Contacts of the helix formed by residues 375 - 398 (chain A) in PDB entry 1OHV
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 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A ILE 3.2 4.8 + - - -
372A LYS* 3.1 14.9 + - - +
373A ARG 3.2 2.9 - - - +
374A GLU* 1.3 80.1 - - - +
376A LEU* 1.3 62.4 + - - +
377A LEU* 3.3 3.6 + - - +
378A SER* 3.4 28.5 + - - -
379A ASN* 3.2 16.6 + - - +
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Residues in contact with LEU 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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77A ILE* 4.0 16.6 - - + -
370A ILE* 4.0 11.7 - - + -
371A ILE* 2.8 33.4 + - + +
374A GLU* 3.4 30.5 - - + +
375A ASP* 1.3 75.0 - - - +
377A LEU* 1.3 61.7 + - - +
378A SER 3.5 0.2 - - - -
379A ASN* 3.6 6.7 + - + +
380A ALA* 3.0 27.5 + - - +
450A LEU* 3.5 48.4 - - + +
451A VAL* 4.5 4.7 - - + -
453A ARG* 3.9 23.3 - - - +
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Residues in contact with LEU 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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304A GLY 4.7 0.2 - - - +
305A GLY* 3.4 35.4 - - - +
308A GLY* 3.5 26.3 - - - +
309A LYS* 4.5 2.2 - - - -
310A PHE* 3.8 36.8 - - + +
371A ILE* 4.0 23.3 - - + +
372A LYS* 6.4 1.3 - - + -
375A ASP* 3.3 1.5 - - - +
376A LEU* 1.3 74.3 - - - +
378A SER* 1.3 66.5 + - - +
380A ALA* 3.2 10.2 + - - +
381A ALA* 3.2 8.5 + - - +
450A LEU* 5.7 0.7 - - + -
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Residues in contact with SER 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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308A GLY 4.5 1.1 + - - -
375A ASP* 3.4 32.6 + - - -
376A LEU 3.5 0.2 - - - -
377A LEU* 1.3 78.3 - - - +
379A ASN* 1.3 62.7 + - - +
381A ALA* 3.2 9.3 + - - +
382A HIS* 3.0 23.3 + - - +
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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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374A GLU 5.1 0.7 - - - +
375A ASP* 3.2 13.2 + - - +
376A LEU* 3.6 11.4 - - + +
377A LEU 3.2 0.8 - - - -
378A SER* 1.3 79.8 - - - +
380A ALA* 1.3 54.9 + - - +
382A HIS* 3.7 13.2 - - - +
383A ALA* 2.7 35.4 + - - +
450A LEU 3.9 12.9 + - - -
452A PHE 2.9 28.7 + - - +
453A ARG* 3.8 37.8 + - - +
454A ASP 5.2 0.2 + - - -
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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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305A GLY 3.5 20.4 - - - +
306A SER* 3.7 16.2 - - - +
308A GLY 4.4 0.7 - - - +
376A LEU 3.0 13.8 + - - +
377A LEU 3.2 9.4 + - - +
379A ASN* 1.3 80.0 - - - +
381A ALA* 1.3 56.5 - - - +
383A ALA* 4.7 0.4 - - - -
384A GLY* 2.8 28.4 + - - -
409A GLY* 4.4 2.0 - - - -
410A THR* 3.3 19.9 + - + +
450A LEU* 4.6 8.7 - - + -
452A PHE 5.5 0.4 - - - -
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Residues in contact with ALA 381 (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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307A THR 5.3 0.7 - - - +
308A GLY* 4.2 12.3 - - - +
377A LEU 3.2 8.2 + - - +
378A SER* 3.2 12.9 + - - +
380A ALA* 1.3 77.9 - - - +
382A HIS* 1.3 58.7 + - - +
384A GLY 3.8 0.2 - - - -
385A LYS* 2.9 40.8 + - - +
409A GLY* 4.3 12.3 - - - -
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Residues in contact with HIS 382 (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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378A SER 3.0 16.1 + - - +
379A ASN* 3.2 15.5 + - - +
381A ALA* 1.3 74.1 - - - +
383A ALA* 1.3 67.9 - - - +
385A LYS* 3.0 14.1 + - - +
386A VAL* 3.0 40.5 + - + +
454A ASP* 2.6 34.8 + - + +
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Residues in contact with ALA 383 (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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379A ASN* 2.7 22.8 + - - +
380A ALA 4.3 1.1 - - - +
382A HIS* 1.3 76.2 - - - +
384A GLY* 1.3 55.8 + - - +
386A VAL* 3.3 4.6 + - - +
387A LEU* 2.9 28.8 + - - +
410A THR* 4.3 3.1 - - + -
452A PHE* 3.5 39.8 - - + +
453A ARG* 3.9 13.9 - - - -
454A ASP* 3.9 11.2 - - - +
457A ALA* 4.3 1.0 - - - +
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Residues in contact with GLY 384 (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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380A ALA 2.8 16.9 + - - -
381A ALA 3.8 0.7 - - - -
383A ALA* 1.3 75.3 - - - +
385A LYS* 1.3 58.3 + - - +
387A LEU* 3.3 5.7 + - - +
388A LEU* 2.8 30.7 + - - +
409A GLY* 3.2 29.4 - - - +
410A THR* 3.6 9.6 - - - +
412A CYS* 4.2 0.5 - - - -
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Residues in contact with LYS 385 (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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381A ALA* 2.9 26.1 + - - +
382A HIS* 3.0 15.9 + - - +
384A GLY* 1.3 73.0 - - - +
386A VAL* 1.3 59.9 + - + +
388A LEU* 3.2 8.2 + - + +
389A THR* 2.9 40.0 + - - +
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Residues in contact with VAL 386 (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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382A HIS* 3.0 28.6 + - + +
383A ALA 3.5 7.0 - - - +
385A LYS* 1.3 76.0 - - + +
387A LEU* 1.3 63.1 + - - +
389A THR* 3.6 6.2 + - - -
390A GLY* 3.2 19.4 + - - -
454A ASP* 3.7 24.0 - - + +
457A ALA* 4.1 14.8 - - + -
458A HIS* 3.6 33.8 - - + +
461A LEU* 4.1 3.2 - - + +
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Residues in contact with LEU 387 (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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383A ALA 2.9 17.1 + - - +
384A GLY* 3.5 5.4 - - - +
386A VAL* 1.3 77.6 - - - +
388A LEU* 1.3 56.9 + - - +
390A GLY* 3.3 3.1 + - - -
391A LEU* 3.0 42.6 + - + +
410A THR* 4.2 10.3 - - - +
412A CYS* 3.9 20.4 - - + -
446A PHE* 4.0 30.3 - - + -
448A PRO* 4.9 1.1 - - + -
452A PHE* 4.5 15.9 - - + -
457A ALA* 4.1 19.7 - - + +
460A PHE* 4.0 31.4 - - + -
461A LEU* 4.4 4.2 - - + +
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Residues in contact with LEU 388 (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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384A GLY 2.8 18.5 + - - +
385A LYS* 3.8 7.4 - - + +
387A LEU* 1.3 74.3 - - - +
389A THR* 1.3 60.1 + - - +
391A LEU* 3.1 7.8 + - + +
392A LEU* 2.8 47.3 + - + +
405A VAL* 3.7 18.6 - - + +
406A ARG* 3.6 33.9 - - - +
407A GLY 3.8 16.6 - - - +
409A GLY 5.5 0.2 - - - +
412A CYS* 4.0 11.2 - - + -
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Residues in contact with THR 389 (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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385A LYS* 2.9 23.4 + - - +
386A VAL* 3.8 7.1 - - - -
388A LEU* 1.3 75.6 - - - +
390A GLY* 1.3 64.0 + - - +
392A LEU* 3.2 14.4 + - + +
393A ASP* 3.0 22.9 + - + +
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Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A VAL 3.2 8.3 + - - -
387A LEU 3.7 0.2 - - - -
389A THR* 1.3 78.3 - - - +
391A LEU* 1.3 57.6 + - - +
393A ASP* 3.2 8.9 + - - +
394A LEU* 3.0 32.1 + - - +
461A LEU* 3.6 32.7 - - - +
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Residues in contact with LEU 391 (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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387A LEU* 3.0 33.0 + - + +
388A LEU* 3.5 9.6 - - + +
390A GLY* 1.3 75.2 - - - +
392A LEU* 1.3 57.6 + - - +
394A LEU* 3.2 12.3 + - + +
395A GLN* 2.9 29.6 + - - +
402A ILE* 4.7 2.2 - - + +
405A VAL* 3.7 23.9 - - + +
412A CYS* 4.2 14.4 - - + -
413A SER 4.8 2.7 - - - +
414A PHE* 3.9 30.3 - - + -
446A PHE* 3.8 29.2 - - + -
460A PHE* 4.2 12.8 - - + -
461A LEU* 4.5 3.8 - - + -
464A PHE* 5.6 0.9 - - + -
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Residues in contact with LEU 392 (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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388A LEU* 2.8 37.7 + - + +
389A THR* 3.5 11.7 - - - +
391A LEU* 1.3 71.8 - - - +
393A ASP* 1.3 56.9 + - - +
395A GLN* 3.3 25.4 + - - +
396A ALA* 3.0 26.7 + - - +
405A VAL* 3.6 26.0 - - + +
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Residues in contact with ASP 393 (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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389A THR* 3.0 14.5 + - + +
390A GLY* 3.5 11.0 - - - +
392A LEU* 1.3 77.5 - - - +
394A LEU* 1.3 63.0 + - - +
396A ALA* 3.2 9.8 + - - +
397A ARG* 3.0 28.3 + - - +
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Residues in contact with LEU 394 (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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390A GLY 3.0 13.0 + - - +
391A LEU* 3.2 15.0 + - + +
393A ASP* 1.3 82.0 - - - +
395A GLN* 1.3 57.4 + - - +
397A ARG* 3.3 3.8 + - + +
398A TYR* 2.8 49.2 + - + +
402A ILE* 4.3 7.2 - - + +
461A LEU* 3.6 35.4 - - + +
464A PHE* 4.3 25.4 - - + -
465A SER* 4.0 28.0 - - - +
468A LEU* 4.4 12.6 - - + -
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Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A TYR* 6.3 0.8 - - - +
226A PRO* 5.8 6.3 - - - +
391A LEU 2.9 12.8 + - - +
392A LEU* 3.3 32.1 + - - +
394A LEU* 1.3 77.8 - - - +
396A ALA* 1.3 62.6 + - - +
398A TYR 3.5 0.2 - - - -
399A PRO* 3.2 26.7 - - + +
402A ILE* 3.7 24.4 - - + +
403A SER* 3.1 4.2 - - - -
404A ARG* 2.9 14.2 + - - -
405A VAL* 2.9 36.6 + - + +
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Residues in contact with ALA 396 (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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392A LEU 3.0 12.3 + - - +
393A ASP* 3.2 15.4 + - - +
395A GLN* 1.3 77.1 - - - +
397A ARG* 1.3 60.4 + - - +
399A PRO* 3.6 10.1 - - - +
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Residues in contact with ARG 397 (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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393A ASP* 3.0 18.3 + - - +
394A LEU* 3.8 3.8 - - + +
396A ALA* 1.3 80.5 - - - +
398A TYR* 1.3 89.3 + - + +
399A PRO* 3.4 5.5 - - - +
400A GLN* 4.1 2.6 + - - +
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Residues in contact with TYR 398 (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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394A LEU* 2.8 29.3 + - + +
395A GLN 3.5 3.8 - - - -
397A ARG* 1.3 100.9 - - + +
399A PRO* 1.3 57.0 - - - +
400A GLN* 3.1 29.6 - - - +
401A PHE* 3.0 21.7 + + + -
402A ILE* 2.8 32.9 + - + +
465A SER* 4.2 7.6 + - - -
468A LEU* 3.8 41.1 - - + -
469A ALA* 3.6 22.7 + - - +
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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
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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