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

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 8YDB entry

There are 12 chains in PDB entry 8YDB (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 2	ILE 255
B	MET 1	LEU 175
C	U 1	G 60
I	LEU 12	LYS 335
H	LEU 12	GLN 333
G	THR 11	LYS 335
F	THR 11	GLN 333
E	VAL 10	GLN 333
D	THR 11	LYS 332
J	MET 1	LYS 340
T	G 22	C 53
N	G 9	A 19

There are 88 helices in PDB entry 8YDB. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	28	46	Right-handed alpha
Helix 2	AA2	A	118	129	Right-handed alpha
Helix 3	AA3	A	150	154	Right-handed 310
Helix 4	AA4	A	163	169	Right-handed alpha
Helix 5	AA5	A	174	186	Right-handed alpha
Helix 6	AA6	A	236	240	Right-handed 310
Helix 7	AA7	B	15	24	Right-handed alpha
Helix 8	AA8	B	24	35	Right-handed alpha
Helix 9	AA9	B	65	72	Right-handed alpha
Helix 10	AB1	B	72	77	Right-handed alpha
Helix 11	AB2	B	107	118	Right-handed alpha
Helix 12	AB3	B	123	139	Right-handed alpha
Helix 13	AB4	I	36	40	Right-handed 310
Helix 14	AB5	I	102	106	Right-handed 310
Helix 15	AB6	I	112	129	Right-handed alpha
Helix 16	AB7	I	131	144	Right-handed alpha
Helix 17	AB8	I	173	177	Right-handed 310
Helix 18	AB9	I	186	202	Right-handed alpha
Helix 19	AC1	I	250	259	Right-handed alpha
Helix 20	AC2	I	267	271	Right-handed 310
Helix 21	AC3	I	296	305	Right-handed alpha
Helix 22	AC4	I	312	326	Right-handed alpha
Helix 23	AC5	H	63	68	Right-handed alpha
Helix 24	AC6	H	102	104	Right-handed 310
Helix 25	AC7	H	112	129	Right-handed alpha
Helix 26	AC8	H	131	144	Right-handed alpha
Helix 27	AC9	H	145	153	Right-handed 310
Helix 28	AD1	H	186	202	Right-handed alpha
Helix 29	AD2	H	250	259	Right-handed alpha
Helix 30	AD3	H	267	272	Right-handed alpha
Helix 31	AD4	H	296	306	Right-handed alpha
Helix 32	AD5	H	312	326	Right-handed alpha
Helix 33	AD6	G	63	71	Right-handed alpha
Helix 34	AD7	G	102	104	Right-handed 310
Helix 35	AD8	G	111	129	Right-handed alpha
Helix 36	AD9	G	131	144	Right-handed alpha
Helix 37	AE1	G	145	153	Right-handed 310
Helix 38	AE2	G	186	201	Right-handed alpha
Helix 39	AE3	G	250	259	Right-handed alpha
Helix 40	AE4	G	267	272	Right-handed alpha
Helix 41	AE5	G	296	307	Right-handed alpha
Helix 42	AE6	G	312	326	Right-handed alpha
Helix 43	AE7	F	63	71	Right-handed alpha
Helix 44	AE8	F	102	104	Right-handed 310
Helix 45	AE9	F	112	129	Right-handed alpha
Helix 46	AF1	F	131	144	Right-handed alpha
Helix 47	AF2	F	145	153	Right-handed 310
Helix 48	AF3	F	186	202	Right-handed alpha
Helix 49	AF4	F	250	260	Right-handed alpha
Helix 50	AF5	F	267	272	Right-handed alpha
Helix 51	AF6	F	296	306	Right-handed alpha
Helix 52	AF7	F	312	326	Right-handed alpha
Helix 53	AF8	E	36	40	Right-handed 310
Helix 54	AF9	E	66	73	Right-handed alpha
Helix 55	AG1	E	102	104	Right-handed 310
Helix 56	AG2	E	111	129	Right-handed alpha
Helix 57	AG3	E	131	144	Right-handed alpha
Helix 58	AG4	E	145	153	Right-handed 310
Helix 59	AG5	E	186	202	Right-handed alpha
Helix 60	AG6	E	250	259	Right-handed alpha
Helix 61	AG7	E	267	272	Right-handed alpha
Helix 62	AG8	E	296	307	Right-handed alpha
Helix 63	AG9	E	312	326	Right-handed alpha
Helix 64	AH1	D	102	104	Right-handed 310
Helix 65	AH2	D	111	129	Right-handed alpha
Helix 66	AH3	D	131	144	Right-handed alpha
Helix 67	AH4	D	145	153	Right-handed 310
Helix 68	AH5	D	175	177	Right-handed 310
Helix 69	AH6	D	186	201	Right-handed alpha
Helix 70	AH7	D	250	260	Right-handed alpha
Helix 71	AH8	D	267	272	Right-handed alpha
Helix 72	AH9	D	296	306	Right-handed alpha
Helix 73	AI1	D	312	326	Right-handed alpha
Helix 74	AI2	J	2	10	Right-handed alpha
Helix 75	AI3	J	15	31	Right-handed alpha
Helix 76	AI4	J	87	94	Right-handed alpha
Helix 77	AI5	J	102	110	Right-handed alpha
Helix 78	AI6	J	111	122	Right-handed alpha
Helix 79	AI7	J	124	134	Right-handed alpha
Helix 80	AI8	J	166	179	Right-handed alpha
Helix 81	AI9	J	191	199	Right-handed alpha
Helix 82	AJ1	J	200	206	Right-handed alpha
Helix 83	AJ2	J	217	221	Right-handed 310
Helix 84	AJ3	J	223	230	Right-handed alpha
Helix 85	AJ4	J	255	265	Right-handed alpha
Helix 86	AJ5	J	281	292	Right-handed alpha
Helix 87	AJ6	J	308	312	Right-handed 310
Helix 88	AJ7	J	325	339	Right-handed alpha

There are 43 sheets in PDB entry 8YDB. 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,

There are 4 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	133	134	first strand
Strand 2	A	137	139	anti-parallel
Strand 3	A	4	17	anti-parallel
Strand 4	A	144	148	anti-parallel

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There are 8 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	133	134	first strand
Strand 2	A	137	139	anti-parallel
Strand 3	A	4	17	anti-parallel
Strand 4	A	101	113	anti-parallel
Strand 5	A	51	64	anti-parallel
Strand 6	A	158	162	anti-parallel
Strand 7	A	221	229	anti-parallel
Strand 8	A	190	195	anti-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	A	23	25	first strand
Strand 2	J	211	214	parallel
Strand 3	J	184	185	anti-parallel

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There are 2 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	66	68	first strand
Strand 2	A	74	76	anti-parallel

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There are 3 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	214	216	first strand
Strand 2	J	157	161	parallel
Strand 3	J	151	154	anti-parallel

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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	242	244	first strand
Strand 2	A	251	253	anti-parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	39	42	first strand
Strand 2	B	58	62	anti-parallel
Strand 3	B	2	8	anti-parallel
Strand 4	B	84	86	anti-parallel

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There are 4 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	39	42	first strand
Strand 2	B	58	62	anti-parallel
Strand 3	B	2	8	anti-parallel
Strand 4	B	91	92	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	B	98	102	first strand
Strand 2	B	154	162	anti-parallel
Strand 3	B	142	147	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	I	19	20	first strand
Strand 2	I	108	109	anti-parallel

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There are 5 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	25	27	first strand
Strand 2	I	90	99	anti-parallel
Strand 3	I	30	35	anti-parallel
Strand 4	I	207	215	first strand
Strand 5	I	158	163	anti-parallel

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There are 5 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	45	46	first strand
Strand 2	I	30	35	anti-parallel
Strand 3	I	90	99	anti-parallel
Strand 4	I	246	249	first strand
Strand 5	I	242	243	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	I	50	57	first strand
Strand 2	I	74	83	anti-parallel
Strand 3	I	222	223	anti-parallel

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There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	106	109	first strand
Strand 2	H	19	21	anti-parallel
Strand 3	H	327	328	anti-parallel

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There are 5 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	25	27	first strand
Strand 2	H	90	99	anti-parallel
Strand 3	H	207	216	anti-parallel
Strand 4	H	157	164	anti-parallel
Strand 5	H	167	168	anti-parallel

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There are 6 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	45	46	first strand
Strand 2	H	31	35	anti-parallel
Strand 3	H	90	99	anti-parallel
Strand 4	H	207	216	anti-parallel
Strand 5	H	157	164	anti-parallel
Strand 6	H	172	173	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	H	50	56	first strand
Strand 2	H	75	81	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	H	242	243	first strand
Strand 2	H	246	247	anti-parallel

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There are 2 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	260	262	first strand
Strand 2	H	275	276	anti-parallel

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There are 2 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	20	21	first strand
Strand 2	G	106	108	anti-parallel

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There are 6 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	25	27	first strand
Strand 2	G	90	99	anti-parallel
Strand 3	G	30	35	anti-parallel
Strand 4	G	207	216	first strand
Strand 5	G	157	163	anti-parallel
Strand 6	G	172	173	anti-parallel

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There are 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	45	46	first strand
Strand 2	G	30	35	anti-parallel
Strand 3	G	90	99	anti-parallel
Strand 4	G	248	249	first strand

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There are 3 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	50	56	first strand
Strand 2	G	75	83	anti-parallel
Strand 3	G	222	223	anti-parallel

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There are 2 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	227	228	first strand
Strand 2	G	239	240	anti-parallel

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There are 2 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	260	262	first strand
Strand 2	G	275	276	anti-parallel

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There are 2 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	282	283	first strand
Strand 2	G	288	289	anti-parallel

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There are 2 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	20	21	first strand
Strand 2	F	106	108	anti-parallel

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There are 5 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	25	27	first strand
Strand 2	F	90	99	anti-parallel
Strand 3	F	207	216	anti-parallel
Strand 4	F	158	164	anti-parallel
Strand 5	F	167	168	anti-parallel

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There are 6 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	45	46	first strand
Strand 2	F	31	35	anti-parallel
Strand 3	F	90	99	anti-parallel
Strand 4	F	207	216	anti-parallel
Strand 5	F	158	164	anti-parallel
Strand 6	F	172	173	anti-parallel

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There are 3 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	50	56	first strand
Strand 2	F	75	83	anti-parallel
Strand 3	F	222	223	anti-parallel

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There are 2 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	227	228	first strand
Strand 2	F	239	240	anti-parallel

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There are 2 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	242	243	first strand
Strand 2	F	246	247	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	E	19	21	first strand
Strand 2	E	106	109	anti-parallel

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There are 5 strands in AD7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	25	27	first strand
Strand 2	E	90	99	anti-parallel
Strand 3	E	30	35	anti-parallel
Strand 4	E	207	216	first strand
Strand 5	E	157	163	anti-parallel

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There are 4 strands in AD8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	45	46	first strand
Strand 2	E	30	35	anti-parallel
Strand 3	E	90	99	anti-parallel
Strand 4	E	248	249	first strand

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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	E	50	55	first strand
Strand 2	E	76	81	anti-parallel

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There are 2 strands in AE1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	260	262	first strand
Strand 2	E	275	276	anti-parallel

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There are 2 strands in AE2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	19	21	first strand
Strand 2	D	106	109	anti-parallel

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There are 4 strands in AE3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	25	27	first strand
Strand 2	D	90	99	anti-parallel
Strand 3	D	32	35	anti-parallel
Strand 4	D	45	46	anti-parallel

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There are 5 strands in AE4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	25	27	first strand
Strand 2	D	90	99	anti-parallel
Strand 3	D	207	215	anti-parallel
Strand 4	D	158	163	anti-parallel
Strand 5	D	172	173	anti-parallel

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There are 2 strands in AE5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	242	243	first strand
Strand 2	D	246	247	anti-parallel

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There are 2 strands in AE6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	35	37	first strand
Strand 2	J	78	80	anti-parallel

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There are 2 strands in AE7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	301	304	first strand
Strand 2	J	321	324	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: 8YDB

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