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

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 9LYP entry

There are 3 chains in PDB entry 9LYP (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
B	ASN 334	PRO 527
i	GLN 1	CYS 218
j	GLN 1	CYS 223

There are 15 helices in PDB entry 9LYP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	B	337	343	Right-handed alpha
Helix 2	AA2	B	364	370	Right-handed alpha
Helix 3	AA3	B	385	390	Right-handed 310
Helix 4	AA4	B	404	408	Right-handed alpha
Helix 5	AA5	B	416	422	Right-handed alpha
Helix 6	AA6	B	438	443	Right-handed alpha
Helix 7	AA7	B	498	500	Right-handed 310
Helix 8	AA8	B	501	506	Right-handed alpha
Helix 9	AA9	i	51	55	Right-handed 310
Helix 10	AB1	i	124	132	Right-handed alpha
Helix 11	AB2	i	186	193	Right-handed alpha
Helix 12	AB3	i	216	218	Right-handed 310
Helix 13	AB4	j	87	91	Right-handed 310
Helix 14	AB5	j	163	166	Right-handed 310
Helix 15	AB6	j	193	197	Right-handed alpha

There are 14 sheets in PDB entry 9LYP. 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,

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	B	354	358	first strand
Strand 2	B	395	403	anti-parallel
Strand 3	B	507	515	anti-parallel
Strand 4	B	433	437	anti-parallel

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There are 2 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	452	454	first strand
Strand 2	B	492	494	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	i	9	12	first strand
Strand 2	i	106	109	parallel

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There are 3 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	i	17	23	first strand
Strand 2	i	72	78	anti-parallel
Strand 3	i	64	69	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	i	47	50	first strand
Strand 2	i	36	40	anti-parallel
Strand 3	i	87	94	anti-parallel
Strand 4	i	98	101	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	i	118	122	first strand
Strand 2	i	134	143	anti-parallel
Strand 3	i	177	185	anti-parallel
Strand 4	i	163	167	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	i	157	159	first strand
Strand 2	i	149	154	anti-parallel
Strand 3	i	195	201	anti-parallel
Strand 4	i	209	214	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	j	3	7	first strand
Strand 2	j	18	25	anti-parallel
Strand 3	j	78	83	anti-parallel
Strand 4	j	69	73	anti-parallel

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There are 2 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	j	11	12	first strand
Strand 2	j	117	118	parallel

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There are 5 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	j	58	60	first strand
Strand 2	j	45	52	anti-parallel
Strand 3	j	33	39	anti-parallel
Strand 4	j	93	98	anti-parallel
Strand 5	j	109	110	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	j	58	60	first strand
Strand 2	j	45	52	anti-parallel
Strand 3	j	33	39	anti-parallel
Strand 4	j	93	98	anti-parallel
Strand 5	j	114	115	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	j	127	130	first strand
Strand 2	j	142	150	anti-parallel
Strand 3	j	186	192	anti-parallel
Strand 4	j	170	172	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	j	158	161	first strand
Strand 2	j	201	207	anti-parallel
Strand 3	j	210	218	anti-parallel

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There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	j	176	177	first strand
Strand 2	j	183	184	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: 9LYP

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