Analysis of interatomic Contacts of Structural Units in PDB entry:
1DKD


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 1DKD entry

There are 8 chains in PDB entry 1DKD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLU 191VAL 336
E
 TRP 602PRO 612
B
 GLU 191VAL 336
F
 TRP 602PRO 612
C
 GLU 191VAL 336
G
 SER 601PRO 612
D
 GLU 191VAL 336
H
 TRP 602PRO 612
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 30 helices in PDB entry 1DKD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
201 205Right-handed 310
Helix 2
2
A
229 232Right-handed 310
Helix 3
3
A
233 244Right-handed alpha
Helix 4
4
A
255 268Right-handed alpha
Helix 5
5
A
281 297Right-handed alpha
Helix 6
6
A
308 312Right-handed 310
Helix 7
7
A
313 317Right-handed 310
Helix 8
8
B
201 205Right-handed 310
Helix 9
9
B
229 232Right-handed 310
Helix 10
10
B
233 244Right-handed alpha
Helix 11
11
B
255 268Right-handed alpha
Helix 12
12
B
281 297Right-handed alpha
Helix 13
13
B
302 306Right-handed 310
Helix 14
14
B
308 312Right-handed 310
Helix 15
15
B
313 317Right-handed 310
Helix 16
16
C
201 205Right-handed 310
Helix 17
17
C
229 232Right-handed 310
Helix 18
18
C
233 244Right-handed alpha
Helix 19
19
C
255 268Right-handed alpha
Helix 20
20
C
281 297Right-handed alpha
Helix 21
21
C
308 312Right-handed 310
Helix 22
22
C
313 317Right-handed 310
Helix 23
23
D
201 205Right-handed 310
Helix 24
24
D
229 232Right-handed 310
Helix 25
25
D
233 243Right-handed alpha
Helix 26
26
D
255 268Right-handed alpha
Helix 27
27
D
281 297Right-handed alpha
Helix 28
28
D
302 306Right-handed 310
Helix 29
29
D
308 312Right-handed 310
Helix 30
30
D
313 317Right-handed 310
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There are 14 sheets in PDB entry 1DKD. Click on sheet of interest to get list of strands forming it: A, A1, B, C, D, D1, E, F, F1, G, H, H1, I, J,

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
193 195first strand
Strand 2
A
330 335anti-parallel
Strand 3
A
318 325anti-parallel
Strand 4
A
213 216anti-parallel
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There are 6 strands in A1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
193 195first strand
Strand 2
A
330 335anti-parallel
Strand 3
A
318 325anti-parallel
Strand 4
A
219 222anti-parallel
Strand 5
A
247 251parallel
Strand 6
A
273 277parallel
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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
226 227first strand
Strand 2
A
253 254parallel
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There are 2 strands in C sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
E
603 604first strand
Strand 2
E
610 611anti-parallel
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There are 5 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
273 277first strand
Strand 2
B
247 254parallel
Strand 3
B
219 227parallel
Strand 4
B
318 325anti-parallel
Strand 5
B
213 216anti-parallel
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There are 6 strands in D1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
273 277first strand
Strand 2
B
247 254parallel
Strand 3
B
219 227parallel
Strand 4
B
318 325anti-parallel
Strand 5
B
330 335anti-parallel
Strand 6
B
192 195anti-parallel
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There are 2 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
F
603 604first strand
Strand 2
F
610 611anti-parallel
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There are 5 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
273 277first strand
Strand 2
C
247 254parallel
Strand 3
C
219 227parallel
Strand 4
C
318 325anti-parallel
Strand 5
C
213 216anti-parallel
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There are 6 strands in F1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
273 277first strand
Strand 2
C
247 254parallel
Strand 3
C
219 227parallel
Strand 4
C
318 325anti-parallel
Strand 5
C
330 335anti-parallel
Strand 6
C
193 195anti-parallel
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There are 2 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
G
603 604first strand
Strand 2
G
610 611anti-parallel
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There are 4 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
193 195first strand
Strand 2
D
330 335anti-parallel
Strand 3
D
318 325anti-parallel
Strand 4
D
213 216anti-parallel
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There are 6 strands in H1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
193 195first strand
Strand 2
D
330 335anti-parallel
Strand 3
D
318 325anti-parallel
Strand 4
D
219 222anti-parallel
Strand 5
D
247 251parallel
Strand 6
D
273 277parallel
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There are 2 strands in I sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
226 227first strand
Strand 2
D
253 254parallel
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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
H
603 604first strand
Strand 2
H
610 611anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il