Analysis of interatomic Contacts of Structural Units in PDB entry:
5VYF

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 5VYF entry

There are 6 chains in PDB entry 5VYF (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
L	ASP 1	GLU 213
H	GLU 1	SER 215
F	THR 6	CYS 162
A	ASP 1	ARG 211
B	VAL 2	GLU 214
C	CYS 7	CYS 162

There are 28 helices in PDB entry 5VYF. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	L	79	83	Right-handed 310
Helix 2	AA2	L	121	128	Right-handed alpha
Helix 3	AA3	L	183	187	Right-handed alpha
Helix 4	AA4	H	28	32	Right-handed 310
Helix 5	AA5	H	62	65	Right-handed 310
Helix 6	AA6	H	87	91	Right-handed 310
Helix 7	AA7	F	7	19	Right-handed alpha
Helix 8	AA8	F	21	32	Right-handed alpha
Helix 9	AA9	F	35	52	Right-handed alpha
Helix 10	AB1	F	53	69	Right-handed alpha
Helix 11	AB2	F	95	108	Right-handed alpha
Helix 12	AB3	F	109	121	Right-handed alpha
Helix 13	AB4	F	123	141	Right-handed alpha
Helix 14	AB5	F	142	158	Right-handed alpha
Helix 15	AB6	A	79	83	Right-handed 310
Helix 16	AB7	A	121	128	Right-handed alpha
Helix 17	AB8	A	183	187	Right-handed alpha
Helix 18	AB9	B	28	32	Right-handed 310
Helix 19	AC1	B	62	65	Right-handed 310
Helix 20	AC2	B	87	91	Right-handed 310
Helix 21	AC3	C	8	19	Right-handed alpha
Helix 22	AC4	C	21	32	Right-handed alpha
Helix 23	AC5	C	35	52	Right-handed alpha
Helix 24	AC6	C	53	69	Right-handed alpha
Helix 25	AC7	C	95	108	Right-handed alpha
Helix 26	AC8	C	109	121	Right-handed alpha
Helix 27	AC9	C	123	141	Right-handed alpha
Helix 28	AD1	C	142	158	Right-handed alpha

There are 20 sheets in PDB entry 5VYF. 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, AC1, AC2,

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	L	4	7	first strand
Strand 2	L	19	25	anti-parallel
Strand 3	L	70	75	anti-parallel
Strand 4	L	62	67	anti-parallel

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There are 6 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	10	13	first strand
Strand 2	L	102	106	parallel
Strand 3	L	85	90	anti-parallel
Strand 4	L	33	38	anti-parallel
Strand 5	L	45	49	anti-parallel
Strand 6	L	53	54	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	L	10	13	first strand
Strand 2	L	102	106	parallel
Strand 3	L	85	90	anti-parallel
Strand 4	L	97	98	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	L	114	118	first strand
Strand 2	L	129	139	anti-parallel
Strand 3	L	173	182	anti-parallel
Strand 4	L	159	163	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	L	153	154	first strand
Strand 2	L	144	150	anti-parallel
Strand 3	L	191	198	anti-parallel
Strand 4	L	205	210	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	H	3	7	first strand
Strand 2	H	18	25	anti-parallel
Strand 3	H	78	83	anti-parallel
Strand 4	H	68	73	anti-parallel

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There are 6 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	11	12	first strand
Strand 2	H	109	113	parallel
Strand 3	H	92	98	anti-parallel
Strand 4	H	34	39	anti-parallel
Strand 5	H	45	51	anti-parallel
Strand 6	H	58	60	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	H	122	126	first strand
Strand 2	H	137	147	anti-parallel
Strand 3	H	178	187	anti-parallel
Strand 4	H	165	167	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	H	122	126	first strand
Strand 2	H	137	147	anti-parallel
Strand 3	H	178	187	anti-parallel
Strand 4	H	171	172	anti-parallel

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There are 3 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	153	156	first strand
Strand 2	H	196	202	anti-parallel
Strand 3	H	207	213	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	A	4	7	first strand
Strand 2	A	19	25	anti-parallel
Strand 3	A	70	75	anti-parallel
Strand 4	A	62	67	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	A	10	13	first strand
Strand 2	A	102	106	parallel
Strand 3	A	85	90	anti-parallel
Strand 4	A	33	38	anti-parallel
Strand 5	A	45	49	anti-parallel
Strand 6	A	53	54	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	A	10	13	first strand
Strand 2	A	102	106	parallel
Strand 3	A	85	90	anti-parallel
Strand 4	A	97	98	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	A	114	118	first strand
Strand 2	A	129	139	anti-parallel
Strand 3	A	173	182	anti-parallel
Strand 4	A	159	163	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	153	154	first strand
Strand 2	A	144	150	anti-parallel
Strand 3	A	192	198	anti-parallel
Strand 4	A	205	209	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	B	3	7	first strand
Strand 2	B	18	25	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	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	B	11	12	first strand
Strand 2	B	109	113	parallel
Strand 3	B	92	98	anti-parallel
Strand 4	B	34	39	anti-parallel
Strand 5	B	45	51	anti-parallel
Strand 6	B	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	B	122	126	first strand
Strand 2	B	137	147	anti-parallel
Strand 3	B	178	187	anti-parallel
Strand 4	B	165	167	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	122	126	first strand
Strand 2	B	137	147	anti-parallel
Strand 3	B	178	187	anti-parallel
Strand 4	B	171	172	anti-parallel

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There are 3 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	153	156	first strand
Strand 2	B	196	202	anti-parallel
Strand 3	B	207	213	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: 5VYF

Analysis of interatomic Contacts of Structural Units in PDB entry:
5VYF