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


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 3PKM entry

There are 4 chains in PDB entry 3PKM (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 HIS 2GLY 245
X
 HIS 2GLY 245
G
 U 2 A 10
R
 U 2 A 10
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 12 helices in PDB entry 3PKM. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
31 42Right-handed alpha
Helix 2
2
A
44 54Right-handed alpha
Helix 3
3
A
93 106Right-handed alpha
Helix 4
4
A
161 179Right-handed alpha
Helix 5
5
A
218 228Right-handed alpha
Helix 6
6
X
2 6Right-handed 310
Helix 7
7
X
27 30Right-handed 310
Helix 8
8
X
31 42Right-handed alpha
Helix 9
9
X
44 54Right-handed alpha
Helix 10
10
X
93 106Right-handed alpha
Helix 11
11
X
161 179Right-handed alpha
Helix 12
12
X
218 228Right-handed alpha
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There are 6 sheets in PDB entry 3PKM. 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
60 62first strand
Strand 2
A
85 91anti-parallel
Strand 3
A
7 13anti-parallel
Strand 4
A
119 124anti-parallel
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There are 4 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
186 200first strand
Strand 2
A
204 217anti-parallel
Strand 3
A
135 138anti-parallel
Strand 4
A
241 244anti-parallel
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There are 4 strands in C sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
X
60 62first strand
Strand 2
X
85 91anti-parallel
Strand 3
X
7 13anti-parallel
Strand 4
X
119 124anti-parallel
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There are 2 strands in D sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
X
23 24first strand
Strand 2
X
79 80anti-parallel
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There are 2 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
X
111 112first strand
Strand 2
X
115 116anti-parallel
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There are 4 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
X
186 199first strand
Strand 2
X
205 217anti-parallel
Strand 3
X
135 138anti-parallel
Strand 4
X
241 244anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il