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

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 5YPZ entry

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

Chain ID	Initial residue	Terminal residue
A	ASP 29	GLN 517
B	ASP 29	GLN 517
C	ASP 29	GLN 517
D	SER 5	PRO 15
E	SER 5	PRO 15
F	SER 5	PRO 15

There are 26 helices in PDB entry 5YPZ. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	29	52	Right-handed alpha
Helix 2	AA2	A	70	73	Right-handed 310
Helix 3	AA3	A	108	114	Right-handed 310
Helix 4	AA4	A	115	119	Right-handed 310
Helix 5	AA5	A	139	144	Right-handed 310
Helix 6	AA6	A	186	198	Right-handed alpha
Helix 7	AA7	A	230	235	Right-handed 310
Helix 8	AA8	A	384	389	Right-handed alpha
Helix 9	AA9	A	451	455	Right-handed 310
Helix 10	AB1	B	30	52	Right-handed alpha
Helix 11	AB2	B	70	73	Right-handed 310
Helix 12	AB3	B	108	114	Right-handed 310
Helix 13	AB4	B	115	119	Right-handed 310
Helix 14	AB5	B	139	144	Right-handed 310
Helix 15	AB6	B	186	199	Right-handed alpha
Helix 16	AB7	B	230	234	Right-handed 310
Helix 17	AB8	B	384	389	Right-handed alpha
Helix 18	AB9	B	392	395	Right-handed 310
Helix 19	AC1	B	451	455	Right-handed 310
Helix 20	AC2	C	30	52	Right-handed alpha
Helix 21	AC3	C	70	73	Right-handed 310
Helix 22	AC4	C	108	114	Right-handed 310
Helix 23	AC5	C	139	144	Right-handed 310
Helix 24	AC6	C	186	198	Right-handed alpha
Helix 25	AC7	C	384	389	Right-handed alpha
Helix 26	AC8	C	451	455	Right-handed 310

There are 26 sheets in PDB entry 5YPZ. 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, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8,

There are 2 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	55	60	first strand
Strand 2	A	63	68	anti-parallel

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There are 6 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	100	102	first strand
Strand 2	A	147	156	anti-parallel
Strand 3	A	165	174	anti-parallel
Strand 4	A	246	253	anti-parallel
Strand 5	A	205	211	anti-parallel
Strand 6	A	220	221	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	A	223	224	first strand
Strand 2	A	227	228	anti-parallel

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There are 10 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	268	269	first strand
Strand 2	C	272	274	parallel
Strand 3	C	284	287	anti-parallel
Strand 4	C	293	297	anti-parallel
Strand 5	B	308	311	parallel
Strand 6	B	320	328	anti-parallel
Strand 7	B	334	341	anti-parallel
Strand 8	A	349	351	parallel
Strand 9	C	353	359	parallel
Strand 10	C	367	371	anti-parallel

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There are 7 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	268	269	first strand
Strand 2	C	272	274	parallel
Strand 3	C	284	287	anti-parallel
Strand 4	C	293	297	anti-parallel
Strand 5	B	308	311	parallel
Strand 6	B	320	328	anti-parallel
Strand 7	C	417	418	anti-parallel

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There are 6 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	367	371	first strand
Strand 2	A	353	359	anti-parallel
Strand 3	B	349	351	parallel
Strand 4	C	334	341	parallel
Strand 5	C	320	328	anti-parallel
Strand 6	A	417	418	anti-parallel

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There are 10 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	367	371	first strand
Strand 2	A	353	359	anti-parallel
Strand 3	B	349	351	parallel
Strand 4	C	334	341	parallel
Strand 5	C	320	328	anti-parallel
Strand 6	C	308	311	anti-parallel
Strand 7	A	293	297	parallel
Strand 8	A	284	287	anti-parallel
Strand 9	A	272	274	anti-parallel
Strand 10	B	268	269	parallel

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There are 9 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	271	273	first strand
Strand 2	B	284	287	anti-parallel
Strand 3	B	293	297	anti-parallel
Strand 4	A	308	311	parallel
Strand 5	A	320	328	anti-parallel
Strand 6	A	334	341	anti-parallel
Strand 7	C	349	351	parallel
Strand 8	B	353	359	parallel
Strand 9	B	367	371	anti-parallel

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There are 6 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	271	273	first strand
Strand 2	B	284	287	anti-parallel
Strand 3	B	293	297	anti-parallel
Strand 4	A	308	311	parallel
Strand 5	A	320	328	anti-parallel
Strand 6	B	417	418	anti-parallel

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There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	374	379	first strand
Strand 2	A	504	513	anti-parallel
Strand 3	A	424	435	anti-parallel
Strand 4	C	464	474	anti-parallel
Strand 5	C	478	489	anti-parallel
Strand 6	C	407	410	anti-parallel

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There are 6 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	374	379	first strand
Strand 2	A	504	513	anti-parallel
Strand 3	A	424	435	anti-parallel
Strand 4	C	464	474	anti-parallel
Strand 5	C	478	489	anti-parallel
Strand 6	C	494	499	anti-parallel

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There are 3 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	407	410	first strand
Strand 2	A	478	489	anti-parallel
Strand 3	A	494	499	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	A	407	410	first strand
Strand 2	A	478	489	anti-parallel
Strand 3	A	464	474	anti-parallel
Strand 4	B	424	435	anti-parallel
Strand 5	B	504	513	anti-parallel
Strand 6	B	374	379	anti-parallel

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There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	461	462	first strand
Strand 2	D	11	12	parallel

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There are 2 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	55	60	first strand
Strand 2	B	63	68	anti-parallel

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There are 6 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	101	102	first strand
Strand 2	B	147	156	anti-parallel
Strand 3	B	165	174	anti-parallel
Strand 4	B	246	253	anti-parallel
Strand 5	B	205	211	anti-parallel
Strand 6	B	220	221	anti-parallel

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There are 2 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	223	224	first strand
Strand 2	B	227	228	anti-parallel

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There are 2 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	397	398	first strand
Strand 2	F	7	8	anti-parallel

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There are 3 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	407	410	first strand
Strand 2	B	478	489	anti-parallel
Strand 3	B	494	499	anti-parallel

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There are 6 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	407	410	first strand
Strand 2	B	478	489	anti-parallel
Strand 3	B	464	474	anti-parallel
Strand 4	C	424	435	anti-parallel
Strand 5	C	504	513	anti-parallel
Strand 6	C	374	379	anti-parallel

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There are 3 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	437	438	first strand
Strand 2	B	461	462	anti-parallel
Strand 3	E	11	12	parallel

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There are 2 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	55	59	first strand
Strand 2	C	64	68	anti-parallel

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There are 6 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	101	102	first strand
Strand 2	C	147	156	anti-parallel
Strand 3	C	165	174	anti-parallel
Strand 4	C	246	253	anti-parallel
Strand 5	C	205	211	anti-parallel
Strand 6	C	220	221	anti-parallel

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There are 2 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	223	224	first strand
Strand 2	C	227	228	anti-parallel

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There are 2 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	397	399	first strand
Strand 2	D	6	8	anti-parallel

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There are 3 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	437	438	first strand
Strand 2	C	461	462	anti-parallel
Strand 3	F	11	12	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: 5YPZ

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