Analysis of interatomic Contacts of Structural Units in PDB entry:
1VYJ

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 1VYJ entry

There are 12 chains in PDB entry 1VYJ (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 1	ASP 257
B	SER 1	LYS 16
C	MET 1	ASP 257
D	SER 1	LYS 16
E	MET 1	ASP 257
F	SER 1	LYS 16
G	MET 1	GLY 260
H	SER 1	LYS 16
I	MET 1	ASP 257
J	SER 1	LYS 16
K	MET 1	ASP 257
L	SER 1	LYS 16

There are 42 helices in PDB entry 1VYJ. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	9	20	Right-handed alpha
Helix 2	2	A	55	57	Right-handed 310
Helix 3	3	A	72	80	Right-handed alpha
Helix 4	4	A	141	155	Right-handed alpha
Helix 5	5	A	209	216	Right-handed alpha
Helix 6	6	A	217	222	Right-handed 310
Helix 7	7	B	7	11	Right-handed 310
Helix 8	8	C	9	20	Right-handed alpha
Helix 9	9	C	55	57	Right-handed 310
Helix 10	10	C	72	80	Right-handed alpha
Helix 11	11	C	141	152	Right-handed alpha
Helix 12	12	C	209	216	Right-handed alpha
Helix 13	13	C	217	222	Right-handed 310
Helix 14	14	D	7	11	Right-handed 310
Helix 15	15	E	9	21	Right-handed alpha
Helix 16	16	E	55	57	Right-handed 310
Helix 17	17	E	72	80	Right-handed alpha
Helix 18	18	E	141	153	Right-handed alpha
Helix 19	19	E	209	216	Right-handed alpha
Helix 20	20	E	217	222	Right-handed 310
Helix 21	21	F	7	11	Right-handed 310
Helix 22	22	G	8	18	Right-handed alpha
Helix 23	23	G	55	57	Right-handed 310
Helix 24	24	G	72	80	Right-handed alpha
Helix 25	25	G	141	153	Right-handed alpha
Helix 26	26	G	209	216	Right-handed alpha
Helix 27	27	G	217	222	Right-handed 310
Helix 28	28	H	7	11	Right-handed 310
Helix 29	29	I	9	18	Right-handed alpha
Helix 30	30	I	55	57	Right-handed 310
Helix 31	31	I	72	81	Right-handed alpha
Helix 32	32	I	141	153	Right-handed alpha
Helix 33	33	I	209	216	Right-handed alpha
Helix 34	34	I	217	222	Right-handed 310
Helix 35	35	J	7	11	Right-handed 310
Helix 36	36	K	9	20	Right-handed alpha
Helix 37	37	K	55	57	Right-handed 310
Helix 38	38	K	72	80	Right-handed alpha
Helix 39	39	K	141	153	Right-handed alpha
Helix 40	40	K	209	216	Right-handed alpha
Helix 41	41	K	217	222	Right-handed 310
Helix 42	42	L	7	11	Right-handed 310

There are 22 sheets in PDB entry 1VYJ. Click on sheet of interest to get list of strands forming it: AA, AB, AC, AD, AE, CA, CB, CC, CD, EA, EB, GA, GB, GC, GD, GE, IA, IB, IC, KA, KB, KC,

There are 8 strands in AA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	2	6	first strand
Strand 2	A	87	92	anti-parallel
Strand 3	A	98	104	anti-parallel
Strand 4	A	110	117	anti-parallel
Strand 5	C	176	183	anti-parallel
Strand 6	C	166	172	anti-parallel
Strand 7	C	157	162	anti-parallel
Strand 8	C	203	208	anti-parallel

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There are 9 strands in AB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	66	71	first strand
Strand 2	A	25	31	anti-parallel
Strand 3	A	34	40	anti-parallel
Strand 4	A	46	53	anti-parallel
Strand 5	A	245	251	anti-parallel
Strand 6	A	235	241	anti-parallel
Strand 7	A	224	229	anti-parallel
Strand 8	A	135	140	anti-parallel
Strand 9	A	196	199	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	126	127	first strand
Strand 2	B	13	14	anti-parallel

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There are 9 strands in AD sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	203	208	first strand
Strand 2	A	157	162	anti-parallel
Strand 3	A	166	173	anti-parallel
Strand 4	A	176	183	anti-parallel
Strand 5	E	111	117	anti-parallel
Strand 6	E	98	104	anti-parallel
Strand 7	E	87	92	anti-parallel
Strand 8	E	2	6	anti-parallel
Strand 9	E	59	62	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	254	255	first strand
Strand 2	B	4	5	anti-parallel

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There are 9 strands in CA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	59	62	first strand
Strand 2	C	2	6	anti-parallel
Strand 3	C	87	92	anti-parallel
Strand 4	C	98	104	anti-parallel
Strand 5	C	110	117	anti-parallel
Strand 6	E	176	183	anti-parallel
Strand 7	E	166	172	anti-parallel
Strand 8	E	157	162	anti-parallel
Strand 9	E	203	208	anti-parallel

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There are 9 strands in CB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	66	71	first strand
Strand 2	C	25	30	anti-parallel
Strand 3	C	34	40	anti-parallel
Strand 4	C	46	53	anti-parallel
Strand 5	C	245	251	anti-parallel
Strand 6	C	235	241	anti-parallel
Strand 7	C	224	229	anti-parallel
Strand 8	C	135	140	anti-parallel
Strand 9	C	196	199	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	126	127	first strand
Strand 2	D	13	14	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	254	255	first strand
Strand 2	D	4	5	anti-parallel

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There are 9 strands in EA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	66	71	first strand
Strand 2	E	25	31	anti-parallel
Strand 3	E	34	40	anti-parallel
Strand 4	E	46	53	anti-parallel
Strand 5	E	245	251	anti-parallel
Strand 6	E	235	241	anti-parallel
Strand 7	E	224	229	anti-parallel
Strand 8	E	135	140	anti-parallel
Strand 9	E	196	199	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	254	255	first strand
Strand 2	F	4	5	anti-parallel

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There are 8 strands in GA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	2	6	first strand
Strand 2	G	87	92	anti-parallel
Strand 3	G	98	104	anti-parallel
Strand 4	G	110	117	anti-parallel
Strand 5	I	176	183	anti-parallel
Strand 6	I	166	173	anti-parallel
Strand 7	I	157	163	anti-parallel
Strand 8	I	203	208	anti-parallel

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There are 9 strands in GB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	66	71	first strand
Strand 2	G	25	31	anti-parallel
Strand 3	G	34	40	anti-parallel
Strand 4	G	46	53	anti-parallel
Strand 5	G	245	251	anti-parallel
Strand 6	G	235	241	anti-parallel
Strand 7	G	224	229	anti-parallel
Strand 8	G	135	140	anti-parallel
Strand 9	G	196	199	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	126	127	first strand
Strand 2	H	13	14	anti-parallel

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There are 9 strands in GD sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	203	208	first strand
Strand 2	G	157	162	anti-parallel
Strand 3	G	166	172	anti-parallel
Strand 4	G	176	183	anti-parallel
Strand 5	K	110	118	anti-parallel
Strand 6	K	97	104	anti-parallel
Strand 7	K	87	92	anti-parallel
Strand 8	K	2	6	anti-parallel
Strand 9	K	59	62	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	254	255	first strand
Strand 2	H	4	5	anti-parallel

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There are 9 strands in IA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	59	62	first strand
Strand 2	I	2	6	anti-parallel
Strand 3	I	87	92	anti-parallel
Strand 4	I	98	104	anti-parallel
Strand 5	I	111	117	anti-parallel
Strand 6	K	176	183	anti-parallel
Strand 7	K	166	173	anti-parallel
Strand 8	K	157	162	anti-parallel
Strand 9	K	203	208	anti-parallel

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There are 9 strands in IB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	66	71	first strand
Strand 2	I	25	30	anti-parallel
Strand 3	I	34	40	anti-parallel
Strand 4	I	46	53	anti-parallel
Strand 5	I	245	251	anti-parallel
Strand 6	I	235	240	anti-parallel
Strand 7	I	224	229	anti-parallel
Strand 8	I	135	140	anti-parallel
Strand 9	I	196	199	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	126	127	first strand
Strand 2	J	13	14	anti-parallel

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There are 8 strands in KA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	66	71	first strand
Strand 2	K	25	31	anti-parallel
Strand 3	K	34	40	anti-parallel
Strand 4	K	46	53	anti-parallel
Strand 5	K	245	251	anti-parallel
Strand 6	K	233	241	anti-parallel
Strand 7	K	224	230	anti-parallel
Strand 8	K	136	140	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	126	127	first strand
Strand 2	L	13	14	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	254	255	first strand
Strand 2	L	4	5	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: 1VYJ

Analysis of interatomic Contacts of Structural Units in PDB entry:
1VYJ