Analysis of interatomic Contacts of Structural Units in PDB entry:
8YJ8

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 8YJ8 entry

There are 4 chains in PDB entry 8YJ8 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 15	LYS 294
B	ASP 16	LYS 294
C	GLU 1	ALA 126
D	VAL 2	ALA 126

There are 29 helices in PDB entry 8YJ8. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	24	36	Right-handed alpha
Helix 2	AA2	A	57	67	Right-handed alpha
Helix 3	AA3	A	83	92	Right-handed alpha
Helix 4	AA4	A	114	118	Right-handed 310
Helix 5	AA5	A	124	127	Right-handed 310
Helix 6	AA6	A	128	147	Right-handed alpha
Helix 7	AA7	A	150	175	Right-handed alpha
Helix 8	AA8	A	193	201	Right-handed alpha
Helix 9	AA9	A	217	231	Right-handed alpha
Helix 10	AB1	A	244	255	Right-handed alpha
Helix 11	AB2	A	276	294	Right-handed alpha
Helix 12	AB3	B	24	36	Right-handed alpha
Helix 13	AB4	B	57	67	Right-handed alpha
Helix 14	AB5	B	83	92	Right-handed alpha
Helix 15	AB6	B	114	118	Right-handed 310
Helix 16	AB7	B	124	127	Right-handed 310
Helix 17	AB8	B	128	147	Right-handed alpha
Helix 18	AB9	B	150	175	Right-handed alpha
Helix 19	AC1	B	180	184	Right-handed 310
Helix 20	AC2	B	193	201	Right-handed alpha
Helix 21	AC3	B	217	231	Right-handed alpha
Helix 22	AC4	B	244	255	Right-handed alpha
Helix 23	AC5	B	276	293	Right-handed alpha
Helix 24	AC6	C	28	30	Right-handed 310
Helix 25	AC7	C	61	65	Right-handed 310
Helix 26	AC8	C	87	91	Right-handed 310
Helix 27	AC9	D	61	65	Right-handed 310
Helix 28	AD1	D	74	76	Right-handed 310
Helix 29	AD2	D	87	91	Right-handed 310

There are 12 sheets in PDB entry 8YJ8. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

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	39	43	first strand
Strand 2	A	18	22	parallel
Strand 3	A	69	72	parallel
Strand 4	A	100	102	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	A	186	190	first strand
Strand 2	A	204	208	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	236	239	first strand
Strand 2	A	258	262	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	40	43	first strand
Strand 2	B	19	22	parallel
Strand 3	B	69	72	parallel
Strand 4	B	100	102	parallel

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There are 2 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	110	111	first strand
Strand 2	B	121	122	anti-parallel

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There are 2 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	186	190	first strand
Strand 2	B	204	208	parallel

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There are 2 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	236	239	first strand
Strand 2	B	258	262	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	4	7	first strand
Strand 2	C	18	24	anti-parallel
Strand 3	C	78	83	anti-parallel
Strand 4	C	68	73	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	C	10	12	first strand
Strand 2	C	119	123	parallel
Strand 3	C	92	100	anti-parallel
Strand 4	C	32	39	anti-parallel
Strand 5	C	46	51	anti-parallel
Strand 6	C	57	58	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	C	10	12	first strand
Strand 2	C	119	123	parallel
Strand 3	C	92	100	anti-parallel
Strand 4	C	114	115	anti-parallel

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There are 4 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	4	7	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 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	119	123	parallel
Strand 3	D	92	100	anti-parallel
Strand 4	D	32	39	anti-parallel
Strand 5	D	46	51	anti-parallel
Strand 6	D	57	58	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: 8YJ8

Analysis of interatomic Contacts of Structural Units in PDB entry:
8YJ8