Analysis of interatomic Contacts of Structural Units in PDB entry:
9YM8

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 9YM8 entry

There are 21 chains in PDB entry 9YM8 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
I	T 2	G 146
J	C 2	A 146
O	MET 1	CYS 76
U	MET 1	CYS 76
A	PRO 38	ARG 134
B	ARG 17	GLY 102
C	LYS 9	LYS 118
D	LYS 30	LYS 125
E	ALA 1	GLY 13
E	ALA 15	ARG 17
E	GLN 19	THR 22
E	ALA 24	ALA 135
F	ARG 19	GLY 102
G	LYS 15	LYS 118
H	ARG 33	SER 124
R	PRO 33	SER 332
N	TYR 13	VAL 473
K	ASP 1358	ASN 5537
T	LEU 325	PRO 625
P	VAL 46	ASN 99
Q	VAL 46	ASN 99

There are 72 helices in PDB entry 9YM8. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	O	22	34	Right-handed alpha
Helix 2	AA2	O	55	60	Right-handed 310
Helix 3	AA3	U	22	34	Right-handed alpha
Helix 4	AA4	U	55	60	Right-handed 310
Helix 5	AA5	A	45	57	Right-handed alpha
Helix 6	AA6	A	63	77	Right-handed alpha
Helix 7	AA7	A	85	114	Right-handed alpha
Helix 8	AA8	A	120	132	Right-handed alpha
Helix 9	AA9	B	25	29	Right-handed 310
Helix 10	AB1	B	30	42	Right-handed alpha
Helix 11	AB2	B	50	76	Right-handed alpha
Helix 12	AB3	B	82	94	Right-handed alpha
Helix 13	AB4	C	16	22	Right-handed alpha
Helix 14	AB5	C	27	36	Right-handed alpha
Helix 15	AB6	C	45	73	Right-handed alpha
Helix 16	AB7	C	79	89	Right-handed alpha
Helix 17	AB8	C	92	97	Right-handed alpha
Helix 18	AB9	D	39	49	Right-handed alpha
Helix 19	AC1	D	55	84	Right-handed alpha
Helix 20	AC2	D	90	102	Right-handed alpha
Helix 21	AC3	D	104	123	Right-handed alpha
Helix 22	AC4	E	44	57	Right-handed alpha
Helix 23	AC5	E	63	77	Right-handed alpha
Helix 24	AC6	E	85	114	Right-handed alpha
Helix 25	AC7	E	120	132	Right-handed alpha
Helix 26	AC8	F	25	29	Right-handed 310
Helix 27	AC9	F	30	42	Right-handed alpha
Helix 28	AD1	F	49	76	Right-handed alpha
Helix 29	AD2	F	82	94	Right-handed alpha
Helix 30	AD3	G	16	22	Right-handed alpha
Helix 31	AD4	G	26	36	Right-handed alpha
Helix 32	AD5	G	45	73	Right-handed alpha
Helix 33	AD6	G	79	90	Right-handed alpha
Helix 34	AD7	G	90	97	Right-handed alpha
Helix 35	AD8	G	112	116	Right-handed 310
Helix 36	AD9	H	37	49	Right-handed alpha
Helix 37	AE1	H	55	84	Right-handed alpha
Helix 38	AE2	H	90	102	Right-handed alpha
Helix 39	AE3	H	104	124	Right-handed alpha
Helix 40	AE4	N	227	234	Right-handed alpha
Helix 41	AE5	N	324	328	Right-handed 310
Helix 42	AE6	N	348	353	Right-handed 310
Helix 43	AE7	N	469	473	Right-handed 310
Helix 44	AE8	K	1414	1421	Right-handed alpha
Helix 45	AE9	K	1498	1503	Right-handed alpha
Helix 46	AF1	K	1533	1536	Right-handed 310
Helix 47	AF2	K	1539	1549	Right-handed alpha
Helix 48	AF3	K	5007	5017	Right-handed alpha
Helix 49	AF4	K	5060	5065	Right-handed alpha
Helix 50	AF5	K	5079	5090	Right-handed alpha
Helix 51	AF6	K	5114	5121	Right-handed alpha
Helix 52	AF7	K	5160	5172	Right-handed alpha
Helix 53	AF8	K	5259	5277	Right-handed alpha
Helix 54	AF9	K	5284	5288	Right-handed 310
Helix 55	AG1	K	5289	5295	Right-handed alpha
Helix 56	AG2	K	5298	5308	Right-handed alpha
Helix 57	AG3	K	5383	5395	Right-handed alpha
Helix 58	AG4	K	5433	5446	Right-handed alpha
Helix 59	AG5	K	5468	5472	Right-handed 310
Helix 60	AG6	T	369	371	Right-handed 310
Helix 61	AG7	T	496	501	Right-handed alpha
Helix 62	AG8	T	525	532	Right-handed alpha
Helix 63	AG9	T	593	595	Right-handed 310
Helix 64	AH1	T	596	619	Right-handed alpha
Helix 65	AH2	P	52	59	Right-handed alpha
Helix 66	AH3	P	61	76	Right-handed alpha
Helix 67	AH4	P	79	91	Right-handed alpha
Helix 68	AH5	P	92	97	Right-handed alpha
Helix 69	AH6	Q	52	59	Right-handed alpha
Helix 70	AH7	Q	61	75	Right-handed alpha
Helix 71	AH8	Q	79	91	Right-handed alpha
Helix 72	AH9	Q	92	97	Right-handed alpha

There are 36 sheets in PDB entry 9YM8. 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,

There are 5 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	O	12	16	first strand
Strand 2	O	2	7	anti-parallel
Strand 3	O	66	70	parallel
Strand 4	O	42	45	anti-parallel
Strand 5	O	48	49	anti-parallel

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There are 5 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	U	12	16	first strand
Strand 2	U	2	7	anti-parallel
Strand 3	U	66	70	parallel
Strand 4	U	42	45	anti-parallel
Strand 5	U	48	49	anti-parallel

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There are 2 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	83	84	first strand
Strand 2	B	80	81	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	B	97	98	first strand
Strand 2	G	101	102	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	77	78	first strand
Strand 2	D	53	54	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	C	101	102	first strand
Strand 2	F	97	98	parallel

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There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	83	84	first strand
Strand 2	F	80	81	parallel

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There are 2 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	77	78	first strand
Strand 2	H	53	54	parallel

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There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	36	41	first strand
Strand 2	R	327	331	anti-parallel
Strand 3	R	315	318	anti-parallel
Strand 4	R	307	309	anti-parallel

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There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	48	53	first strand
Strand 2	R	59	64	anti-parallel
Strand 3	R	69	73	anti-parallel
Strand 4	R	79	83	anti-parallel

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There are 4 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	90	95	first strand
Strand 2	R	101	106	anti-parallel
Strand 3	R	110	115	anti-parallel
Strand 4	R	120	126	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	R	134	137	first strand
Strand 2	R	143	147	anti-parallel
Strand 3	R	153	157	anti-parallel
Strand 4	R	163	167	anti-parallel

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There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	174	179	first strand
Strand 2	R	185	190	anti-parallel
Strand 3	R	194	199	anti-parallel
Strand 4	R	205	210	anti-parallel

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There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	217	222	first strand
Strand 2	R	228	233	anti-parallel
Strand 3	R	237	242	anti-parallel
Strand 4	R	248	252	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	264	267	first strand
Strand 2	R	273	277	anti-parallel
Strand 3	R	282	287	anti-parallel
Strand 4	R	293	298	anti-parallel

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There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	20	21	first strand
Strand 2	N	317	321	anti-parallel
Strand 3	N	310	314	anti-parallel
Strand 4	N	298	303	anti-parallel

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There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	27	32	first strand
Strand 2	N	38	43	anti-parallel
Strand 3	N	47	52	anti-parallel
Strand 4	N	57	63	anti-parallel

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There are 5 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	69	74	first strand
Strand 2	N	80	85	anti-parallel
Strand 3	N	89	94	anti-parallel
Strand 4	N	100	105	anti-parallel
Strand 5	N	453	456	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	N	110	115	first strand
Strand 2	N	122	127	anti-parallel
Strand 3	N	133	136	anti-parallel
Strand 4	N	143	144	anti-parallel

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There are 4 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	157	159	first strand
Strand 2	N	165	168	anti-parallel
Strand 3	N	174	179	anti-parallel
Strand 4	N	185	190	anti-parallel

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There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	201	206	first strand
Strand 2	N	212	217	anti-parallel
Strand 3	N	222	226	anti-parallel
Strand 4	N	243	245	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	N	254	259	first strand
Strand 2	N	265	270	anti-parallel
Strand 3	N	275	280	anti-parallel
Strand 4	N	286	291	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	N	343	344	first strand
Strand 2	K	5429	5432	parallel
Strand 3	K	5459	5462	anti-parallel
Strand 4	K	5452	5456	anti-parallel

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There are 3 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	1364	1368	first strand
Strand 2	K	5176	5180	anti-parallel
Strand 3	K	5183	5184	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	K	1443	1444	first strand
Strand 2	K	1451	1452	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	K	1520	1522	first strand
Strand 2	K	1529	1531	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	K	5049	5053	first strand
Strand 2	K	5056	5059	anti-parallel

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There are 2 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	5076	5077	first strand
Strand 2	K	5156	5157	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	K	5124	5125	first strand
Strand 2	K	5131	5132	anti-parallel

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There are 5 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	5187	5190	first strand
Strand 2	K	5208	5217	anti-parallel
Strand 3	K	5225	5234	anti-parallel
Strand 4	K	5239	5246	anti-parallel
Strand 5	K	5254	5257	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	K	5399	5403	first strand
Strand 2	K	5409	5413	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	K	5422	5426	first strand
Strand 2	K	5492	5498	anti-parallel
Strand 3	K	5481	5487	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	K	5474	5475	first strand
Strand 2	K	5509	5510	parallel

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There are 4 strands in AD7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	T	373	375	first strand
Strand 2	T	341	348	anti-parallel
Strand 3	T	517	523	anti-parallel
Strand 4	T	510	514	anti-parallel

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There are 7 strands in AD8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	T	383	388	first strand
Strand 2	T	407	412	anti-parallel
Strand 3	T	563	569	anti-parallel
Strand 4	T	435	441	anti-parallel
Strand 5	T	457	461	anti-parallel
Strand 6	T	467	469	anti-parallel
Strand 7	T	472	474	anti-parallel

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There are 7 strands in AD9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	T	393	394	first strand
Strand 2	T	400	402	anti-parallel
Strand 3	T	573	577	anti-parallel
Strand 4	T	419	429	anti-parallel
Strand 5	T	485	492	anti-parallel
Strand 6	T	540	545	anti-parallel
Strand 7	T	548	555	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: 9YM8

Analysis of interatomic Contacts of Structural Units in PDB entry:
9YM8