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_49036.211GNRA with one bulged base
10HL_48039.111MS2 virus RNA Hairpin
11HL_56824.210LSU Helix 60A. LSU Helix 63A.
12HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13HL_68081.310LSU Helix 20 Hairpin loop
14HL_80459.210
15HL_46175.11016S helix 23 and 24 hairpin loops
16HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
17HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_28436.39LSU Helix 96 (H96) Hairpin Loop
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_82294.28SSU Helix 37 (h37) Hairpin loop.
21HL_34027.285S Loop C - Upper part of Hairpin Loop.
22HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
23HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
24HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_46489.26LSU H89 Hairpin Loop
26HL_39942.26LSU Helix 91 (H91) Hairpin Loop
27HL_42677.16
28HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
29HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
30HL_70420.26LSU Helix 97 Hairpin loop
31HL_75579.26
32HL_87136.26LSU Helix 39A Hairpin loop
33HL_18156.26LSU Helix 72 (H72) Hairpin Loop
34HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
35HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
36HL_41833.26LSU Helix 81 (H81) Hairpin Loop
37HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
38HL_88311.25LSU Helix 35 (H35) Hairpin Loop
39HL_45018.35Hairpin-Hairpin Interacting HL
40HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
41HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
42HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
43HL_06643.25tRNA D-loop. Sec tRNA
44HL_57514.15Two base, cross-stacked hairpin loop
45HL_72273.15tRNA D-loop
46HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
47HL_64543.14SSU Helix 31 (h31) Hairpin Loop
48HL_98523.14GNRA-like. Closed by tSH UC.
49HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
50HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
51HL_62881.14RNase P Structured Hairpin Loop
52HL_18798.14UNCG-like. cWW Closing pair.
53HL_61547.34
54HL_29831.14GNRA-like with bulged base.
55HL_47784.14SSU Central Pseudoknot (forms helix 2)
56HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
57HL_46794.23
58HL_80492.23tRNA D-loop
59HL_90579.23
60HL_54751.13
61HL_13707.23cSH AA Platform containing Hairpin Loop
62HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
63HL_42687.23
64HL_27429.33
65HL_25124.13tSW GA closed tetraloops
66HL_41827.13
67HL_98833.13
68HL_19221.23
69HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
70HL_08382.23
71HL_42077.23LSU Helix 28 (H28) Hairpin Loop
72HL_58083.23
73HL_32644.13LSU Helix 69 (H69) Hairpin Loop
74HL_78361.13
75HL_23182.13
76HL_74686.13SSU Central Pseudoknot (forms helix 2)
77HL_82253.23
78HL_76036.33LSU Helix 8 (H8) Hairpin Loop
79HL_81752.12
80HL_67367.12
81HL_98577.12
82HL_49210.12
83HL_77555.12
84HL_42553.12
85HL_87554.12
86HL_60200.12
87HL_53753.12
88HL_12595.12
89HL_23290.12
90HL_58687.12
91HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
92HL_06122.12
93HL_57904.12
94HL_24473.32tRNA D-loop
95HL_94578.12
96HL_33451.12
97HL_06312.12
98HL_76766.12
99HL_64371.22
100HL_62967.12
101HL_84353.12
102HL_65924.12
103HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
104HL_50312.12
105HL_57014.12
106HL_26057.12
107HL_03791.12
108HL_16770.12
109HL_38130.22
110HL_44467.12
111HL_99633.12
112HL_96915.12
113HL_45440.12
114HL_75575.12
115HL_05361.12
116HL_97512.12LSU Helix 8 (H8) Hairpin Loop
117HL_19399.12
118HL_68697.12
119HL_24711.12
120HL_26495.12
121HL_67692.12
122HL_55543.11
123HL_77692.11tRNA D-loop
124HL_25197.11
125HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
126HL_87223.11
127HL_58223.11
128HL_19132.11
129HL_91613.11
130HL_70912.11
131HL_13786.11
132HL_13105.11
133HL_25175.11
134HL_95716.11
135HL_71607.11
136HL_66900.11
137HL_31969.11
138HL_96994.11
139HL_17468.11
140HL_52393.11Double tSH (double sheared) with bulged base
141HL_59604.11
142HL_97499.11
143HL_63690.11
144HL_00721.11
145HL_26579.11
146HL_58601.11
147HL_88960.11
148HL_29084.11
149HL_62970.11
150HL_80746.11
151HL_97971.11
152HL_82243.11
153HL_10116.11Kink-turn-like Hairpin Loop
154HL_01418.11
155HL_24108.11
156HL_33524.11tRNA T-loop distorted by RS binding
157HL_30128.11
158HL_48480.11
159HL_37962.11
160HL_65071.11
161HL_44522.11
162HL_66877.11cSH GU/cWS double platform, intercalation site
163HL_85753.11
164HL_62880.11
165HL_04194.11
166HL_78228.11
167HL_35200.11
168HL_69403.11GNRA-like
169HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
170HL_20028.11
171HL_59182.11
172HL_93567.11
173HL_57217.11cHS platform Intercalation Site
174HL_35004.11
175HL_39422.11
176HL_66880.11
177HL_44390.11
178HL_67000.11
179HL_96192.11
180HL_75850.11
181HL_39486.11
182HL_82288.11
183HL_17537.11
184HL_16118.11
185HL_34375.11
186HL_55202.11U2B"-U2A" binding hairpin loop
187HL_38138.11
188HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
189HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
190HL_57923.11
191HL_99779.11
192HL_20806.11
193HL_84289.11
194HL_27397.11
195HL_56809.11
196HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
197HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
198HL_33277.11
199HL_36842.11
200HL_85018.11
201HL_99584.11
202HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
203HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
204HL_07315.11
205HL_45411.11
206HL_19226.11
207HL_52109.11
208HL_95049.11Two base, cross-stacked hairpin loop
209HL_05113.11
210HL_34440.11
211HL_07915.11
212HL_63304.11
213HL_66467.11
214HL_19452.11tRNA D-loop
215HL_08203.11
216HL_38898.11
217HL_56775.11
218HL_12984.11
219HL_33640.11
220HL_53789.11
221HL_78507.11
222HL_20914.11
223HL_45358.11Double hairpin loop based on GGA triple
224HL_42969.11
225HL_79902.11
226HL_30731.11
227HL_27819.11
228HL_00090.11
229HL_55272.11
230HL_47337.11
231HL_68733.11LSU Yeast Hairpin Loop
232HL_99207.11Tetrahymena LSU hairpin poorly modeled
233HL_98233.11
234HL_30008.11
235HL_17008.11Nova-2 KH3 domain binding hairpin
236HL_81295.11UNCG-like. cWW Closing pair.
237HL_59610.11
238HL_65802.11
239HL_35865.11
240HL_24707.11
241HL_25195.11
242HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
243HL_60203.11
244HL_68435.11
245HL_84888.11T-loop like but without tWH UA
246HL_57843.11
247HL_68579.11
248HL_12706.11
249HL_67761.11
250HL_53015.11
251HL_78420.11
252HL_90102.11Kink-turn-like Hairpin Loop
253HL_93530.11
254HL_97784.11
255HL_73465.11
256HL_42345.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription