This analysis is straightforward, and takes virtually no time. The command is shown in the output file as well:
x3dna-dssr -i=1ehz.pdb --u-turn --non-pair --po4 -o=1ehz.outFor completeness, here is the original
1ehz.out file included in the Supplementary Data file of the DSSR paper.
****************************************************************************
DSSR: an Integrated Software Tool for
Dissecting the Spatial Structure of RNA
v1.2.8-2015jun15 by xiangjun@x3dna.org
This program 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.
****************************************************************************
Note: Each nucleotide is identified by model:chainId.name#, where the
'model:' portion is omitted if no model number is available (as
is often the case for x-ray crystal structures in the PDB). So a
common example 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=1ehz.pdb --u-turn --non-pair --po4 -o=1ehz.out
Date and time: Mon Jun 15 02:58:49 2015
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 -- n/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 -- n/a 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 -- n/a tSW tm+W
18 A.G18 A.PSU55 G+P -- n/a 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 -- n/a cWW cW-W
27 A.OMC32 A.A38 c-A -- n/a c.W c.-W
28 A.U33 A.A36 U-A -- n/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 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[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 -- n/a 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 -- n/a tHS tM-m
2 A.A38 A.OMC32 A-c -- n/a cW. cW-.
3 A.PSU39 A.A31 P-A -- n/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 -- n/a tSW tm+W
****************************************************************************
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=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 92 non-pairing interactions
1 A.G1 A.C2 stacking: 5.4(2.6)--pm(>>,forward) H-bonds[1]: "OP2*OP2[2.99]"
2 A.G1 A.A73 stacking: 2.4(1.2)--mm(<>,outward)
3 A.C2 A.G3 stacking: 0.5(0.0)--pm(>>,forward)
4 A.G3 A.G4 stacking: 3.2(1.8)--pm(>>,forward)
5 A.G3 A.G71 stacking: 2.6(0.3)--mm(<>,outward)
6 A.G4 A.A5 stacking: 5.6(3.5)--pm(>>,forward)
7 A.A5 A.U6 stacking: 5.9(4.3)--pm(>>,forward)
8 A.U6 A.U7 stacking: 0.6(0.0)--pm(>>,forward)
9 A.U7 A.5MC49 stacking: 1.2(0.0)--pm(>>,forward) H-bonds[1]: "O2'(hydroxyl)-OP2[2.68]"
10 A.U8 A.C13 stacking: 2.0(0.0)--pp(><,inward)
11 A.U8 A.G15 stacking: 0.5(0.0)--mm(<>,outward)
12 A.A9 A.C11 H-bonds[1]: "O2'(hydroxyl)-N4(amino)[2.90]"
13 A.A9 A.C13 H-bonds[1]: "OP2-N4(amino)[3.01]"
14 A.A9 A.G22 stacking: 0.1(0.0)--mp(<<,backward)
15 A.A9 A.G45 stacking: 1.6(0.5)--pp(><,inward)
16 A.A9 A.7MG46 stacking: 1.6(0.7)--mm(<>,outward) H-bonds[1]: "O5'-N2(amino)[3.34]"
17 A.2MG10 A.C11 stacking: 4.2(1.3)--pm(>>,forward)
18 A.2MG10 A.M2G26 stacking: 1.0(0.0)--mm(<>,outward)
19 A.C11 A.U12 stacking: 0.9(0.0)--pm(>>,forward)
20 A.U12 A.C13 stacking: 1.3(0.3)--pm(>>,forward)
21 A.A14 A.G15 stacking: 2.4(0.8)--pm(>>,forward)
22 A.A14 A.G22 stacking: 1.9(0.1)--mm(<>,outward)
23 A.G15 A.H2U16 stacking: 0.4(0.0)--pm(>>,forward)
24 A.G15 A.U59 stacking: 0.4(0.0)--pm(>>,forward)
25 A.H2U16 A.C60 stacking: 1.4(0.0)--pm(>>,forward) H-bonds[1]: "O2'(hydroxyl)-N3[3.46]"
26 A.H2U17 A.G18 H-bonds[1]: "O2'(hydroxyl)-OP1[2.97]"
27 A.G18 A.G57 stacking: 4.3(1.5)--pp(><,inward) H-bonds[3]: "O3'-N2(amino)[3.29],O2'(hydroxyl)-N1(imino)[3.04],O2'(hydroxyl)-N2(amino)[2.71]"
28 A.G18 A.1MA58 stacking: 8.3(3.6)--mm(<>,outward) H-bonds[2]: "N2(amino)-O5'[3.22],N2(amino)-O4'[3.11]"
29 A.G19 A.G57 stacking: 3.3(0.9)--mm(<>,outward) H-bonds[1]: "O4'-N2(amino)[3.17]"
30 A.G19 A.C60 H-bonds[1]: "OP1-N4(amino)[3.27]"
31 A.G20 A.A21 H-bonds[1]: "OP1*OP2[2.74]"
32 A.G20 A.G22 H-bonds[1]: "N2(amino)-O4'[3.24]"
33 A.A21 A.G22 H-bonds[1]: "O2'(hydroxyl)-O4'[3.44]"
34 A.A21 A.7MG46 stacking: 5.0(2.1)--pp(><,inward)
35 A.A21 A.C48 stacking: 5.9(2.9)--mm(<>,outward)
36 A.G22 A.A23 stacking: 1.1(0.1)--pm(>>,forward)
37 A.A23 A.G24 stacking: 4.1(3.3)--pm(>>,forward)
38 A.G24 A.C25 stacking: 7.5(4.2)--pm(>>,forward)
39 A.C25 A.M2G26 stacking: 2.0(1.0)--pm(>>,forward)
40 A.M2G26 A.C27 stacking: 6.8(3.6)--pm(>>,forward)
41 A.C27 A.C28 stacking: 0.9(0.1)--pm(>>,forward)
42 A.C28 A.G43 stacking: 0.2(0.0)--mm(<>,outward)
43 A.A29 A.G30 stacking: 2.4(2.2)--pm(>>,forward)
44 A.A29 A.G42 stacking: 2.8(1.6)--mm(<>,outward)
45 A.G30 A.A31 stacking: 6.3(3.5)--pm(>>,forward)
46 A.G30 A.U41 stacking: 0.8(0.0)--mm(<>,outward)
47 A.A31 A.OMC32 stacking: 6.2(4.1)--pm(>>,forward)
48 A.OMC32 A.U33 stacking: 3.6(1.3)--pm(>>,forward)
49 A.U33 A.A35 H-bonds[1]: "O2'(hydroxyl)-N7[2.37]"
50 A.U33 A.YYG37 H-bonds[1]: "O2'(hydroxyl)-O22[3.41]"
51 A.OMG34 A.A35 stacking: 6.0(4.1)--pm(>>,forward) H-bonds[1]: "O2'(hydroxyl)-O4'[3.33]"
52 A.A35 A.A36 stacking: 4.7(2.1)--pm(>>,forward)
53 A.A36 A.YYG37 stacking: 5.3(3.9)--pm(>>,forward) H-bonds[4]: "O2'(hydroxyl)-O4'[2.49],N6(amino)-O17[3.25],N6(amino)*N20[2.94],N6(amino)-O22[3.25]"
54 A.YYG37 A.A38 stacking: 7.7(3.5)--pm(>>,forward)
55 A.A38 A.PSU39 stacking: 5.9(4.1)--pm(>>,forward)
56 A.PSU39 A.5MC40 stacking: 5.4(1.1)--pm(>>,forward)
57 A.G42 A.G43 stacking: 3.3(1.8)--pm(>>,forward)
58 A.G43 A.A44 stacking: 4.7(2.9)--pm(>>,forward)
59 A.A44 A.G45 stacking: 5.4(2.5)--pm(>>,forward)
60 A.7MG46 A.C48 H-bonds[1]: "O2'(hydroxyl)-OP2[3.55]"
61 A.U47 A.5MC49 H-bonds[1]: "O2'(hydroxyl)-O3'[3.21]"
62 A.U47 A.U50 H-bonds[1]: "O2'(hydroxyl)-OP1[2.71]"
63 A.C48 A.5MC49 H-bonds[1]: "O2'(hydroxyl)-OP1[3.13]"
64 A.C48 A.U59 H-bonds[1]: "O2'(hydroxyl)-O2'(hydroxyl)[3.07]"
65 A.U50 A.G51 stacking: 0.4(0.0)--pm(>>,forward)
66 A.U50 A.G65 stacking: 0.4(0.0)--mm(<>,outward)
67 A.G51 A.U52 stacking: 6.8(4.0)--pm(>>,forward)
68 A.G51 A.A64 stacking: 2.5(1.1)--mm(<>,outward)
69 A.G53 A.5MU54 stacking: 7.9(3.4)--pm(>>,forward)
70 A.G53 A.A62 stacking: 4.2(2.0)--mm(<>,outward)
71 A.5MU54 A.PSU55 stacking: 5.7(2.2)--pm(>>,forward)
72 A.PSU55 A.G57 H-bonds[1]: "O2'(hydroxyl)-N7[2.72]"
73 A.PSU55 A.1MA58 H-bonds[1]: "N3-OP2[2.77]"
74 A.C56 A.G57 stacking: 1.9(1.2)--pm(>>,forward)
75 A.1MA58 A.C60 H-bonds[1]: "O2'(hydroxyl)-OP2[2.42]"
76 A.1MA58 A.C61 stacking: 4.8(1.3)--pm(>>,forward)
77 A.U59 A.C60 stacking: 6.7(4.2)--pm(>>,forward)
78 A.C60 A.C61 H-bonds[1]: "OP1-N4(amino)[3.12]"
79 A.A62 A.C63 stacking: 4.7(3.0)--pm(>>,forward)
80 A.C63 A.A64 stacking: 0.6(0.0)--pm(>>,forward)
81 A.A64 A.G65 stacking: 4.0(2.9)--pm(>>,forward)
82 A.G65 A.A66 stacking: 3.3(1.7)--pm(>>,forward)
83 A.A66 A.A67 stacking: 4.7(3.9)--pm(>>,forward)
84 A.A67 A.U68 stacking: 4.5(3.1)--pm(>>,forward)
85 A.U68 A.U69 stacking: 2.6(1.0)--pm(>>,forward)
86 A.U69 A.C70 stacking: 0.4(0.0)--pm(>>,forward) H-bonds[1]: "O2'(hydroxyl)-O4'[3.16]"
87 A.C70 A.G71 stacking: 1.4(0.2)--pm(>>,forward)
88 A.G71 A.C72 stacking: 7.4(4.2)--pm(>>,forward)
89 A.C72 A.A73 stacking: 0.3(0.1)--pm(>>,forward)
90 A.A73 A.C74 stacking: 6.0(4.0)--pm(>>,forward)
91 A.C74 A.C75 stacking: 4.8(2.5)--pm(>>,forward)
92 A.C75 A.A76 H-bonds[1]: "O5'*OP1[3.27]"
****************************************************************************
List of 11 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
****************************************************************************
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=10; [8]; linked by [#2]
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]
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]
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]
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 2 U-turns
1 A.U33-A.A36 H-bonds[1]: "N3(imino)-OP2[2.80]" nts=6 cUgAAg A.OMC32,A.U33,A.OMG34,A.A35,A.A36,A.YYG37
2 A.PSU55-A.1MA58 H-bonds[1]: "N3-OP2[2.77]" nts=6 tPCGaU A.5MU54,A.PSU55,A.C56,A.G57,A.1MA58,A.U59
****************************************************************************
List of 18 phosphate interactions
1 A.U7 OP1-hbonds[1]: "MG@A.MG580[2.60]"
2 A.A9 OP2-hbonds[1]: "N4@A.C13[3.01]"
3 A.A14 OP2-hbonds[1]: "MG@A.MG580[1.93]"
4 A.H2U16 OP2-cap: "A.H2U16"
5 A.G18 OP1-hbonds[1]: "O2'@A.H2U17[2.97]"
6 A.G19 OP1-hbonds[2]: "N4@A.C60[3.27],MN@A.MN530[2.19]"
7 A.G20 OP1-hbonds[1]: "MG@A.MG540[2.07]"
8 A.A21 OP2-hbonds[1]: "MG@A.MG540[2.11]"
9 A.A23 OP2-hbonds[1]: "N6@A.A9[3.12]"
10 A.A35 OP2-cap: "A.U33"
11 A.A36 OP2-hbonds[1]: "N3@A.U33[2.80]"
12 A.YYG37 OP2-hbonds[1]: "MG@A.MG590[2.53]"
13 A.C48 OP2-hbonds[1]: "O2'@A.7MG46[3.55]"
14 A.5MC49 OP1-hbonds[1]: "O2'@A.C48[3.13]" OP2-hbonds[1]: "O2'@A.U7[2.68]"
15 A.U50 OP1-hbonds[1]: "O2'@A.U47[2.71]"
16 A.G57 OP2-cap: "A.PSU55"
17 A.1MA58 OP2-hbonds[1]: "N3@A.PSU55[2.77]"
18 A.C60 OP1-hbonds[1]: "N4@A.C61[3.12]" OP2-hbonds[1]: "O2'@A.1MA58[2.42]"
****************************************************************************
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 [chain] RNA
GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAPcUGGAGgUCcUGUGtPCGaUCCACAGAAUUCGCACCA
(((((((..((((.....[..)))).((((.........)))).....(((((..]....))))))))))))....
****************************************************************************
List of 12 additional files
1 dssr-stems.pdb -- an ensemble of stems
2 dssr-helices.pdb -- an ensemble of helices (coaxial stacking)
3 dssr-pairs.pdb -- an ensemble of base pairs
4 dssr-multiplets.pdb -- an ensemble of multiplets
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 connect table format
9 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation
10 dssr-torsions.txt -- backbone torsion angles and suite names
11 dssr-Uturns.pdb -- an ensemble of U-turn motifs
12 dssr-stacks.pdb -- an ensemble of stacks
Note the 14 modified nucleotides (shown below) auto-identified by DSSR:
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.YYG37For simplicity, the
--more option is excluded from the sample DSSR run. Otherwise, neat listings would be distracted by additional auxiliary parameters. For example, the section listing base pairs (without specifying
--more as in the above
1ehz.out file) is shown below:
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
......
With the
--more option, it would become
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
[-167.8(anti) ~C3'-endo lambda=51.3] [-161.6(anti) ~C3'-endo lambda=56.2]
d(C1'-C1')=10.58 d(N1-N9)=8.85 d(C6-C8)=9.75 tor(C1'-N1-N9-C1')=-0.7
H-bonds[3]: "O6(carbonyl)-N4(amino)[2.83],N1(imino)-N3[2.88],N2(amino)-O2(carbonyl)[2.84]"
bp-pars: [-0.55 -0.28 -0.43 -6.30 -9.83 -0.70]
2 A.C2 A.G71 C-G WC 19-XIX cWW cW-W
[-163.8(anti) ~C3'-endo lambda=53.0] [-162.8(anti) ~C3'-endo lambda=52.7]
d(C1'-C1')=10.83 d(N1-N9)=9.06 d(C6-C8)=9.93 tor(C1'-N1-N9-C1')=-8.3
H-bonds[3]: "O2(carbonyl)-N2(amino)[3.01],N3-N1(imino)[2.97],N4(amino)-O6(carbonyl)[2.86]"
bp-pars: [0.13 -0.08 0.03 -7.96 -10.30 -2.67]
......More informative, but less intuitive. As noted in the User Manual, "There is more to DSSR than meets the eye. By connecting dots in RNA structural bioinformatics, the program makes many common tasks simple and advanced applications feasible."
Topic: Output of a sample DSSR run on yeast phenylalanine tRNA (1ehz) (Read 31559 times)