Analysis of interatomic
Contacts of Structural
Units in PDB entry:
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).
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 5VDK entry
There is 1 chain in PDB entry 5VDK
(CSU analysis of residue contacts immediately below table)
| Chain ID |
Initial residue | Terminal residue |
|---|
A
|
MET 204 | LEU 486 |
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There are 10
helices in PDB entry 5VDK. Click on helix of interest for
CSU analysis.
Helix
number
| Helix
ID | Chain
ID |
Initial
residue | Terminal
residue |
Helix class |
|---|
| Helix 1 |
AA1 | A
| 206 |
211 | Right-handed alpha |
| Helix 2 |
AA2 | A
| 254 |
266 | Right-handed alpha |
| Helix 3 |
AA3 | A
| 296 |
307 | Right-handed alpha |
| Helix 4 |
AA4 | A
| 312 |
333 | Right-handed alpha |
| Helix 5 |
AA5 | A
| 396 |
400 | Right-handed 310 |
| Helix 6 |
AA6 | A
| 401 |
406 | Right-handed alpha |
| Helix 7 |
AA7 | A
| 412 |
429 | Right-handed alpha |
| Helix 8 |
AA8 | A
| 436 |
444 | Right-handed alpha |
| Helix 9 |
AA9 | A
| 456 |
468 | Right-handed alpha |
| Helix 10 |
AB1 | A
| 476 |
482 | Right-handed alpha |
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There are
3 sheets in PDB entry 5VDK. Click on sheet of
interest to get list of strands forming it:
AA1,
AA2,
AA3,
There are 5
strands in AA1 sheet. Click on strand of interest
for CSU analysis.
Strand
number
| Chain
ID |
Initial
residue | Terminal
residue |
Strand sense |
|---|
| Strand 1 |
A
| 212 |
221 | first strand |
| Strand 2 |
A
| 224 |
231 | anti-parallel |
| Strand 3 |
A
| 237 |
243 | anti-parallel |
| Strand 4 |
A
| 284 |
290 | anti-parallel |
| Strand 5 |
A
| 275 |
281 | anti-parallel |
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There are 2
strands in AA2 sheet. Click on strand of interest
for CSU analysis.
Strand
number
| Chain
ID |
Initial
residue | Terminal
residue |
Strand sense |
|---|
| Strand 1 |
A
| 335 |
336 | first strand |
| Strand 2 |
A
| 385 |
386 | anti-parallel |
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There are 2
strands in AA3 sheet. Click on strand of interest
for CSU analysis.
Strand
number
| Chain
ID |
Initial
residue | Terminal
residue |
Strand sense |
|---|
| Strand 1 |
A
| 345 |
348 | first strand |
| Strand 2 |
A
| 375 |
378 | anti-parallel |
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Please mail
questions/suggestions concerning this page
to
Vladimir.Sobolev@weizmann.
ac.il