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


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 3KMD entry

There are 6 chains in PDB entry 3KMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 PRO 92LYS 291
B
 PRO 92LYS 291
D
 PRO 92LYS 291
C
 PRO 92LYS 291
E
 G 1 C 19
F
 G 1 C 19
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 3KMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
165 169Right-handed 310
Helix 2
2
A
176 182Right-handed alpha
Helix 3
3
A
277 288Right-handed alpha
Helix 4
4
A
289 291Right-handed 310
Helix 5
5
B
165 169Right-handed 310
Helix 6
6
B
176 182Right-handed alpha
Helix 7
7
B
277 288Right-handed alpha
Helix 8
8
B
289 291Right-handed 310
Helix 9
9
D
165 169Right-handed 310
Helix 10
10
D
176 182Right-handed alpha
Helix 11
11
D
277 288Right-handed alpha
Helix 12
12
D
289 291Right-handed 310
Helix 13
13
C
165 169Right-handed 310
Helix 14
14
C
176 182Right-handed alpha
Helix 15
15
C
277 289Right-handed alpha
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There are 8 sheets in PDB entry 3KMD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H,

There are 4 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
110 112first strand
Strand 2
A
141 146anti-parallel
Strand 3
A
230 236anti-parallel
Strand 4
A
195 197anti-parallel
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There are 7 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
124 127first strand
Strand 2
A
132 135anti-parallel
Strand 3
A
264 274parallel
Strand 4
A
251 258anti-parallel
Strand 5
A
156 163anti-parallel
Strand 6
A
214 219anti-parallel
Strand 7
A
204 207anti-parallel
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There are 4 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
110 112first strand
Strand 2
B
141 146anti-parallel
Strand 3
B
230 236anti-parallel
Strand 4
B
195 197anti-parallel
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There are 7 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
124 127first strand
Strand 2
B
132 135anti-parallel
Strand 3
B
264 274parallel
Strand 4
B
251 258anti-parallel
Strand 5
B
156 163anti-parallel
Strand 6
B
214 219anti-parallel
Strand 7
B
204 207anti-parallel
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There are 4 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
110 112first strand
Strand 2
D
141 146anti-parallel
Strand 3
D
230 236anti-parallel
Strand 4
D
195 197anti-parallel
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There are 7 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
124 127first strand
Strand 2
D
132 135anti-parallel
Strand 3
D
264 274parallel
Strand 4
D
251 258anti-parallel
Strand 5
D
156 163anti-parallel
Strand 6
D
214 219anti-parallel
Strand 7
D
204 207anti-parallel
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There are 4 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
110 112first strand
Strand 2
C
141 146anti-parallel
Strand 3
C
230 236anti-parallel
Strand 4
C
195 197anti-parallel
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There are 7 strands in H sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
124 127first strand
Strand 2
C
132 135anti-parallel
Strand 3
C
263 274parallel
Strand 4
C
251 259anti-parallel
Strand 5
C
155 163anti-parallel
Strand 6
C
214 219anti-parallel
Strand 7
C
204 207anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il