 A.G66 A.C73 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.U20 A.A45 U-A WC 20-XX cWW cW-W **************************************************************************** List of 2 coaxial stacks 1 Helix#1 contains 2 stems: [#1,#2] 2 Helix#3 contains 2 stems: [#4,#5] **************************************************************************** List of 15 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.U14,A.C15 2 nts=2 GA A.G21,A.A43 3 nts=2 AG A.A41,A.G42 4 nts=2 GA A.G51,A.A85 5 nts=3 GGU A.G18,A.G19,A.U20 6 nts=3 AAG A.A34,A.A35,A.G36 7 nts=3 CUG A.C38,A.U39,A.G40 8 nts=3 CAA A.C57,A.A56,A.A84 9 nts=3 GAU A.G66,A.A67,A.U68 10 nts=3 GCG A.G76,A.C77,A.G78 11 nts=4 AAAC A.A44,A.A45,A.A47,A.C48 12 nts=4 UAGG A.U52,A.A53,A.G83,A.G82 13 nts=4 UGAC A.U59,A.G60,A.A61,A.C63 14 nts=4 AAUC A.A69,A.A70,A.U71,A.C73 15 nts=6 CCGUGC A.C23,A.C24,A.G33,A.U32,A.G31,A.C30 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 UUGa A.U25,A.U62,A.G72,A.A23/91 **************************************************************************** List of 7 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP2@A.G42 A.G40 3.17 2 other N3'@A.TPP114 A.G42 3.33 3 other N3'@A.TPP114 A.A43 3.42 4 sugar O4'@A.A44 A.A45 2.94 5 sugar O4'@A.U52 A.A53 3.11 6 phosphate OP2@A.A70 A.U68 2.93 7 sugar O4'@A.G51 A.A84 2.93 **************************************************************************** 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 1 hairpin loop 1 hairpin loop: nts=8; [6]; linked by [#5] summary: [1] 6 [A.66 A.73] 4 nts=8 GAUAAUGC A.G66,A.A67,A.U68,A.A69,A.A70,A.U71,A.G72,A.C73 nts=6 AUAAUG A.A67,A.U68,A.A69,A.A70,A.U71,A.G72 **************************************************************************** List of 1 bulge 1 bulge: nts=10; [0,6]; linked by [#-1,#3] summary: [2] 0 6 [A.20 A.45 A.21 A.38] 1 3 nts=10 UGCUGAGAAA A.U20,A.G21,A.C38,A.U39,A.G40,A.A41,A.G42,A.A43,A.A44,A.A45 nts=0 nts=6 UGAGAA A.U39,A.G40,A.A41,A.G42,A.A43,A.A44 **************************************************************************** List of 2 internal loops 1 asymmetric internal loop: nts=7; [1,2]; linked by [#2,#-1] summary: [2] 1 2 [A.18 A.48 A.20 A.45] 4 1 nts=7 GGUAUAC A.G18,A.G19,A.U20,A.A45,A.U46,A.A47,A.C48 nts=1 G A.G19 nts=2 UA A.U46,A.A47 2 symmetric internal loop: nts=10; [3,3]; linked by [#4,#5] summary: [2] 3 3 [A.59 A.80 A.63 A.76] 3 4 nts=10 UGAUCGCGUA A.U59,A.G60,A.A61,A.U62,A.C63,A.G76,A.C77,A.G78,A.U79,A.A80 nts=3 GAU A.G60,A.A61,A.U62 nts=3 CGU A.C77,A.G78,A.U79 **************************************************************************** List of 1 junction 1 3-way junction: nts=13; [0,5,2]; linked by [#1,#2,#4] summary: [3] 0 5 2 [A.14 A.85 A.15 A.51 A.57 A.82] 6 4 3 nts=13 UCGUAUCACGGAA A.U14,A.C15,A.G51,A.U52,A.A53,A.U54,A.C55,A.A56,A.C57,A.G82,A.G83,A.A84,A.A85 nts=0 nts=5 UAUCA A.U52,A.A53,A.U54,A.C55,A.A56 nts=2 GA A.G83,A.A84 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=8* CUCGUGAA A.C24,A.U25,A.C30,A.G31,A.U32,A.G33,A.A34,A.A35 2 nts=1 a A.A23/91 **************************************************************************** List of 6 A-minor motifs (types I, II, or X) 1 type=II A|G-C A.A41|A.G18,A.C48 WC +A.G18 H-bonds[0]: "" -A.C48 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.92],N3-O2'(hydroxyl)[2.53]" 2 type=X A|G-C A.A43|A.G21,A.C38 WC +A.G21 H-bonds[1]: "O2'(hydroxyl)-N7[2.63]" -A.C38 H-bonds[0]: "" 3 type=I A|G-C A.A56|A.G17,A.C49 WC +A.G17 H-bonds[2]: "N1-O2'(hydroxyl)[2.93],N3-N2(amino)[3.19]" -A.C49 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.06]" 4 type=X A|C-G A.A69|A.C22,A.G37 WC -A.C22 H-bonds[0]: "" +A.G37 H-bonds[1]: "N1-N2(amino)[3.32]" 5 type=II A|C-G A.A70|A.C22,A.G37 WC -A.C22 H-bonds[3]: "O2'(hydroxyl)-O3'[3.01],O2'(hydroxyl)-O2'(hydroxyl)[2.64],N3-O2'(hydroxyl)[2.81]" +A.G37 H-bonds[0]: "" 6 type=I A|G-C A.A84|A.G16,A.C50 WC -A.G16 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.93],N3-N2(amino)[3.13]" +A.C50 H-bonds[1]: "N1-O2'(hydroxyl)[2.56]" **************************************************************************** List of 1 ribose zipper 1 nts=4 GCAU A.G21,A.C22,A.A70,A.U71 **************************************************************************** List of 7 splayed-apart dinucleotides 1 A.U20 A.G21 angle=98 distance=14.3 ratio=0.75 2 A.G51 A.U52 angle=96 distance=13.7 ratio=0.75 3 A.A61 A.U62 angle=138 distance=18.0 ratio=0.93 4 A.U62 A.C63 angle=162 distance=18.9 ratio=0.99 5 A.U71 A.G72 angle=106 distance=12.1 ratio=0.81 6 A.G72 A.C73 angle=93 distance=12.6 ratio=0.73 7 A.C90 A.A23/91 angle=141 distance=17.5 ratio=0.94 ---------------------------------------------------------------- Summary of 5 splayed-apart units 1 nts=2 UG A.U20,A.G21 2 nts=2 GU A.G51,A.U52 3 nts=3 AUC A.A61,A.U62,A.C63 4 nts=3 UGC A.U71,A.G72,A.C73 5 nts=2 Ca A.C90,A.A23/91 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2hoj nts=79 [whole] GCGACUCGGGGUGCCCU&CGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCGCa ((((((((((.((((..&......)))......)..)))).....(((...((((......))))...)))..)))))). >2hoj-A #1 nts=79 0.13(3.25) [chain] RNA* GCGACUCGGGGUGCCCU&CGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCGCa ((((((((((.((((..&......)))......)..)))).....(((...((((......))))...)))..)))))). **************************************************************************** Summary of structural features of 79 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.G9 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 C ( A.C10 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 G ( A.G11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 A ( A.A12 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 C ( A.C13 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 U ( A.U14 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 7 C ( A.C15 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 8 G ( A.G16 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 9 G ( A.G17 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 10 G ( A.G18 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 11 G . A.G19 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 12 U ( A.U20 0.011 anti,isolated-canonical,non-pair-contact,helix-end,bulge,internal-loop,splayed-apart 13 G ( A.G21 0.006 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet,bulge,A-minor,ribose-zipper,phosphate,splayed-apart 14 C ( A.C22 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,multiplet,A-minor,ribose-zipper 15 C ( A.C23 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet 16 C . A.C24 0.006 turn,anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 17 U . A.U25 0.003 break,anti,~C3'-endo,non-stack,non-canonical,non-pair-contact,multiplet,ss-non-loop,phosphate 18 C . A.C30 0.001 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 19 G . A.G31 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 20 U . A.U32 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop 21 G . A.G33 0.014 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 22 A . A.A34 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 23 A . A.A35 0.003 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 24 G ) A.G36 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,multiplet 25 G ) A.G37 0.006 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,multiplet,A-minor 26 C ) A.C38 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,multiplet,bulge,A-minor,phosphate 27 U . A.U39 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,bulge 28 G . A.G40 0.014 u-turn,anti,~C3'-endo,BI,non-pair-contact,bulge,cap-acceptor 29 A . A.A41 0.013 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,A-minor 30 G . A.G42 0.006 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,bulge,cap-donor,cap-acceptor,phosphate 31 A . A.A43 0.006 turn,u-turn,anti,non-canonical,non-pair-contact,helix-end,bulge,A-minor,cap-acceptor,phosphate 32 A . A.A44 0.006 syn,~C2'-endo,non-pair-contact,bulge,cap-donor 33 A ) A.A45 0.006 ~C3'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,internal-loop,cap-acceptor,phosphate 34 U . A.U46 --- turn,~C3'-endo,non-stack,internal-loop 35 A . A.A47 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop 36 C ) A.C48 0.003 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 37 C ) A.C49 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 38 C ) A.C50 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet,A-minor 39 G ) A.G51 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,cap-donor,splayed-apart 40 U . A.U52 0.009 turn,anti,non-pair-contact,junction-loop,cap-donor,splayed-apart 41 A . A.A53 0.005 syn,~C3'-endo,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,cap-acceptor,phosphate 42 U . A.U54 --- turn,~C3'-endo,non-stack,junction-loop 43 C . A.C55 --- ~C3'-endo,non-stack,junction-loop,phosphate 44 A . A.A56 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop,A-minor 45 C ( A.C57 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop,phosphate 46 C ( A.C58 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 47 U ( A.U59 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 48 G . A.G60 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 49 A . A.A61 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,splayed-apart 50 U . A.U62 0.005 turn,anti,~C2'-endo,non-stack,internal-loop,splayed-apart 51 C ( A.C63 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 52 U ( A.U64 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 53 G ( A.G65 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 54 G ( A.G66 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 55 A . A.A67 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop 56 U . A.U68 0.004 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor 57 A . A.A69 0.009 turn,u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,multiplet,hairpin-loop,A-minor,phosphate 58 A . A.A70 0.009 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,A-minor,ribose-zipper,cap-donor,phosphate 59 U . A.U71 0.005 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,ribose-zipper,phosphate,splayed-apart 60 G . A.G72 0.011 turn,syn,~C3'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 61 C ) A.C73 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop,phosphate,splayed-apart 62 C ) A.C74 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 63 A ) A.A75 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 64 G ) A.G76 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 65 C . A.C77 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 66 G . A.G78 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 67 U . A.U79 --- turn,~C3'-endo,non-stack,internal-loop,phosphate 68 A ) A.A80 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 69 G ) A.G81 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 70 G ) A.G82 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 71 G . A.G83 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,junction-loop 72 A . A.A84 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,junction-loop,A-minor,cap-acceptor 73 A ) A.A85 0.009 ~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,junction-loop 74 G ) A.G86 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 75 U ) A.U87 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 76 C ) A.C88 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 77 G ) A.G89 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 78 C ) A.C90 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,splayed-apart 79 a . A.A23/91 0.005 modified,anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart **************************************************************************** List of 20 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-bulges.pdb -- an ensemble of bulges 7 dssr-iloops.pdb -- an ensemble of internal loops 8 dssr-junctions.pdb -- an ensemble of junctions (multi-branch) 9 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 10 dssr-2ndstrs.ct -- secondary structure in connectivity table format 11 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 12 dssr-torsions.txt -- backbone torsion angles and suite names 13 dssr-splays.pdb -- an ensemble of splayed-apart units 14 dssr-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 15 dssr-stacks.pdb -- an ensemble of base stacks 16 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 17 dssr-rotmat.txt -- position vector and rotation matrix 18 dssr-viewV.pdb -- vertical view of the principal moment of inertia 19 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 20 dssr-viewT.pdb -- top view of the principal moment of inertia