Analysis of interatomic Contacts of Structural Units in PDB entry:
8D87

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 8D87 entry

There are 3 chains in PDB entry 8D87 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	TYR 1	ALA 391
B	TYR 1	ALA 391
C	TYR 1	ALA 391

There are 12 helices in PDB entry 8D87. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	113	117	Right-handed 310
Helix 2	AA2	A	191	195	Right-handed 310
Helix 3	AA3	A	238	247	Right-handed alpha
Helix 4	AA4	A	250	254	Right-handed 310
Helix 5	AA5	B	113	117	Right-handed 310
Helix 6	AA6	B	191	195	Right-handed 310
Helix 7	AA7	B	238	247	Right-handed alpha
Helix 8	AA8	B	250	254	Right-handed 310
Helix 9	AA9	C	113	117	Right-handed 310
Helix 10	AB1	C	191	195	Right-handed 310
Helix 11	AB2	C	238	247	Right-handed alpha
Helix 12	AB3	C	250	254	Right-handed 310

There are 33 sheets in PDB entry 8D87. 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, AC9, AD1, AD2, AD3, AD4, AD5, AD6,

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	3	8	first strand
Strand 2	A	275	280	anti-parallel

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There are 5 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	140	146	first strand
Strand 2	A	126	137	anti-parallel
Strand 3	A	27	40	anti-parallel
Strand 4	A	267	269	anti-parallel
Strand 5	A	260	262	anti-parallel

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There are 5 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	140	146	first strand
Strand 2	A	126	137	anti-parallel
Strand 3	A	27	40	anti-parallel
Strand 4	A	15	19	anti-parallel
Strand 5	A	289	290	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	46	48	first strand
Strand 2	A	119	122	anti-parallel
Strand 3	A	177	179	anti-parallel
Strand 4	A	184	185	anti-parallel

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There are 3 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	51	54	first strand
Strand 2	A	101	110	anti-parallel
Strand 3	A	59	60	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	A	51	54	first strand
Strand 2	A	101	110	anti-parallel
Strand 3	A	77	82	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	A	153	156	first strand
Strand 2	A	159	162	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	A	203	204	first strand
Strand 2	A	214	215	anti-parallel

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There are 2 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	220	221	first strand
Strand 2	A	233	234	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	A	296	306	first strand
Strand 2	A	314	322	anti-parallel
Strand 3	A	351	357	anti-parallel
Strand 4	A	338	339	anti-parallel

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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	A	343	346	first strand
Strand 2	A	326	332	anti-parallel
Strand 3	A	364	369	anti-parallel
Strand 4	A	372	377	anti-parallel

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There are 2 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	3	8	first strand
Strand 2	B	275	280	anti-parallel

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There are 5 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	140	147	first strand
Strand 2	B	126	137	anti-parallel
Strand 3	B	27	40	anti-parallel
Strand 4	B	267	269	anti-parallel
Strand 5	B	260	262	anti-parallel

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There are 5 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	140	147	first strand
Strand 2	B	126	137	anti-parallel
Strand 3	B	27	40	anti-parallel
Strand 4	B	15	19	anti-parallel
Strand 5	B	289	290	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	46	48	first strand
Strand 2	B	119	122	anti-parallel
Strand 3	B	177	179	anti-parallel
Strand 4	B	184	185	anti-parallel

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There are 3 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	51	54	first strand
Strand 2	B	101	110	anti-parallel
Strand 3	B	59	61	anti-parallel

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There are 3 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	51	54	first strand
Strand 2	B	101	110	anti-parallel
Strand 3	B	77	81	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	153	156	first strand
Strand 2	B	159	162	anti-parallel

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There are 2 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	203	204	first strand
Strand 2	B	214	215	anti-parallel

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There are 2 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	220	221	first strand
Strand 2	B	233	234	anti-parallel

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There are 4 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	296	306	first strand
Strand 2	B	314	322	anti-parallel
Strand 3	B	351	357	anti-parallel
Strand 4	B	338	339	anti-parallel

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There are 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	343	346	first strand
Strand 2	B	326	332	anti-parallel
Strand 3	B	364	369	anti-parallel
Strand 4	B	372	377	anti-parallel

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There are 2 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	3	8	first strand
Strand 2	C	275	280	anti-parallel

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There are 5 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	140	146	first strand
Strand 2	C	126	137	anti-parallel
Strand 3	C	27	40	anti-parallel
Strand 4	C	267	269	anti-parallel
Strand 5	C	260	262	anti-parallel

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There are 5 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	140	146	first strand
Strand 2	C	126	137	anti-parallel
Strand 3	C	27	40	anti-parallel
Strand 4	C	15	19	anti-parallel
Strand 5	C	289	290	anti-parallel

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There are 4 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	46	48	first strand
Strand 2	C	119	122	anti-parallel
Strand 3	C	177	179	anti-parallel
Strand 4	C	184	185	anti-parallel

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There are 3 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	51	54	first strand
Strand 2	C	102	110	anti-parallel
Strand 3	C	59	60	anti-parallel

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There are 3 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	51	54	first strand
Strand 2	C	102	110	anti-parallel
Strand 3	C	77	81	anti-parallel

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There are 2 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	153	156	first strand
Strand 2	C	159	162	anti-parallel

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There are 2 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	203	204	first strand
Strand 2	C	214	215	anti-parallel

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There are 2 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	220	221	first strand
Strand 2	C	233	234	anti-parallel

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There are 4 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	296	306	first strand
Strand 2	C	314	322	anti-parallel
Strand 3	C	351	357	anti-parallel
Strand 4	C	338	339	anti-parallel

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There are 4 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	343	346	first strand
Strand 2	C	326	332	anti-parallel
Strand 3	C	364	369	anti-parallel
Strand 4	C	372	377	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: 8D87

Analysis of interatomic Contacts of Structural Units in PDB entry:
8D87