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


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 5YDR entry

There are 3 chains in PDB entry 5YDR (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ALA -1LEU 73
B
 MET 350ALA 599
D
 HIS 0ARG 72
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 15 helices in PDB entry 5YDR. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
22 35Right-handed alpha
Helix 2
AA2
A
37 39Right-handed 310
Helix 3
AA3
B
362 366Right-handed 310
Helix 4
AA4
B
376 382Right-handed alpha
Helix 5
AA5
B
383 387Right-handed 310
Helix 6
AA6
B
495 502Right-handed alpha
Helix 7
AA7
B
502 519Right-handed alpha
Helix 8
AA8
B
523 534Right-handed alpha
Helix 9
AA9
B
546 553Right-handed alpha
Helix 10
AB1
B
553 568Right-handed alpha
Helix 11
AB2
B
578 589Right-handed alpha
Helix 12
AB3
B
591 598Right-handed alpha
Helix 13
AB4
D
22 35Right-handed alpha
Helix 14
AB5
D
37 39Right-handed 310
Helix 15
AB6
D
55 60Right-handed 310
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There are 3 sheets in PDB entry 5YDR. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3,

There are 5 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
12 17first strand
Strand 2
A
1 6anti-parallel
Strand 3
A
66 71parallel
Strand 4
A
41 45anti-parallel
Strand 5
A
48 49anti-parallel
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There are 6 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
453 458first strand
Strand 2
B
433 440anti-parallel
Strand 3
B
404 414anti-parallel
Strand 4
B
485 488parallel
Strand 5
B
476 480anti-parallel
Strand 6
B
463 467anti-parallel
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There are 5 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
12 17first strand
Strand 2
D
1 7anti-parallel
Strand 3
D
66 71parallel
Strand 4
D
41 45anti-parallel
Strand 5
D
48 49anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il