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


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 5CMD entry

There are 6 chains in PDB entry 5CMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 SER 5SER 68
B
 SER 4MET 67
C
 SER 5SER 68
D
 SER 5SER 68
E
 SER 5SER 68
F
 SER 5MET 67
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 5CMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
20 22Right-handed 310
Helix 2
AA2
A
55 67Right-handed alpha
Helix 3
AA3
B
20 22Right-handed 310
Helix 4
AA4
B
55 66Right-handed alpha
Helix 5
AA5
C
20 22Right-handed 310
Helix 6
AA6
C
55 65Right-handed alpha
Helix 7
AA7
D
20 22Right-handed 310
Helix 8
AA8
D
55 67Right-handed alpha
Helix 9
AA9
E
20 22Right-handed 310
Helix 10
AB1
E
55 68Right-handed alpha
Helix 11
AB2
F
20 22Right-handed 310
Helix 12
AB3
F
55 65Right-handed alpha
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There are 9 sheets in PDB entry 5CMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9,

There are 2 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
8 10first strand
Strand 2
B
8 10anti-parallel
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There are 3 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
24 29first strand
Strand 2
A
39 43anti-parallel
Strand 3
A
48 51anti-parallel
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There are 3 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
24 29first strand
Strand 2
B
39 43anti-parallel
Strand 3
B
48 51anti-parallel
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There are 2 strands in AA4 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
8 10first strand
Strand 2
D
8 10anti-parallel
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There are 3 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
24 29first strand
Strand 2
C
39 43anti-parallel
Strand 3
C
48 51anti-parallel
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There are 3 strands in AA6 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
24 29first strand
Strand 2
D
39 43anti-parallel
Strand 3
D
48 51anti-parallel
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There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
8 10first strand
Strand 2
F
8 10anti-parallel
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There are 3 strands in AA8 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
24 29first strand
Strand 2
E
39 43anti-parallel
Strand 3
E
48 51anti-parallel
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There are 3 strands in AA9 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
24 29first strand
Strand 2
F
39 43anti-parallel
Strand 3
F
48 51anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il