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


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 3DYD entry

There are 2 chains in PDB entry 3DYD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 TRP 41CYS 444
B
 TRP 41CYS 444
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 3DYD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
90 104Right-handed alpha
Helix 2
2
A
115 127Right-handed alpha
Helix 3
3
A
134 136Right-handed 310
Helix 4
4
A
143 156Right-handed alpha
Helix 5
5
A
170 179Right-handed alpha
Helix 6
6
A
189 193Right-handed 310
Helix 7
7
A
197 203Right-handed alpha
Helix 8
8
A
226 240Right-handed alpha
Helix 9
9
A
262 267Right-handed 310
Helix 10
10
A
284 288Right-handed 310
Helix 11
11
A
301 317Right-handed alpha
Helix 12
12
A
320 334Right-handed alpha
Helix 13
13
A
335 360Right-handed alpha
Helix 14
14
A
380 383Right-handed 310
Helix 15
15
A
388 401Right-handed alpha
Helix 16
16
A
408 411Right-handed 310
Helix 17
17
A
423 442Right-handed alpha
Helix 18
18
B
90 104Right-handed alpha
Helix 19
19
B
115 127Right-handed alpha
Helix 20
20
B
134 136Right-handed 310
Helix 21
21
B
142 156Right-handed alpha
Helix 22
22
B
170 179Right-handed alpha
Helix 23
23
B
189 193Right-handed 310
Helix 24
24
B
197 205Right-handed alpha
Helix 25
25
B
226 241Right-handed alpha
Helix 26
26
B
262 267Right-handed 310
Helix 27
27
B
284 288Right-handed 310
Helix 28
28
B
301 314Right-handed alpha
Helix 29
29
B
320 334Right-handed alpha
Helix 30
30
B
335 359Right-handed alpha
Helix 31
31
B
380 383Right-handed 310
Helix 32
32
B
388 401Right-handed alpha
Helix 33
33
B
408 411Right-handed 310
Helix 34
34
B
423 442Right-handed alpha
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There are 6 sheets in PDB entry 3DYD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F,

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
74 75first strand
Strand 2
A
402 403parallel
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There are 7 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
138 141first strand
Strand 2
A
290 295anti-parallel
Strand 3
A
272 277anti-parallel
Strand 4
A
244 247parallel
Strand 5
A
209 215parallel
Strand 6
A
161 166parallel
Strand 7
A
182 187parallel
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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
363 366first strand
Strand 2
A
373 378anti-parallel
Strand 3
A
415 419anti-parallel
Strand 4
A
405 406anti-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
B
74 75first strand
Strand 2
B
402 403parallel
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There are 7 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
138 141first strand
Strand 2
B
290 295anti-parallel
Strand 3
B
272 277anti-parallel
Strand 4
B
244 247parallel
Strand 5
B
209 215parallel
Strand 6
B
161 166parallel
Strand 7
B
182 187parallel
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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
B
363 365first strand
Strand 2
B
373 378anti-parallel
Strand 3
B
415 419anti-parallel
Strand 4
B
405 406anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il