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

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 8YVI entry

There are 15 chains in PDB entry 8YVI (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLY 6	GLN 97
B	GLY 6	GLN 97
C	GLY 6	GLN 97
D	GLY 6	GLN 97
E	GLY 6	GLN 97
F	GLY 6	GLN 97
G	GLY 6	GLN 97
H	MET 1	ASN 81
I	GLY 6	GLN 97
J	GLY 6	GLN 97
K	GLY 6	GLN 97
L	GLY 6	GLN 97
M	GLY 6	GLN 97
X	ARG 712	ARG 731
Y	ARG 701	GLY 869

There are 43 helices in PDB entry 8YVI. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	17	31	Right-handed alpha
Helix 2	AA2	A	53	69	Right-handed alpha
Helix 3	AA3	A	87	92	Right-handed 310
Helix 4	AA4	B	16	31	Right-handed alpha
Helix 5	AA5	B	53	68	Right-handed alpha
Helix 6	AA6	B	85	92	Right-handed alpha
Helix 7	AA7	C	16	31	Right-handed alpha
Helix 8	AA8	C	53	69	Right-handed alpha
Helix 9	AA9	C	87	92	Right-handed 310
Helix 10	AB1	D	17	31	Right-handed alpha
Helix 11	AB2	D	53	69	Right-handed alpha
Helix 12	AB3	D	86	92	Right-handed 310
Helix 13	AB4	E	16	30	Right-handed alpha
Helix 14	AB5	E	53	69	Right-handed alpha
Helix 15	AB6	E	87	91	Right-handed 310
Helix 16	AB7	F	16	31	Right-handed alpha
Helix 17	AB8	F	53	69	Right-handed alpha
Helix 18	AB9	F	85	92	Right-handed 310
Helix 19	AC1	G	16	31	Right-handed alpha
Helix 20	AC2	G	53	69	Right-handed alpha
Helix 21	AC3	G	85	90	Right-handed alpha
Helix 22	AC4	H	16	20	Right-handed 310
Helix 23	AC5	H	56	62	Right-handed alpha
Helix 24	AC6	I	17	30	Right-handed alpha
Helix 25	AC7	I	53	69	Right-handed alpha
Helix 26	AC8	I	87	92	Right-handed 310
Helix 27	AC9	J	16	31	Right-handed alpha
Helix 28	AD1	J	53	69	Right-handed alpha
Helix 29	AD2	J	85	92	Right-handed 310
Helix 30	AD3	K	17	31	Right-handed alpha
Helix 31	AD4	K	53	69	Right-handed alpha
Helix 32	AD5	K	87	91	Right-handed 310
Helix 33	AD6	L	16	31	Right-handed alpha
Helix 34	AD7	L	53	69	Right-handed alpha
Helix 35	AD8	L	85	90	Right-handed alpha
Helix 36	AD9	M	17	31	Right-handed alpha
Helix 37	AE1	M	53	69	Right-handed alpha
Helix 38	AE2	M	87	92	Right-handed 310
Helix 39	AE3	Y	715	719	Right-handed 310
Helix 40	AE4	Y	727	732	Right-handed alpha
Helix 41	AE5	Y	786	790	Right-handed 310
Helix 42	AE6	Y	811	816	Right-handed alpha
Helix 43	AE7	Y	833	838	Right-handed 310

There are 14 sheets in PDB entry 8YVI. 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,

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	34	40	first strand
Strand 2	A	45	52	anti-parallel
Strand 3	A	8	15	anti-parallel
Strand 4	A	75	81	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	B	33	42	first strand
Strand 2	B	45	52	anti-parallel
Strand 3	B	8	15	anti-parallel
Strand 4	B	75	81	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	C	34	42	first strand
Strand 2	C	45	52	anti-parallel
Strand 3	C	8	15	anti-parallel
Strand 4	C	75	81	anti-parallel

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There are 5 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	33	40	first strand
Strand 2	D	46	52	anti-parallel
Strand 3	D	9	14	anti-parallel
Strand 4	D	75	81	anti-parallel
Strand 5	Y	703	704	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	E	34	40	first strand
Strand 2	E	46	52	anti-parallel
Strand 3	E	8	14	anti-parallel
Strand 4	E	75	81	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	F	34	42	first strand
Strand 2	F	45	52	anti-parallel
Strand 3	F	8	15	anti-parallel
Strand 4	F	75	81	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	G	34	42	first strand
Strand 2	G	45	52	anti-parallel
Strand 3	G	8	15	anti-parallel
Strand 4	G	75	81	anti-parallel

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There are 6 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	2	10	first strand
Strand 2	H	24	28	anti-parallel
Strand 3	H	36	40	anti-parallel
Strand 4	H	72	76	parallel
Strand 5	H	49	53	anti-parallel
Strand 6	H	2	10	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	I	34	42	first strand
Strand 2	I	45	52	anti-parallel
Strand 3	I	8	15	anti-parallel
Strand 4	I	74	81	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	J	33	40	first strand
Strand 2	J	45	52	anti-parallel
Strand 3	J	8	15	anti-parallel
Strand 4	J	75	81	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	K	33	42	first strand
Strand 2	K	45	52	anti-parallel
Strand 3	K	8	15	anti-parallel
Strand 4	K	74	81	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	L	34	42	first strand
Strand 2	L	45	52	anti-parallel
Strand 3	L	8	15	anti-parallel
Strand 4	L	75	81	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	M	34	40	first strand
Strand 2	M	45	52	anti-parallel
Strand 3	M	8	15	anti-parallel
Strand 4	M	75	81	anti-parallel
Strand 5	Y	796	797	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	Y	862	863	first strand
Strand 2	Y	867	868	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: 8YVI

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