1.5 | 1.6

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: 3NPB → 4KQY.

No new PDB files have been added.

Obsolete: 3NPB → 4KQY.

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

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.9	226	GNRA Hairpin motifs
2	HL_18781.4	20	Double sheared (tSH) with U-turn
3	HL_17723.4	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.

Removed motif groups

#	Motif id	Instances	Description

Added motif groups

#	Motif id	Instances	Description