Contacts of the helix formed by residues 355 - 383 (chain A) in PDB entry 2VKZ
Residue contacts within the protein 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). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A ASP* 3.1 10.2 + - - +
354A LEU* 1.3 88.1 - - - +
356A ASN* 1.3 63.9 + - - +
357A GLY 3.2 3.8 + - - -
358A GLU* 3.2 10.9 + - - +
359A ARG* 3.1 23.3 + - - +
1153C ASP* 4.3 13.4 - - - +
1155C PHE* 3.5 35.1 - - + -
1166C LYS* 4.8 15.0 + - - +
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Residues in contact with ASN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ASP* 3.4 32.0 + - + +
354A LEU 3.5 1.6 - - - -
355A ASP* 1.3 75.7 - - - +
357A GLY* 1.3 69.3 + - - +
359A ARG* 3.2 20.8 + - - +
360A LYS* 3.1 46.5 + - - +
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Residues in contact with GLY 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP 5.2 0.2 + - - -
354A LEU 4.7 2.8 + - - -
355A ASP 3.2 1.2 + - - -
356A ASN* 1.3 80.7 - - - +
358A GLU* 1.3 63.1 + - - +
360A LYS* 3.2 6.6 + - - +
361A PHE* 2.9 24.4 + - - +
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ASP* 3.2 10.2 + - + +
357A GLY* 1.3 74.8 - - - +
359A ARG* 1.3 64.3 + - - +
361A PHE* 3.6 20.2 - - + +
362A LEU* 2.9 49.8 + - - +
1155C PHE* 3.6 25.5 - - + -
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Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 3.5 29.6 + - - -
355A ASP* 3.1 18.4 + - - +
356A ASN* 3.4 24.2 - - - +
357A GLY 3.1 0.8 + - - -
358A GLU* 1.3 80.8 - - - +
360A LYS* 1.3 65.9 + - + +
362A LEU* 3.0 11.8 + - - +
363A LYS* 3.1 12.2 + - - +
1150C ASP* 4.9 5.5 + - - +
1153C ASP* 2.4 46.2 + - - +
1155C PHE* 4.5 8.5 - - + -
1168C LEU* 4.4 14.5 - - - +
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Residues in contact with LYS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ASN* 3.1 39.9 + - - +
357A GLY* 3.7 6.5 - - - +
359A ARG* 1.3 78.6 - - + +
361A PHE* 1.3 62.5 + - - +
363A LYS* 3.1 10.8 + - - +
364A GLU* 3.1 30.1 + - + +
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A GLY 2.9 17.9 + - - +
358A GLU* 3.6 23.3 - - - +
359A ARG 3.1 0.2 + - - -
360A LYS* 1.3 77.4 - - - +
362A LEU* 1.3 80.7 + - + +
363A LYS 3.2 0.3 + - - -
364A GLU* 3.2 8.5 + - + +
365A LYS* 2.9 50.7 + - + +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A GLU* 2.9 37.1 + - - +
359A ARG* 3.5 5.6 - - - +
361A PHE* 1.3 100.4 - - + +
363A LYS* 1.3 60.4 + - - +
365A LYS* 3.6 16.1 + - + +
366A ASP* 3.3 26.8 + - - +
1154C ILE 5.0 4.5 - - - +
1155C PHE* 4.1 21.1 - - + -
1156C GLU 6.3 0.2 - - - +
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ARG 3.1 10.4 + - - +
360A LYS* 3.5 12.3 - - - +
361A PHE 3.1 0.4 - - - -
362A LEU* 1.3 76.2 - - - +
364A GLU* 1.3 73.7 + - - +
366A ASP* 3.3 10.0 + - + +
367A THR* 3.2 31.5 + - + +
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LYS* 3.1 16.9 + - + +
361A PHE* 3.8 8.5 - - + +
363A LYS* 1.3 85.7 - - - +
365A LYS* 1.3 67.2 + - - +
366A ASP 3.0 2.2 - - - -
367A THR* 3.0 18.0 + - - +
368A VAL* 3.0 30.0 + - + +
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Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A PHE* 2.9 45.2 + - + +
362A LEU* 3.6 17.2 - - + +
364A GLU* 1.3 76.7 - - - +
366A ASP* 1.3 65.6 + - - +
368A VAL* 3.4 15.4 + - + +
369A ALA* 3.4 13.5 + - - +
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Residues in contact with ASP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A LEU 3.3 13.1 + - - +
363A LYS* 3.3 14.2 + - + +
364A GLU 3.0 0.2 - - - -
365A LYS* 1.3 77.9 - - - +
367A THR* 1.3 58.9 + - + +
368A VAL 2.8 11.0 + - - -
369A ALA* 3.1 7.9 + - - +
370A GLU* 3.1 23.1 + - - +
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Residues in contact with THR 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A LYS* 3.3 25.1 - - + +
364A GLU* 3.0 28.1 + - - +
366A ASP* 1.3 75.3 - - + +
368A VAL* 1.3 58.5 + - - +
370A GLU* 3.5 20.5 + - - +
371A LEU* 3.1 34.5 + - - +
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLU* 3.0 18.6 + - + +
365A LYS* 3.5 13.7 - - + +
366A ASP 2.8 3.0 + - - -
367A THR* 1.3 78.4 - - - +
369A ALA* 1.3 59.3 + - + +
370A GLU 2.9 1.3 - - - -
371A LEU* 3.3 3.7 + - - +
372A GLN* 2.7 44.1 + - + +
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LYS 3.4 7.7 + - - +
366A ASP* 3.1 7.9 + - - +
368A VAL* 1.3 83.1 - - + +
370A GLU* 1.3 56.6 + - - +
372A GLN* 3.9 8.5 - - - +
373A ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ASP* 3.1 12.4 + - - +
367A THR* 3.5 27.7 + - - +
369A ALA* 1.3 75.1 - - - +
371A LEU* 1.3 70.3 + - + +
373A ALA* 3.1 19.3 - - - +
374A GLN* 3.3 21.3 + - - +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A THR* 3.1 19.7 + - - +
368A VAL* 3.9 3.6 - - - +
370A GLU* 1.3 79.3 - - + +
372A GLN* 1.3 68.5 + - - +
373A ALA 2.8 3.3 + - - -
374A GLN* 2.8 35.4 + - - +
375A LEU* 3.0 15.2 + - + +
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A VAL* 2.7 30.9 + - + +
369A ALA* 3.9 7.9 - - - +
371A LEU* 1.3 72.6 - - - +
373A ALA* 1.3 56.1 + - - +
375A LEU* 3.6 17.5 - - - +
376A ASP* 2.8 68.2 + - - +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ALA 2.9 20.3 + - - +
370A GLU* 3.1 10.1 - - - +
371A LEU 2.8 1.0 + - - -
372A GLN* 1.3 75.8 - - - +
374A GLN* 1.3 60.7 + - + +
376A ASP* 3.0 12.2 + - - +
377A TYR* 2.9 26.7 + - - +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A GLU* 3.3 19.2 - - + +
371A LEU* 2.8 33.9 + - - +
373A ALA* 1.3 73.8 - - + +
375A LEU* 1.3 58.3 + - - +
377A TYR* 3.1 9.4 + - - +
378A LEU* 2.9 34.4 + - + +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LEU* 3.0 11.9 + - + +
372A GLN* 3.6 24.0 - - - +
374A GLN* 1.3 77.1 - - - +
376A ASP* 1.3 66.2 + - - +
378A LEU* 3.3 13.0 + - + +
379A ASN* 3.1 40.6 + - - +
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLN* 2.8 48.4 + - - +
373A ALA* 3.0 13.7 + - - +
375A LEU* 1.3 78.9 - - - +
377A TYR* 1.3 56.4 + - - +
379A ASN* 3.4 7.3 + - - +
380A ALA* 2.9 25.3 + - - +
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ALA 2.9 12.7 + - - +
374A GLN* 3.1 10.9 + - - +
376A ASP* 1.3 72.7 - - - +
378A LEU* 1.3 72.0 + - + +
379A ASN 3.0 1.6 - - - -
380A ALA* 2.7 31.8 + - + +
381A GLU* 2.9 47.5 + - + +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A GLN* 2.9 17.4 + - + +
375A LEU* 3.7 13.7 - - + +
377A TYR* 1.3 90.5 - - + +
379A ASN* 1.3 57.6 + - - +
381A GLU* 3.4 5.0 + - + +
382A LEU* 2.9 50.6 + - + +
387A VAL* 4.7 4.5 - - + -
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Residues in contact with ASN 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LEU* 3.1 32.5 + - - +
376A ASP* 3.4 11.6 - - - +
377A TYR 3.0 0.6 - - - -
378A LEU* 1.3 76.6 - - - +
380A ALA* 1.3 61.3 + - - +
383A GLY* 2.9 37.6 + - - -
384A GLU* 4.4 12.3 - - - +
387A VAL* 3.8 35.2 - - - +
388A ASN* 5.8 1.4 + - - -
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ASP 2.9 13.6 + - - +
377A TYR* 2.7 29.9 + - + +
379A ASN* 1.3 74.1 - - - +
381A GLU* 1.3 59.6 + - + +
383A GLY* 4.6 1.2 + - - -
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 2.9 51.4 + - + +
378A LEU* 3.8 10.5 - - + +
380A ALA* 1.3 79.7 - - - +
382A LEU* 1.3 70.1 + - + +
383A GLY 3.5 0.4 - - - -
789A GLU* 4.7 5.7 - - - +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 2.9 35.4 + - + +
381A GLU* 1.3 81.6 - - + +
383A GLY* 1.3 59.6 + - - +
386A PHE* 3.2 45.4 - - + +
387A VAL* 3.6 18.2 - - + -
786A SER* 2.9 22.1 + - - -
789A GLU* 4.5 18.5 - - - +
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Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASN* 2.9 22.1 + - - -
380A ALA 4.6 1.3 + - - -
381A GLU 3.5 1.4 - - - -
382A LEU* 1.3 77.8 - - - +
384A GLU* 1.3 66.6 + - - -
387A VAL* 3.1 26.0 + - - +
786A SER* 3.4 13.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il