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

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 1YBU entry

There are 4 chains in PDB entry 1YBU (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ALA 291	ASP 456
B	ALA 291	ASP 456
C	ALA 291	ASP 456
D	ALA 291	ASP 456

There are 20 helices in PDB entry 1YBU. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	305	314	Right-handed alpha
Helix 2	2	A	314	336	Right-handed alpha
Helix 3	3	A	354	371	Right-handed alpha
Helix 4	4	A	398	411	Right-handed alpha
Helix 5	5	A	420	425	Right-handed alpha
Helix 6	6	B	305	314	Right-handed alpha
Helix 7	7	B	314	336	Right-handed alpha
Helix 8	8	B	354	371	Right-handed alpha
Helix 9	9	B	398	409	Right-handed alpha
Helix 10	10	B	420	427	Right-handed alpha
Helix 11	11	C	305	314	Right-handed alpha
Helix 12	12	C	314	336	Right-handed alpha
Helix 13	13	C	354	371	Right-handed alpha
Helix 14	14	C	398	409	Right-handed alpha
Helix 15	15	C	420	427	Right-handed alpha
Helix 16	16	D	305	314	Right-handed alpha
Helix 17	17	D	314	336	Right-handed alpha
Helix 18	18	D	354	371	Right-handed alpha
Helix 19	19	D	398	411	Right-handed alpha
Helix 20	20	D	420	425	Right-handed alpha

There are 8 sheets in PDB entry 1YBU. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H,

There are 5 strands in A sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	339	340	first strand
Strand 2	A	349	352	anti-parallel
Strand 3	A	293	303	anti-parallel
Strand 4	A	376	388	anti-parallel
Strand 5	A	395	397	anti-parallel

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There are 7 strands in B sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	339	340	first strand
Strand 2	A	349	352	anti-parallel
Strand 3	A	293	303	anti-parallel
Strand 4	A	376	388	anti-parallel
Strand 5	A	416	419	parallel
Strand 6	A	449	453	anti-parallel
Strand 7	A	433	438	anti-parallel

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There are 5 strands in C sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	339	343	first strand
Strand 2	B	348	352	anti-parallel
Strand 3	B	293	303	anti-parallel
Strand 4	B	376	388	anti-parallel
Strand 5	B	395	397	anti-parallel

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There are 7 strands in D sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	339	343	first strand
Strand 2	B	348	352	anti-parallel
Strand 3	B	293	303	anti-parallel
Strand 4	B	376	388	anti-parallel
Strand 5	B	416	419	parallel
Strand 6	B	448	453	anti-parallel
Strand 7	B	433	439	anti-parallel

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There are 5 strands in E sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	339	343	first strand
Strand 2	C	348	352	anti-parallel
Strand 3	C	293	303	anti-parallel
Strand 4	C	376	387	anti-parallel
Strand 5	C	396	397	anti-parallel

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There are 7 strands in F sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	339	343	first strand
Strand 2	C	348	352	anti-parallel
Strand 3	C	293	303	anti-parallel
Strand 4	C	376	387	anti-parallel
Strand 5	C	416	419	parallel
Strand 6	C	448	453	anti-parallel
Strand 7	C	433	439	anti-parallel

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There are 5 strands in G sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	339	340	first strand
Strand 2	D	347	352	anti-parallel
Strand 3	D	293	303	anti-parallel
Strand 4	D	376	388	anti-parallel
Strand 5	D	395	397	anti-parallel

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There are 7 strands in H sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	339	340	first strand
Strand 2	D	347	352	anti-parallel
Strand 3	D	293	303	anti-parallel
Strand 4	D	376	388	anti-parallel
Strand 5	D	416	419	parallel
Strand 6	D	449	453	anti-parallel
Strand 7	D	433	438	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: 1YBU

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