Analysis of interatomic Contacts of Structural Units in PDB entry:
8PKD


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 8PKD entry

There are 4 chains in PDB entry 8PKD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLU 2ARG 151
B
 GLU 2ARG 151
C
 GLU 2ARG 151
D
 GLU 2ARG 151
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 28 helices in PDB entry 8PKD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
2 12Right-handed alpha
Helix 2
AA2
A
18 33Right-handed alpha
Helix 3
AA3
A
34 53Right-handed alpha
Helix 4
AA4
A
60 74Right-handed alpha
Helix 5
AA5
A
97 103Right-handed alpha
Helix 6
AA6
A
106 111Right-handed alpha
Helix 7
AA7
A
111 125Right-handed alpha
Helix 8
AA8
B
3 12Right-handed alpha
Helix 9
AA9
B
18 33Right-handed alpha
Helix 10
AB1
B
34 53Right-handed alpha
Helix 11
AB2
B
60 74Right-handed alpha
Helix 12
AB3
B
97 103Right-handed alpha
Helix 13
AB4
B
106 111Right-handed alpha
Helix 14
AB5
B
111 125Right-handed alpha
Helix 15
AB6
C
3 12Right-handed alpha
Helix 16
AB7
C
18 33Right-handed alpha
Helix 17
AB8
C
34 53Right-handed alpha
Helix 18
AB9
C
60 74Right-handed alpha
Helix 19
AC1
C
97 103Right-handed alpha
Helix 20
AC2
C
106 111Right-handed alpha
Helix 21
AC3
C
111 125Right-handed alpha
Helix 22
AC4
D
3 12Right-handed alpha
Helix 23
AC5
D
18 33Right-handed alpha
Helix 24
AC6
D
34 53Right-handed alpha
Helix 25
AC7
D
60 74Right-handed alpha
Helix 26
AC8
D
97 103Right-handed alpha
Helix 27
AC9
D
106 111Right-handed alpha
Helix 28
AD1
D
111 125Right-handed alpha
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There are 4 sheets in PDB entry 8PKD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4,

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
79 85first strand
Strand 2
A
88 94anti-parallel
Strand 3
A
145 150anti-parallel
Strand 4
A
132 135anti-parallel
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There are 4 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
79 85first strand
Strand 2
B
88 94anti-parallel
Strand 3
B
145 150anti-parallel
Strand 4
B
132 135anti-parallel
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There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
79 85first strand
Strand 2
C
88 94anti-parallel
Strand 3
C
145 150anti-parallel
Strand 4
C
132 135anti-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
D
79 85first strand
Strand 2
D
88 94anti-parallel
Strand 3
D
145 150anti-parallel
Strand 4
D
132 135anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il