Analysis of interatomic Contacts of Structural Units in PDB entry:
5VDF

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 5VDF entry

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

Chain ID	Initial residue	Terminal residue
A	ALA 2	LEU 73
B	ALA 2	LEU 73
C	ALA 2	LEU 73
D	ALA 2	LEU 73
E	ALA 2	LEU 73
F	ALA 2	LEU 73
G	ALA 2	LEU 73
H	ALA 2	LEU 73

There are 16 helices in PDB entry 5VDF. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	15	28	Right-handed alpha
Helix 2	AA2	A	52	62	Right-handed alpha
Helix 3	AA3	B	15	28	Right-handed alpha
Helix 4	AA4	B	52	62	Right-handed alpha
Helix 5	AA5	C	15	28	Right-handed alpha
Helix 6	AA6	C	52	62	Right-handed alpha
Helix 7	AA7	D	15	28	Right-handed alpha
Helix 8	AA8	D	52	62	Right-handed alpha
Helix 9	AA9	E	15	28	Right-handed alpha
Helix 10	AB1	E	52	62	Right-handed alpha
Helix 11	AB2	F	15	28	Right-handed alpha
Helix 12	AB3	F	52	62	Right-handed alpha
Helix 13	AB4	G	15	27	Right-handed alpha
Helix 14	AB5	G	52	62	Right-handed alpha
Helix 15	AB6	H	15	28	Right-handed alpha
Helix 16	AB7	H	52	62	Right-handed alpha

There are 8 sheets in PDB entry 5VDF. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

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	39	first strand
Strand 2	A	44	49	anti-parallel
Strand 3	A	5	11	anti-parallel
Strand 4	A	67	73	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	39	first strand
Strand 2	B	44	49	anti-parallel
Strand 3	B	5	11	anti-parallel
Strand 4	B	67	73	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	39	first strand
Strand 2	C	44	49	anti-parallel
Strand 3	C	5	11	anti-parallel
Strand 4	C	67	72	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	D	33	39	first strand
Strand 2	D	44	49	anti-parallel
Strand 3	D	5	11	anti-parallel
Strand 4	D	67	72	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	E	33	39	first strand
Strand 2	E	44	49	anti-parallel
Strand 3	E	5	11	anti-parallel
Strand 4	E	67	72	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	39	first strand
Strand 2	F	44	49	anti-parallel
Strand 3	F	5	11	anti-parallel
Strand 4	F	67	72	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	39	first strand
Strand 2	G	44	49	anti-parallel
Strand 3	G	5	11	anti-parallel
Strand 4	G	67	73	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	H	33	39	first strand
Strand 2	H	44	49	anti-parallel
Strand 3	H	5	11	anti-parallel
Strand 4	H	67	72	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: 5VDF

Analysis of interatomic Contacts of Structural Units in PDB entry:
5VDF