1.7 | 1.8

Changes in PDB files used for clustering

Release 1.7 has 218 PDB files, release 1.8 has 221 PDB files, 218 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.8: 4L8H, 4MGM, 4MGN.

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 1.7 has 250 motif groups, release 1.8 has 254 motif groups, 232 of them are identical.

10 motif groups were updated, 8 groups are present only in release 1.7, 12 groups are only in release 1.8.

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_67042.9	226	GNRA Hairpin motifs
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_49036.3	12	GNRA with one bulged base
8	HL_48039.2	11	MS2 virus RNA Hairpin
9	HL_68081.3	10	LSU Helix 20 Hairpin loop
10	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.
11	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
12	HL_27271.1	10	LSU Helix 96 (H96) Hairpin Loop
13	HL_17723.4	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14	HL_46175.2	10	16S helix 23 and 24 hairpin loops
15	HL_80459.3	9
16	HL_87844.2	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
18	HL_24544.2	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
20	HL_33402.3	8	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
21	HL_15603.1	8	U1A protein-binding Hairpin Loop.
22	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
23	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
24	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
25	HL_46489.2	6	LSU H89 Hairpin Loop
26	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
27	HL_57514.2	6	Two base, cross-stacked hairpin loop
28	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
29	HL_70420.2	6	LSU Helix 97 Hairpin loop
30	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
31	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
32	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
33	HL_75579.2	6
34	HL_87136.2	6	LSU Helix 39A Hairpin loop
35	HL_45018.3	5	Hairpin-Hairpin Interacting HL
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_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
39	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
40	HL_62228.3	5	LSU Helix 35A (H35A) Hairpin Loop
41	HL_06643.2	5	tRNA D-loop. Sec tRNA
42	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
43	HL_72273.1	5	tRNA D-loop
44	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
46	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
47	HL_62881.1	4	RNase P Structured Hairpin Loop
48	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
49	HL_47784.2	4	SSU Central Pseudoknot (forms helix 2)
50	HL_98523.2	4	GNRA-like. Closed by tSH UC.
51	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
52	HL_23971.1	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
53	HL_29831.1	4	GNRA-like with bulged base.
54	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
55	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
56	HL_23182.1	3
57	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
58	HL_61547.4	3
59	HL_08382.2	3
60	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
61	HL_25124.1	3	tSW GA closed tetraloops
62	HL_68697.2	3
63	HL_41827.1	3
64	HL_19221.2	3
65	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
66	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
67	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
68	HL_78361.1	3
69	HL_58083.2	3
70	HL_80492.2	3	tRNA D-loop
71	HL_27429.3	3
72	HL_16770.1	2
73	HL_38130.2	2
74	HL_42553.1	2
75	HL_19399.1	2
76	HL_99633.1	2
77	HL_33451.1	2
78	HL_98577.1	2
79	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
80	HL_96915.1	2
81	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
82	HL_54751.2	2
83	HL_94578.1	2
84	HL_49210.1	2
85	HL_19528.1	2
86	HL_87554.1	2
87	HL_86398.1	2
88	HL_23290.1	2
89	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
90	HL_64371.2	2
91	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
92	HL_23129.1	2
93	HL_91872.1	2
94	HL_60200.1	2
95	HL_90542.1	2
96	HL_93771.1	2	tRNA T-loop distorted by RS binding
97	HL_65924.1	2
98	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
99	HL_24711.1	2
100	HL_24473.3	2	tRNA D-loop
101	HL_05361.1	2
102	HL_74559.1	2	Two base, cross-stacked hairpin loop
103	HL_06122.1	2
104	HL_91693.1	2
105	HL_26495.1	2
106	HL_50312.1	2
107	HL_03791.1	2
108	HL_62967.1	2
109	HL_84353.1	2
110	HL_17790.1	2	UNCG-like. cWW Closing pair.
111	HL_44467.1	2
112	HL_18587.1	2
113	HL_59610.1	1
114	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
115	HL_25197.1	1
116	HL_93633.1	1
117	HL_20806.1	1
118	HL_68435.1	1
119	HL_84888.1	1	T-loop like but without tWH UA
120	HL_57843.1	1
121	HL_68579.1	1
122	HL_27819.1	1
123	HL_00090.1	1
124	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
125	HL_39486.1	1
126	HL_36842.1	1
127	HL_23195.1	1
128	HL_20028.1	1
129	HL_29196.1	1
130	HL_55202.1	1	U2B"-U2A" binding hairpin loop
131	HL_65802.1	1
132	HL_35865.1	1
133	HL_48480.1	1
134	HL_78507.1	1
135	HL_60203.1	1
136	HL_58223.1	1
137	HL_19132.1	1
138	HL_12706.1	1
139	HL_67761.1	1
140	HL_63304.1	1
141	HL_47337.1	1
142	HL_33277.1	1
143	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
144	HL_99584.1	1
145	HL_38138.1	1
146	HL_33640.1	1
147	HL_30128.1	1
148	HL_99779.1	1
149	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
150	HL_87223.1	1
151	HL_26579.1	1
152	HL_58601.1	1
153	HL_88960.1	1
154	HL_91613.1	1
155	HL_70912.1	1
156	HL_13786.1	1
157	HL_55272.1	1
158	HL_78420.1	1
159	HL_68733.1	1	LSU Yeast Hairpin Loop
160	HL_66467.1	1
161	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
162	HL_17537.1	1
163	HL_08203.1	1
164	HL_38898.1	1
165	HL_93567.1	1
166	HL_57923.1	1
167	HL_97499.1	1
168	HL_00721.1	1
169	HL_44522.1	1
170	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
171	HL_53015.1	1
172	HL_25175.1	1
173	HL_90102.1	1	Kink-turn-like Hairpin Loop
174	HL_97784.1	1
175	HL_85018.1	1
176	HL_30008.1	1
177	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
178	HL_56775.1	1
179	HL_45411.1	1
180	HL_37962.1	1
181	HL_65071.1	1
182	HL_39422.1	1
183	HL_66880.1	1
184	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
185	HL_93530.1	1
186	HL_19452.1	1	tRNA D-loop
187	HL_42345.1	1
188	HL_77692.1	1	tRNA D-loop
189	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
190	HL_53789.1	1
191	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
192	HL_57217.1	1	cHS platform Intercalation Site
193	HL_52540.1	1
194	HL_84289.1	1
195	HL_27397.1	1
196	HL_44390.1	1
197	HL_67000.1	1
198	HL_62970.1	1
199	HL_04194.1	1
200	HL_95716.1	1
201	HL_82243.1	1
202	HL_10116.1	1	Kink-turn-like Hairpin Loop
203	HL_98233.1	1
204	HL_96994.1	1
205	HL_25195.1	1
206	HL_59604.1	1
207	HL_95049.1	1	Two base, cross-stacked hairpin loop
208	HL_05113.1	1
209	HL_34440.1	1
210	HL_56809.1	1
211	HL_62880.1	1
212	HL_78228.1	1
213	HL_97971.1	1
214	HL_69403.1	1	GNRA-like
215	HL_46570.1	1
216	HL_73465.1	1
217	HL_24108.1	1
218	HL_73972.1	1
219	HL_24707.1	1
220	HL_19226.1	1
221	HL_45358.1	1	Double hairpin loop based on GGA triple
222	HL_42969.1	1
223	HL_79902.1	1
224	HL_30731.1	1
225	HL_07915.1	1
226	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
227	HL_75850.1	1
228	HL_35200.1	1
229	HL_82288.1	1
230	HL_83865.1	1
231	HL_01418.1	1
232	HL_59182.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_72498.10	66	T-loops with two bulged bases
2	HL_74465.3	13	tRNA Anti-Codon loop
3	HL_42677.2	7
4	HL_06997.2	3
5	HL_90579.3	3	LSU Helix 69 (H69) Hairpin Loop
6	HL_21675.2	3	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7	HL_98833.3	3
8	HL_42687.4	3
9	HL_76766.3	2
10	HL_32644.2	2	LSU Helix 69 (H69) Hairpin Loop

Removed motif groups

#	Motif id	Instances
1	HL_12595.2	3
2	HL_81752.1	2
3	HL_06312.1	2
4	HL_26143.1	2
5	HL_53753.1	2
6	HL_75575.1	2
7	HL_07315.1	1
8	HL_71607.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_35619.1	3
2	HL_74505.1	2
3	HL_42094.1	2
4	HL_63941.1	2
5	HL_65249.1	2
6	HL_28676.1	1
7	HL_76585.1	1
8	HL_76679.1	1
9	HL_84768.1	1
10	HL_52116.1	1
11	HL_98234.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
12	HL_59225.1	1