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


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 3DPD entry

There is 1 chain in PDB entry 3DPD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 MET 143ILE 1094
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 39 helices in PDB entry 3DPD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
144 159Right-handed alpha
Helix 2
2
A
171 189Right-handed alpha
Helix 3
3
A
192 199Right-handed alpha
Helix 4
4
A
208 213Right-handed alpha
Helix 5
5
A
242 250Right-handed alpha
Helix 6
6
A
286 289Right-handed 310
Helix 7
7
A
290 299Right-handed alpha
Helix 8
8
A
312 317Right-handed 310
Helix 9
9
A
421 423Right-handed 310
Helix 10
10
A
498 503Right-handed 310
Helix 11
11
A
548 560Right-handed alpha
Helix 12
12
A
568 578Right-handed alpha
Helix 13
13
A
578 584Right-handed alpha
Helix 14
14
A
585 587Right-handed 310
Helix 15
15
A
588 593Right-handed alpha
Helix 16
16
A
600 612Right-handed alpha
Helix 17
17
A
614 620Right-handed alpha
Helix 18
18
A
623 630Right-handed alpha
Helix 19
19
A
637 649Right-handed alpha
Helix 20
20
A
652 667Right-handed alpha
Helix 21
21
A
668 670Right-handed 310
Helix 22
22
A
675 688Right-handed alpha
Helix 23
23
A
688 706Right-handed alpha
Helix 24
24
A
709 722Right-handed alpha
Helix 25
25
A
725 752Right-handed alpha
Helix 26
26
A
762 776Right-handed alpha
Helix 27
27
A
797 801Right-handed 310
Helix 28
28
A
837 858Right-handed alpha
Helix 29
29
A
888 896Right-handed alpha
Helix 30
30
A
904 915Right-handed alpha
Helix 31
31
A
917 943Right-handed alpha
Helix 32
32
A
948 950Right-handed 310
Helix 33
33
A
988 996Right-handed alpha
Helix 34
34
A
1005 1022Right-handed alpha
Helix 35
35
A
1023 1039Right-handed alpha
Helix 36
36
A
1044 1049Right-handed alpha
Helix 37
37
A
1049 1055Right-handed alpha
Helix 38
38
A
1060 1077Right-handed alpha
Helix 39
39
A
1080 1091Right-handed alpha
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There are 7 sheets in PDB entry 3DPD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G,

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
220 221first strand
Strand 2
A
234 235anti-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
230 231first strand
Strand 2
A
224 225anti-parallel
Strand 3
A
305 308parallel
Strand 4
A
271 274anti-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
407 419first strand
Strand 2
A
360 369anti-parallel
Strand 3
A
515 520anti-parallel
Strand 4
A
478 483anti-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
392 398first strand
Strand 2
A
380 389anti-parallel
Strand 3
A
402 403anti-parallel
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There are 5 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
392 398first strand
Strand 2
A
380 389anti-parallel
Strand 3
A
428 434anti-parallel
Strand 4
A
460 467anti-parallel
Strand 5
A
485 486anti-parallel
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There are 4 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
811 815first strand
Strand 2
A
828 834anti-parallel
Strand 3
A
876 880anti-parallel
Strand 4
A
869 871anti-parallel
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There are 3 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
885 887first strand
Strand 2
A
952 955anti-parallel
Strand 3
A
960 962anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il