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


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 3PFD entry

There are 4 chains in PDB entry 3PFD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLU 18ARG 389
B
 GLU 18ARG 389
C
 HIS 19ARG 389
D
 GLU 18ILE 271
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 3PFD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
18 34Right-handed alpha
Helix 2
2
A
37 44Right-handed alpha
Helix 3
3
A
48 58Right-handed alpha
Helix 4
4
A
66 70Right-handed 310
Helix 5
5
A
75 88Right-handed alpha
Helix 6
6
A
90 103Right-handed alpha
Helix 7
7
A
104 111Right-handed alpha
Helix 8
8
A
112 125Right-handed alpha
Helix 9
9
A
142 146Right-handed 310
Helix 10
10
A
182 188Right-handed 310
Helix 11
11
A
239 250Right-handed alpha
Helix 12
12
A
251 277Right-handed alpha
Helix 13
13
A
287 318Right-handed alpha
Helix 14
14
A
323 348Right-handed alpha
Helix 15
15
A
349 354Right-handed 310
Helix 16
16
A
358 370Right-handed alpha
Helix 17
17
A
375 388Right-handed alpha
Helix 18
18
B
18 34Right-handed alpha
Helix 19
19
B
37 44Right-handed alpha
Helix 20
20
B
48 58Right-handed alpha
Helix 21
21
B
66 70Right-handed 310
Helix 22
22
B
75 88Right-handed alpha
Helix 23
23
B
90 103Right-handed alpha
Helix 24
24
B
104 111Right-handed alpha
Helix 25
25
B
112 125Right-handed alpha
Helix 26
26
B
142 146Right-handed 310
Helix 27
27
B
182 188Right-handed 310
Helix 28
28
B
239 250Right-handed alpha
Helix 29
29
B
251 277Right-handed alpha
Helix 30
30
B
287 318Right-handed alpha
Helix 31
31
B
323 348Right-handed alpha
Helix 32
32
B
349 354Right-handed 310
Helix 33
33
B
358 370Right-handed alpha
Helix 34
34
B
375 389Right-handed alpha
Helix 35
35
C
19 34Right-handed alpha
Helix 36
36
C
34 44Right-handed alpha
Helix 37
37
C
48 58Right-handed alpha
Helix 38
38
C
66 70Right-handed 310
Helix 39
39
C
75 88Right-handed alpha
Helix 40
40
C
90 111Right-handed alpha
Helix 41
41
C
112 125Right-handed alpha
Helix 42
42
C
142 146Right-handed 310
Helix 43
43
C
182 188Right-handed 310
Helix 44
44
C
239 250Right-handed alpha
Helix 45
45
C
251 277Right-handed alpha
Helix 46
46
C
287 318Right-handed alpha
Helix 47
47
C
321 349Right-handed alpha
Helix 48
48
C
350 354Right-handed 310
Helix 49
49
C
358 370Right-handed alpha
Helix 50
50
C
375 388Right-handed alpha
Helix 51
51
D
18 34Right-handed alpha
Helix 52
52
D
37 44Right-handed alpha
Helix 53
53
D
48 58Right-handed alpha
Helix 54
54
D
66 70Right-handed 310
Helix 55
55
D
75 88Right-handed alpha
Helix 56
56
D
90 111Right-handed alpha
Helix 57
57
D
112 125Right-handed alpha
Helix 58
58
D
142 146Right-handed 310
Helix 59
59
D
185 188Right-handed 310
Helix 60
60
D
229 231Right-handed 310
Helix 61
61
D
239 250Right-handed alpha
Helix 62
62
D
251 277Right-handed alpha
Helix 63
63
D
287 318Right-handed alpha
Helix 64
64
D
322 348Right-handed alpha
Helix 65
65
D
349 354Right-handed 310
Helix 66
66
D
358 369Right-handed alpha
Helix 67
67
D
375 388Right-handed alpha
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There are 12 sheets in PDB entry 3PFD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L,

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
130 133first strand
Strand 2
A
174 180parallel
Strand 3
A
190 196anti-parallel
Strand 4
A
233 234anti-parallel
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There are 4 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
149 153first strand
Strand 2
A
156 167anti-parallel
Strand 3
A
218 229anti-parallel
Strand 4
A
202 207anti-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
A
278 279first strand
Strand 2
A
282 283anti-parallel
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There are 4 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
130 133first strand
Strand 2
B
174 180parallel
Strand 3
B
190 196anti-parallel
Strand 4
B
233 234anti-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
B
149 153first strand
Strand 2
B
156 167anti-parallel
Strand 3
B
218 229anti-parallel
Strand 4
B
202 207anti-parallel
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There are 2 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
278 279first strand
Strand 2
B
282 283anti-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
130 133first strand
Strand 2
C
174 180parallel
Strand 3
C
190 196anti-parallel
Strand 4
C
233 234anti-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
C
149 153first strand
Strand 2
C
156 167anti-parallel
Strand 3
C
218 229anti-parallel
Strand 4
C
202 207anti-parallel
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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
C
278 279first strand
Strand 2
C
282 283anti-parallel
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There are 4 strands in J sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
130 133first strand
Strand 2
D
174 180parallel
Strand 3
D
190 196anti-parallel
Strand 4
D
233 234anti-parallel
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There are 4 strands in K sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
149 153first strand
Strand 2
D
156 167anti-parallel
Strand 3
D
218 228anti-parallel
Strand 4
D
202 207anti-parallel
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There are 2 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
D
278 279first strand
Strand 2
D
282 283anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il