Analysis of interatomic Contacts of Structural Units in PDB entry:
4DKM


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 4DKM entry

There are 16 chains in PDB entry 4DKM (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 LEU 3ILE 57
A
 PHE 61LEU 218
B
 LEU 3ILE 57
B
 PHE 61LEU 218
C
 LEU 3ILE 57
C
 PHE 61LEU 218
D
 LEU 3ILE 57
D
 PHE 61LEU 218
E
 LEU 3ILE 57
E
 PHE 61LEU 218
F
 LEU 3ILE 57
F
 PHE 61LEU 218
G
 LEU 3ILE 57
G
 PHE 61LEU 218
H
 LEU 3ILE 57
H
 PHE 61LEU 218
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 32 helices in PDB entry 4DKM. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
49 53Right-handed 310
Helix 2
2
A
61 64Right-handed 310
Helix 3
3
A
72 81Right-handed alpha
Helix 4
4
A
182 188Right-handed alpha
Helix 5
5
B
49 53Right-handed 310
Helix 6
6
B
61 64Right-handed 310
Helix 7
7
B
72 81Right-handed alpha
Helix 8
8
B
182 188Right-handed alpha
Helix 9
9
C
49 53Right-handed 310
Helix 10
10
C
61 64Right-handed 310
Helix 11
11
C
72 81Right-handed alpha
Helix 12
12
C
182 188Right-handed alpha
Helix 13
13
D
49 53Right-handed 310
Helix 14
14
D
61 64Right-handed 310
Helix 15
15
D
72 81Right-handed alpha
Helix 16
16
D
182 188Right-handed alpha
Helix 17
17
E
49 53Right-handed 310
Helix 18
18
E
61 64Right-handed 310
Helix 19
19
E
72 81Right-handed alpha
Helix 20
20
E
182 188Right-handed alpha
Helix 21
21
F
49 53Right-handed 310
Helix 22
22
F
61 64Right-handed 310
Helix 23
23
F
72 81Right-handed alpha
Helix 24
24
F
182 188Right-handed alpha
Helix 25
25
G
49 53Right-handed 310
Helix 26
26
G
61 64Right-handed 310
Helix 27
27
G
72 81Right-handed alpha
Helix 28
28
G
182 188Right-handed alpha
Helix 29
29
H
49 53Right-handed 310
Helix 30
30
H
61 64Right-handed 310
Helix 31
31
H
72 81Right-handed alpha
Helix 32
32
H
182 188Right-handed alpha
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There are 16 sheets in PDB entry 4DKM. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P,

There are 12 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
6 15first strand
Strand 2
A
18 28anti-parallel
Strand 3
A
35 41anti-parallel
Strand 4
A
205 215anti-parallel
Strand 5
A
191 201anti-parallel
Strand 6
A
139 147anti-parallel
Strand 7
A
150 160anti-parallel
Strand 8
A
166 177anti-parallel
Strand 9
A
84 92anti-parallel
Strand 10
A
97 107anti-parallel
Strand 11
A
110 120anti-parallel
Strand 12
A
6 15parallel
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There are 2 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
66 67first strand
Strand 2
A
70 71anti-parallel
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There are 12 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 15first strand
Strand 2
B
18 28anti-parallel
Strand 3
B
35 41anti-parallel
Strand 4
B
205 215anti-parallel
Strand 5
B
191 201anti-parallel
Strand 6
B
139 147anti-parallel
Strand 7
B
150 160anti-parallel
Strand 8
B
166 177anti-parallel
Strand 9
B
84 92anti-parallel
Strand 10
B
97 107anti-parallel
Strand 11
B
110 120anti-parallel
Strand 12
B
6 15parallel
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There are 2 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
66 67first strand
Strand 2
B
70 71anti-parallel
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There are 12 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
6 15first strand
Strand 2
C
18 28anti-parallel
Strand 3
C
35 41anti-parallel
Strand 4
C
205 215anti-parallel
Strand 5
C
191 201anti-parallel
Strand 6
C
139 147anti-parallel
Strand 7
C
150 160anti-parallel
Strand 8
C
166 177anti-parallel
Strand 9
C
84 92anti-parallel
Strand 10
C
97 107anti-parallel
Strand 11
C
110 120anti-parallel
Strand 12
C
6 15parallel
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There are 2 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
66 67first strand
Strand 2
C
70 71anti-parallel
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There are 12 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
6 15first strand
Strand 2
D
18 28anti-parallel
Strand 3
D
35 41anti-parallel
Strand 4
D
205 215anti-parallel
Strand 5
D
191 201anti-parallel
Strand 6
D
139 147anti-parallel
Strand 7
D
150 160anti-parallel
Strand 8
D
166 177anti-parallel
Strand 9
D
84 92anti-parallel
Strand 10
D
97 107anti-parallel
Strand 11
D
110 120anti-parallel
Strand 12
D
6 15parallel
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There are 2 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
66 67first strand
Strand 2
D
70 71anti-parallel
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There are 12 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
6 15first strand
Strand 2
E
18 28anti-parallel
Strand 3
E
35 41anti-parallel
Strand 4
E
205 215anti-parallel
Strand 5
E
191 201anti-parallel
Strand 6
E
139 147anti-parallel
Strand 7
E
150 160anti-parallel
Strand 8
E
166 177anti-parallel
Strand 9
E
84 92anti-parallel
Strand 10
E
97 107anti-parallel
Strand 11
E
110 120anti-parallel
Strand 12
E
6 15parallel
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There are 2 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
66 67first strand
Strand 2
E
70 71anti-parallel
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There are 12 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
6 15first strand
Strand 2
F
18 28anti-parallel
Strand 3
F
35 41anti-parallel
Strand 4
F
205 215anti-parallel
Strand 5
F
191 201anti-parallel
Strand 6
F
139 147anti-parallel
Strand 7
F
150 160anti-parallel
Strand 8
F
166 177anti-parallel
Strand 9
F
84 92anti-parallel
Strand 10
F
97 107anti-parallel
Strand 11
F
110 120anti-parallel
Strand 12
F
6 15parallel
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There are 2 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
66 67first strand
Strand 2
F
70 71anti-parallel
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There are 12 strands in M sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
G
6 15first strand
Strand 2
G
18 28anti-parallel
Strand 3
G
35 41anti-parallel
Strand 4
G
205 215anti-parallel
Strand 5
G
191 201anti-parallel
Strand 6
G
139 147anti-parallel
Strand 7
G
150 160anti-parallel
Strand 8
G
166 177anti-parallel
Strand 9
G
84 92anti-parallel
Strand 10
G
97 107anti-parallel
Strand 11
G
110 120anti-parallel
Strand 12
G
6 15parallel
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There are 2 strands in N sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
G
66 67first strand
Strand 2
G
70 71anti-parallel
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There are 12 strands in O sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
6 15first strand
Strand 2
H
18 28anti-parallel
Strand 3
H
35 41anti-parallel
Strand 4
H
205 215anti-parallel
Strand 5
H
191 201anti-parallel
Strand 6
H
139 147anti-parallel
Strand 7
H
150 160anti-parallel
Strand 8
H
166 177anti-parallel
Strand 9
H
84 92anti-parallel
Strand 10
H
97 107anti-parallel
Strand 11
H
110 120anti-parallel
Strand 12
H
6 15parallel
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There are 2 strands in P sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
H
66 67first strand
Strand 2
H
70 71anti-parallel
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