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


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 3CMD entry

There are 2 chains in PDB entry 3CMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 LEU -6GLU 187
B
 SER -8GLU 187
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 14 helices in PDB entry 3CMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
3 7Right-handed 310
Helix 2
2
A
12 17Right-handed 310
Helix 3
3
A
27 46Right-handed alpha
Helix 4
4
A
46 53Right-handed alpha
Helix 5
5
A
64 67Right-handed 310
Helix 6
6
A
149 162Right-handed alpha
Helix 7
7
A
166 171Right-handed 310
Helix 8
8
B
3 7Right-handed 310
Helix 9
9
B
12 17Right-handed 310
Helix 10
10
B
27 46Right-handed alpha
Helix 11
11
B
46 53Right-handed alpha
Helix 12
12
B
64 67Right-handed 310
Helix 13
13
B
149 162Right-handed alpha
Helix 14
14
B
166 171Right-handed 310
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There are 4 sheets in PDB entry 3CMD. Click on sheet of interest to get list of strands forming it: A, B, C, D,

There are 5 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
72 77anti-parallel
Strand 3
A
89 101anti-parallel
Strand 4
A
130 136anti-parallel
Strand 5
A
142 148anti-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
127 128first strand
Strand 2
A
105 108anti-parallel
Strand 3
A
184 186parallel
Strand 4
B
-2 -1anti-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
B
60 62first strand
Strand 2
B
72 77anti-parallel
Strand 3
B
89 101anti-parallel
Strand 4
B
130 136anti-parallel
Strand 5
B
142 148anti-parallel
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There are 3 strands in D sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
127 128first strand
Strand 2
B
105 108anti-parallel
Strand 3
B
184 186parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il