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

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 8RYD entry

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

Chain ID	Initial residue	Terminal residue
A	ALA 16	GLY 240
B	ALA 16	PHE 245
C	ALA 16	PHE 245
D	SER 15	GLU 239

There are 46 helices in PDB entry 8RYD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	16	20	Right-handed 310
Helix 2	AA2	A	22	29	Right-handed alpha
Helix 3	AA3	A	30	33	Right-handed 310
Helix 4	AA4	A	34	36	Right-handed 310
Helix 5	AA5	A	37	55	Right-handed alpha
Helix 6	AA6	A	70	77	Right-handed alpha
Helix 7	AA7	A	87	102	Right-handed alpha
Helix 8	AA8	A	113	121	Right-handed alpha
Helix 9	AA9	A	136	140	Right-handed 310
Helix 10	AB1	A	143	154	Right-handed alpha
Helix 11	AB2	A	165	180	Right-handed alpha
Helix 12	AB3	A	207	218	Right-handed alpha
Helix 13	AB4	B	16	20	Right-handed 310
Helix 14	AB5	B	22	29	Right-handed alpha
Helix 15	AB6	B	30	33	Right-handed 310
Helix 16	AB7	B	37	55	Right-handed alpha
Helix 17	AB8	B	70	77	Right-handed alpha
Helix 18	AB9	B	87	101	Right-handed alpha
Helix 19	AC1	B	113	121	Right-handed alpha
Helix 20	AC2	B	136	140	Right-handed 310
Helix 21	AC3	B	143	154	Right-handed alpha
Helix 22	AC4	B	165	180	Right-handed alpha
Helix 23	AC5	B	207	218	Right-handed alpha
Helix 24	AC6	C	22	29	Right-handed alpha
Helix 25	AC7	C	30	33	Right-handed 310
Helix 26	AC8	C	34	36	Right-handed 310
Helix 27	AC9	C	37	55	Right-handed alpha
Helix 28	AD1	C	70	77	Right-handed alpha
Helix 29	AD2	C	87	101	Right-handed alpha
Helix 30	AD3	C	113	121	Right-handed alpha
Helix 31	AD4	C	136	140	Right-handed 310
Helix 32	AD5	C	143	154	Right-handed alpha
Helix 33	AD6	C	165	180	Right-handed alpha
Helix 34	AD7	C	207	218	Right-handed alpha
Helix 35	AD8	D	16	20	Right-handed 310
Helix 36	AD9	D	22	29	Right-handed alpha
Helix 37	AE1	D	30	33	Right-handed 310
Helix 38	AE2	D	34	36	Right-handed 310
Helix 39	AE3	D	37	55	Right-handed alpha
Helix 40	AE4	D	70	78	Right-handed alpha
Helix 41	AE5	D	87	101	Right-handed alpha
Helix 42	AE6	D	113	121	Right-handed alpha
Helix 43	AE7	D	136	140	Right-handed 310
Helix 44	AE8	D	143	152	Right-handed alpha
Helix 45	AE9	D	165	180	Right-handed alpha
Helix 46	AF1	D	207	218	Right-handed alpha

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

There are 7 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	107	111	first strand
Strand 2	A	80	85	parallel
Strand 3	A	59	63	parallel
Strand 4	A	128	132	parallel
Strand 5	A	157	162	parallel
Strand 6	A	231	238	anti-parallel
Strand 7	A	220	227	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	A	185	188	first strand
Strand 2	A	193	196	anti-parallel
Strand 3	A	202	204	anti-parallel

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There are 7 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	107	110	first strand
Strand 2	B	80	84	parallel
Strand 3	B	59	63	parallel
Strand 4	B	128	132	parallel
Strand 5	B	156	162	parallel
Strand 6	B	231	238	anti-parallel
Strand 7	B	220	227	anti-parallel

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There are 3 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	185	188	first strand
Strand 2	B	193	196	anti-parallel
Strand 3	B	202	204	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	C	107	111	first strand
Strand 2	C	80	85	parallel
Strand 3	C	59	63	parallel
Strand 4	C	128	132	parallel
Strand 5	C	156	162	parallel
Strand 6	C	231	238	anti-parallel
Strand 7	C	220	227	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	C	185	188	first strand
Strand 2	C	193	196	anti-parallel
Strand 3	C	202	204	anti-parallel

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There are 7 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	107	111	first strand
Strand 2	D	80	85	parallel
Strand 3	D	59	63	parallel
Strand 4	D	128	132	parallel
Strand 5	D	156	162	parallel
Strand 6	D	231	238	anti-parallel
Strand 7	D	220	227	anti-parallel

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There are 3 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	185	188	first strand
Strand 2	D	193	196	anti-parallel
Strand 3	D	202	204	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: 8RYD

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