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


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 3PDE entry

There are 4 chains in PDB entry 3PDE (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 SER 1ASN 300
B
 SER 1ARG 298
C
 SER 1ARG 298
D
 SER 1ASN 300
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 67 helices in PDB entry 3PDE. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
5 20Right-handed alpha
Helix 2
2
A
21 29Right-handed alpha
Helix 3
3
A
32 45Right-handed alpha
Helix 4
4
A
49 62Right-handed alpha
Helix 5
5
A
67 91Right-handed alpha
Helix 6
6
A
105 111Right-handed alpha
Helix 7
7
A
111 131Right-handed alpha
Helix 8
8
A
136 152Right-handed alpha
Helix 9
9
A
155 166Right-handed alpha
Helix 10
10
A
172 184Right-handed alpha
Helix 11
11
A
184 199Right-handed alpha
Helix 12
12
A
202 204Right-handed 310
Helix 13
13
A
205 231Right-handed alpha
Helix 14
14
A
250 256Right-handed alpha
Helix 15
15
A
256 277Right-handed alpha
Helix 16
16
A
281 289Right-handed alpha
Helix 17
17
A
290 294Right-handed 310
Helix 18
18
B
1 20Right-handed alpha
Helix 19
19
B
21 29Right-handed alpha
Helix 20
20
B
32 45Right-handed alpha
Helix 21
21
B
49 62Right-handed alpha
Helix 22
22
B
67 91Right-handed alpha
Helix 23
23
B
105 111Right-handed alpha
Helix 24
24
B
111 131Right-handed alpha
Helix 25
25
B
136 152Right-handed alpha
Helix 26
26
B
155 166Right-handed alpha
Helix 27
27
B
172 184Right-handed alpha
Helix 28
28
B
184 199Right-handed alpha
Helix 29
29
B
202 204Right-handed 310
Helix 30
30
B
205 231Right-handed alpha
Helix 31
31
B
243 249Right-handed alpha
Helix 32
32
B
250 277Right-handed alpha
Helix 33
33
B
280 289Right-handed alpha
Helix 34
34
B
290 296Right-handed 310
Helix 35
35
C
1 20Right-handed alpha
Helix 36
36
C
21 29Right-handed alpha
Helix 37
37
C
32 45Right-handed alpha
Helix 38
38
C
49 62Right-handed alpha
Helix 39
39
C
67 91Right-handed alpha
Helix 40
40
C
105 111Right-handed alpha
Helix 41
41
C
111 131Right-handed alpha
Helix 42
42
C
136 152Right-handed alpha
Helix 43
43
C
155 166Right-handed alpha
Helix 44
44
C
172 184Right-handed alpha
Helix 45
45
C
184 199Right-handed alpha
Helix 46
46
C
202 204Right-handed 310
Helix 47
47
C
205 231Right-handed alpha
Helix 48
48
C
250 277Right-handed alpha
Helix 49
49
C
280 289Right-handed alpha
Helix 50
50
C
290 296Right-handed 310
Helix 51
51
D
4 20Right-handed alpha
Helix 52
52
D
21 29Right-handed alpha
Helix 53
53
D
32 45Right-handed alpha
Helix 54
54
D
49 62Right-handed alpha
Helix 55
55
D
67 91Right-handed alpha
Helix 56
56
D
105 111Right-handed alpha
Helix 57
57
D
111 131Right-handed alpha
Helix 58
58
D
136 152Right-handed alpha
Helix 59
59
D
155 166Right-handed alpha
Helix 60
60
D
172 184Right-handed alpha
Helix 61
61
D
184 199Right-handed alpha
Helix 62
62
D
202 204Right-handed 310
Helix 63
63
D
205 230Right-handed alpha
Helix 64
64
D
245 249Right-handed 310
Helix 65
65
D
250 276Right-handed alpha
Helix 66
66
D
281 289Right-handed alpha
Helix 67
67
D
290 294Right-handed 310
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There are 5 sheets in PDB entry 3PDE. Click on sheet of interest to get list of strands forming it: A, B, C, D, E,

There are 2 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
3 4first strand
Strand 2
D
231 232parallel
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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
99 100first strand
Strand 2
A
103 104anti-parallel
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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
B
99 100first strand
Strand 2
B
103 104anti-parallel
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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
C
99 100first strand
Strand 2
C
103 104anti-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
D
99 100first strand
Strand 2
D
103 104anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il