Changes in PDB files used for clustering

Release 1.5 has 212 PDB files, release 1.6 has 212 PDB files, 211 of them are identical.

1 equivalence classes changed representatives: 3NPB4KQY.

No new PDB files have been added.

Obsolete: 3NPB4KQY.

Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.

Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.

PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.

Redistribution of motif instances

Loading the Sankey diagram...

Changes in motif groups

Release 1.5 has 249 motif groups, release 1.6 has 249 motif groups, 246 of them are identical.

3 motif groups were updated, 0 groups are present only in release 1.5, 0 groups are only in release 1.6.

Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:

Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey

Hover over the links connecting the motif groups to see which motif instances were exchanged.


Identical motif groups

#Motif idInstancesDescription
1HL_72498.964T-loops with two bulged bases
2HL_39895.635UNCG Hairpin motifs
3HL_91226.317Kissing Hairpin motif
4HL_97270.315T-loops with 1 bulged base
5HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6HL_74465.212tRNA Anti-Codon loop
7HL_49036.312GNRA with one bulged base
8HL_48039.211MS2 virus RNA Hairpin
9HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
10HL_27271.110LSU Helix 96 (H96) Hairpin Loop
11HL_46175.21016S helix 23 and 24 hairpin loops
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_56824.210LSU Helix 60A. LSU Helix 63A.
14HL_80459.39
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_82294.38SSU Helix 37 (h37) Hairpin loop.
17HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18HL_34027.285S Loop C - Upper part of Hairpin Loop.
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
22HL_57514.26Two base, cross-stacked hairpin loop
23HL_41833.26LSU Helix 81 (H81) Hairpin Loop
24HL_87136.26LSU Helix 39A Hairpin loop
25HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
26HL_70420.26LSU Helix 97 Hairpin loop
27HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
28HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
29HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_18156.26LSU Helix 72 (H72) Hairpin Loop
31HL_42677.16
32HL_46489.26LSU H89 Hairpin Loop
33HL_39942.26LSU Helix 91 (H91) Hairpin Loop
34HL_75579.26
35HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
36HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
37HL_45018.35Hairpin-Hairpin Interacting HL
38HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
39HL_06643.25tRNA D-loop. Sec tRNA
40HL_88311.25LSU Helix 35 (H35) Hairpin Loop
41HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
42HL_72273.15tRNA D-loop
43HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
45HL_47784.24SSU Central Pseudoknot (forms helix 2)
46HL_64543.24SSU Helix 31 (h31) Hairpin Loop
47HL_11376.14LSU Helix 8 (H8) Hairpin Loop
48HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
49HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
50HL_98523.24GNRA-like. Closed by tSH UC.
51HL_62881.14RNase P Structured Hairpin Loop
52HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
53HL_29831.14GNRA-like with bulged base.
54HL_08382.23
55HL_13707.23cSH AA Platform containing Hairpin Loop
56HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
57HL_41827.13
58HL_68697.23
59HL_19221.23
60HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
61HL_90579.23
62HL_42077.23LSU Helix 28 (H28) Hairpin Loop
63HL_58083.23
64HL_61547.43
65HL_76036.33LSU Helix 8 (H8) Hairpin Loop
66HL_23182.13
67HL_32644.13LSU Helix 69 (H69) Hairpin Loop
68HL_76766.23
69HL_25124.13tSW GA closed tetraloops
70HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
71HL_80492.23tRNA D-loop
72HL_27429.33
73HL_74686.13SSU Central Pseudoknot (forms helix 2)
74HL_12595.23
75HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
76HL_78361.13
77HL_42687.33
78HL_21545.12LSU Helix 96 (H96) Hairpin Loop
79HL_24473.32tRNA D-loop
80HL_26143.12
81HL_38130.22
82HL_54751.22
83HL_60200.12
84HL_86398.12
85HL_90542.12
86HL_93771.12tRNA T-loop distorted by RS binding
87HL_99633.12
88HL_05361.12
89HL_26495.12
90HL_64371.22
91HL_94578.12
92HL_06122.12
93HL_23129.12
94HL_50312.12
95HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
96HL_06312.12
97HL_16770.12
98HL_19399.12
99HL_24711.12
100HL_84353.12
101HL_87554.12
102HL_91693.12
103HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
104HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
105HL_74559.12Two base, cross-stacked hairpin loop
106HL_91872.12
107HL_06997.12
108HL_17790.12UNCG-like. cWW Closing pair.
109HL_19528.12
110HL_23290.12
111HL_42553.12
112HL_81752.12
113HL_98577.12
114HL_33451.12
115HL_53753.12
116HL_62967.12
117HL_65924.12
118HL_75575.12
119HL_96915.12
120HL_98833.22
121HL_03791.12
122HL_18587.12
123HL_49210.12
124HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
125HL_04194.11
126HL_19132.11
127HL_30008.11
128HL_42969.11
129HL_47337.11
130HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
131HL_63304.11
132HL_66467.11
133HL_78507.11
134HL_10116.11Kink-turn-like Hairpin Loop
135HL_13786.11
136HL_30128.11
137HL_38138.11
138HL_44390.11
139HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
140HL_55202.11U2B"-U2A" binding hairpin loop
141HL_57843.11
142HL_60203.11
143HL_66877.11cSH GU/cWS double platform, intercalation site
144HL_68733.11LSU Yeast Hairpin Loop
145HL_73465.11
146HL_75850.11
147HL_83865.11
148HL_97499.11
149HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
150HL_19226.11
151HL_24707.11
152HL_26579.11
153HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
154HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
155HL_44522.11
156HL_55272.11
157HL_69403.11GNRA-like
158HL_73972.11
159HL_79902.11
160HL_84289.11
161HL_87223.11
162HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
163HL_97784.11
164HL_00090.11
165HL_34440.11
166HL_39422.11
167HL_42345.11
168HL_52540.11
169HL_58223.11
170HL_65071.11
171HL_67000.11
172HL_95049.11Two base, cross-stacked hairpin loop
173HL_97971.11
174HL_01418.11
175HL_17537.11
176HL_19452.11tRNA D-loop
177HL_23195.11
178HL_27397.11
179HL_33277.11
180HL_35200.11
181HL_39486.11
182HL_45411.11
183HL_56775.11
184HL_58601.11
185HL_62880.11
186HL_67761.11
187HL_70912.11
188HL_77692.11tRNA D-loop
189HL_84888.11T-loop like but without tWH UA
190HL_95716.11
191HL_25175.11
192HL_35865.11
193HL_48480.11
194HL_53015.11
195HL_56809.11
196HL_59182.11
197HL_65802.11
198HL_71607.11
199HL_78228.11
200HL_85018.11
201HL_93530.11
202HL_03785.11LSU Helix 8 (H8) Hairpin Loop
203HL_07315.11
204HL_25195.11
205HL_27819.11
206HL_36842.11
207HL_59604.11
208HL_68435.11
209HL_82243.11
210HL_88960.11
211HL_93567.11
212HL_07915.11
213HL_12706.11
214HL_20806.11
215HL_24108.11
216HL_25197.11
217HL_33640.11
218HL_37962.11
219HL_46570.11
220HL_53789.11
221HL_57217.11cHS platform Intercalation Site
222HL_59610.11
223HL_62970.11
224HL_68579.11
225HL_78420.11
226HL_82288.11
227HL_90102.11Kink-turn-like Hairpin Loop
228HL_93633.11
229HL_96994.11
230HL_99207.11Tetrahymena LSU hairpin poorly modeled

Updated motif groups

#Motif idInstancesDescription
1HL_67042.9226GNRA Hairpin motifs
2HL_18781.420Double sheared (tSH) with U-turn
3HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription