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

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 8YDD entry

There are 5 chains in PDB entry 8YDD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	VAL 31	CYS 334
B	VAL 31	CYS 334
C	PRO 30	CYS 334
D	VAL 102	GLN 155
E	LYS 96	GLN 155

There are 7 helices in PDB entry 8YDD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	D	104	118	Right-handed alpha
Helix 2	AA2	D	122	133	Right-handed alpha
Helix 3	AA3	D	136	148	Right-handed alpha
Helix 4	AA4	E	98	102	Right-handed 310
Helix 5	AA5	E	104	118	Right-handed alpha
Helix 6	AA6	E	122	134	Right-handed alpha
Helix 7	AA7	E	136	149	Right-handed alpha

There are 20 sheets in PDB entry 8YDD. 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,

There are 8 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	304	309	first strand
Strand 2	A	315	320	anti-parallel
Strand 3	A	327	331	anti-parallel
Strand 4	A	36	41	anti-parallel
Strand 5	B	36	42	parallel
Strand 6	B	326	331	anti-parallel
Strand 7	B	315	320	anti-parallel
Strand 8	B	304	309	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	48	53	first strand
Strand 2	A	59	64	anti-parallel
Strand 3	A	69	73	anti-parallel
Strand 4	A	79	83	anti-parallel

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There are 4 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	90	95	first strand
Strand 2	A	101	106	anti-parallel
Strand 3	A	110	115	anti-parallel
Strand 4	A	120	126	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	132	137	first strand
Strand 2	A	143	148	anti-parallel
Strand 3	A	153	157	anti-parallel
Strand 4	A	163	167	anti-parallel

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There are 4 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	174	179	first strand
Strand 2	A	185	190	anti-parallel
Strand 3	A	195	199	anti-parallel
Strand 4	A	205	209	anti-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	217	222	first strand
Strand 2	A	229	233	anti-parallel
Strand 3	A	237	242	anti-parallel
Strand 4	A	247	252	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	264	267	first strand
Strand 2	A	273	276	anti-parallel
Strand 3	A	282	287	anti-parallel
Strand 4	A	293	298	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	B	48	53	first strand
Strand 2	B	59	64	anti-parallel
Strand 3	B	69	73	anti-parallel
Strand 4	B	79	83	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	90	95	first strand
Strand 2	B	101	106	anti-parallel
Strand 3	B	110	115	anti-parallel
Strand 4	B	120	126	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	132	137	first strand
Strand 2	B	143	148	anti-parallel
Strand 3	B	153	157	anti-parallel
Strand 4	B	163	167	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	B	174	179	first strand
Strand 2	B	185	190	anti-parallel
Strand 3	B	194	199	anti-parallel
Strand 4	B	205	210	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	217	222	first strand
Strand 2	B	229	233	anti-parallel
Strand 3	B	237	242	anti-parallel
Strand 4	B	247	252	anti-parallel

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There are 4 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	264	267	first strand
Strand 2	B	273	277	anti-parallel
Strand 3	B	283	287	anti-parallel
Strand 4	B	293	297	anti-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	C	36	41	first strand
Strand 2	C	327	331	anti-parallel
Strand 3	C	315	320	anti-parallel
Strand 4	C	304	309	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	C	48	53	first strand
Strand 2	C	59	64	anti-parallel
Strand 3	C	69	73	anti-parallel
Strand 4	C	79	83	anti-parallel

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There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	90	95	first strand
Strand 2	C	101	106	anti-parallel
Strand 3	C	110	115	anti-parallel
Strand 4	C	121	126	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	C	132	137	first strand
Strand 2	C	143	148	anti-parallel
Strand 3	C	153	157	anti-parallel
Strand 4	C	163	167	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	174	179	first strand
Strand 2	C	185	190	anti-parallel
Strand 3	C	195	199	anti-parallel
Strand 4	C	205	209	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	217	222	first strand
Strand 2	C	228	233	anti-parallel
Strand 3	C	237	242	anti-parallel
Strand 4	C	247	252	anti-parallel

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There are 4 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	264	267	first strand
Strand 2	C	273	277	anti-parallel
Strand 3	C	283	287	anti-parallel
Strand 4	C	293	297	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: 8YDD

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