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

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 9YAF entry

There are 10 chains in PDB entry 9YAF (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 3	PRO 182
B	SER 3	GLN 191
C	ALA -1	GLY 11
D	GLN 2	PRO 218
E	GLY 3	SER 258
F	ILE 3	PRO 182
G	SER 3	ARG 189
H	ALA -1	PRO 10
I	GLN 2	PRO 216
J	GLY 3	ASP 256

There are 21 helices in PDB entry 9YAF. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	47	53	Right-handed 310
Helix 2	AA2	A	58	78	Right-handed alpha
Helix 3	AA3	B	54	64	Right-handed alpha
Helix 4	AA4	B	64	78	Right-handed alpha
Helix 5	AA5	B	78	87	Right-handed alpha
Helix 6	AA6	B	88	93	Right-handed 310
Helix 7	AA7	D	180	183	Right-handed 310
Helix 8	AA8	E	95	99	Right-handed 310
Helix 9	AA9	E	128	132	Right-handed 310
Helix 10	AB1	E	143	151	Right-handed alpha
Helix 11	AB2	E	210	214	Right-handed alpha
Helix 12	AB3	F	47	53	Right-handed 310
Helix 13	AB4	F	58	78	Right-handed alpha
Helix 14	AB5	G	54	64	Right-handed alpha
Helix 15	AB6	G	64	78	Right-handed alpha
Helix 16	AB7	G	78	87	Right-handed alpha
Helix 17	AB8	I	180	183	Right-handed 310
Helix 18	AB9	J	95	99	Right-handed 310
Helix 19	AC1	J	128	132	Right-handed 310
Helix 20	AC2	J	143	151	Right-handed alpha
Helix 21	AC3	J	210	214	Right-handed alpha

There are 34 sheets in PDB entry 9YAF. 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,

There are 8 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	42	45	first strand
Strand 2	A	31	37	anti-parallel
Strand 3	A	21	28	anti-parallel
Strand 4	A	7	16	anti-parallel
Strand 5	B	8	18	anti-parallel
Strand 6	B	23	32	anti-parallel
Strand 7	B	35	41	anti-parallel
Strand 8	B	47	49	anti-parallel

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There are 4 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	90	95	first strand
Strand 2	A	105	114	anti-parallel
Strand 3	A	147	155	anti-parallel
Strand 4	A	134	136	anti-parallel

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There are 4 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	90	95	first strand
Strand 2	A	105	114	anti-parallel
Strand 3	A	147	155	anti-parallel
Strand 4	A	140	141	anti-parallel

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There are 4 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	128	130	first strand
Strand 2	A	120	125	anti-parallel
Strand 3	A	163	168	anti-parallel
Strand 4	A	176	180	anti-parallel

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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	98	103	first strand
Strand 2	B	114	122	anti-parallel
Strand 3	B	155	162	anti-parallel
Strand 4	B	142	144	anti-parallel

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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	98	103	first strand
Strand 2	B	114	122	anti-parallel
Strand 3	B	155	162	anti-parallel
Strand 4	B	148	149	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	137	138	first strand
Strand 2	B	128	133	anti-parallel
Strand 3	B	171	176	anti-parallel
Strand 4	B	184	188	anti-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	D	10	14	first strand
Strand 2	D	121	126	parallel
Strand 3	D	100	107	anti-parallel
Strand 4	D	39	44	anti-parallel
Strand 5	D	51	56	anti-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	D	10	14	first strand
Strand 2	D	121	126	parallel
Strand 3	D	100	107	anti-parallel
Strand 4	D	115	117	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	D	19	21	first strand
Strand 2	D	87	91	anti-parallel
Strand 3	D	76	80	anti-parallel
Strand 4	D	66	68	anti-parallel

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There are 8 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	169	171	first strand
Strand 2	D	188	193	anti-parallel
Strand 3	D	148	153	anti-parallel
Strand 4	D	135	141	anti-parallel
Strand 5	E	136	141	anti-parallel
Strand 6	E	152	162	anti-parallel
Strand 7	E	200	209	anti-parallel
Strand 8	E	182	184	anti-parallel

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There are 8 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	169	171	first strand
Strand 2	D	188	193	anti-parallel
Strand 3	D	148	153	anti-parallel
Strand 4	D	135	141	anti-parallel
Strand 5	E	136	141	anti-parallel
Strand 6	E	152	162	anti-parallel
Strand 7	E	200	209	anti-parallel
Strand 8	E	189	190	anti-parallel

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There are 2 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	177	179	first strand
Strand 2	D	184	186	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	E	5	7	first strand
Strand 2	E	19	24	anti-parallel
Strand 3	E	87	91	anti-parallel
Strand 4	E	76	80	anti-parallel

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There are 6 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	10	14	first strand
Strand 2	E	121	126	parallel
Strand 3	E	100	107	anti-parallel
Strand 4	E	38	45	anti-parallel
Strand 5	E	49	57	anti-parallel
Strand 6	E	64	68	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	E	10	14	first strand
Strand 2	E	121	126	parallel
Strand 3	E	100	107	anti-parallel
Strand 4	E	116	117	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	E	176	178	first strand
Strand 2	E	167	173	anti-parallel
Strand 3	E	219	226	anti-parallel
Strand 4	E	245	252	anti-parallel

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There are 8 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	42	45	first strand
Strand 2	F	31	37	anti-parallel
Strand 3	F	21	28	anti-parallel
Strand 4	F	7	16	anti-parallel
Strand 5	G	8	18	anti-parallel
Strand 6	G	23	32	anti-parallel
Strand 7	G	35	41	anti-parallel
Strand 8	G	47	49	anti-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	F	90	95	first strand
Strand 2	F	105	114	anti-parallel
Strand 3	F	147	155	anti-parallel
Strand 4	F	134	136	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	F	90	95	first strand
Strand 2	F	105	114	anti-parallel
Strand 3	F	147	155	anti-parallel
Strand 4	F	140	141	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	F	128	129	first strand
Strand 2	F	120	125	anti-parallel
Strand 3	F	163	168	anti-parallel
Strand 4	F	176	180	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	98	102	first strand
Strand 2	G	115	122	anti-parallel
Strand 3	G	155	161	anti-parallel
Strand 4	G	142	144	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	G	98	102	first strand
Strand 2	G	115	122	anti-parallel
Strand 3	G	155	161	anti-parallel
Strand 4	G	148	149	anti-parallel

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There are 4 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	137	138	first strand
Strand 2	G	128	133	anti-parallel
Strand 3	G	171	176	anti-parallel
Strand 4	G	184	186	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	I	5	6	first strand
Strand 2	I	16	24	anti-parallel
Strand 3	I	86	93	anti-parallel
Strand 4	I	76	78	anti-parallel
Strand 5	I	66	68	anti-parallel

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There are 5 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	10	14	first strand
Strand 2	I	121	126	parallel
Strand 3	I	100	107	anti-parallel
Strand 4	I	38	44	anti-parallel
Strand 5	I	50	56	anti-parallel

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There are 4 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	10	14	first strand
Strand 2	I	121	126	parallel
Strand 3	I	100	107	anti-parallel
Strand 4	I	115	117	anti-parallel

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There are 8 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	169	171	first strand
Strand 2	I	188	193	anti-parallel
Strand 3	I	148	153	anti-parallel
Strand 4	I	135	141	anti-parallel
Strand 5	J	136	141	anti-parallel
Strand 6	J	152	162	anti-parallel
Strand 7	J	200	209	anti-parallel
Strand 8	J	182	184	anti-parallel

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There are 8 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	169	171	first strand
Strand 2	I	188	193	anti-parallel
Strand 3	I	148	153	anti-parallel
Strand 4	I	135	141	anti-parallel
Strand 5	J	136	141	anti-parallel
Strand 6	J	152	162	anti-parallel
Strand 7	J	200	209	anti-parallel
Strand 8	J	189	190	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	I	177	179	first strand
Strand 2	I	184	186	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	J	5	7	first strand
Strand 2	J	19	24	anti-parallel
Strand 3	J	87	91	anti-parallel
Strand 4	J	76	80	anti-parallel

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There are 6 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	10	14	first strand
Strand 2	J	121	126	parallel
Strand 3	J	100	107	anti-parallel
Strand 4	J	38	45	anti-parallel
Strand 5	J	49	57	anti-parallel
Strand 6	J	64	67	anti-parallel

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There are 4 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	10	14	first strand
Strand 2	J	121	126	parallel
Strand 3	J	100	107	anti-parallel
Strand 4	J	116	117	anti-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	J	176	178	first strand
Strand 2	J	167	173	anti-parallel
Strand 3	J	219	226	anti-parallel
Strand 4	J	245	252	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: 9YAF

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