Analysis of interatomic Contacts of Structural Units in PDB entry:
8YDX

Contacts of Structural Units (CSU) are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).
This page provides analyses of contacts formed by:

chains
helices
sheets
residues

For analysis of ligand-protein contacts, use:

LPC software

3D structure can be seen in additional window with STING software for 8YDX entry

There are 6 chains in PDB entry 8YDX (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
D	ASP 1	ASP 39
F	ASP 1	ASP 39
E	ASP 1	ASP 39
C	ALA 27	ASP 1146
B	ALA 27	ASP 1146
A	ALA 27	ASP 1146

There are 72 helices in PDB entry 8YDX. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	D	1	19	Right-handed alpha
Helix 2	AA2	D	21	38	Right-handed alpha
Helix 3	AA3	F	2	19	Right-handed alpha
Helix 4	AA4	F	21	38	Right-handed alpha
Helix 5	AA5	E	2	19	Right-handed alpha
Helix 6	AA6	E	21	38	Right-handed alpha
Helix 7	AA7	C	294	304	Right-handed alpha
Helix 8	AA8	C	337	343	Right-handed alpha
Helix 9	AA9	C	365	371	Right-handed alpha
Helix 10	AB1	C	383	388	Right-handed alpha
Helix 11	AB2	C	405	410	Right-handed 310
Helix 12	AB3	C	416	422	Right-handed alpha
Helix 13	AB4	C	438	443	Right-handed alpha
Helix 14	AB5	C	502	505	Right-handed 310
Helix 15	AB6	C	737	743	Right-handed alpha
Helix 16	AB7	C	746	755	Right-handed alpha
Helix 17	AB8	C	758	783	Right-handed alpha
Helix 18	AB9	C	816	826	Right-handed alpha
Helix 19	AC1	C	866	885	Right-handed alpha
Helix 20	AC2	C	886	891	Right-handed alpha
Helix 21	AC3	C	897	909	Right-handed alpha
Helix 22	AC4	C	912	919	Right-handed alpha
Helix 23	AC5	C	919	941	Right-handed alpha
Helix 24	AC6	C	945	965	Right-handed alpha
Helix 25	AC7	C	966	968	Right-handed 310
Helix 26	AC8	C	976	984	Right-handed alpha
Helix 27	AC9	C	985	1032	Right-handed alpha
Helix 28	AD1	C	1140	1146	Right-handed alpha
Helix 29	AD2	B	294	304	Right-handed alpha
Helix 30	AD3	B	337	343	Right-handed alpha
Helix 31	AD4	B	365	371	Right-handed alpha
Helix 32	AD5	B	383	388	Right-handed alpha
Helix 33	AD6	B	405	410	Right-handed 310
Helix 34	AD7	B	416	422	Right-handed alpha
Helix 35	AD8	B	438	443	Right-handed alpha
Helix 36	AD9	B	502	505	Right-handed 310
Helix 37	AE1	B	737	743	Right-handed alpha
Helix 38	AE2	B	746	757	Right-handed alpha
Helix 39	AE3	B	758	783	Right-handed alpha
Helix 40	AE4	B	816	826	Right-handed alpha
Helix 41	AE5	B	866	885	Right-handed alpha
Helix 42	AE6	B	886	891	Right-handed alpha
Helix 43	AE7	B	897	909	Right-handed alpha
Helix 44	AE8	B	912	919	Right-handed alpha
Helix 45	AE9	B	919	941	Right-handed alpha
Helix 46	AF1	B	945	965	Right-handed alpha
Helix 47	AF2	B	966	968	Right-handed 310
Helix 48	AF3	B	976	984	Right-handed alpha
Helix 49	AF4	B	985	1033	Right-handed alpha
Helix 50	AF5	B	1140	1146	Right-handed alpha
Helix 51	AF6	A	294	304	Right-handed alpha
Helix 52	AF7	A	337	343	Right-handed alpha
Helix 53	AF8	A	365	371	Right-handed alpha
Helix 54	AF9	A	383	388	Right-handed alpha
Helix 55	AG1	A	405	410	Right-handed 310
Helix 56	AG2	A	416	422	Right-handed alpha
Helix 57	AG3	A	438	443	Right-handed alpha
Helix 58	AG4	A	502	505	Right-handed 310
Helix 59	AG5	A	737	743	Right-handed alpha
Helix 60	AG6	A	746	755	Right-handed alpha
Helix 61	AG7	A	758	783	Right-handed alpha
Helix 62	AG8	A	816	826	Right-handed alpha
Helix 63	AG9	A	866	885	Right-handed alpha
Helix 64	AH1	A	886	891	Right-handed alpha
Helix 65	AH2	A	897	909	Right-handed alpha
Helix 66	AH3	A	912	919	Right-handed alpha
Helix 67	AH4	A	919	941	Right-handed alpha
Helix 68	AH5	A	945	965	Right-handed alpha
Helix 69	AH6	A	966	968	Right-handed 310
Helix 70	AH7	A	976	984	Right-handed alpha
Helix 71	AH8	A	985	1033	Right-handed alpha
Helix 72	AH9	A	1140	1146	Right-handed alpha

There are 52 sheets in PDB entry 8YDX. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8, AC9, AD1, AD2, AD3, AD4, AD5, AD6, AD7, AD8, AD9, AE1, AE2, AE3, AE4, AE5, AE6, AE7, AE8, AE9, AF1, AF2, AF3, AF4, AF5, AF6, AF7,

There are 7 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	28	30	first strand
Strand 2	C	61	65	anti-parallel
Strand 3	C	264	269	anti-parallel
Strand 4	C	89	95	anti-parallel
Strand 5	C	188	197	anti-parallel
Strand 6	C	200	209	anti-parallel
Strand 7	C	225	230	anti-parallel

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There are 7 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	42	43	first strand
Strand 2	A	565	568	parallel
Strand 3	A	572	577	anti-parallel
Strand 4	A	584	588	anti-parallel
Strand 5	A	546	554	anti-parallel
Strand 6	A	538	543	anti-parallel
Strand 7	A	325	328	parallel

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There are 3 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	47	55	first strand
Strand 2	C	271	279	anti-parallel
Strand 3	C	285	290	anti-parallel

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There are 6 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	84	85	first strand
Strand 2	C	237	242	anti-parallel
Strand 3	C	101	107	anti-parallel
Strand 4	C	116	120	anti-parallel
Strand 5	C	126	132	anti-parallel
Strand 6	C	164	172	anti-parallel

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There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	135	144	first strand
Strand 2	C	153	160	anti-parallel

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There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	311	319	first strand
Strand 2	C	592	599	anti-parallel
Strand 3	C	609	612	anti-parallel
Strand 4	C	648	651	anti-parallel
Strand 5	C	642	645	anti-parallel

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There are 7 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	325	328	first strand
Strand 2	C	538	543	parallel
Strand 3	C	546	554	anti-parallel
Strand 4	C	584	589	anti-parallel
Strand 5	C	572	577	anti-parallel
Strand 6	C	565	568	anti-parallel
Strand 7	B	42	43	parallel

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There are 5 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	354	358	first strand
Strand 2	C	394	403	anti-parallel
Strand 3	C	507	516	anti-parallel
Strand 4	C	431	437	anti-parallel
Strand 5	C	376	379	anti-parallel

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There are 3 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	361	362	first strand
Strand 2	C	524	525	parallel
Strand 3	C	391	392	anti-parallel

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There are 2 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	452	454	first strand
Strand 2	C	492	494	anti-parallel

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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	473	474	first strand
Strand 2	C	488	489	anti-parallel

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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	654	655	first strand
Strand 2	C	691	696	parallel
Strand 3	C	670	672	anti-parallel
Strand 4	C	665	667	anti-parallel

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There are 3 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	654	655	first strand
Strand 2	C	691	696	parallel
Strand 3	C	688	688	anti-parallel

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There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	701	703	first strand
Strand 2	B	787	789	parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	711	715	first strand
Strand 2	C	1072	1076	anti-parallel

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There are 3 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	718	728	first strand
Strand 2	C	1059	1069	anti-parallel
Strand 3	C	1047	1056	anti-parallel

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There are 2 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	733	735	first strand
Strand 2	C	859	861	anti-parallel

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There are 2 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	788	790	first strand
Strand 2	A	702	704	parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	1120	1125	first strand
Strand 2	C	1086	1090	anti-parallel
Strand 3	C	1080	1083	anti-parallel
Strand 4	C	1132	1134	parallel

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There are 3 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	1094	1097	first strand
Strand 2	C	1102	1105	anti-parallel
Strand 3	C	1113	1114	anti-parallel

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There are 7 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	28	30	first strand
Strand 2	B	61	66	anti-parallel
Strand 3	B	264	269	anti-parallel
Strand 4	B	90	96	anti-parallel
Strand 5	B	186	197	anti-parallel
Strand 6	B	200	212	anti-parallel
Strand 7	B	224	230	anti-parallel

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There are 3 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	47	55	first strand
Strand 2	B	271	279	anti-parallel
Strand 3	B	285	290	anti-parallel

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There are 4 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	83	85	first strand
Strand 2	B	237	246	anti-parallel
Strand 3	B	141	145	parallel
Strand 4	B	152	157	anti-parallel

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There are 6 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	83	85	first strand
Strand 2	B	237	246	anti-parallel
Strand 3	B	101	107	anti-parallel
Strand 4	B	116	121	anti-parallel
Strand 5	B	126	131	anti-parallel
Strand 6	B	168	171	anti-parallel

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There are 5 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	314	319	first strand
Strand 2	B	592	598	anti-parallel
Strand 3	B	609	613	anti-parallel
Strand 4	B	648	651	anti-parallel
Strand 5	B	642	645	anti-parallel

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There are 7 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	325	328	first strand
Strand 2	B	539	543	parallel
Strand 3	B	546	554	anti-parallel
Strand 4	B	583	588	anti-parallel
Strand 5	B	573	578	anti-parallel
Strand 6	B	565	567	anti-parallel
Strand 7	A	42	43	parallel

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There are 5 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	354	358	first strand
Strand 2	B	394	403	anti-parallel
Strand 3	B	507	516	anti-parallel
Strand 4	B	431	437	anti-parallel
Strand 5	B	376	379	anti-parallel

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There are 3 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	361	362	first strand
Strand 2	B	524	525	parallel
Strand 3	B	391	392	anti-parallel

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There are 2 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	452	454	first strand
Strand 2	B	492	494	anti-parallel

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There are 2 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	473	474	first strand
Strand 2	B	488	489	anti-parallel

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There are 4 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	654	655	first strand
Strand 2	B	691	696	parallel
Strand 3	B	670	672	anti-parallel
Strand 4	B	665	667	anti-parallel

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There are 3 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	654	655	first strand
Strand 2	B	691	696	parallel
Strand 3	B	688	688	anti-parallel

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There are 2 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	701	703	first strand
Strand 2	A	787	789	parallel

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There are 3 strands in AD7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	711	728	first strand
Strand 2	B	1059	1078	anti-parallel
Strand 3	B	1047	1056	anti-parallel

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There are 5 strands in AD8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	711	728	first strand
Strand 2	B	1059	1078	anti-parallel
Strand 3	B	1094	1097	anti-parallel
Strand 4	B	1102	1105	anti-parallel
Strand 5	B	1113	1114	anti-parallel

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There are 2 strands in AD9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	733	736	first strand
Strand 2	B	858	861	anti-parallel

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There are 4 strands in AE1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	1120	1125	first strand
Strand 2	B	1086	1090	anti-parallel
Strand 3	B	1081	1083	anti-parallel
Strand 4	B	1133	1134	parallel

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There are 7 strands in AE2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	28	30	first strand
Strand 2	A	61	66	anti-parallel
Strand 3	A	264	269	anti-parallel
Strand 4	A	89	95	anti-parallel
Strand 5	A	189	197	anti-parallel
Strand 6	A	200	208	anti-parallel
Strand 7	A	224	229	anti-parallel

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There are 3 strands in AE3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	48	55	first strand
Strand 2	A	271	279	anti-parallel
Strand 3	A	285	290	anti-parallel

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There are 4 strands in AE4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	84	85	first strand
Strand 2	A	237	245	anti-parallel
Strand 3	A	140	144	parallel
Strand 4	A	153	158	anti-parallel

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There are 6 strands in AE5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	84	85	first strand
Strand 2	A	237	245	anti-parallel
Strand 3	A	101	107	anti-parallel
Strand 4	A	116	121	anti-parallel
Strand 5	A	126	133	anti-parallel
Strand 6	A	163	172	anti-parallel

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There are 5 strands in AE6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	311	319	first strand
Strand 2	A	592	599	anti-parallel
Strand 3	A	609	613	anti-parallel
Strand 4	A	648	651	anti-parallel
Strand 5	A	642	645	anti-parallel

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There are 5 strands in AE7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	354	358	first strand
Strand 2	A	394	403	anti-parallel
Strand 3	A	507	516	anti-parallel
Strand 4	A	431	437	anti-parallel
Strand 5	A	376	379	anti-parallel

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There are 3 strands in AE8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	361	362	first strand
Strand 2	A	524	525	parallel
Strand 3	A	391	392	anti-parallel

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There are 2 strands in AE9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	452	454	first strand
Strand 2	A	492	494	anti-parallel

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There are 2 strands in AF1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	473	474	first strand
Strand 2	A	488	489	anti-parallel

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There are 4 strands in AF2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	654	655	first strand
Strand 2	A	691	696	parallel
Strand 3	A	670	672	anti-parallel
Strand 4	A	665	667	anti-parallel

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There are 3 strands in AF3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	654	655	first strand
Strand 2	A	691	696	parallel
Strand 3	A	688	688	anti-parallel

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There are 3 strands in AF4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	711	728	first strand
Strand 2	A	1059	1076	anti-parallel
Strand 3	A	1047	1056	anti-parallel

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There are 2 strands in AF5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	733	736	first strand
Strand 2	A	858	861	anti-parallel

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There are 4 strands in AF6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	1120	1125	first strand
Strand 2	A	1086	1090	anti-parallel
Strand 3	A	1081	1083	anti-parallel
Strand 4	A	1133	1134	parallel

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There are 2 strands in AF7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	1094	1097	first strand
Strand 2	A	1102	1105	anti-parallel

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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 8YDX

Analysis of interatomic Contacts of Structural Units in PDB entry:
8YDX