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

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 9YXD entry

There are 5 chains in PDB entry 9YXD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 6	SER 92
B	SER 2	GLY 107
C	ASP 1	GLY 218
D	GLN 3	LYS 218
K	VAL 2	SER 120

There are 17 helices in PDB entry 9YXD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	16	19	Right-handed 310
Helix 2	AA2	A	40	45	Right-handed alpha
Helix 3	AA3	B	15	18	Right-handed 310
Helix 4	AA4	C	83	87	Right-handed 310
Helix 5	AA5	C	127	133	Right-handed alpha
Helix 6	AA6	C	189	194	Right-handed alpha
Helix 7	AA7	D	28	32	Right-handed 310
Helix 8	AA8	D	62	65	Right-handed 310
Helix 9	AA9	D	87	91	Right-handed 310
Helix 10	AB1	D	131	133	Right-handed 310
Helix 11	AB2	D	160	162	Right-handed 310
Helix 12	AB3	D	191	193	Right-handed 310
Helix 13	AB4	D	205	208	Right-handed 310
Helix 14	AB5	K	28	32	Right-handed 310
Helix 15	AB6	K	62	65	Right-handed 310
Helix 16	AB7	K	74	76	Right-handed 310
Helix 17	AB8	K	87	91	Right-handed 310

There are 18 sheets in PDB entry 9YXD. 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,

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	11	14	first strand
Strand 2	A	26	38	anti-parallel
Strand 3	B	19	35	anti-parallel
Strand 4	B	4	14	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	11	14	first strand
Strand 2	A	26	38	anti-parallel
Strand 3	A	53	57	anti-parallel
Strand 4	B	92	95	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	59	70	first strand
Strand 2	A	74	85	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	B	49	63	first strand
Strand 2	B	72	86	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	C	4	7	first strand
Strand 2	C	19	25	anti-parallel
Strand 3	C	74	79	anti-parallel
Strand 4	C	66	70	anti-parallel

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There are 6 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	10	14	first strand
Strand 2	C	108	113	parallel
Strand 3	C	88	96	anti-parallel
Strand 4	C	35	42	anti-parallel
Strand 5	C	49	53	anti-parallel
Strand 6	C	57	58	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	C	10	14	first strand
Strand 2	C	108	113	parallel
Strand 3	C	88	96	anti-parallel
Strand 4	C	101	104	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	C	120	124	first strand
Strand 2	C	135	145	anti-parallel
Strand 3	C	179	188	anti-parallel
Strand 4	C	165	169	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	C	159	160	first strand
Strand 2	C	150	156	anti-parallel
Strand 3	C	197	204	anti-parallel
Strand 4	C	211	216	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	4	6	first strand
Strand 2	D	18	24	anti-parallel
Strand 3	D	78	83	anti-parallel
Strand 4	D	68	73	anti-parallel

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There are 6 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	10	12	first strand
Strand 2	D	111	115	parallel
Strand 3	D	92	100	anti-parallel
Strand 4	D	34	39	anti-parallel
Strand 5	D	45	51	anti-parallel
Strand 6	D	58	60	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	D	10	12	first strand
Strand 2	D	111	115	parallel
Strand 3	D	92	100	anti-parallel
Strand 4	D	103	107	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	D	124	128	first strand
Strand 2	D	139	149	anti-parallel
Strand 3	D	180	189	anti-parallel
Strand 4	D	167	169	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	D	135	136	first strand
Strand 2	D	139	149	anti-parallel
Strand 3	D	180	189	anti-parallel
Strand 4	D	173	174	anti-parallel

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There are 3 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	155	158	first strand
Strand 2	D	199	204	anti-parallel
Strand 3	D	209	214	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	K	3	7	first strand
Strand 2	K	18	25	anti-parallel
Strand 3	K	78	83	anti-parallel
Strand 4	K	68	73	anti-parallel

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There are 6 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	10	12	first strand
Strand 2	K	115	119	parallel
Strand 3	K	92	98	anti-parallel
Strand 4	K	34	39	anti-parallel
Strand 5	K	46	51	anti-parallel
Strand 6	K	58	60	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	10	12	first strand
Strand 2	K	115	119	parallel
Strand 3	K	92	98	anti-parallel
Strand 4	K	110	111	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: 9YXD

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