Analysis of interatomic Contacts of Structural Units in PDB entry:
4Y8D

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 4Y8D entry

There are 4 chains in PDB entry 4Y8D (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 27	GLU 333
C	GLN 1	SER 120
B	ASP 27	GLU 333
D	GLN 1	SER 121

There are 22 helices in PDB entry 4Y8D. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	75	93	Right-handed alpha
Helix 2	AA2	A	130	138	Right-handed alpha
Helix 3	AA3	A	139	141	Right-handed 310
Helix 4	AA4	A	144	164	Right-handed alpha
Helix 5	AA5	A	175	177	Right-handed 310
Helix 6	AA6	A	241	259	Right-handed alpha
Helix 7	AA7	A	285	296	Right-handed alpha
Helix 8	AA8	A	305	320	Right-handed alpha
Helix 9	AA9	A	328	332	Right-handed 310
Helix 10	AB1	C	84	88	Right-handed 310
Helix 11	AB2	C	98	106	Right-handed alpha
Helix 12	AB3	B	75	93	Right-handed alpha
Helix 13	AB4	B	130	138	Right-handed alpha
Helix 14	AB5	B	144	164	Right-handed alpha
Helix 15	AB6	B	175	177	Right-handed 310
Helix 16	AB7	B	241	259	Right-handed alpha
Helix 17	AB8	B	285	287	Right-handed 310
Helix 18	AB9	B	288	296	Right-handed alpha
Helix 19	AC1	B	305	320	Right-handed alpha
Helix 20	AC2	B	328	332	Right-handed 310
Helix 21	AC3	D	84	88	Right-handed 310
Helix 22	AC4	D	98	106	Right-handed alpha

There are 10 sheets in PDB entry 4Y8D. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1,

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	32	35	first strand
Strand 2	A	38	47	anti-parallel
Strand 3	A	52	59	anti-parallel
Strand 4	A	65	73	anti-parallel
Strand 5	A	117	123	anti-parallel
Strand 6	A	101	107	anti-parallel

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There are 3 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	128	129	first strand
Strand 2	A	179	181	anti-parallel
Strand 3	A	187	189	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	C	4	8	first strand
Strand 2	C	18	24	anti-parallel
Strand 3	C	75	80	anti-parallel
Strand 4	C	65	69	anti-parallel

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There are 6 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	10	12	first strand
Strand 2	C	115	119	parallel
Strand 3	C	89	95	anti-parallel
Strand 4	C	30	36	anti-parallel
Strand 5	C	43	49	anti-parallel
Strand 6	C	55	57	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	10	12	first strand
Strand 2	C	115	119	parallel
Strand 3	C	89	95	anti-parallel
Strand 4	C	110	111	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	B	32	35	first strand
Strand 2	B	38	47	anti-parallel
Strand 3	B	52	59	anti-parallel
Strand 4	B	65	73	anti-parallel
Strand 5	B	117	123	anti-parallel
Strand 6	B	101	107	anti-parallel

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There are 3 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	128	129	first strand
Strand 2	B	179	181	anti-parallel
Strand 3	B	187	189	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	D	4	8	first strand
Strand 2	D	18	24	anti-parallel
Strand 3	D	75	80	anti-parallel
Strand 4	D	65	69	anti-parallel

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There are 6 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	12	first strand
Strand 2	D	115	119	parallel
Strand 3	D	89	95	anti-parallel
Strand 4	D	30	36	anti-parallel
Strand 5	D	43	49	anti-parallel
Strand 6	D	55	57	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	10	12	first strand
Strand 2	D	115	119	parallel
Strand 3	D	89	95	anti-parallel
Strand 4	D	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: 4Y8D

Analysis of interatomic Contacts of Structural Units in PDB entry:
4Y8D