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

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 8YDT entry

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

Chain ID	Initial residue	Terminal residue
A	ASP 1	ASP 39
B	ASN 334	SER 529
C	ASP 1	ASP 39
D	ASN 334	SER 529

There are 18 helices in PDB entry 8YDT. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	2	19	Right-handed alpha
Helix 2	AA2	A	21	38	Right-handed alpha
Helix 3	AA3	B	338	343	Right-handed alpha
Helix 4	AA4	B	349	353	Right-handed 310
Helix 5	AA5	B	364	372	Right-handed alpha
Helix 6	AA6	B	405	410	Right-handed 310
Helix 7	AA7	B	416	422	Right-handed alpha
Helix 8	AA8	B	438	443	Right-handed alpha
Helix 9	AA9	B	502	505	Right-handed 310
Helix 10	AB1	C	2	20	Right-handed alpha
Helix 11	AB2	C	21	36	Right-handed alpha
Helix 12	AB3	D	337	343	Right-handed alpha
Helix 13	AB4	D	364	370	Right-handed alpha
Helix 14	AB5	D	383	388	Right-handed alpha
Helix 15	AB6	D	404	408	Right-handed alpha
Helix 16	AB7	D	416	422	Right-handed alpha
Helix 17	AB8	D	438	443	Right-handed alpha
Helix 18	AB9	D	502	505	Right-handed 310

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

There are 5 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	354	358	first strand
Strand 2	B	394	403	anti-parallel
Strand 3	B	507	516	anti-parallel
Strand 4	B	431	437	anti-parallel
Strand 5	B	376	380	anti-parallel

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There are 3 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	361	363	first strand
Strand 2	B	524	526	parallel
Strand 3	B	391	392	anti-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	B	452	454	first strand
Strand 2	B	492	494	anti-parallel

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There are 2 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	473	474	first strand
Strand 2	B	488	489	anti-parallel

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There are 5 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	354	358	first strand
Strand 2	D	394	403	anti-parallel
Strand 3	D	507	516	anti-parallel
Strand 4	D	431	437	anti-parallel
Strand 5	D	376	380	anti-parallel

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There are 3 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	361	363	first strand
Strand 2	D	524	526	parallel
Strand 3	D	391	392	anti-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	D	452	454	first strand
Strand 2	D	492	494	anti-parallel

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There are 2 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	473	474	first strand
Strand 2	D	488	489	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: 8YDT

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