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


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 5YJD entry

There are 2 chains in PDB entry 5YJD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 TYR 2ALA 216
B
 SER 3ALA 216
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 5YJD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
47 63Right-handed alpha
Helix 2
AA2
A
76 84Right-handed alpha
Helix 3
AA3
A
104 115Right-handed alpha
Helix 4
AA4
A
158 160Right-handed 310
Helix 5
AA5
A
161 178Right-handed alpha
Helix 6
AA6
A
184 188Right-handed 310
Helix 7
AA7
B
47 63Right-handed alpha
Helix 8
AA8
B
77 84Right-handed alpha
Helix 9
AA9
B
104 115Right-handed alpha
Helix 10
AB1
B
158 160Right-handed 310
Helix 11
AB2
B
161 178Right-handed alpha
Helix 12
AB3
B
184 188Right-handed 310
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There are 6 sheets in PDB entry 5YJD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6,

There are 4 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
45 46first strand
Strand 2
A
101 103anti-parallel
Strand 3
A
147 156anti-parallel
Strand 4
A
96 98anti-parallel
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There are 5 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
45 46first strand
Strand 2
A
101 103anti-parallel
Strand 3
A
147 156anti-parallel
Strand 4
A
3 13anti-parallel
Strand 5
A
192 203anti-parallel
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There are 2 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
119 123first strand
Strand 2
A
138 142anti-parallel
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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
45 46first strand
Strand 2
B
101 103anti-parallel
Strand 3
B
147 155anti-parallel
Strand 4
B
96 98anti-parallel
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There are 5 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
45 46first strand
Strand 2
B
101 103anti-parallel
Strand 3
B
147 155anti-parallel
Strand 4
B
4 13anti-parallel
Strand 5
B
192 203anti-parallel
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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
119 123first strand
Strand 2
B
138 142anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il