Analysis of interatomic Contacts of Structural Units in PDB entry:
3VPD


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 3VPD entry

There are 2 chains in PDB entry 3VPD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 MET 1GLY 281
B
 MET 1GLY 281
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 25 helices in PDB entry 3VPD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
10 23Right-handed alpha
Helix 2
2
A
33 35Right-handed 310
Helix 3
3
A
43 47Right-handed 310
Helix 4
4
A
58 72Right-handed alpha
Helix 5
5
A
79 88Right-handed alpha
Helix 6
6
A
88 100Right-handed alpha
Helix 7
7
A
111 123Right-handed alpha
Helix 8
8
A
144 159Right-handed alpha
Helix 9
9
A
160 165Right-handed 310
Helix 10
10
A
202 206Right-handed 310
Helix 11
11
A
215 229Right-handed alpha
Helix 12
12
A
258 264Right-handed alpha
Helix 13
13
A
266 278Right-handed alpha
Helix 14
14
B
10 24Right-handed alpha
Helix 15
15
B
33 35Right-handed 310
Helix 16
16
B
43 47Right-handed 310
Helix 17
17
B
58 72Right-handed alpha
Helix 18
18
B
79 88Right-handed alpha
Helix 19
19
B
88 99Right-handed alpha
Helix 20
20
B
111 123Right-handed alpha
Helix 21
21
B
144 159Right-handed alpha
Helix 22
22
B
160 165Right-handed 310
Helix 23
23
B
215 229Right-handed alpha
Helix 24
24
B
256 264Right-handed alpha
Helix 25
25
B
266 279Right-handed alpha
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There are 6 sheets in PDB entry 3VPD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F,

There are 4 strands in A sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
27 31first strand
Strand 2
A
2 6parallel
Strand 3
A
51 54parallel
Strand 4
A
76 77parallel
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There are 5 strands in B sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
37 38first strand
Strand 2
B
106 109anti-parallel
Strand 3
B
166 170anti-parallel
Strand 4
B
126 129anti-parallel
Strand 5
B
140 142anti-parallel
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There are 5 strands in C sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
140 142first strand
Strand 2
A
126 129anti-parallel
Strand 3
A
166 170anti-parallel
Strand 4
A
106 109anti-parallel
Strand 5
B
37 38anti-parallel
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There are 5 strands in D sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
208 211first strand
Strand 2
A
187 195anti-parallel
Strand 3
A
177 184anti-parallel
Strand 4
A
233 241anti-parallel
Strand 5
A
244 251anti-parallel
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There are 4 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
27 31first strand
Strand 2
B
2 6parallel
Strand 3
B
51 54parallel
Strand 4
B
76 77parallel
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There are 5 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
210 211first strand
Strand 2
B
187 194anti-parallel
Strand 3
B
178 184anti-parallel
Strand 4
B
233 241anti-parallel
Strand 5
B
244 251anti-parallel
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