Analysis of interatomic Contacts of Structural Units in PDB entry:
2VPD


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).
For CSU analysis of other PDB entry

This page provides analyses of contacts formed by:
For analysis of ligand-protein contacts, use: 3D structure can be seen in additional window with STING software for 2VPD entry

There are 4 chains in PDB entry 2VPD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 VAL 340ASP 398
B
 MET 172ILE 205
C
 MET 332ALA 397
D
 ALA 171ILE 205
Residue contacts

1. List of contacts for up to 10 consecutive residues:
Chain ID from residue number to residue number


2. Detailed analyses of contacts for any single residue:
Residue number chain ID
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There are 7 helices in PDB entry 2VPD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
369 373Right-handed alpha
Helix 2
2
A
375 385Right-handed alpha
Helix 3
3
A
392 398Right-handed alpha
Helix 4
4
B
181 194Right-handed alpha
Helix 5
5
C
375 385Right-handed alpha
Helix 6
6
C
392 397Right-handed alpha
Helix 7
7
D
181 194Right-handed alpha
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There are 4 sheets in PDB entry 2VPD. Click on sheet of interest to get list of strands forming it: AA, AB, CA, CB,

There are 2 strands in AA sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
356 358first strand
Strand 2
A
366 368anti-parallel
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There are 4 strands in AB sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
388 390first strand
Strand 2
B
173 180parallel
Strand 3
D
172 180anti-parallel
Strand 4
C
388 390parallel
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There are 2 strands in CA sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
341 342first strand
Strand 2
C
349 350anti-parallel
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There are 2 strands in CB sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
356 358first strand
Strand 2
C
366 368anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il