1.4 | 1.5

Changes in PDB files used for clustering

Release 1.4 has 216 PDB files, release 1.5 has 217 PDB files, 214 of them are identical.

1 equivalence classes changed representatives: 2XZM → 4BPP.

2 new structures in release 1.5: 4L8R, 4LCK.

Obsolete: 2XZM → 4V5O, 4HXH → 4L8R.

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 1.4 has 256 motif groups, release 1.5 has 249 motif groups, 193 of them are identical.

27 motif groups were updated, 36 groups are present only in release 1.4, 29 groups are only in release 1.5.

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_91226.3	17	Kissing Hairpin motif
2	HL_74465.2	12	tRNA Anti-Codon loop
3	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
4	HL_17723.3	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
5	HL_68081.3	10	LSU Helix 20 Hairpin loop
6	HL_87844.2	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
7	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
8	HL_15603.1	8	U1A protein-binding Hairpin Loop.
9	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
10	HL_42677.1	6
11	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
12	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
13	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
14	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
15	HL_87136.2	6	LSU Helix 39A Hairpin loop
16	HL_46489.2	6	LSU H89 Hairpin Loop
17	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
18	HL_75579.2	6
19	HL_70420.2	6	LSU Helix 97 Hairpin loop
20	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
21	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
22	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
23	HL_45018.3	5	Hairpin-Hairpin Interacting HL
24	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
25	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
26	HL_06643.2	5	tRNA D-loop. Sec tRNA
27	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
28	HL_72273.1	5	tRNA D-loop
29	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
30	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
31	HL_29831.1	4	GNRA-like with bulged base.
32	HL_62881.1	4	RNase P Structured Hairpin Loop
33	HL_23182.1	3
34	HL_58083.2	3
35	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
36	HL_08382.2	3
37	HL_90579.2	3
38	HL_25124.1	3	tSW GA closed tetraloops
39	HL_41827.1	3
40	HL_19221.2	3
41	HL_27429.3	3
42	HL_78361.1	3
43	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
44	HL_80492.2	3	tRNA D-loop
45	HL_32644.1	3	LSU Helix 69 (H69) Hairpin Loop
46	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
47	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
48	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
49	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
50	HL_65924.1	2
51	HL_03791.1	2
52	HL_81752.1	2
53	HL_49210.1	2
54	HL_05361.1	2
55	HL_64371.2	2
56	HL_44467.1	2
57	HL_24711.1	2
58	HL_23290.1	2
59	HL_60200.1	2
60	HL_06122.1	2
61	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
62	HL_24473.3	2	tRNA D-loop
63	HL_26495.1	2
64	HL_06312.1	2
65	HL_84353.1	2
66	HL_42553.1	2
67	HL_50312.1	2
68	HL_62967.1	2
69	HL_16770.1	2
70	HL_38130.2	2
71	HL_33451.1	2
72	HL_53753.1	2
73	HL_75575.1	2
74	HL_94578.1	2
75	HL_19399.1	2
76	HL_98577.1	2
77	HL_87554.1	2
78	HL_99633.1	2
79	HL_96915.1	2
80	HL_38898.1	1
81	HL_38138.1	1
82	HL_30128.1	1
83	HL_57923.1	1
84	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
85	HL_60203.1	1
86	HL_26579.1	1
87	HL_58601.1	1
88	HL_88960.1	1
89	HL_67000.1	1
90	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
91	HL_47337.1	1
92	HL_68733.1	1	LSU Yeast Hairpin Loop
93	HL_93530.1	1
94	HL_10116.1	1	Kink-turn-like Hairpin Loop
95	HL_20028.1	1
96	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
97	HL_77692.1	1	tRNA D-loop
98	HL_35865.1	1
99	HL_93567.1	1
100	HL_45411.1	1
101	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
102	HL_87223.1	1
103	HL_44522.1	1
104	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
105	HL_44390.1	1
106	HL_63304.1	1
107	HL_78420.1	1
108	HL_90102.1	1	Kink-turn-like Hairpin Loop
109	HL_71607.1	1
110	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
111	HL_99584.1	1
112	HL_56775.1	1
113	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
114	HL_07315.1	1
115	HL_59604.1	1
116	HL_97499.1	1
117	HL_00721.1	1
118	HL_39422.1	1
119	HL_66880.1	1
120	HL_56809.1	1
121	HL_55272.1	1
122	HL_25175.1	1
123	HL_95716.1	1
124	HL_82243.1	1
125	HL_17537.1	1
126	HL_08203.1	1
127	HL_65802.1	1
128	HL_53789.1	1
129	HL_25195.1	1
130	HL_37962.1	1
131	HL_65071.1	1
132	HL_84289.1	1
133	HL_27397.1	1
134	HL_07915.1	1
135	HL_00090.1	1
136	HL_53015.1	1
137	HL_97971.1	1
138	HL_69403.1	1	GNRA-like
139	HL_85018.1	1
140	HL_30008.1	1
141	HL_33640.1	1
142	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
143	HL_57217.1	1	cHS platform Intercalation Site
144	HL_95049.1	1	Two base, cross-stacked hairpin loop
145	HL_05113.1	1
146	HL_34440.1	1
147	HL_27819.1	1
148	HL_67761.1	1
149	HL_04194.1	1
150	HL_78228.1	1
151	HL_35200.1	1
152	HL_82288.1	1
153	HL_19452.1	1	tRNA D-loop
154	HL_42345.1	1
155	HL_20806.1	1
156	HL_45358.1	1	Double hairpin loop based on GGA triple
157	HL_42969.1	1
158	HL_79902.1	1
159	HL_30731.1	1
160	HL_12706.1	1
161	HL_13786.1	1
162	HL_75850.1	1
163	HL_39486.1	1
164	HL_36842.1	1
165	HL_98233.1	1
166	HL_96994.1	1
167	HL_59610.1	1
168	HL_24707.1	1
169	HL_48480.1	1
170	HL_19226.1	1
171	HL_68435.1	1
172	HL_84888.1	1	T-loop like but without tWH UA
173	HL_57843.1	1
174	HL_68579.1	1
175	HL_70912.1	1
176	HL_62970.1	1
177	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
178	HL_33277.1	1
179	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
180	HL_73465.1	1
181	HL_24108.1	1
182	HL_55202.1	1	U2B"-U2A" binding hairpin loop
183	HL_25197.1	1
184	HL_99779.1	1
185	HL_78507.1	1
186	HL_58223.1	1
187	HL_19132.1	1
188	HL_91613.1	1
189	HL_62880.1	1
190	HL_66467.1	1
191	HL_97784.1	1
192	HL_01418.1	1
193	HL_59182.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.8	226	GNRA Hairpin motifs
2	HL_72498.9	64	T-loops with two bulged bases
3	HL_39895.6	35	UNCG Hairpin motifs
4	HL_18781.3	20	Double sheared (tSH) with U-turn
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_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.
10	HL_46175.2	10	16S helix 23 and 24 hairpin loops
11	HL_80459.3	9
12	HL_24544.2	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
13	HL_33402.3	8	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
14	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
15	HL_57514.2	6	Two base, cross-stacked hairpin loop
16	HL_62228.3	5	LSU Helix 35A (H35A) Hairpin Loop
17	HL_47784.2	4	SSU Central Pseudoknot (forms helix 2)
18	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
19	HL_98523.2	4	GNRA-like. Closed by tSH UC.
20	HL_76766.2	3
21	HL_42687.3	3
22	HL_61547.4	3
23	HL_12595.2	3
24	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
25	HL_68697.2	3
26	HL_54751.2	2
27	HL_98833.2	2

Removed motif groups

#	Motif id	Instances	Description
1	HL_28436.3	9	LSU Helix 96 (H96) Hairpin Loop
2	HL_12811.2	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
3	HL_18798.1	4	UNCG-like. cWW Closing pair.
4	HL_77235.3	4	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
5	HL_82253.2	3
6	HL_46794.2	3
7	HL_57014.1	2
8	HL_77555.1	2
9	HL_97512.1	2	LSU Helix 8 (H8) Hairpin Loop
10	HL_57904.1	2
11	HL_58687.1	2
12	HL_45440.1	2
13	HL_26057.1	2
14	HL_67367.1	2
15	HL_67692.1	2
16	HL_16118.1	1
17	HL_33524.1	1	tRNA T-loop distorted by RS binding
18	HL_17468.1	1
19	HL_34375.1	1
20	HL_80746.1	1
21	HL_35004.1	1
22	HL_81295.1	1	UNCG-like. cWW Closing pair.
23	HL_20914.1	1
24	HL_63690.1	1
25	HL_66900.1	1
26	HL_83053.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
27	HL_52109.1	1
28	HL_85753.1	1
29	HL_12984.1	1
30	HL_29084.1	1
31	HL_52393.1	1	Double tSH (double sheared) with bulged base
32	HL_94145.1	1	SSU Helix 43 (h43) Hairpin Loop E.coli
33	HL_13105.1	1
34	HL_31969.1	1
35	HL_55543.1	1
36	HL_96192.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_27271.1	10	LSU Helix 96 (H96) Hairpin Loop
2	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
3	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
4	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
5	HL_23971.1	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
6	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
7	HL_21675.1	3	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
8	HL_17790.1	2	UNCG-like. cWW Closing pair.
9	HL_26143.1	2
10	HL_93771.1	2	tRNA T-loop distorted by RS binding
11	HL_18587.1	2
12	HL_74559.1	2	Two base, cross-stacked hairpin loop
13	HL_19528.1	2
14	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
15	HL_86398.1	2
16	HL_90542.1	2
17	HL_23129.1	2
18	HL_91693.1	2
19	HL_06997.1	2
20	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
21	HL_91872.1	2
22	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
23	HL_73972.1	1
24	HL_83865.1	1
25	HL_46570.1	1
26	HL_52540.1	1
27	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
28	HL_23195.1	1
29	HL_93633.1	1