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

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 5YMV entry

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

Chain ID	Initial residue	Terminal residue
A	MET 0	TRP 270
B	ASP 1	PHE 98
C	ALA 1	VAL 9
D	MET 0	TRP 270
E	ASP 1	PHE 98
F	ALA 1	VAL 9

There are 14 helices in PDB entry 5YMV. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	47	54	Right-handed alpha
Helix 2	AA2	A	55	84	Right-handed alpha
Helix 3	AA3	A	134	136	Right-handed 310
Helix 4	AA4	A	137	147	Right-handed alpha
Helix 5	AA5	A	148	159	Right-handed alpha
Helix 6	AA6	A	159	177	Right-handed alpha
Helix 7	AA7	A	249	251	Right-handed 310
Helix 8	AA8	D	47	54	Right-handed alpha
Helix 9	AA9	D	55	84	Right-handed alpha
Helix 10	AB1	D	134	136	Right-handed 310
Helix 11	AB2	D	137	147	Right-handed alpha
Helix 12	AB3	D	148	159	Right-handed alpha
Helix 13	AB4	D	159	177	Right-handed alpha
Helix 14	AB5	D	249	251	Right-handed 310

There are 12 sheets in PDB entry 5YMV. 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 8 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	44	45	first strand
Strand 2	A	31	37	anti-parallel
Strand 3	A	22	28	anti-parallel
Strand 4	A	2	12	anti-parallel
Strand 5	A	92	102	anti-parallel
Strand 6	A	105	115	anti-parallel
Strand 7	A	118	124	anti-parallel
Strand 8	A	129	132	anti-parallel

Back to list of sheets
Back to top of page

There are 4 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	183	191	first strand
Strand 2	A	194	204	anti-parallel
Strand 3	A	237	245	anti-parallel
Strand 4	A	224	231	anti-parallel

Back to list of sheets
Back to top of page

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	A	218	219	first strand
Strand 2	A	210	215	anti-parallel
Strand 3	A	253	258	anti-parallel
Strand 4	A	266	268	anti-parallel

Back to list of sheets
Back to top of page

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	5	10	first strand
Strand 2	B	20	29	anti-parallel
Strand 3	B	61	69	anti-parallel
Strand 4	B	49	50	anti-parallel

Back to list of sheets
Back to top of page

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	B	5	10	first strand
Strand 2	B	20	29	anti-parallel
Strand 3	B	61	69	anti-parallel
Strand 4	B	54	55	anti-parallel

Back to list of sheets
Back to top of page

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	B	43	44	first strand
Strand 2	B	35	40	anti-parallel
Strand 3	B	77	82	anti-parallel
Strand 4	B	90	93	anti-parallel

Back to list of sheets
Back to top of page

There are 8 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	44	45	first strand
Strand 2	D	31	37	anti-parallel
Strand 3	D	22	28	anti-parallel
Strand 4	D	2	12	anti-parallel
Strand 5	D	92	102	anti-parallel
Strand 6	D	105	115	anti-parallel
Strand 7	D	118	124	anti-parallel
Strand 8	D	129	132	anti-parallel

Back to list of sheets
Back to top of page

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	183	191	first strand
Strand 2	D	194	204	anti-parallel
Strand 3	D	237	245	anti-parallel
Strand 4	D	224	231	anti-parallel

Back to list of sheets
Back to top of page

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	D	218	219	first strand
Strand 2	D	210	215	anti-parallel
Strand 3	D	253	258	anti-parallel
Strand 4	D	266	268	anti-parallel

Back to list of sheets
Back to top of page

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	E	5	10	first strand
Strand 2	E	20	29	anti-parallel
Strand 3	E	61	69	anti-parallel
Strand 4	E	49	50	anti-parallel

Back to list of sheets
Back to top of page

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	E	5	10	first strand
Strand 2	E	20	29	anti-parallel
Strand 3	E	61	69	anti-parallel
Strand 4	E	54	55	anti-parallel

Back to list of sheets
Back to top of page

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	E	43	44	first strand
Strand 2	E	35	40	anti-parallel
Strand 3	E	77	82	anti-parallel
Strand 4	E	90	93	anti-parallel

Back to list of sheets
Back to top of page

Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

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

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