1.5 | 1.6

Changes in PDB files used for clustering

Release 1.5 has 217 PDB files, release 1.6 has 217 PDB files, 216 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_68081.3	10	LSU Helix 20 Hairpin loop
11	HL_46175.2	10	16S helix 23 and 24 hairpin loops
12	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.
13	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
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_33402.3	8	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
19	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
20	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
21	HL_24544.2	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22	HL_57514.2	6	Two base, cross-stacked hairpin loop
23	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
24	HL_70420.2	6	LSU Helix 97 Hairpin loop
25	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
26	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
27	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28	HL_42677.1	6
29	HL_75579.2	6
30	HL_87136.2	6	LSU Helix 39A Hairpin loop
31	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
32	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
33	HL_46489.2	6	LSU H89 Hairpin Loop
34	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
35	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
36	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
37	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
38	HL_62228.3	5	LSU Helix 35A (H35A) Hairpin Loop
39	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40	HL_72273.1	5	tRNA D-loop
41	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
42	HL_45018.3	5	Hairpin-Hairpin Interacting HL
43	HL_06643.2	5	tRNA D-loop. Sec tRNA
44	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
45	HL_47784.2	4	SSU Central Pseudoknot (forms helix 2)
46	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
47	HL_62881.1	4	RNase P Structured Hairpin Loop
48	HL_29831.1	4	GNRA-like with bulged base.
49	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
50	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
51	HL_98523.2	4	GNRA-like. Closed by tSH UC.
52	HL_23971.1	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
53	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
54	HL_21675.1	3	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
55	HL_19221.2	3
56	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
57	HL_12595.2	3
58	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
59	HL_42687.3	3
60	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
61	HL_90579.2	3
62	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
63	HL_41827.1	3
64	HL_58083.2	3
65	HL_61547.4	3
66	HL_80492.2	3	tRNA D-loop
67	HL_27429.3	3
68	HL_25124.1	3	tSW GA closed tetraloops
69	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
70	HL_08382.2	3
71	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
72	HL_23182.1	3
73	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
74	HL_76766.2	3
75	HL_68697.2	3
76	HL_32644.1	3	LSU Helix 69 (H69) Hairpin Loop
77	HL_78361.1	3
78	HL_91693.1	2
79	HL_23290.1	2
80	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
81	HL_19399.1	2
82	HL_44467.1	2
83	HL_18587.1	2
84	HL_62967.1	2
85	HL_81752.1	2
86	HL_54751.2	2
87	HL_24473.3	2	tRNA D-loop
88	HL_53753.1	2
89	HL_17790.1	2	UNCG-like. cWW Closing pair.
90	HL_05361.1	2
91	HL_98577.1	2
92	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
93	HL_99633.1	2
94	HL_93771.1	2	tRNA T-loop distorted by RS binding
95	HL_98833.2	2
96	HL_38130.2	2
97	HL_26495.1	2
98	HL_96915.1	2
99	HL_06997.1	2
100	HL_06122.1	2
101	HL_65924.1	2
102	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
103	HL_75575.1	2
104	HL_19528.1	2
105	HL_87554.1	2
106	HL_86398.1	2
107	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
108	HL_84353.1	2
109	HL_42553.1	2
110	HL_06312.1	2
111	HL_64371.2	2
112	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
113	HL_23129.1	2
114	HL_91872.1	2
115	HL_16770.1	2
116	HL_33451.1	2
117	HL_50312.1	2
118	HL_26143.1	2
119	HL_60200.1	2
120	HL_24711.1	2
121	HL_49210.1	2
122	HL_94578.1	2
123	HL_03791.1	2
124	HL_74559.1	2	Two base, cross-stacked hairpin loop
125	HL_90542.1	2
126	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
127	HL_57923.1	1
128	HL_78507.1	1
129	HL_45358.1	1	Double hairpin loop based on GGA triple
130	HL_42969.1	1
131	HL_79902.1	1
132	HL_30731.1	1
133	HL_07915.1	1
134	HL_78228.1	1
135	HL_97971.1	1
136	HL_82243.1	1
137	HL_10116.1	1	Kink-turn-like Hairpin Loop
138	HL_98233.1	1
139	HL_96994.1	1
140	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
141	HL_07315.1	1
142	HL_45411.1	1
143	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
144	HL_60203.1	1
145	HL_68435.1	1
146	HL_84888.1	1	T-loop like but without tWH UA
147	HL_57843.1	1
148	HL_68579.1	1
149	HL_27819.1	1
150	HL_00090.1	1
151	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
152	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
153	HL_75850.1	1
154	HL_35200.1	1
155	HL_69403.1	1	GNRA-like
156	HL_46570.1	1
157	HL_73465.1	1
158	HL_24108.1	1
159	HL_73972.1	1
160	HL_53789.1	1
161	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
162	HL_87223.1	1
163	HL_58223.1	1
164	HL_19132.1	1
165	HL_12706.1	1
166	HL_67761.1	1
167	HL_63304.1	1
168	HL_39486.1	1
169	HL_82288.1	1
170	HL_83865.1	1
171	HL_01418.1	1
172	HL_59182.1	1
173	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
174	HL_24707.1	1
175	HL_25195.1	1
176	HL_59604.1	1
177	HL_97499.1	1
178	HL_00721.1	1
179	HL_26579.1	1
180	HL_58601.1	1
181	HL_88960.1	1
182	HL_91613.1	1
183	HL_70912.1	1
184	HL_13786.1	1
185	HL_55272.1	1
186	HL_47337.1	1
187	HL_33277.1	1
188	HL_36842.1	1
189	HL_23195.1	1
190	HL_20028.1	1
191	HL_38138.1	1
192	HL_25197.1	1
193	HL_37962.1	1
194	HL_65071.1	1
195	HL_44522.1	1
196	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
197	HL_53015.1	1
198	HL_78420.1	1
199	HL_68733.1	1	LSU Yeast Hairpin Loop
200	HL_66467.1	1
201	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
202	HL_99584.1	1
203	HL_33640.1	1
204	HL_65802.1	1
205	HL_35865.1	1
206	HL_93633.1	1
207	HL_57217.1	1	cHS platform Intercalation Site
208	HL_39422.1	1
209	HL_66880.1	1
210	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
211	HL_25175.1	1
212	HL_90102.1	1	Kink-turn-like Hairpin Loop
213	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
214	HL_17537.1	1
215	HL_08203.1	1
216	HL_55202.1	1	U2B"-U2A" binding hairpin loop
217	HL_56775.1	1
218	HL_30128.1	1
219	HL_48480.1	1
220	HL_20806.1	1
221	HL_52540.1	1
222	HL_84289.1	1
223	HL_27397.1	1
224	HL_44390.1	1
225	HL_67000.1	1
226	HL_62970.1	1
227	HL_93530.1	1
228	HL_97784.1	1
229	HL_85018.1	1
230	HL_30008.1	1
231	HL_38898.1	1
232	HL_59610.1	1
233	HL_77692.1	1	tRNA D-loop
234	HL_93567.1	1
235	HL_99779.1	1
236	HL_19226.1	1
237	HL_95049.1	1	Two base, cross-stacked hairpin loop
238	HL_05113.1	1
239	HL_34440.1	1
240	HL_56809.1	1
241	HL_62880.1	1
242	HL_04194.1	1
243	HL_95716.1	1
244	HL_71607.1	1
245	HL_19452.1	1	tRNA D-loop
246	HL_42345.1	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