Changes in PDB files used for clustering

Release 1.3 has 211 PDB files, release 1.4 has 211 PDB files, 211 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

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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_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_68081.310LSU Helix 20 Hairpin loop
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_80459.210
17HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_28436.39LSU Helix 96 (H96) Hairpin Loop
19HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
22HL_15603.18U1A protein-binding Hairpin Loop.
23HL_82294.28SSU Helix 37 (h37) Hairpin loop.
24HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
26HL_75579.26
27HL_18156.26LSU Helix 72 (H72) Hairpin Loop
28HL_42677.16
29HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
30HL_39942.26LSU Helix 91 (H91) Hairpin Loop
31HL_46489.26LSU H89 Hairpin Loop
32HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
33HL_41833.26LSU Helix 81 (H81) Hairpin Loop
34HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
35HL_70420.26LSU Helix 97 Hairpin loop
36HL_87136.26LSU Helix 39A Hairpin loop
37HL_72273.15tRNA D-loop
38HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
39HL_88311.25LSU Helix 35 (H35) Hairpin Loop
40HL_06643.25tRNA D-loop. Sec tRNA
41HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
42HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
43HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
44HL_45018.35Hairpin-Hairpin Interacting HL
45HL_57514.15Two base, cross-stacked hairpin loop
46HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
47HL_61547.34
48HL_18798.14UNCG-like. cWW Closing pair.
49HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
50HL_64543.14SSU Helix 31 (h31) Hairpin Loop
51HL_47784.14SSU Central Pseudoknot (forms helix 2)
52HL_62881.14RNase P Structured Hairpin Loop
53HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
54HL_29831.14GNRA-like with bulged base.
55HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
56HL_98523.14GNRA-like. Closed by tSH UC.
57HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
58HL_13707.23cSH AA Platform containing Hairpin Loop
59HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
60HL_58083.23
61HL_78361.13
62HL_98833.13
63HL_42687.23
64HL_25124.13tSW GA closed tetraloops
65HL_27429.33
66HL_41827.13
67HL_46794.23
68HL_76036.33LSU Helix 8 (H8) Hairpin Loop
69HL_23182.13
70HL_32644.13LSU Helix 69 (H69) Hairpin Loop
71HL_82253.23
72HL_19221.23
73HL_42077.23LSU Helix 28 (H28) Hairpin Loop
74HL_54751.13
75HL_74686.13SSU Central Pseudoknot (forms helix 2)
76HL_90579.23
77HL_08382.23
78HL_80492.23tRNA D-loop
79HL_26495.12
80HL_42553.12
81HL_45440.12
82HL_57904.12
83HL_60200.12
84HL_96915.12
85HL_98577.12
86HL_05361.12
87HL_84353.12
88HL_87554.12
89HL_06122.12
90HL_24711.12
91HL_64371.22
92HL_81752.12
93HL_06312.12
94HL_38130.22
95HL_49210.12
96HL_53753.12
97HL_68697.12
98HL_94578.12
99HL_99633.12
100HL_12595.12
101HL_57014.12
102HL_58687.12
103HL_76766.12
104HL_97512.12LSU Helix 8 (H8) Hairpin Loop
105HL_16770.12
106HL_23290.12
107HL_67367.12
108HL_50312.12
109HL_62967.12
110HL_65924.12
111HL_67692.12
112HL_77555.12
113HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
114HL_03791.12
115HL_19399.12
116HL_24473.32tRNA D-loop
117HL_26057.12
118HL_33451.12
119HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
120HL_75575.12
121HL_04194.11
122HL_10116.11Kink-turn-like Hairpin Loop
123HL_13105.11
124HL_19452.11tRNA D-loop
125HL_30008.11
126HL_33524.11tRNA T-loop distorted by RS binding
127HL_35865.11
128HL_52393.11Double tSH (double sheared) with bulged base
129HL_55543.11
130HL_63304.11
131HL_66467.11
132HL_71607.11
133HL_78228.11
134HL_80746.11
135HL_84289.11
136HL_87223.11
137HL_93530.11
138HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
139HL_24707.11
140HL_26579.11
141HL_30128.11
142HL_33640.11
143HL_36842.11
144HL_48480.11
145HL_56775.11
146HL_60203.11
147HL_63690.11
148HL_66877.11cSH GU/cWS double platform, intercalation site
149HL_68435.11
150HL_81295.11UNCG-like. cWW Closing pair.
151HL_93567.11
152HL_96994.11
153HL_13786.11
154HL_20806.11
155HL_27397.11
156HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
157HL_37962.11
158HL_53015.11
159HL_56809.11
160HL_58223.11
161HL_66900.11
162HL_68579.11
163HL_75850.11
164HL_78420.11
165HL_84888.11T-loop like but without tWH UA
166HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
167HL_99207.11Tetrahymena LSU hairpin poorly modeled
168HL_20914.11
169HL_31969.11
170HL_42969.11
171HL_58601.11
172HL_67000.11
173HL_78507.11
174HL_82243.11
175HL_85018.11
176HL_97499.11
177HL_00090.11
178HL_16118.11
179HL_19132.11
180HL_25175.11
181HL_27819.11
182HL_34375.11
183HL_38138.11
184HL_44390.11
185HL_47337.11
186HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
187HL_53789.11
188HL_62880.11
189HL_65071.11
190HL_68733.11LSU Yeast Hairpin Loop
191HL_73465.11
192HL_88960.11
193HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
194HL_01418.11
195HL_07315.11
196HL_12706.11
197HL_25195.11
198HL_33277.11
199HL_34440.11
200HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
201HL_44522.11
202HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
203HL_57217.11cHS platform Intercalation Site
204HL_59182.11
205HL_65802.11
206HL_69403.11GNRA-like
207HL_79902.11
208HL_82288.11
209HL_85753.11
210HL_90102.11Kink-turn-like Hairpin Loop
211HL_95049.11Two base, cross-stacked hairpin loop
212HL_97784.11
213HL_07915.11
214HL_17468.11
215HL_19226.11
216HL_24108.11
217HL_25197.11
218HL_29084.11
219HL_35004.11
220HL_39422.11
221HL_42345.11
222HL_55202.11U2B"-U2A" binding hairpin loop
223HL_59604.11
224HL_95716.11
225HL_97971.11
226HL_12984.11
227HL_17537.11
228HL_35200.11
229HL_39486.11
230HL_45411.11
231HL_52109.11
232HL_55272.11
233HL_57843.11
234HL_59610.11
235HL_62970.11
236HL_67761.11
237HL_70912.11
238HL_77692.11tRNA D-loop
239HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
240HL_96192.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription