Analysis of interatomic Contacts of Structural Units in PDB entry:
8VD4

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 8VD4 entry

There are 4 chains in PDB entry 8VD4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 16	ALA 313
B	SER 16	ALA 313
C	SER 16	ALA 313
D	SER 16	ALA 313

There are 33 helices in PDB entry 8VD4. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	55	61	Right-handed alpha
Helix 2	AA2	A	116	122	Right-handed alpha
Helix 3	AA3	A	125	147	Right-handed alpha
Helix 4	AA4	A	158	167	Right-handed alpha
Helix 5	AA5	A	175	188	Right-handed alpha
Helix 6	AA6	A	199	201	Right-handed 310
Helix 7	AA7	A	202	208	Right-handed alpha
Helix 8	AA8	A	283	287	Right-handed alpha
Helix 9	AA9	B	55	61	Right-handed alpha
Helix 10	AB1	B	117	122	Right-handed alpha
Helix 11	AB2	B	125	147	Right-handed alpha
Helix 12	AB3	B	158	167	Right-handed alpha
Helix 13	AB4	B	175	188	Right-handed alpha
Helix 14	AB5	B	202	208	Right-handed alpha
Helix 15	AB6	B	303	305	Right-handed 310
Helix 16	AB7	C	55	61	Right-handed alpha
Helix 17	AB8	C	116	122	Right-handed alpha
Helix 18	AB9	C	125	147	Right-handed alpha
Helix 19	AC1	C	158	167	Right-handed alpha
Helix 20	AC2	C	175	188	Right-handed alpha
Helix 21	AC3	C	199	201	Right-handed 310
Helix 22	AC4	C	202	207	Right-handed alpha
Helix 23	AC5	C	221	223	Right-handed 310
Helix 24	AC6	C	303	305	Right-handed 310
Helix 25	AC7	D	55	61	Right-handed alpha
Helix 26	AC8	D	116	122	Right-handed alpha
Helix 27	AC9	D	125	130	Right-handed alpha
Helix 28	AD1	D	130	147	Right-handed alpha
Helix 29	AD2	D	158	167	Right-handed alpha
Helix 30	AD3	D	175	188	Right-handed alpha
Helix 31	AD4	D	199	201	Right-handed 310
Helix 32	AD5	D	202	208	Right-handed alpha
Helix 33	AD6	D	303	305	Right-handed 310

There are 16 sheets in PDB entry 8VD4. 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,

There are 3 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	24	25	first strand
Strand 2	A	269	275	anti-parallel
Strand 3	A	280	282	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	62	63	first strand
Strand 2	A	252	265	parallel
Strand 3	A	288	301	anti-parallel
Strand 4	A	97	115	anti-parallel
Strand 5	A	70	78	anti-parallel

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There are 3 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	169	171	first strand
Strand 2	A	307	311	parallel
Strand 3	A	244	247	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	196	198	first strand
Strand 2	A	229	233	parallel
Strand 3	A	225	226	anti-parallel
Strand 4	A	219	220	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	B	24	25	first strand
Strand 2	B	269	275	anti-parallel
Strand 3	B	280	282	anti-parallel

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There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	62	63	first strand
Strand 2	B	252	265	parallel
Strand 3	B	288	301	anti-parallel
Strand 4	B	98	115	anti-parallel
Strand 5	B	70	76	anti-parallel

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There are 5 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	62	63	first strand
Strand 2	B	252	265	parallel
Strand 3	B	288	301	anti-parallel
Strand 4	B	98	115	anti-parallel
Strand 5	C	83	85	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	B	169	171	first strand
Strand 2	B	307	311	parallel
Strand 3	B	244	247	anti-parallel

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There are 3 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	196	199	first strand
Strand 2	B	229	234	parallel
Strand 3	B	225	226	anti-parallel

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There are 3 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	24	25	first strand
Strand 2	C	269	275	anti-parallel
Strand 3	C	280	282	anti-parallel

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There are 5 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	62	63	first strand
Strand 2	C	252	265	parallel
Strand 3	C	288	301	anti-parallel
Strand 4	C	97	115	anti-parallel
Strand 5	C	70	78	anti-parallel

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There are 5 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	62	63	first strand
Strand 2	C	252	265	parallel
Strand 3	C	288	301	anti-parallel
Strand 4	C	97	115	anti-parallel
Strand 5	D	83	85	anti-parallel

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There are 7 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	169	171	first strand
Strand 2	C	307	311	parallel
Strand 3	C	244	247	anti-parallel
Strand 4	C	195	198	anti-parallel
Strand 5	C	229	233	parallel
Strand 6	C	225	226	anti-parallel
Strand 7	C	219	220	anti-parallel

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There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	24	25	first strand
Strand 2	D	269	275	anti-parallel
Strand 3	D	280	282	anti-parallel

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There are 5 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	62	63	first strand
Strand 2	D	252	265	parallel
Strand 3	D	288	301	anti-parallel
Strand 4	D	98	115	anti-parallel
Strand 5	D	70	76	anti-parallel

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There are 7 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	169	171	first strand
Strand 2	D	307	311	parallel
Strand 3	D	244	247	anti-parallel
Strand 4	D	195	198	anti-parallel
Strand 5	D	229	233	parallel
Strand 6	D	225	226	anti-parallel
Strand 7	D	219	220	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: 8VD4

Analysis of interatomic Contacts of Structural Units in PDB entry:
8VD4