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


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 3GDE entry

There is 1 chain in PDB entry 3GDE (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 GLY -2PHE 550
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 23 helices in PDB entry 3GDE. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
2 14Right-handed alpha
Helix 2
2
A
18 32Right-handed alpha
Helix 3
3
A
35 47Right-handed alpha
Helix 4
4
A
62 75Right-handed alpha
Helix 5
5
A
77 89Right-handed alpha
Helix 6
6
A
90 106Right-handed alpha
Helix 7
7
A
113 127Right-handed alpha
Helix 8
8
A
131 147Right-handed alpha
Helix 9
9
A
148 160Right-handed alpha
Helix 10
10
A
168 180Right-handed alpha
Helix 11
11
A
183 195Right-handed alpha
Helix 12
12
A
196 214Right-handed alpha
Helix 13
13
A
233 241Right-handed alpha
Helix 14
14
A
274 277Right-handed 310
Helix 15
15
A
278 289Right-handed alpha
Helix 16
16
A
309 319Right-handed alpha
Helix 17
17
A
323 330Right-handed alpha
Helix 18
18
A
350 362Right-handed alpha
Helix 19
19
A
378 392Right-handed alpha
Helix 20
20
A
438 441Right-handed 310
Helix 21
21
A
469 481Right-handed alpha
Helix 22
22
A
532 536Right-handed 310
Helix 23
23
A
538 548Right-handed alpha
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There are 6 sheets in PDB entry 3GDE. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F,

There are 5 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
227 230first strand
Strand 2
A
411 419parallel
Strand 3
A
396 400anti-parallel
Strand 4
A
244 249anti-parallel
Strand 5
A
373 376anti-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
265 268first strand
Strand 2
A
253 259anti-parallel
Strand 3
A
293 303anti-parallel
Strand 4
A
306 308anti-parallel
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There are 5 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
265 268first strand
Strand 2
A
253 259anti-parallel
Strand 3
A
293 303anti-parallel
Strand 4
A
332 342anti-parallel
Strand 5
A
368 370parallel
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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
A
458 464first strand
Strand 2
A
443 451anti-parallel
Strand 3
A
425 434anti-parallel
Strand 4
A
491 494anti-parallel
Strand 5
A
484 488anti-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
458 464first strand
Strand 2
A
443 451anti-parallel
Strand 3
A
425 434anti-parallel
Strand 4
A
499 503anti-parallel
Strand 5
A
523 527anti-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
A
506 509first strand
Strand 2
A
517 520anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il