1.4 | 1.5

Changes in PDB files used for clustering

Release 1.4 has 211 PDB files, release 1.5 has 212 PDB files, 209 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_17723.3	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
4	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
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_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
11	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
12	HL_75579.2	6
13	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
14	HL_46489.2	6	LSU H89 Hairpin Loop
15	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
16	HL_42677.1	6
17	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
18	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
19	HL_87136.2	6	LSU Helix 39A Hairpin loop
20	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
21	HL_70420.2	6	LSU Helix 97 Hairpin loop
22	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
23	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
24	HL_06643.2	5	tRNA D-loop. Sec tRNA
25	HL_72273.1	5	tRNA D-loop
26	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
27	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
28	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
29	HL_45018.3	5	Hairpin-Hairpin Interacting HL
30	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
31	HL_62881.1	4	RNase P Structured Hairpin Loop
32	HL_29831.1	4	GNRA-like with bulged base.
33	HL_23182.1	3
34	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
35	HL_80492.2	3	tRNA D-loop
36	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
37	HL_19221.2	3
38	HL_32644.1	3	LSU Helix 69 (H69) Hairpin Loop
39	HL_90579.2	3
40	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
41	HL_58083.2	3
42	HL_08382.2	3
43	HL_27429.3	3
44	HL_41827.1	3
45	HL_78361.1	3
46	HL_25124.1	3	tSW GA closed tetraloops
47	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
48	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
49	HL_06122.1	2
50	HL_98577.1	2
51	HL_06312.1	2
52	HL_23290.1	2
53	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
54	HL_50312.1	2
55	HL_64371.2	2
56	HL_26495.1	2
57	HL_42553.1	2
58	HL_60200.1	2
59	HL_99633.1	2
60	HL_24473.3	2	tRNA D-loop
61	HL_53753.1	2
62	HL_81752.1	2
63	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
64	HL_96915.1	2
65	HL_65924.1	2
66	HL_03791.1	2
67	HL_19399.1	2
68	HL_24711.1	2
69	HL_33451.1	2
70	HL_16770.1	2
71	HL_38130.2	2
72	HL_49210.1	2
73	HL_62967.1	2
74	HL_87554.1	2
75	HL_05361.1	2
76	HL_75575.1	2
77	HL_84353.1	2
78	HL_94578.1	2
79	HL_25195.1	1
80	HL_30008.1	1
81	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
82	HL_42345.1	1
83	HL_45411.1	1
84	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
85	HL_56809.1	1
86	HL_59604.1	1
87	HL_63304.1	1
88	HL_67000.1	1
89	HL_70912.1	1
90	HL_84888.1	1	T-loop like but without tWH UA
91	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
92	HL_25197.1	1
93	HL_30128.1	1
94	HL_34440.1	1
95	HL_39422.1	1
96	HL_59610.1	1
97	HL_67761.1	1
98	HL_71607.1	1
99	HL_75850.1	1
100	HL_79902.1	1
101	HL_85018.1	1
102	HL_88960.1	1
103	HL_95049.1	1	Two base, cross-stacked hairpin loop
104	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
105	HL_00090.1	1
106	HL_12706.1	1
107	HL_19132.1	1
108	HL_24108.1	1
109	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
110	HL_35200.1	1
111	HL_39486.1	1
112	HL_47337.1	1
113	HL_53015.1	1
114	HL_57217.1	1	cHS platform Intercalation Site
115	HL_65071.1	1
116	HL_90102.1	1	Kink-turn-like Hairpin Loop
117	HL_95716.1	1
118	HL_01418.1	1
119	HL_07315.1	1
120	HL_26579.1	1
121	HL_35865.1	1
122	HL_57843.1	1
123	HL_60203.1	1
124	HL_65802.1	1
125	HL_68435.1	1
126	HL_77692.1	1	tRNA D-loop
127	HL_07915.1	1
128	HL_13786.1	1
129	HL_19226.1	1
130	HL_24707.1	1
131	HL_27397.1	1
132	HL_33277.1	1
133	HL_36842.1	1
134	HL_42969.1	1
135	HL_53789.1	1
136	HL_62880.1	1
137	HL_68579.1	1
138	HL_73465.1	1
139	HL_78228.1	1
140	HL_82243.1	1
141	HL_96994.1	1
142	HL_37962.1	1
143	HL_44390.1	1
144	HL_48480.1	1
145	HL_55202.1	1	U2B"-U2A" binding hairpin loop
146	HL_58223.1	1
147	HL_68733.1	1	LSU Yeast Hairpin Loop
148	HL_82288.1	1
149	HL_87223.1	1
150	HL_93530.1	1
151	HL_97499.1	1
152	HL_04194.1	1
153	HL_10116.1	1	Kink-turn-like Hairpin Loop
154	HL_19452.1	1	tRNA D-loop
155	HL_27819.1	1
156	HL_33640.1	1
157	HL_44522.1	1
158	HL_55272.1	1
159	HL_58601.1	1
160	HL_66467.1	1
161	HL_69403.1	1	GNRA-like
162	HL_78420.1	1
163	HL_84289.1	1
164	HL_93567.1	1
165	HL_97784.1	1
166	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
167	HL_17537.1	1
168	HL_20806.1	1
169	HL_25175.1	1
170	HL_38138.1	1
171	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
172	HL_56775.1	1
173	HL_59182.1	1
174	HL_62970.1	1
175	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
176	HL_78507.1	1
177	HL_97971.1	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_12595.2	3
21	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
22	HL_68697.2	3
23	HL_76766.2	3
24	HL_42687.3	3
25	HL_61547.4	3
26	HL_98833.2	2
27	HL_54751.2	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_77235.3	4	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
4	HL_18798.1	4	UNCG-like. cWW Closing pair.
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_13105.1	1
17	HL_31969.1	1
18	HL_55543.1	1
19	HL_96192.1	1
20	HL_16118.1	1
21	HL_33524.1	1	tRNA T-loop distorted by RS binding
22	HL_17468.1	1
23	HL_34375.1	1
24	HL_80746.1	1
25	HL_35004.1	1
26	HL_81295.1	1	UNCG-like. cWW Closing pair.
27	HL_20914.1	1
28	HL_63690.1	1
29	HL_66900.1	1
30	HL_83053.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
31	HL_52109.1	1
32	HL_85753.1	1
33	HL_12984.1	1
34	HL_29084.1	1
35	HL_52393.1	1	Double tSH (double sheared) with bulged base
36	HL_94145.1	1	SSU Helix 43 (h43) Hairpin Loop E.coli

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_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
4	HL_23971.1	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
5	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
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_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
9	HL_17790.1	2	UNCG-like. cWW Closing pair.
10	HL_26143.1	2
11	HL_93771.1	2	tRNA T-loop distorted by RS binding
12	HL_18587.1	2
13	HL_74559.1	2	Two base, cross-stacked hairpin loop
14	HL_19528.1	2
15	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
16	HL_86398.1	2
17	HL_90542.1	2
18	HL_23129.1	2
19	HL_91693.1	2
20	HL_06997.1	2
21	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
22	HL_91872.1	2
23	HL_93633.1	1
24	HL_73972.1	1
25	HL_83865.1	1
26	HL_46570.1	1
27	HL_52540.1	1
28	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
29	HL_23195.1	1