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

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 8YBF entry

There are 2 chains in PDB entry 8YBF (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LYS 161	CYS 602
B	GLY 158	CYS 602

There are 9 helices in PDB entry 8YBF. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	163	168	Right-handed alpha
Helix 2	AA2	A	204	212	Right-handed alpha
Helix 3	AA3	A	260	262	Right-handed 310
Helix 4	AA4	A	370	380	Right-handed alpha
Helix 5	AA5	B	160	168	Right-handed alpha
Helix 6	AA6	B	169	174	Right-handed alpha
Helix 7	AA7	B	204	212	Right-handed alpha
Helix 8	AA8	B	260	262	Right-handed 310
Helix 9	AA9	B	371	380	Right-handed alpha

There are 17 sheets in PDB entry 8YBF. 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,

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	A	193	199	first strand
Strand 2	A	589	601	anti-parallel
Strand 3	A	573	583	anti-parallel
Strand 4	A	557	568	anti-parallel

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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	215	223	first strand
Strand 2	A	227	235	anti-parallel
Strand 3	A	248	258	anti-parallel
Strand 4	A	264	273	anti-parallel

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There are 3 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	282	283	first strand
Strand 2	A	291	297	anti-parallel
Strand 3	A	286	288	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	A	282	283	first strand
Strand 2	A	291	297	anti-parallel
Strand 3	A	315	321	anti-parallel
Strand 4	A	330	334	anti-parallel

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There are 6 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	301	303	first strand
Strand 2	A	342	346	anti-parallel
Strand 3	A	358	367	anti-parallel
Strand 4	A	405	412	anti-parallel
Strand 5	A	422	426	anti-parallel
Strand 6	A	337	338	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	A	301	303	first strand
Strand 2	A	342	346	anti-parallel
Strand 3	A	358	367	anti-parallel
Strand 4	A	353	355	anti-parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	438	441	first strand
Strand 2	A	447	452	anti-parallel
Strand 3	A	462	467	anti-parallel
Strand 4	A	474	476	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	A	504	512	first strand
Strand 2	A	520	526	anti-parallel
Strand 3	A	533	540	anti-parallel
Strand 4	A	545	552	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	B	193	199	first strand
Strand 2	B	589	601	anti-parallel
Strand 3	B	573	583	anti-parallel
Strand 4	B	557	568	anti-parallel

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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	B	215	223	first strand
Strand 2	B	227	235	anti-parallel
Strand 3	B	248	258	anti-parallel
Strand 4	B	264	273	anti-parallel

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There are 3 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	282	283	first strand
Strand 2	B	291	297	anti-parallel
Strand 3	B	286	288	anti-parallel

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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	B	282	283	first strand
Strand 2	B	291	297	anti-parallel
Strand 3	B	315	321	anti-parallel
Strand 4	B	330	334	anti-parallel

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There are 6 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	301	303	first strand
Strand 2	B	342	346	anti-parallel
Strand 3	B	358	367	anti-parallel
Strand 4	B	405	412	anti-parallel
Strand 5	B	422	426	anti-parallel
Strand 6	B	337	338	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	B	301	303	first strand
Strand 2	B	342	346	anti-parallel
Strand 3	B	358	367	anti-parallel
Strand 4	B	353	355	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	B	438	441	first strand
Strand 2	B	447	452	anti-parallel
Strand 3	B	462	467	anti-parallel
Strand 4	B	474	478	anti-parallel

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There are 2 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	480	481	first strand
Strand 2	B	492	493	anti-parallel

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There are 4 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	511	512	first strand
Strand 2	B	520	526	anti-parallel
Strand 3	B	533	540	anti-parallel
Strand 4	B	545	552	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: 8YBF

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