**************************************************************************** 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=5h9f.pdb -o=5h9f.out File name: 5h9f.pdb no. of DNA/RNA chains: 3 [L=61,M=28,N=50] no. of nucleotides: 139 no. of atoms: 28930 no. of waters: 1050 no. of metals: 1 [Zn=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 23G-g 1 L.23G61 **************************************************************************** List of 54 base pairs nt1 nt2 bp name Saenger LW DSSR 1 L.A9 N.DT32 A-T WC 20-XX cWW cW-W 2 L.C10 N.DG31 C-G WC 19-XIX cWW cW-W 3 L.G11 N.DC30 G-C WC 19-XIX cWW cW-W 4 L.G12 N.DC29 G-C WC 19-XIX cWW cW-W 5 L.U13 N.DA28 U-A WC 20-XX cWW cW-W 6 L.U15 N.DA26 U-A WC 20-XX cWW cW-W 7 L.U16 N.DA25 U-A WC 20-XX cWW cW-W 8 L.G17 N.DC24 G-C WC 19-XIX cWW cW-W 9 L.U18 N.DA23 U-A WC 20-XX cWW cW-W 10 L.U19 N.DA22 U-A WC 20-XX cWW cW-W 11 L.A21 N.DT20 A-T WC 20-XX cWW cW-W 12 L.G22 N.DC19 G-C WC 19-XIX cWW cW-W 13 L.A23 N.DT18 A-T WC 20-XX cWW cW-W 14 L.U24 N.DA17 U-A WC 20-XX cWW cW-W 15 L.C25 N.DG16 C-G WC 19-XIX cWW cW-W 16 L.U27 N.DA14 U-A WC 20-XX cWW cW-W 17 L.G28 N.DC13 G-C WC 19-XIX cWW cW-W 18 L.G29 N.DC12 G-C WC 19-XIX cWW cW-W 19 L.C30 N.DG11 C-G WC 19-XIX cWW cW-W 20 L.U31 N.DA10 U-A WC 20-XX cWW cW-W 21 L.G33 N.DC8 G-C WC 19-XIX cWW cW-W 22 L.C34 N.DG7 C-G WC 19-XIX cWW cW-W 23 L.C35 N.DG6 C-G WC 19-XIX cWW cW-W 24 L.A36 N.DT5 A-T WC 20-XX cWW cW-W 25 L.A37 N.DT4 A-T WC 20-XX cWW cW-W 26 L.A39 N.DT2 A-T WC 20-XX cWW cW-W 27 L.G40 N.DC1 G-C WC 19-XIX cWW cW-W 28 L.U45 L.C46 U+C Platform -- cSH cm+M 29 L.C46 L.23G61 C-g WC 19-XIX cWW cW-W 30 L.C47 L.G60 C-G WC 19-XIX cWW cW-W 31 L.C48 L.G59 C-G WC 19-XIX cWW cW-W 32 L.C49 L.G58 C-G WC 19-XIX cWW cW-W 33 L.G50 L.C57 G-C WC 19-XIX cWW cW-W 34 L.C51 L.G56 C-G WC 19-XIX cWW cW-W 35 L.G52 L.A55 G+A -- -- cHH cM+M 36 L.G52 L.G56 G+G -- 06-VI cHW cM+W 37 M.DT1 N.DA50 T-A WC 20-XX cWW cW-W 38 M.DC2 N.DG49 C-G WC 19-XIX cWW cW-W 39 M.DT3 N.DA48 T-A WC 20-XX cWW cW-W 40 M.DG4 N.DC47 G-C WC 19-XIX cWW cW-W 41 M.DT5 N.DA46 T-A -- -- cWW cW-W 42 M.DG6 N.DC45 G-C WC 19-XIX cWW cW-W 43 M.DC7 N.DG44 C-G -- -- cWW cW-W 44 M.DA8 N.DT43 A-T -- -- cWW cW-W 45 M.DG9 N.DC42 G-C WC 19-XIX cWW cW-W 46 M.DT10 N.DA41 T-A WC 20-XX cWW cW-W 47 M.DG11 N.DC40 G-C WC 19-XIX cWW cW-W 48 M.DC12 N.DG39 C-G WC 19-XIX cWW cW-W 49 M.DT13 N.DA38 T-A WC 20-XX cWW cW-W 50 M.DC14 N.DG37 C-G WC 19-XIX cWW cW-W 51 M.DG15 N.DC36 G-C WC 19-XIX cWW cW-W 52 M.DA16 N.DT35 A-T WC 20-XX cWW cW-W 53 M.DT17 N.DA34 T-A WC 20-XX cWW cW-W 54 M.DG18 N.DC33 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 multiplet 1 nts=3 UCg L.U45,L.C46,L.23G61 **************************************************************************** List of 8 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=5 strand-1 5'-ACGGU-3' bp-type ||||| strand-2 3'-TGCCA-5' helix-form .... 1 L.A9 N.DT32 A-T WC 20-XX cWW cW-W 2 L.C10 N.DG31 C-G WC 19-XIX cWW cW-W 3 L.G11 N.DC30 G-C WC 19-XIX cWW cW-W 4 L.G12 N.DC29 G-C WC 19-XIX cWW cW-W 5 L.U13 N.DA28 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=5 strand-1 5'-UUGUU-3' bp-type ||||| strand-2 3'-AACAA-5' helix-form B... 1 L.U15 N.DA26 U-A WC 20-XX cWW cW-W 2 L.U16 N.DA25 U-A WC 20-XX cWW cW-W 3 L.G17 N.DC24 G-C WC 19-XIX cWW cW-W 4 L.U18 N.DA23 U-A WC 20-XX cWW cW-W 5 L.U19 N.DA22 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=5 strand-1 5'-AGAUC-3' bp-type ||||| strand-2 3'-TCTAG-5' helix-form .... 1 L.A21 N.DT20 A-T WC 20-XX cWW cW-W 2 L.G22 N.DC19 G-C WC 19-XIX cWW cW-W 3 L.A23 N.DT18 A-T WC 20-XX cWW cW-W 4 L.U24 N.DA17 U-A WC 20-XX cWW cW-W 5 L.C25 N.DG16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[1] bps=5 strand-1 5'-UGGCU-3' bp-type ||||| strand-2 3'-ACCGA-5' helix-form B... 1 L.U27 N.DA14 U-A WC 20-XX cWW cW-W 2 L.G28 N.DC13 G-C WC 19-XIX cWW cW-W 3 L.G29 N.DC12 G-C WC 19-XIX cWW cW-W 4 L.C30 N.DG11 C-G WC 19-XIX cWW cW-W 5 L.U31 N.DA10 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#5[1] bps=5 strand-1 5'-GCCAA-3' bp-type ||||| strand-2 3'-CGGTT-5' helix-form .B.. 1 L.G33 N.DC8 G-C WC 19-XIX cWW cW-W 2 L.C34 N.DG7 C-G WC 19-XIX cWW cW-W 3 L.C35 N.DG6 C-G WC 19-XIX cWW cW-W 4 L.A36 N.DT5 A-T WC 20-XX cWW cW-W 5 L.A37 N.DT4 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#6[1] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-TC-5' helix-form . 1 L.A39 N.DT2 A-T WC 20-XX cWW cW-W 2 L.G40 N.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#7[1] bps=7 strand-1 5'-CCCCGCG-3' bp-type ||||||. strand-2 3'-gGGGCGA-5' helix-form ...... 1 L.C46 L.23G61 C-g WC 19-XIX cWW cW-W 2 L.C47 L.G60 C-G WC 19-XIX cWW cW-W 3 L.C48 L.G59 C-G WC 19-XIX cWW cW-W 4 L.C49 L.G58 C-G WC 19-XIX cWW cW-W 5 L.G50 L.C57 G-C WC 19-XIX cWW cW-W 6 L.C51 L.G56 C-G WC 19-XIX cWW cW-W 7 L.G52 L.A55 G+A -- -- cHH cM+M -------------------------------------------------------------------------- helix#8[2] bps=18 strand-1 5'-TCTGTGCAGTGCTCGATG-3' bp-type ||||.|..|||||||||| strand-2 3'-AGACACGTCACGAGCTAC-5' helix-form .............BB.. 1 M.DT1 N.DA50 T-A WC 20-XX cWW cW-W 2 M.DC2 N.DG49 C-G WC 19-XIX cWW cW-W 3 M.DT3 N.DA48 T-A WC 20-XX cWW cW-W 4 M.DG4 N.DC47 G-C WC 19-XIX cWW cW-W 5 M.DT5 N.DA46 T-A -- -- cWW cW-W 6 M.DG6 N.DC45 G-C WC 19-XIX cWW cW-W 7 M.DC7 N.DG44 C-G -- -- cWW cW-W 8 M.DA8 N.DT43 A-T -- -- cWW cW-W 9 M.DG9 N.DC42 G-C WC 19-XIX cWW cW-W 10 M.DT10 N.DA41 T-A WC 20-XX cWW cW-W 11 M.DG11 N.DC40 G-C WC 19-XIX cWW cW-W 12 M.DC12 N.DG39 C-G WC 19-XIX cWW cW-W 13 M.DT13 N.DA38 T-A WC 20-XX cWW cW-W 14 M.DC14 N.DG37 C-G WC 19-XIX cWW cW-W 15 M.DG15 N.DC36 G-C WC 19-XIX cWW cW-W 16 M.DA16 N.DT35 A-T WC 20-XX cWW cW-W 17 M.DT17 N.DA34 T-A WC 20-XX cWW cW-W 18 M.DG18 N.DC33 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 9 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'-ACGGU-3' bp-type ||||| strand-2 3'-TGCCA-5' helix-form .... 1 L.A9 N.DT32 A-T WC 20-XX cWW cW-W 2 L.C10 N.DG31 C-G WC 19-XIX cWW cW-W 3 L.G11 N.DC30 G-C WC 19-XIX cWW cW-W 4 L.G12 N.DC29 G-C WC 19-XIX cWW cW-W 5 L.U13 N.DA28 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=5 strand-1 5'-UUGUU-3' bp-type ||||| strand-2 3'-AACAA-5' helix-form B... 1 L.U15 N.DA26 U-A WC 20-XX cWW cW-W 2 L.U16 N.DA25 U-A WC 20-XX cWW cW-W 3 L.G17 N.DC24 G-C WC 19-XIX cWW cW-W 4 L.U18 N.DA23 U-A WC 20-XX cWW cW-W 5 L.U19 N.DA22 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#3] bps=5 strand-1 5'-AGAUC-3' bp-type ||||| strand-2 3'-TCTAG-5' helix-form .... 1 L.A21 N.DT20 A-T WC 20-XX cWW cW-W 2 L.G22 N.DC19 G-C WC 19-XIX cWW cW-W 3 L.A23 N.DT18 A-T WC 20-XX cWW cW-W 4 L.U24 N.DA17 U-A WC 20-XX cWW cW-W 5 L.C25 N.DG16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#4] bps=5 strand-1 5'-UGGCU-3' bp-type ||||| strand-2 3'-ACCGA-5' helix-form B... 1 L.U27 N.DA14 U-A WC 20-XX cWW cW-W 2 L.G28 N.DC13 G-C WC 19-XIX cWW cW-W 3 L.G29 N.DC12 G-C WC 19-XIX cWW cW-W 4 L.C30 N.DG11 C-G WC 19-XIX cWW cW-W 5 L.U31 N.DA10 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#5[#5] bps=5 strand-1 5'-GCCAA-3' bp-type ||||| strand-2 3'-CGGTT-5' helix-form .B.. 1 L.G33 N.DC8 G-C WC 19-XIX cWW cW-W 2 L.C34 N.DG7 C-G WC 19-XIX cWW cW-W 3 L.C35 N.DG6 C-G WC 19-XIX cWW cW-W 4 L.A36 N.DT5 A-T WC 20-XX cWW cW-W 5 L.A37 N.DT4 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#6[#6] bps=2 strand-1 5'-AG-3' bp-type || strand-2 3'-TC-5' helix-form . 1 L.A39 N.DT2 A-T WC 20-XX cWW cW-W 2 L.G40 N.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#7[#7] bps=6 strand-1 5'-CCCCGC-3' bp-type |||||| strand-2 3'-gGGGCG-5' helix-form ..... 1 L.C46 L.23G61 C-g WC 19-XIX cWW cW-W 2 L.C47 L.G60 C-G WC 19-XIX cWW cW-W 3 L.C48 L.G59 C-G WC 19-XIX cWW cW-W 4 L.C49 L.G58 C-G WC 19-XIX cWW cW-W 5 L.G50 L.C57 G-C WC 19-XIX cWW cW-W 6 L.C51 L.G56 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#8[#8] bps=4 strand-1 5'-TCTG-3' bp-type |||| strand-2 3'-AGAC-5' helix-form ... 1 M.DT1 N.DA50 T-A WC 20-XX cWW cW-W 2 M.DC2 N.DG49 C-G WC 19-XIX cWW cW-W 3 M.DT3 N.DA48 T-A WC 20-XX cWW cW-W 4 M.DG4 N.DC47 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#9[#8] bps=10 strand-1 5'-GTGCTCGATG-3' bp-type |||||||||| strand-2 3'-CACGAGCTAC-5' helix-form .....BB.. 1 M.DG9 N.DC42 G-C WC 19-XIX cWW cW-W 2 M.DT10 N.DA41 T-A WC 20-XX cWW cW-W 3 M.DG11 N.DC40 G-C WC 19-XIX cWW cW-W 4 M.DC12 N.DG39 C-G WC 19-XIX cWW cW-W 5 M.DT13 N.DA38 T-A WC 20-XX cWW cW-W 6 M.DC14 N.DG37 C-G WC 19-XIX cWW cW-W 7 M.DG15 N.DC36 G-C WC 19-XIX cWW cW-W 8 M.DA16 N.DT35 A-T WC 20-XX cWW cW-W 9 M.DT17 N.DA34 T-A WC 20-XX cWW cW-W 10 M.DG18 N.DC33 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. -------------------------------------------------------------------- [#8] -1 M.DG6 N.DC45 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#8 contains 2 stems: [#8,#9] **************************************************************************** List of 28 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 QC A.GLN354,N.DC33 2 nts=2 HA B.HIS123,N.DA9 3 nts=2 HG C.HIS123,N.DG21 4 nts=2 HT E.HIS213,N.DT4 5 nts=2 FU F.PHE200,L.U31 6 nts=2 HA F.HIS213,N.DA10 7 nts=2 FC G.PHE200,L.C25 8 nts=2 HG G.HIS213,N.DG16 9 nts=2 RA H.ARG46,L.A14 10 nts=2 FU H.PHE200,L.U19 11 nts=2 HA H.HIS213,N.DA22 12 nts=2 RG I.ARG46,L.G8 13 nts=2 FU I.PHE200,L.U13 14 nts=2 HA I.HIS213,N.DA28 15 nts=2 QT J.GLN105,N.DT32 16 nts=2 YU J.TYR145,L.U2 17 nts=2 FA J.PHE208,L.A3 18 nts=2 AG L.A55,L.G56 19 nts=2 GT M.DG18,M.DT19 20 nts=2 TA M.DT22,M.DA23 21 nts=3 ETT A.GLU401,M.DT24,M.DT25 22 nts=3 DAY I.ASP179,L.A1,J.TYR142 23 nts=3 GGA L.G40,L.G41,L.A42 24 nts=3 CGC L.C51,L.G52,L.C54 25 nts=3 TAT M.DT26,M.DA27,M.DT28 26 nts=5 FCAAR A.PHE129,L.C6,L.A5,L.A4,J.ARG206 27 nts=6 GTGCAG M.DG4,M.DT5,M.DG6,M.DC7,M.DA8,M.DG9 28 nts=6 CTGCAC N.DC42,N.DT43,N.DG44,N.DC45,N.DA46,N.DC47 **************************************************************************** Nucleotides not involved in stacking interactions nts=9 CCUCGUCTT L.C20,L.C26,L.U32,L.C38,L.G43,L.U44,L.C53,M.DT20,M.DT21 **************************************************************************** List of 7 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other SD@H.MET166 L.G12 3.30 2 other SD@G.MET166 L.U18 3.20 3 other SD@F.MET166 L.A23 3.50 4 other SD@F.MET166 L.U24 3.44 5 other SD@E.MET166 L.C30 3.42 6 other SD@D.MET166 L.A36 3.33 7 sugar O4'@L.G56 L.A55 3.41 **************************************************************************** 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 hairpin loop 1 hairpin loop: nts=6; [4]; linked by [#7] summary: [1] 4 [L.51 L.56] 6 nts=6 CGCCAG L.C51,L.G52,L.C53,L.C54,L.A55,L.G56 nts=4 GCCA L.G52,L.C53,L.C54,L.A55 **************************************************************************** List of 7 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [L.13 N.28 L.15 N.26] 5 5 nts=6 UAUATA L.U13,L.A14,L.U15,N.DA26,N.DT27,N.DA28 nts=1 A L.A14 nts=1 T N.DT27 2 symmetric internal loop: nts=6; [1,1]; linked by [#2,#3] summary: [2] 1 1 [L.19 N.22 L.21 N.20] 5 5 nts=6 UCATGA L.U19,L.C20,L.A21,N.DT20,N.DG21,N.DA22 nts=1 C L.C20 nts=1 G N.DG21 3 symmetric internal loop: nts=6; [1,1]; linked by [#3,#4] summary: [2] 1 1 [L.25 N.16 L.27 N.14] 5 5 nts=6 CCUAGG L.C25,L.C26,L.U27,N.DA14,N.DG15,N.DG16 nts=1 C L.C26 nts=1 G N.DG15 4 symmetric internal loop: nts=6; [1,1]; linked by [#4,#5] summary: [2] 1 1 [L.31 N.10 L.33 N.8] 5 5 nts=6 UUGCAA L.U31,L.U32,L.G33,N.DC8,N.DA9,N.DA10 nts=1 U L.U32 nts=1 A N.DA9 5 symmetric internal loop: nts=6; [1,1]; linked by [#5,#6] summary: [2] 1 1 [L.37 N.4 L.39 N.2] 5 2 nts=6 ACATGT L.A37,L.C38,L.A39,N.DT2,N.DG3,N.DT4 nts=1 C L.C38 nts=1 G N.DG3 6 symmetric internal loop: nts=6; [1,1]; linked by [#8,#-1] summary: [2] 1 1 [M.4 N.47 M.6 N.45] 4 1 nts=6 GTGCAC M.DG4,M.DT5,M.DG6,N.DC45,N.DA46,N.DC47 nts=1 T M.DT5 nts=1 A N.DA46 7 symmetric internal loop: nts=8; [2,2]; linked by [#-1,#9] summary: [2] 2 2 [M.6 N.45 M.9 N.42] 1 10 nts=8 GCAGCTGC M.DG6,M.DC7,M.DA8,M.DG9,N.DC42,N.DT43,N.DG44,N.DC45 nts=2 CA M.DC7,M.DA8 nts=2 TG N.DT43,N.DG44 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=8 AUAAACCG L.A1,L.U2,L.A3,L.A4,L.A5,L.C6,L.C7,L.G8 2 nts=5 GAGUU L.G41,L.A42,L.G43,L.U44,L.U45 3 nts=10 TTTTATTTAT M.DT19,M.DT20,M.DT21,M.DT22,M.DA23,M.DT24,M.DT25,M.DT26,M.DA27,M.DT28 **************************************************************************** List of 21 splayed-apart dinucleotides 1 L.A1 L.U2 angle=100 distance=13.9 ratio=0.76 2 L.U2 L.A3 angle=138 distance=15.4 ratio=0.94 3 L.A3 L.A4 angle=85 distance=13.0 ratio=0.68 4 L.C7 L.G8 angle=129 distance=17.0 ratio=0.90 5 L.U13 L.A14 angle=107 distance=15.5 ratio=0.81 6 L.U19 L.C20 angle=101 distance=15.0 ratio=0.77 7 L.C25 L.C26 angle=100 distance=14.9 ratio=0.77 8 L.U31 L.U32 angle=101 distance=14.9 ratio=0.77 9 L.A37 L.C38 angle=106 distance=15.3 ratio=0.80 10 L.A42 L.G43 angle=107 distance=14.2 ratio=0.80 11 L.U44 L.U45 angle=104 distance=15.3 ratio=0.79 12 L.G52 L.C53 angle=113 distance=14.2 ratio=0.83 13 L.C53 L.C54 angle=100 distance=14.9 ratio=0.77 14 M.DT20 M.DT21 angle=104 distance=15.2 ratio=0.79 15 M.DT25 M.DT26 angle=94 distance=14.6 ratio=0.73 16 N.DG3 N.DT4 angle=93 distance=13.7 ratio=0.72 17 N.DA9 N.DA10 angle=98 distance=13.6 ratio=0.76 18 N.DG15 N.DG16 angle=101 distance=13.8 ratio=0.77 19 N.DG21 N.DA22 angle=117 distance=15.2 ratio=0.85 20 N.DT27 N.DA28 angle=102 distance=14.3 ratio=0.78 21 N.DT32 N.DC33 angle=129 distance=19.4 ratio=0.90 ---------------------------------------------------------------- Summary of 18 splayed-apart units 1 nts=4 AUAA L.A1,L.U2,L.A3,L.A4 2 nts=2 CG L.C7,L.G8 3 nts=2 UA L.U13,L.A14 4 nts=2 UC L.U19,L.C20 5 nts=2 CC L.C25,L.C26 6 nts=2 UU L.U31,L.U32 7 nts=2 AC L.A37,L.C38 8 nts=2 AG L.A42,L.G43 9 nts=2 UU L.U44,L.U45 10 nts=3 GCC L.G52,L.C53,L.C54 11 nts=2 TT M.DT20,M.DT21 12 nts=2 TT M.DT25,M.DT26 13 nts=2 GT N.DG3,N.DT4 14 nts=2 AA N.DA9,N.DA10 15 nts=2 GG N.DG15,N.DG16 16 nts=2 GA N.DG21,N.DA22 17 nts=2 TA N.DT27,N.DA28 18 nts=2 TC N.DT32,N.DC33 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** 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. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5h9f nts=139 [whole] AUAAACCGACGGUAUUGUUCAGAUCCUGGCUUGCCAACAGGAGUUCCCCGCGCCAGCGGGg&TCTGTGCAGTGCTCGATGTTTTATTTAT&CTGTTGGCAAGCCAGGATCTGAACAATACCGTCATCGAGCACTGCACAGA ........(((((.(((((.(((((.(((((.(((((.((.....((((((....))))))&[[[[.[..[[[[[[[[[[..........&)).))))).))))).))))).))))).)))))]]]]]]]]]]..].]]]] >5h9f-L #1 nts=61 0.73(3.23) [chain] RNA AUAAACCGACGGUAUUGUUCAGAUCCUGGCUUGCCAACAGGAGUUCCCCGCGCCAGCGGGg ........(((((.(((((.(((((.(((((.(((((.((.....((((((....)))))) >5h9f-M #2 nts=28 3.56(0.79) [chain] DNA TCTGTGCAGTGCTCGATGTTTTATTTAT [[[[.[..[[[[[[[[[[.......... >5h9f-N #3 nts=50 1.34(2.45) [chain] DNA CTGTTGGCAAGCCAGGATCTGAACAATACCGTCATCGAGCACTGCACAGA )).))))).))))).))))).))))).)))))]]]]]]]]]]..].]]]] **************************************************************************** Summary of structural features of 139 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 A . L.A1 0.007 anti,~C3'-endo,ss-non-loop,splayed-apart 2 U . L.U2 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 3 A . L.A3 0.006 turn,syn,~C2'-endo,ss-non-loop,phosphate,splayed-apart 4 A . L.A4 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 5 A . L.A5 0.006 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 6 C . L.C6 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 7 C . L.C7 0.008 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 8 G . L.G8 0.016 syn,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 9 A ( L.A9 0.009 turn,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 10 C ( L.C10 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 11 G ( L.G11 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 G ( L.G12 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor 13 U ( L.U13 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 14 A . L.A14 0.009 syn,~C3'-endo,BI,non-pair-contact,internal-loop,phosphate,splayed-apart 15 U ( L.U15 0.007 turn,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 16 U ( L.U16 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 17 G ( L.G17 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 U ( L.U18 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor 19 U ( L.U19 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 20 C . L.C20 0.010 syn,~C3'-endo,BI,non-stack,non-pair-contact,internal-loop,phosphate,splayed-apart 21 A ( L.A21 0.009 turn,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 22 G ( L.G22 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 23 A ( L.A23 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor,phosphate 24 U ( L.U24 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor 25 C ( L.C25 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 26 C . L.C26 0.011 syn,~C3'-endo,BI,non-stack,non-pair-contact,internal-loop,phosphate,splayed-apart 27 U ( L.U27 0.010 turn,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 28 G ( L.G28 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 G ( L.G29 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 30 C ( L.C30 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor 31 U ( L.U31 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 32 U . L.U32 0.013 syn,~C3'-endo,BI,non-stack,non-pair-contact,internal-loop,phosphate,splayed-apart 33 G ( L.G33 0.007 turn,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 34 C ( L.C34 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 35 C ( L.C35 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 36 A ( L.A36 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,cap-acceptor 37 A ( L.A37 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,splayed-apart 38 C . L.C38 0.016 ~C3'-endo,non-stack,non-pair-contact,internal-loop,phosphate,splayed-apart 39 A ( L.A39 0.005 turn,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate 40 G ( L.G40 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 41 G . L.G41 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop 42 A . L.A42 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 43 G . L.G43 0.005 syn,~C3'-endo,non-stack,ss-non-loop,splayed-apart 44 U . L.U44 0.006 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 45 U . L.U45 0.004 anti,~C2'-endo,non-canonical,multiplet,ss-non-loop,splayed-apart 46 C ( L.C46 0.004 anti,~C3'-endo,canonical,non-canonical,helix-end,stem-end,multiplet 47 C ( L.C47 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 48 C ( L.C48 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 49 C ( L.C49 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 50 G ( L.G50 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 51 C ( L.C51 0.000 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 52 G . L.G52 0.001 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 53 C . L.C53 0.001 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 54 C . L.C54 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart 55 A . L.A55 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor 56 G ) L.G56 0.002 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,hairpin-loop,cap-donor 57 C ) L.C57 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 58 G ) L.G58 0.007 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 59 G ) L.G59 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 60 G ) L.G60 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 61 g ) L.23G61 0.081 modified,anti,canonical,non-pair-contact,helix-end,stem-end,multiplet 62 T [ M.DT1 0.002 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 63 C [ M.DC2 0.002 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 64 T [ M.DT3 0.006 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 65 G [ M.DG4 0.018 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 66 T . M.DT5 0.006 anti,non-canonical,non-pair-contact,helix,internal-loop 67 G [ M.DG6 0.015 pseudoknotted,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix,internal-loop 68 C . M.DC7 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 69 A . M.DA8 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 70 G [ M.DG9 0.017 pseudoknotted,anti,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 71 T [ M.DT10 0.003 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 72 G [ M.DG11 0.007 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 73 C [ M.DC12 0.002 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 74 T [ M.DT13 0.004 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 75 C [ M.DC14 0.001 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 76 G [ M.DG15 0.001 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 77 A [ M.DA16 0.001 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 78 T [ M.DT17 0.005 pseudoknotted,anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 79 G [ M.DG18 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 80 T . M.DT19 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 81 T . M.DT20 0.002 anti,BI,non-stack,ss-non-loop,phosphate,splayed-apart 82 T . M.DT21 0.004 anti,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 83 T . M.DT22 0.002 anti,non-pair-contact,ss-non-loop 84 A . M.DA23 0.005 syn,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 85 T . M.DT24 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 86 T . M.DT25 0.003 anti,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 87 T . M.DT26 0.005 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 88 A . M.DA27 0.005 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 89 T . M.DT28 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 90 C ) N.DC1 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 91 T ) N.DT2 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 92 G . N.DG3 0.006 syn,~C2'-endo,internal-loop,splayed-apart 93 T ) N.DT4 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 94 T ) N.DT5 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 95 G ) N.DG6 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 96 G ) N.DG7 0.006 anti,BI,canonical,non-pair-contact,helix,stem 97 C ) N.DC8 0.006 anti,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 98 A . N.DA9 0.007 anti,~C2'-endo,internal-loop,splayed-apart 99 A ) N.DA10 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,splayed-apart 100 G ) N.DG11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 101 C ) N.DC12 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 102 C ) N.DC13 0.005 anti,BI,canonical,non-pair-contact,helix,stem 103 A ) N.DA14 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 104 G . N.DG15 0.006 syn,~C2'-endo,internal-loop,phosphate,splayed-apart 105 G ) N.DG16 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 106 A ) N.DA17 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 107 T ) N.DT18 0.006 anti,BI,canonical,non-pair-contact,helix,stem 108 C ) N.DC19 0.006 anti,BI,canonical,non-pair-contact,helix,stem 109 T ) N.DT20 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 110 G . N.DG21 0.010 syn,~C2'-endo,internal-loop,phosphate,splayed-apart 111 A ) N.DA22 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,splayed-apart 112 A ) N.DA23 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 113 C ) N.DC24 0.005 anti,BI,canonical,non-pair-contact,helix,stem 114 A ) N.DA25 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 115 A ) N.DA26 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 116 T . N.DT27 0.005 syn,~C2'-endo,internal-loop,splayed-apart 117 A ) N.DA28 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,phosphate,splayed-apart 118 C ) N.DC29 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 119 C ) N.DC30 0.003 anti,BI,canonical,non-pair-contact,helix,stem 120 G ) N.DG31 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 121 T ) N.DT32 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 122 C ] N.DC33 0.004 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate,splayed-apart 123 A ] N.DA34 0.007 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 124 T ] N.DT35 0.006 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 125 C ] N.DC36 0.003 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 126 G ] N.DG37 0.004 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 127 A ] N.DA38 0.005 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 128 G ] N.DG39 0.016 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 129 C ] N.DC40 0.014 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 130 A ] N.DA41 0.004 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 131 C ] N.DC42 0.019 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 132 T . N.DT43 0.004 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 133 G . N.DG44 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 134 C ] N.DC45 0.003 pseudoknotted,anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,internal-loop,phosphate 135 A . N.DA46 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 136 C ] N.DC47 0.014 pseudoknotted,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 137 A ] N.DA48 0.007 pseudoknotted,anti,canonical,non-pair-contact,helix,stem,coaxial-stack 138 G ] N.DG49 0.005 pseudoknotted,anti,canonical,non-pair-contact,helix,stem,coaxial-stack 139 A ] N.DA50 0.003 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,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-hairpins.pdb -- an ensemble of hairpin loops 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