Analysis of interatomic Contacts of Structural Units in PDB entry:
2PKD


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 2PKD entry

There are 6 chains in PDB entry 2PKD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLU 5ARG 111
B
 SER 4ARG 111
C
 GLU 5ARG 111
D
 GLU 5ARG 111
E
 ASP 3ARG 111
F
 GLU 5ARG 111
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 2PKD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
58 62Right-handed 310
Helix 2
2
A
80 84Right-handed 310
Helix 3
3
B
25 27Right-handed 310
Helix 4
4
B
58 62Right-handed 310
Helix 5
5
C
25 27Right-handed 310
Helix 6
6
C
58 62Right-handed 310
Helix 7
7
C
80 84Right-handed 310
Helix 8
8
D
25 27Right-handed 310
Helix 9
9
D
58 62Right-handed 310
Helix 10
10
D
80 84Right-handed 310
Helix 11
11
E
25 27Right-handed 310
Helix 12
12
E
58 62Right-handed 310
Helix 13
13
E
80 84Right-handed 310
Helix 14
14
F
58 62Right-handed 310
Helix 15
15
F
80 84Right-handed 310
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There are 12 sheets in PDB entry 2PKD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L,

There are 6 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
7 12first strand
Strand 2
A
99 109parallel
Strand 3
A
85 93anti-parallel
Strand 4
A
29 35anti-parallel
Strand 5
A
39 44anti-parallel
Strand 6
A
53 56anti-parallel
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There are 3 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
17 19first strand
Strand 2
A
74 76anti-parallel
Strand 3
A
65 67anti-parallel
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There are 6 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
6 12first strand
Strand 2
B
99 109parallel
Strand 3
B
85 93anti-parallel
Strand 4
B
29 35anti-parallel
Strand 5
B
39 44anti-parallel
Strand 6
B
53 56anti-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
17 19first strand
Strand 2
B
74 76anti-parallel
Strand 3
B
65 67anti-parallel
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There are 6 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
7 12first strand
Strand 2
C
99 109parallel
Strand 3
C
85 93anti-parallel
Strand 4
C
29 35anti-parallel
Strand 5
C
39 44anti-parallel
Strand 6
C
53 56anti-parallel
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There are 3 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
17 19first strand
Strand 2
C
74 76anti-parallel
Strand 3
C
65 67anti-parallel
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There are 6 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
7 12first strand
Strand 2
D
99 109parallel
Strand 3
D
85 93anti-parallel
Strand 4
D
29 35anti-parallel
Strand 5
D
39 44anti-parallel
Strand 6
D
53 56anti-parallel
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There are 3 strands in H sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
17 19first strand
Strand 2
D
74 76anti-parallel
Strand 3
D
65 67anti-parallel
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There are 6 strands in I sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
7 12first strand
Strand 2
E
99 109parallel
Strand 3
E
85 93anti-parallel
Strand 4
E
29 35anti-parallel
Strand 5
E
39 44anti-parallel
Strand 6
E
53 56anti-parallel
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There are 3 strands in J sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
17 19first strand
Strand 2
E
74 76anti-parallel
Strand 3
E
65 67anti-parallel
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There are 6 strands in K sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
7 12first strand
Strand 2
F
99 109parallel
Strand 3
F
85 93anti-parallel
Strand 4
F
29 35anti-parallel
Strand 5
F
39 44anti-parallel
Strand 6
F
53 56anti-parallel
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There are 3 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
17 19first strand
Strand 2
F
74 76anti-parallel
Strand 3
F
65 67anti-parallel
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