Analysis of interatomic Contacts of Structural Units in PDB entry:
3NKD


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 3NKD entry

There are 2 chains in PDB entry 3NKD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ASP 13PRO 280
B
 ILE 9PRO 280
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 27 helices in PDB entry 3NKD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
45 49Right-handed 310
Helix 2
2
A
61 71Right-handed alpha
Helix 3
3
A
80 83Right-handed 310
Helix 4
4
A
95 108Right-handed alpha
Helix 5
5
A
108 125Right-handed alpha
Helix 6
6
A
133 144Right-handed alpha
Helix 7
7
A
144 157Right-handed alpha
Helix 8
8
A
174 185Right-handed alpha
Helix 9
9
A
186 199Right-handed alpha
Helix 10
10
A
213 227Right-handed alpha
Helix 11
11
A
227 239Right-handed alpha
Helix 12
12
A
243 253Right-handed alpha
Helix 13
13
A
254 256Right-handed 310
Helix 14
14
A
257 263Right-handed alpha
Helix 15
15
A
263 274Right-handed alpha
Helix 16
16
B
10 14Right-handed 310
Helix 17
17
B
45 47Right-handed 310
Helix 18
18
B
62 71Right-handed alpha
Helix 19
19
B
80 82Right-handed 310
Helix 20
20
B
95 108Right-handed alpha
Helix 21
21
B
108 125Right-handed alpha
Helix 22
22
B
133 157Right-handed alpha
Helix 23
23
B
174 198Right-handed alpha
Helix 24
24
B
213 224Right-handed alpha
Helix 25
25
B
227 237Right-handed alpha
Helix 26
26
B
243 259Right-handed alpha
Helix 27
27
B
259 274Right-handed alpha
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There are 2 sheets in PDB entry 3NKD. Click on sheet of interest to get list of strands forming it: A, B,

There are 8 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
17 20first strand
Strand 2
A
51 54parallel
Strand 3
A
74 78parallel
Strand 4
A
85 89anti-parallel
Strand 5
B
84 89anti-parallel
Strand 6
B
74 78anti-parallel
Strand 7
B
49 54parallel
Strand 8
B
15 20parallel
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There are 8 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
41 43first strand
Strand 2
A
31 36anti-parallel
Strand 3
A
23 28anti-parallel
Strand 4
A
58 60parallel
Strand 5
B
59 61anti-parallel
Strand 6
B
24 28parallel
Strand 7
B
31 35anti-parallel
Strand 8
B
42 43anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il