1.11 | 1.12

Changes in PDB files used for clustering

Release 1.11 has 224 PDB files, release 1.12 has 226 PDB files, 224 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 1.12: 4C4W, 4OO8.

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 1.11 has 253 motif groups, release 1.12 has 253 motif groups, 249 of them are identical.

4 motif groups were updated, 0 groups are present only in release 1.11, 0 groups are only in release 1.12.

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 id	Instances	Description
1	HL_72498.12	66	T-loops with two bulged bases
2	HL_39895.6	35	UNCG Hairpin motifs
3	HL_18781.4	20	Double sheared (tSH) with U-turn
4	HL_91226.3	17	Kissing Hairpin motif
5	HL_97270.3	15	T-loops with 1 bulged base
6	HL_52574.3	14	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7	HL_74465.5	13	tRNA Anti-Codon loop
8	HL_49036.3	12	GNRA with one bulged base
9	HL_27271.2	12	LSU Helix 96 (H96) Hairpin Loop
10	HL_48039.2	11	MS2 virus RNA Hairpin
11	HL_46175.2	10	16S helix 23 and 24 hairpin loops
12	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
13	HL_68081.3	10	LSU Helix 20 Hairpin loop
14	HL_17723.4	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
15	HL_80459.3	9
16	HL_87844.2	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17	HL_24544.2	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
19	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
20	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
21	HL_33402.3	8	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
22	HL_42677.2	7
23	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
24	HL_46489.2	6	LSU H89 Hairpin Loop
25	HL_70420.2	6	LSU Helix 97 Hairpin loop
26	HL_87136.2	6	LSU Helix 39A Hairpin loop
27	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
28	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
29	HL_57514.2	6	Two base, cross-stacked hairpin loop
30	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
31	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
32	HL_75579.2	6
33	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
34	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
35	HL_72273.1	5	tRNA D-loop
36	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
37	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
38	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
39	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
40	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
41	HL_45018.3	5	Hairpin-Hairpin Interacting HL
42	HL_82538.1	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
43	HL_62228.3	5	LSU Helix 35A (H35A) Hairpin Loop
44	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45	HL_29831.1	4	GNRA-like with bulged base.
46	HL_62881.1	4	RNase P Structured Hairpin Loop
47	HL_47784.2	4	SSU Central Pseudoknot (forms helix 2)
48	HL_98523.2	4	GNRA-like. Closed by tSH UC.
49	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
50	HL_25124.2	4	tSW GA closed tetraloops
51	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
52	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
53	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
54	HL_86115.1	4
55	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
56	HL_06997.2	3
57	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
58	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
59	HL_76766.4	3
60	HL_90579.3	3	LSU Helix 69 (H69) Hairpin Loop
61	HL_08382.2	3
62	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
63	HL_80492.2	3	tRNA D-loop
64	HL_19221.2	3
65	HL_41827.1	3
66	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
67	HL_78361.1	3
68	HL_23182.1	3
69	HL_27429.3	3
70	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
71	HL_58083.2	3
72	HL_68697.2	3
73	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
74	HL_98833.3	3
75	HL_35619.2	3
76	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
77	HL_18587.1	2
78	HL_33451.1	2
79	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
80	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
81	HL_86398.1	2
82	HL_90542.1	2
83	HL_93771.1	2	tRNA T-loop distorted by RS binding
84	HL_99633.1	2
85	HL_24473.3	2	tRNA D-loop
86	HL_26495.1	2
87	HL_42553.1	2
88	HL_65249.1	2
89	HL_74505.1	2
90	HL_84353.1	2
91	HL_94578.1	2
92	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
93	HL_49210.1	2
94	HL_62967.1	2
95	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
96	HL_74559.1	2	Two base, cross-stacked hairpin loop
97	HL_16770.1	2
98	HL_21675.3	2	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
99	HL_38130.2	2
100	HL_54751.2	2
101	HL_87554.1	2
102	HL_91693.1	2
103	HL_23129.1	2
104	HL_24711.1	2
105	HL_60200.1	2
106	HL_65924.1	2
107	HL_91872.1	2
108	HL_19399.1	2
109	HL_32644.2	2	LSU Helix 69 (H69) Hairpin Loop
110	HL_50312.1	2
111	HL_63941.1	2
112	HL_98577.1	2
113	HL_05361.1	2
114	HL_17790.1	2	UNCG-like. cWW Closing pair.
115	HL_42094.1	2
116	HL_64371.2	2
117	HL_96915.1	2
118	HL_06122.1	2
119	HL_19528.1	2
120	HL_23290.1	2
121	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
122	HL_12706.1	1
123	HL_24108.1	1
124	HL_25197.1	1
125	HL_29196.1	1
126	HL_35865.1	1
127	HL_48480.1	1
128	HL_56809.1	1
129	HL_59182.1	1
130	HL_62880.1	1
131	HL_65071.1	1
132	HL_69403.1	1	GNRA-like
133	HL_76679.1	1
134	HL_79902.1	1
135	HL_84289.1	1
136	HL_00090.1	1
137	HL_07915.1	1
138	HL_20806.1	1
139	HL_33640.1	1
140	HL_36842.1	1
141	HL_53015.1	1
142	HL_59225.1	1
143	HL_67000.1	1
144	HL_97499.1	1
145	HL_01418.1	1
146	HL_13786.1	1
147	HL_19132.1	1
148	HL_26579.1	1
149	HL_30008.1	1
150	HL_37962.1	1
151	HL_46570.1	1
152	HL_53789.1	1
153	HL_57217.1	1	cHS platform Intercalation Site
154	HL_59604.1	1
155	HL_67761.1	1
156	HL_70912.1	1
157	HL_77692.1	1	tRNA D-loop
158	HL_84768.1	1
159	HL_87223.1	1
160	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
161	HL_97784.1	1
162	HL_10116.1	1	Kink-turn-like Hairpin Loop
163	HL_24707.1	1
164	HL_30128.1	1
165	HL_42969.1	1
166	HL_47337.1	1
167	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
168	HL_59610.1	1
169	HL_62970.1	1
170	HL_65802.1	1
171	HL_78228.1	1
172	HL_82243.1	1
173	HL_84888.1	1	T-loop like but without tWH UA
174	HL_95049.1	1	Two base, cross-stacked hairpin loop
175	HL_97971.1	1
176	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
177	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
178	HL_17537.1	1
179	HL_19226.1	1
180	HL_27397.1	1
181	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
182	HL_38138.1	1
183	HL_44390.1	1
184	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
185	HL_55202.1	1	U2B"-U2A" binding hairpin loop
186	HL_57843.1	1
187	HL_63304.1	1
188	HL_68435.1	1
189	HL_82288.1	1
190	HL_85018.1	1
191	HL_95716.1	1
192	HL_04194.1	1
193	HL_34440.1	1
194	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
195	HL_44522.1	1
196	HL_55272.1	1
197	HL_60203.1	1
198	HL_68579.1	1
199	HL_75850.1	1
200	HL_78420.1	1
201	HL_93263.1	1
202	HL_19452.1	1	tRNA D-loop
203	HL_23195.1	1
204	HL_25175.1	1
205	HL_27819.1	1
206	HL_33277.1	1
207	HL_35200.1	1
208	HL_39422.1	1
209	HL_52116.1	1
210	HL_58223.1	1
211	HL_66467.1	1
212	HL_73465.1	1
213	HL_78507.1	1
214	HL_88960.1	1
215	HL_93530.1	1
216	HL_25195.1	1
217	HL_28676.1	1
218	HL_39486.1	1
219	HL_42345.1	1
220	HL_45411.1	1
221	HL_52540.1	1
222	HL_56775.1	1
223	HL_58601.1	1
224	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
225	HL_68733.1	1	LSU Yeast Hairpin Loop
226	HL_73972.1	1
227	HL_76585.1	1
228	HL_83865.1	1
229	HL_90102.1	1	Kink-turn-like Hairpin Loop
230	HL_93567.1	1
231	HL_96994.1	1
232	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.11	231	GNRA Hairpin motifs
2	HL_75759.4	11
3	HL_15603.2	9	U1A protein-binding Hairpin Loop.
4	HL_06643.3	6	tRNA D-loop. Sec tRNA

Removed motif groups

#	Motif id	Instances	Description

Added motif groups

#	Motif id	Instances	Description