Contacts of the helix formed by residues 375 - 398 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371D ILE 3.1 5.2 + - - -
372D LYS* 3.1 14.5 + - - +
373D ARG 3.3 2.2 - - - +
374D GLU* 1.3 79.7 - - - +
376D LEU* 1.3 59.6 + - - +
377D LEU* 3.4 3.6 + - - +
378D SER* 3.4 28.0 + - - -
379D ASN* 3.2 19.6 + - - +
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Residues in contact with LEU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ILE* 4.0 17.0 - - + -
370D ILE* 4.1 11.2 - - + -
371D ILE* 2.8 41.4 + - + +
374D GLU* 3.5 27.1 - - + +
375D ASP* 1.3 70.8 - - - +
377D LEU* 1.3 60.0 - - - +
379D ASN* 3.7 7.6 + - + +
380D ALA* 3.0 27.2 + - - +
450D LEU* 3.5 45.8 - - + +
451D VAL* 4.7 4.9 - - + -
453D ARG* 3.8 23.1 - - - +
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Residues in contact with LEU 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D GLY 4.7 0.2 - - - +
305D GLY* 3.4 35.4 - - - +
308D GLY* 3.5 22.3 - - - +
309D LYS* 4.0 2.5 - - - -
310D PHE* 3.8 35.9 - - + +
371D ILE* 4.1 22.0 - - + +
372D LYS* 6.3 2.9 - - + -
375D ASP* 3.4 1.7 - - - +
376D LEU* 1.3 73.6 - - - +
378D SER* 1.3 66.9 + - - +
380D ALA* 3.1 12.8 + - - +
381D ALA 3.2 9.0 + - - -
450D LEU* 5.7 1.1 - - + -
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Residues in contact with SER 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D GLY 5.1 1.3 - - - -
375D ASP* 3.4 32.7 + - - -
377D LEU* 1.3 79.5 - - - +
379D ASN* 1.3 57.5 + - - +
381D ALA* 3.2 8.9 + - - +
382D HIS* 3.0 28.5 + - - +
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Residues in contact with ASN 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D GLU 5.1 0.4 - - - +
375D ASP* 3.2 16.1 + - - +
376D LEU* 3.7 12.1 - - + +
377D LEU 3.2 0.8 - - - -
378D SER* 1.3 79.8 - - - +
380D ALA* 1.3 55.2 + - - +
382D HIS* 4.4 12.9 - - - -
383D ALA* 2.7 34.7 + - - +
450D LEU 3.8 15.2 + - - -
452D PHE 3.1 27.1 + - - -
453D ARG* 3.7 33.3 + - - +
454D ASP 5.1 0.3 + - - -
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Residues in contact with ALA 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D GLY 3.5 20.0 - - - +
306D SER* 3.7 16.6 - - - +
308D GLY 4.4 0.7 - - - +
376D LEU 3.0 14.7 + - - +
377D LEU 3.1 9.2 + - - +
379D ASN* 1.3 78.9 - - - +
381D ALA* 1.3 57.3 + - - +
383D ALA* 4.7 0.2 - - - -
384D GLY* 2.8 24.6 + - - -
409D GLY* 4.4 2.0 - - - -
410D THR* 3.3 21.4 + - + +
450D LEU* 4.5 8.1 - - + -
452D PHE 5.5 0.4 - - - -
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D THR 5.4 0.4 - - - +
308D GLY* 4.2 12.7 - - - +
377D LEU 3.2 11.1 + - - +
378D SER* 3.2 12.9 + - - +
380D ALA* 1.3 75.9 - - - +
382D HIS* 1.3 57.6 + - - +
384D GLY 3.8 0.3 - - - -
385D LYS* 2.9 40.1 + - - +
409D GLY* 4.3 12.0 - - - -
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Residues in contact with HIS 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D SER 3.0 15.5 + - - +
379D ASN* 3.7 14.6 - - - +
381D ALA* 1.3 74.5 - - - +
383D ALA* 1.3 67.8 + - - +
385D LYS* 3.1 13.0 + - - +
386D VAL* 3.0 40.6 + - + +
454D ASP* 2.7 34.2 + - + +
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Residues in contact with ALA 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379D ASN* 2.7 22.6 + - - +
380D ALA 4.3 1.6 - - - +
382D HIS* 1.3 74.6 - - - +
384D GLY* 1.3 56.6 + - - +
386D VAL* 3.3 4.3 + - - +
387D LEU* 2.9 27.5 + - - +
410D THR* 4.3 2.5 - - + -
452D PHE* 3.6 34.1 - - + +
453D ARG* 3.8 4.0 - - - -
454D ASP* 3.8 26.5 - - - +
457D ALA* 4.1 4.0 - - - +
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Residues in contact with GLY 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D ALA 2.8 18.1 + - - -
381D ALA 3.8 0.4 - - - -
383D ALA* 1.3 75.9 - - - +
385D LYS* 1.3 58.8 + - - +
387D LEU* 3.4 5.0 + - - +
388D LEU* 2.9 30.7 + - - +
409D GLY* 3.3 29.8 - - - +
410D THR* 3.6 9.1 - - - +
412D CYS* 4.2 0.5 - - - -
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Residues in contact with LYS 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ALA* 2.9 25.1 + - - +
382D HIS* 3.1 16.4 + - - +
384D GLY* 1.3 72.5 - - - +
386D VAL* 1.3 62.5 + - + +
388D LEU* 3.3 7.4 + - + +
389D THR* 2.9 38.3 + - - +
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Residues in contact with VAL 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D HIS* 3.0 28.2 + - + +
383D ALA 3.5 7.0 - - - +
385D LYS* 1.3 75.8 - - + +
387D LEU* 1.3 63.8 + - - +
389D THR* 3.5 5.9 + - - -
390D GLY 3.2 17.3 + - - -
454D ASP* 3.7 23.6 - - + +
457D ALA* 3.9 15.7 - - + -
458D HIS* 3.5 34.3 - - + +
461D LEU* 4.0 4.2 - - + +
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Residues in contact with LEU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU* 5.7 0.2 - - + -
383D ALA 2.9 16.7 + - - +
384D GLY* 3.5 5.6 - - - +
385D LYS 3.2 0.2 - - - -
386D VAL* 1.3 76.3 - - - +
388D LEU* 1.3 57.9 + - - +
390D GLY* 3.3 3.1 + - - -
391D LEU* 3.0 41.3 + - + +
410D THR* 4.2 8.7 - - - +
412D CYS* 4.0 20.2 - - + -
446D PHE* 4.0 30.1 - - + -
448D PRO* 5.0 0.9 - - + -
452D PHE* 4.4 18.8 - - + -
457D ALA* 4.0 19.3 - - + +
460D PHE* 3.9 31.9 - - + -
461D LEU* 4.1 5.0 - - + +
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Residues in contact with LEU 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D GLY 2.9 17.5 + - - +
385D LYS* 3.3 7.8 + - + +
387D LEU* 1.3 76.0 - - - +
389D THR* 1.3 59.7 + - - +
391D LEU* 3.2 7.0 + - + +
392D LEU* 2.8 47.2 + - + +
405D VAL* 3.7 18.8 - - + -
406D ARG* 3.6 33.0 - - - +
407D GLY 3.8 15.7 - - - +
412D CYS* 4.1 13.7 - - + -
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Residues in contact with THR 389 (chain D).
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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385D LYS* 2.9 24.5 + - - +
386D VAL* 3.8 7.6 - - - -
388D LEU* 1.3 74.8 - - - +
390D GLY* 1.3 62.7 + - - +
392D LEU* 3.2 14.5 + - + +
393D ASP* 3.0 22.5 + - + +
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Residues in contact with GLY 390 (chain D).
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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386D VAL 3.2 8.5 + - - -
387D LEU 3.7 3.1 - - - -
389D THR* 1.3 79.6 - - - +
391D LEU* 1.3 56.1 + - - +
393D ASP* 3.2 9.3 + - - +
394D LEU* 2.9 31.2 + - - +
461D LEU* 3.6 26.5 - - - -
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D LEU* 3.0 33.9 + - + +
388D LEU* 3.6 9.6 - - + +
390D GLY* 1.3 75.5 - - - +
392D LEU* 1.3 58.8 + - - +
394D LEU* 3.3 11.6 + - + +
395D GLN* 2.9 28.4 + - - +
402D ILE* 4.7 2.0 - - + +
405D VAL* 3.6 23.4 - - + +
412D CYS* 4.2 14.4 - - + -
413D SER 4.9 2.9 - - - +
414D PHE* 4.0 26.9 - - + -
446D PHE* 3.7 20.4 - - + -
460D PHE* 3.8 25.8 - - + -
461D LEU* 4.3 3.4 - - + -
464D PHE* 5.4 0.9 - - + -
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Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D LEU* 2.8 34.4 + - + +
389D THR* 3.2 13.4 + - + +
391D LEU* 1.3 75.4 - - - +
393D ASP* 1.3 62.4 + - - +
395D GLN* 3.3 25.2 + - - +
396D ALA* 3.0 21.8 + - - +
405D VAL* 3.7 24.7 - - + +
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Residues in contact with ASP 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D THR* 3.0 13.9 + - + +
390D GLY* 3.2 12.3 + - - +
392D LEU* 1.3 77.7 - - - +
394D LEU* 1.3 69.1 + - - +
396D ALA* 3.2 9.9 + - - +
397D ARG* 3.0 23.9 + - - +
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D GLY 2.9 15.8 + - - +
391D LEU* 3.7 11.4 - - + +
393D ASP* 1.3 78.5 - - - +
395D GLN* 1.3 60.0 + - - +
397D ARG* 3.2 4.8 + - + +
398D TYR* 2.8 41.7 + - + +
402D ILE* 4.3 6.6 - - + +
461D LEU* 3.9 34.8 - - + +
464D PHE* 4.0 27.1 - - + -
465D SER* 4.0 30.7 - - - +
468D LEU* 4.1 14.8 - - + -
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Residues in contact with GLN 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D TYR* 5.9 1.0 - - - +
226D PRO* 5.8 6.9 - - - +
391D LEU 2.9 14.3 + - - +
392D LEU* 3.3 32.3 + - - +
394D LEU* 1.3 77.0 - - - +
396D ALA* 1.3 61.4 + - - +
398D TYR 3.5 0.2 - - - -
399D PRO* 3.3 26.0 - - + +
402D ILE* 3.7 24.6 - - + +
403D SER* 3.2 3.4 - - - -
404D ARG 2.9 14.7 + - - -
405D VAL* 2.9 35.8 + - + +
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Residues in contact with ALA 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D LEU 3.0 13.0 + - - +
393D ASP* 3.2 15.0 + - - +
395D GLN* 1.3 76.5 - - - +
397D ARG* 1.3 59.2 + - - +
399D PRO* 3.6 10.1 - - - +
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Residues in contact with ARG 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D ASP* 3.0 18.9 + - - +
394D LEU* 4.4 3.1 - - + -
396D ALA* 1.3 77.0 - - - +
398D TYR* 1.3 90.1 + - + +
399D PRO* 3.3 7.7 - - - +
400D GLN* 4.1 2.9 + - - +
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Residues in contact with TYR 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D LEU* 2.8 24.3 + - + +
395D GLN 3.5 3.4 - - - -
397D ARG* 1.3 100.4 - - + +
399D PRO* 1.3 58.5 - - - +
400D GLN* 3.1 26.0 - - - -
401D PHE* 3.0 16.6 + + + -
402D ILE* 2.8 27.8 + - + +
465D SER* 4.2 8.5 + - - -
468D LEU* 3.5 50.9 - - + -
469D ALA* 3.3 30.5 - - - +
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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