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


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 3PDK entry

There are 2 chains in PDB entry 3PDK (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLY 2GLY 446
B
 LYS 3GLY 446
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 34 helices in PDB entry 3PDK. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
19 36Right-handed alpha
Helix 2
2
A
52 66Right-handed alpha
Helix 3
3
A
78 90Right-handed alpha
Helix 4
4
A
120 133Right-handed alpha
Helix 5
5
A
142 146Right-handed 310
Helix 6
6
A
153 165Right-handed alpha
Helix 7
7
A
187 196Right-handed alpha
Helix 8
8
A
221 232Right-handed alpha
Helix 9
9
A
257 272Right-handed alpha
Helix 10
10
A
275 277Right-handed 310
Helix 11
11
A
287 297Right-handed alpha
Helix 12
12
A
307 319Right-handed alpha
Helix 13
13
A
340 356Right-handed alpha
Helix 14
14
A
358 364Right-handed alpha
Helix 15
15
A
380 385Right-handed alpha
Helix 16
16
A
387 401Right-handed alpha
Helix 17
17
A
426 446Right-handed alpha
Helix 18
18
B
19 36Right-handed alpha
Helix 19
19
B
52 66Right-handed alpha
Helix 20
20
B
78 89Right-handed alpha
Helix 21
21
B
120 132Right-handed alpha
Helix 22
22
B
142 146Right-handed 310
Helix 23
23
B
154 166Right-handed alpha
Helix 24
24
B
187 196Right-handed alpha
Helix 25
25
B
221 231Right-handed alpha
Helix 26
26
B
257 272Right-handed alpha
Helix 27
27
B
275 277Right-handed 310
Helix 28
28
B
287 296Right-handed alpha
Helix 29
29
B
307 319Right-handed alpha
Helix 30
30
B
340 356Right-handed alpha
Helix 31
31
B
358 364Right-handed alpha
Helix 32
32
B
380 386Right-handed alpha
Helix 33
33
B
387 402Right-handed alpha
Helix 34
34
B
426 445Right-handed alpha
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There are 8 sheets in PDB entry 3PDK. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H,

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
10 13first strand
Strand 2
A
106 113anti-parallel
Strand 3
A
93 97anti-parallel
Strand 4
A
42 47parallel
Strand 5
A
70 76parallel
Strand 6
A
149 151parallel
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There are 5 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
199 203first strand
Strand 2
A
175 179parallel
Strand 3
A
235 239parallel
Strand 4
A
246 250anti-parallel
Strand 5
A
255 256anti-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
A
300 304first strand
Strand 2
A
279 283parallel
Strand 3
A
322 324parallel
Strand 4
A
330 332anti-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
A
371 376first strand
Strand 2
A
418 423anti-parallel
Strand 3
A
406 410anti-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
B
10 13first strand
Strand 2
B
106 113anti-parallel
Strand 3
B
93 97anti-parallel
Strand 4
B
42 47parallel
Strand 5
B
70 76parallel
Strand 6
B
149 151parallel
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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
B
199 203first strand
Strand 2
B
175 179parallel
Strand 3
B
235 239parallel
Strand 4
B
246 249anti-parallel
Strand 5
B
255 256anti-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
B
300 304first strand
Strand 2
B
279 283parallel
Strand 3
B
323 324parallel
Strand 4
B
330 331anti-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
B
371 377first strand
Strand 2
B
417 423anti-parallel
Strand 3
B
406 411anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il