Changes in PDB files used for clustering

Release 1.3 has 216 PDB files, release 1.4 has 216 PDB files, 216 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

No equivalence class representatives have been obsoleted.

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 1.3 has 256 motif groups, release 1.4 has 256 motif groups, 256 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.3, 0 groups are only in release 1.4.

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_67042.7227GNRA Hairpin motifs
2HL_72498.863T-loops with two bulged bases
3HL_39895.535UNCG Hairpin motifs
4HL_18781.220Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_52574.215LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_97270.215T-loops with 1 bulged base
8HL_74465.212tRNA Anti-Codon loop
9HL_48039.111MS2 virus RNA Hairpin
10HL_49036.211GNRA with one bulged base
11HL_68081.310LSU Helix 20 Hairpin loop
12HL_80459.210
13HL_46175.11016S helix 23 and 24 hairpin loops
14HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
15HL_56824.210LSU Helix 60A. LSU Helix 63A.
16HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
17HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_28436.39LSU Helix 96 (H96) Hairpin Loop
19HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
20HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_15603.18U1A protein-binding Hairpin Loop.
22HL_82294.28SSU Helix 37 (h37) Hairpin loop.
23HL_34027.285S Loop C - Upper part of Hairpin Loop.
24HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
26HL_41833.26LSU Helix 81 (H81) Hairpin Loop
27HL_46489.26LSU H89 Hairpin Loop
28HL_39942.26LSU Helix 91 (H91) Hairpin Loop
29HL_42677.16
30HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
31HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
32HL_70420.26LSU Helix 97 Hairpin loop
33HL_75579.26
34HL_87136.26LSU Helix 39A Hairpin loop
35HL_18156.26LSU Helix 72 (H72) Hairpin Loop
36HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
37HL_57514.15Two base, cross-stacked hairpin loop
38HL_72273.15tRNA D-loop
39HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
40HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41HL_88311.25LSU Helix 35 (H35) Hairpin Loop
42HL_45018.35Hairpin-Hairpin Interacting HL
43HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
45HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
46HL_06643.25tRNA D-loop. Sec tRNA
47HL_29831.14GNRA-like with bulged base.
48HL_47784.14SSU Central Pseudoknot (forms helix 2)
49HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
50HL_64543.14SSU Helix 31 (h31) Hairpin Loop
51HL_98523.14GNRA-like. Closed by tSH UC.
52HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
53HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
54HL_62881.14RNase P Structured Hairpin Loop
55HL_18798.14UNCG-like. cWW Closing pair.
56HL_61547.34
57HL_08382.23
58HL_42077.23LSU Helix 28 (H28) Hairpin Loop
59HL_58083.23
60HL_32644.13LSU Helix 69 (H69) Hairpin Loop
61HL_78361.13
62HL_23182.13
63HL_74686.13SSU Central Pseudoknot (forms helix 2)
64HL_82253.23
65HL_76036.33LSU Helix 8 (H8) Hairpin Loop
66HL_46794.23
67HL_80492.23tRNA D-loop
68HL_90579.23
69HL_54751.13
70HL_13707.23cSH AA Platform containing Hairpin Loop
71HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
72HL_42687.23
73HL_27429.33
74HL_25124.13tSW GA closed tetraloops
75HL_41827.13
76HL_98833.13
77HL_19221.23
78HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
79HL_16770.12
80HL_38130.22
81HL_44467.12
82HL_99633.12
83HL_96915.12
84HL_45440.12
85HL_75575.12
86HL_05361.12
87HL_97512.12LSU Helix 8 (H8) Hairpin Loop
88HL_19399.12
89HL_68697.12
90HL_24711.12
91HL_26495.12
92HL_67692.12
93HL_81752.12
94HL_67367.12
95HL_98577.12
96HL_49210.12
97HL_77555.12
98HL_42553.12
99HL_87554.12
100HL_60200.12
101HL_53753.12
102HL_12595.12
103HL_23290.12
104HL_58687.12
105HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
106HL_06122.12
107HL_57904.12
108HL_24473.32tRNA D-loop
109HL_94578.12
110HL_33451.12
111HL_06312.12
112HL_76766.12
113HL_64371.22
114HL_62967.12
115HL_84353.12
116HL_65924.12
117HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
118HL_50312.12
119HL_57014.12
120HL_26057.12
121HL_03791.12
122HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
123HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
124HL_07315.11
125HL_45411.11
126HL_19226.11
127HL_52109.11
128HL_95049.11Two base, cross-stacked hairpin loop
129HL_05113.11
130HL_34440.11
131HL_07915.11
132HL_63304.11
133HL_66467.11
134HL_19452.11tRNA D-loop
135HL_08203.11
136HL_38898.11
137HL_56775.11
138HL_12984.11
139HL_33640.11
140HL_53789.11
141HL_78507.11
142HL_20914.11
143HL_45358.11Double hairpin loop based on GGA triple
144HL_42969.11
145HL_79902.11
146HL_30731.11
147HL_27819.11
148HL_00090.11
149HL_55272.11
150HL_47337.11
151HL_68733.11LSU Yeast Hairpin Loop
152HL_99207.11Tetrahymena LSU hairpin poorly modeled
153HL_98233.11
154HL_30008.11
155HL_17008.11Nova-2 KH3 domain binding hairpin
156HL_81295.11UNCG-like. cWW Closing pair.
157HL_59610.11
158HL_65802.11
159HL_35865.11
160HL_24707.11
161HL_25195.11
162HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
163HL_60203.11
164HL_68435.11
165HL_84888.11T-loop like but without tWH UA
166HL_57843.11
167HL_68579.11
168HL_12706.11
169HL_67761.11
170HL_53015.11
171HL_78420.11
172HL_90102.11Kink-turn-like Hairpin Loop
173HL_93530.11
174HL_97784.11
175HL_73465.11
176HL_42345.11
177HL_55543.11
178HL_77692.11tRNA D-loop
179HL_25197.11
180HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
181HL_87223.11
182HL_58223.11
183HL_19132.11
184HL_91613.11
185HL_70912.11
186HL_13786.11
187HL_13105.11
188HL_25175.11
189HL_95716.11
190HL_71607.11
191HL_66900.11
192HL_31969.11
193HL_96994.11
194HL_17468.11
195HL_52393.11Double tSH (double sheared) with bulged base
196HL_59604.11
197HL_97499.11
198HL_63690.11
199HL_00721.11
200HL_26579.11
201HL_58601.11
202HL_88960.11
203HL_29084.11
204HL_62970.11
205HL_80746.11
206HL_97971.11
207HL_82243.11
208HL_10116.11Kink-turn-like Hairpin Loop
209HL_01418.11
210HL_24108.11
211HL_33524.11tRNA T-loop distorted by RS binding
212HL_30128.11
213HL_48480.11
214HL_37962.11
215HL_65071.11
216HL_44522.11
217HL_66877.11cSH GU/cWS double platform, intercalation site
218HL_85753.11
219HL_62880.11
220HL_04194.11
221HL_78228.11
222HL_35200.11
223HL_69403.11GNRA-like
224HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
225HL_20028.11
226HL_59182.11
227HL_93567.11
228HL_57217.11cHS platform Intercalation Site
229HL_35004.11
230HL_39422.11
231HL_66880.11
232HL_44390.11
233HL_67000.11
234HL_96192.11
235HL_75850.11
236HL_39486.11
237HL_82288.11
238HL_17537.11
239HL_16118.11
240HL_34375.11
241HL_55202.11U2B"-U2A" binding hairpin loop
242HL_38138.11
243HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
244HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
245HL_57923.11
246HL_99779.11
247HL_20806.11
248HL_84289.11
249HL_27397.11
250HL_56809.11
251HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
252HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
253HL_33277.11
254HL_36842.11
255HL_85018.11
256HL_99584.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription