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

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 9YDP entry

There are 7 chains in PDB entry 9YDP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 1	PHE 241
B	SER 2	ASN 340
G	ASN 5	ARG 62
N	GLN 1	SER 128
R	SER 42	ARG 334
P	TYR 1	TYR 1
P	GLY 3	PHE 4

There are 29 helices in PDB entry 9YDP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	1	27	Right-handed alpha
Helix 2	AA2	A	37	44	Right-handed 310
Helix 3	AA3	A	90	96	Right-handed 310
Helix 4	AA4	A	109	111	Right-handed 310
Helix 5	AA5	A	112	125	Right-handed alpha
Helix 6	AA6	A	140	151	Right-handed alpha
Helix 7	AA7	A	154	158	Right-handed 310
Helix 8	AA8	A	159	165	Right-handed 310
Helix 9	AA9	A	178	199	Right-handed alpha
Helix 10	AB1	A	217	238	Right-handed alpha
Helix 11	AB2	B	3	26	Right-handed alpha
Helix 12	AB3	B	29	34	Right-handed alpha
Helix 13	AB4	G	6	24	Right-handed alpha
Helix 14	AB5	G	29	44	Right-handed alpha
Helix 15	AB6	N	28	32	Right-handed 310
Helix 16	AB7	N	62	65	Right-handed 310
Helix 17	AB8	N	87	91	Right-handed 310
Helix 18	AB9	R	43	77	Right-handed alpha
Helix 19	AC1	R	82	100	Right-handed alpha
Helix 20	AC2	R	101	112	Right-handed alpha
Helix 21	AC3	R	116	152	Right-handed alpha
Helix 22	AC4	R	152	160	Right-handed alpha
Helix 23	AC5	R	161	176	Right-handed alpha
Helix 24	AC6	R	176	186	Right-handed alpha
Helix 25	AC7	R	205	222	Right-handed alpha
Helix 26	AC8	R	222	241	Right-handed alpha
Helix 27	AC9	R	248	287	Right-handed alpha
Helix 28	AD1	R	293	319	Right-handed alpha
Helix 29	AD2	R	322	334	Right-handed alpha

There are 11 sheets in PDB entry 9YDP. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2,

There are 6 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	64	71	first strand
Strand 2	A	74	81	anti-parallel
Strand 3	A	28	35	parallel
Strand 4	A	100	106	parallel
Strand 5	A	133	139	parallel
Strand 6	A	206	210	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	B	47	52	first strand
Strand 2	B	335	339	anti-parallel
Strand 3	B	327	331	anti-parallel
Strand 4	B	315	320	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	B	58	63	first strand
Strand 2	B	69	74	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	88	94	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	B	100	105	first strand
Strand 2	B	111	116	anti-parallel
Strand 3	B	120	125	anti-parallel
Strand 4	B	134	140	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	146	151	first strand
Strand 2	B	156	161	anti-parallel
Strand 3	B	166	170	anti-parallel
Strand 4	B	175	180	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	187	192	first strand
Strand 2	B	198	203	anti-parallel
Strand 3	B	207	212	anti-parallel
Strand 4	B	218	223	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	229	234	first strand
Strand 2	B	240	245	anti-parallel
Strand 3	B	250	254	anti-parallel
Strand 4	B	259	264	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	273	278	first strand
Strand 2	B	284	289	anti-parallel
Strand 3	B	294	298	anti-parallel
Strand 4	B	304	308	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	N	3	7	first strand
Strand 2	N	18	25	anti-parallel
Strand 3	N	78	83	anti-parallel
Strand 4	N	68	73	anti-parallel

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There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	11	12	first strand
Strand 2	N	122	126	parallel
Strand 3	N	92	98	anti-parallel
Strand 4	N	34	39	anti-parallel
Strand 5	N	45	51	anti-parallel
Strand 6	N	58	60	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	R	187	192	first strand
Strand 2	R	195	200	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: 9YDP

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