Analysis of interatomic Contacts of Structural Units in PDB entry:
2VDM


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 2VDM entry

There are 4 chains in PDB entry 2VDM (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
LEU 1PRO 452
B
GLY 1ARG 461
H
GLU 1PRO 221
L
ASP 1CYS 214
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 29 helices in PDB entry 2VDM. Click on helix of interest for CSU analysis.
Helix
number
Helix
ID
Chain
ID
Initial
residue
Terminal
residue
Helix class
Helix 1
1
A
151 158Right-handed alpha
Helix 2
2
A
187 192Right-handed alpha
Helix 3
3
A
200 207Right-handed alpha
Helix 4
4
A
227 231Right-handed 310
Helix 5
5
A
259 264Right-handed alpha
Helix 6
6
A
440 442Right-handed 310
Helix 7
7
B
12 20Right-handed alpha
Helix 8
8
B
41 47Right-handed alpha
Helix 9
9
B
50 52Right-handed 310
Helix 10
10
B
121 125Right-handed 310
Helix 11
11
B
127 146Right-handed alpha
Helix 12
12
B
169 174Right-handed 310
Helix 13
13
B
177 181Right-handed 310
Helix 14
14
B
199 210Right-handed alpha
Helix 15
15
B
221 232Right-handed alpha
Helix 16
16
B
232 237Right-handed alpha
Helix 17
17
B
259 264Right-handed 310
Helix 18
18
B
291 302Right-handed alpha
Helix 19
19
B
314 323Right-handed alpha
Helix 20
20
B
337 350Right-handed alpha
Helix 21
21
B
435 439Right-handed 310
Helix 22
22
H
28 32Right-handed 310
Helix 23
23
H
62 64Right-handed 310
Helix 24
24
H
87 91Right-handed 310
Helix 25
25
H
162 164Right-handed 310
Helix 26
26
H
206 209Right-handed 310
Helix 27
27
L
79 83Right-handed 310
Helix 28
28
L
121 128Right-handed alpha
Helix 29
29
L
183 187Right-handed alpha
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There are 25 sheets in PDB entry 2VDM. Click on sheet of interest to get list of strands forming it: AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, BA, BB, BC, BD, HA, HB, HC, HD, HE, HF, LA, LB, LC, LD, LE,

There are 4 strands in AA sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
3 12first strand
Strand 2
A
444 450anti-parallel
Strand 3
A
434 439anti-parallel
Strand 4
A
420 425anti-parallel
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There are 4 strands in AB sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
23 27first strand
Strand 2
A
33 39anti-parallel
Strand 3
A
52 57anti-parallel
Strand 4
A
67 68anti-parallel
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There are 4 strands in AC sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
75 79first strand
Strand 2
A
82 87anti-parallel
Strand 3
A
112 117anti-parallel
Strand 4
A
120 121anti-parallel
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There are 4 strands in AD sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
97 100first strand
Strand 2
A
103 108anti-parallel
Strand 3
A
129 133anti-parallel
Strand 4
A
140 143anti-parallel
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There are 4 strands in AE sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
172 175first strand
Strand 2
A
180 185anti-parallel
Strand 3
A
194 199anti-parallel
Strand 4
A
220 221anti-parallel
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There are 4 strands in AF sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
239 242first strand
Strand 2
A
252 257anti-parallel
Strand 3
A
266 270anti-parallel
Strand 4
A
276 281anti-parallel
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There are 4 strands in AG sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
292 296first strand
Strand 2
A
305 310anti-parallel
Strand 3
A
327 331anti-parallel
Strand 4
A
345 348anti-parallel
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There are 2 strands in AH sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
314 317first strand
Strand 2
A
321 324anti-parallel
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There are 4 strands in AI sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
360 364first strand
Strand 2
A
373 378anti-parallel
Strand 3
A
388 392anti-parallel
Strand 4
A
405 408anti-parallel
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There are 2 strands in AJ sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
A
394 395first strand
Strand 2
A
398 399anti-parallel
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There are 3 strands in BA sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
38 40first strand
Strand 2
B
23 26anti-parallel
Strand 3
B
54 55anti-parallel
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There are 6 strands in BB sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
60 65first strand
Strand 2
B
87 92anti-parallel
Strand 3
B
425 431parallel
Strand 4
B
411 418anti-parallel
Strand 5
B
353 360anti-parallel
Strand 6
B
385 389anti-parallel
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There are 5 strands in BC sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
83 84first strand
Strand 2
B
97 105anti-parallel
Strand 3
B
394 402anti-parallel
Strand 4
B
367 373anti-parallel
Strand 5
B
379 381anti-parallel
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There are 6 strands in BD sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
B
190 197first strand
Strand 2
B
149 156anti-parallel
Strand 3
B
112 119parallel
Strand 4
B
243 250parallel
Strand 5
B
305 311parallel
Strand 6
B
329 333parallel
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There are 4 strands in HA sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
3 6first strand
Strand 2
H
18 25anti-parallel
Strand 3
H
78 83anti-parallel
Strand 4
H
68 73anti-parallel
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There are 6 strands in HB sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
10 12first strand
Strand 2
H
113 117parallel
Strand 3
H
92 98anti-parallel
Strand 4
H
34 40anti-parallel
Strand 5
H
44 51anti-parallel
Strand 6
H
58 60anti-parallel
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There are 4 strands in HC sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
10 12first strand
Strand 2
H
113 117parallel
Strand 3
H
92 98anti-parallel
Strand 4
H
108 109anti-parallel
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There are 4 strands in HD sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
126 130first strand
Strand 2
H
141 151anti-parallel
Strand 3
H
180 190anti-parallel
Strand 4
H
169 171anti-parallel
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There are 4 strands in HE sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
126 130first strand
Strand 2
H
141 151anti-parallel
Strand 3
H
180 190anti-parallel
Strand 4
H
175 177anti-parallel
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There are 3 strands in HF sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
H
157 160first strand
Strand 2
H
200 205anti-parallel
Strand 3
H
210 215anti-parallel
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There are 4 strands in LA sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
4 7first strand
Strand 2
L
19 25anti-parallel
Strand 3
L
70 75anti-parallel
Strand 4
L
62 67anti-parallel
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There are 6 strands in LB sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
10 13first strand
Strand 2
L
102 106parallel
Strand 3
L
85 90anti-parallel
Strand 4
L
33 38anti-parallel
Strand 5
L
44 49anti-parallel
Strand 6
L
53 54anti-parallel
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There are 4 strands in LC sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
10 13first strand
Strand 2
L
102 106parallel
Strand 3
L
85 90anti-parallel
Strand 4
L
97 98anti-parallel
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There are 4 strands in LD sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
114 118first strand
Strand 2
L
129 139anti-parallel
Strand 3
L
173 182anti-parallel
Strand 4
L
159 163anti-parallel
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There are 4 strands in LE sheet. Click on strand of interest for CSU analysis.
Strand
number
Chain
ID
Initial
residue
Terminal
residue
Strand sense
Strand 1
L
153 154first strand
Strand 2
L
145 150anti-parallel
Strand 3
L
191 197anti-parallel
Strand 4
L
205 210anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il