Contacts of the helix formed by residues 375 - 398 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B ILE 3.3 8.0 + - - -
372B LYS 3.3 7.9 + - - +
373B ARG 3.3 5.4 - - - +
374B GLU* 1.3 80.9 - - - +
376B LEU* 1.3 59.4 + - - +
377B LEU* 3.3 5.0 + - - +
378B SER* 3.3 28.1 + - - -
379B ASN* 3.2 21.1 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 4.0 17.0 - - + -
370B ILE* 4.0 11.4 - - + -
371B ILE* 3.0 33.3 + - + +
374B GLU* 3.5 28.5 - - + +
375B ASP* 1.3 73.6 - - - +
377B LEU* 1.3 60.8 + - - +
379B ASN* 3.7 6.9 + - + +
380B ALA* 3.0 27.4 + - - +
450B LEU* 3.5 47.4 - - + +
451B VAL* 4.5 5.8 - - + -
453B ARG* 3.9 24.2 - - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B GLY 4.8 0.2 - - - +
305B GLY* 3.4 35.4 - - - +
308B GLY* 3.5 25.1 - - - +
309B LYS* 4.0 2.7 - - - -
310B PHE* 3.8 35.0 - - + +
371B ILE* 4.1 22.2 - - + +
372B LYS* 6.4 1.6 - - + -
375B ASP* 3.3 1.7 - - - +
376B LEU* 1.3 75.0 - - - +
378B SER* 1.3 66.9 + - - +
380B ALA* 3.2 9.5 + - - +
381B ALA* 3.2 9.5 + - - +
450B LEU* 5.7 1.1 - - + -
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B GLY 5.1 1.1 - - - -
375B ASP* 3.3 32.5 + - - -
377B LEU* 1.3 79.7 - - - +
379B ASN* 1.3 59.1 + - - +
381B ALA* 3.2 9.6 + - - +
382B HIS* 3.0 27.8 + - - +
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Residues in contact with ASN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B GLU 5.2 0.2 - - - +
375B ASP* 3.2 13.6 + - - +
376B LEU* 3.7 11.4 - - - +
377B LEU 3.2 0.8 - - - -
378B SER* 1.3 79.6 - - - +
380B ALA* 1.3 59.4 + - - +
382B HIS* 3.7 12.1 - - - +
383B ALA* 2.8 30.4 + - - +
450B LEU 3.9 14.3 + - - -
452B PHE 2.9 29.1 + - - -
453B ARG* 3.4 38.8 + - - +
454B ASP* 5.0 0.7 + - - -
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B GLY 3.6 20.2 - - - +
306B SER* 3.8 17.3 - - - +
308B GLY 4.4 0.7 - - - +
376B LEU 3.0 18.0 + - - +
377B LEU 3.2 5.8 + - - +
379B ASN* 1.3 80.6 - - - +
381B ALA* 1.3 57.5 + - - +
383B ALA* 4.7 0.2 - - - -
384B GLY* 2.8 27.9 + - - -
409B GLY* 4.4 2.0 - - - -
410B THR* 3.3 18.3 + - + +
450B LEU* 4.6 8.1 - - + -
452B PHE 5.5 0.4 - - - -
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B THR 5.4 0.7 - - - +
308B GLY* 4.2 12.3 - - - +
377B LEU 3.2 9.4 + - - +
378B SER* 3.4 11.9 - - - +
380B ALA* 1.3 78.2 - - - +
382B HIS* 1.3 58.4 + - - +
384B GLY 3.8 0.5 - - - -
385B LYS* 2.9 39.8 + - - +
409B GLY* 4.3 12.4 - - - -
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Residues in contact with HIS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B SER 3.0 15.5 + - - +
379B ASN* 3.7 13.9 - - - +
381B ALA* 1.3 75.1 - - - +
383B ALA* 1.3 66.8 + - - +
385B LYS* 3.0 14.3 + - - +
386B VAL* 3.0 36.0 + - + +
454B ASP* 2.4 33.8 + - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ASN* 2.8 22.0 + - - +
380B ALA 4.3 1.1 - - - +
382B HIS* 1.3 73.1 - - - +
384B GLY* 1.3 57.9 + - - +
386B VAL* 3.3 4.2 + - - +
387B LEU* 2.9 27.7 + - - +
410B THR* 4.4 1.8 - - + -
452B PHE* 3.7 39.3 - - + +
453B ARG* 3.8 13.5 - - - -
454B ASP* 3.8 12.8 - - - +
457B ALA* 4.1 3.8 - - - +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ALA 2.8 18.4 + - - -
381B ALA 3.8 0.2 - - - -
383B ALA* 1.3 75.5 - - - +
385B LYS* 1.3 58.5 + - - +
387B LEU* 3.3 5.1 + - - +
388B LEU* 2.8 31.6 + - - +
409B GLY* 3.3 28.6 - - - +
410B THR* 3.6 10.2 - - - +
412B CYS* 4.2 0.5 - - - -
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ALA* 2.9 26.2 + - - +
382B HIS* 3.0 16.5 + - - +
384B GLY* 1.3 73.2 - - - +
386B VAL* 1.3 60.2 + - + +
388B LEU* 3.2 7.3 + - + +
389B THR* 2.9 38.8 + - - +
409B GLY* 5.3 0.2 - - - -
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B HIS* 3.0 28.8 + - + +
383B ALA 3.3 7.2 + - - +
385B LYS* 1.3 75.4 - - + +
387B LEU* 1.3 63.2 - - - +
389B THR* 3.5 6.2 + - - -
390B GLY 3.2 17.3 + - - -
454B ASP* 3.7 20.6 - - + -
457B ALA* 3.9 15.5 - - + -
458B HIS* 3.4 37.2 - - + +
461B LEU* 3.8 6.2 - - + +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 5.7 0.4 - - + -
383B ALA 2.9 16.6 + - - +
384B GLY* 3.5 5.4 - - - +
386B VAL* 1.3 77.8 - - - +
388B LEU* 1.3 57.7 + - - +
390B GLY* 3.3 3.1 + - - -
391B LEU* 3.0 39.6 + - + +
410B THR* 4.2 11.2 - - - +
412B CYS* 4.0 18.2 - - + -
446B PHE* 4.0 32.5 - - + -
448B PRO* 4.9 1.3 - - + -
452B PHE* 4.6 16.2 - - + -
457B ALA* 4.1 16.6 - - + -
460B PHE* 3.8 34.3 - - + -
461B LEU* 4.1 5.1 - - + +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B GLY 2.8 17.2 + - - +
385B LYS* 3.8 7.4 - - + +
387B LEU* 1.3 74.4 - - - +
389B THR* 1.3 60.4 + - - +
391B LEU* 3.2 7.8 + - + +
392B LEU* 2.9 42.3 + - + +
405B VAL* 3.7 18.4 - - + -
406B ARG* 3.6 32.8 - - - +
407B GLY 3.8 17.9 - - - +
409B GLY 5.5 0.4 - - - +
412B CYS* 4.0 13.0 - - + -
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LYS* 2.9 25.0 + - - +
386B VAL* 3.8 7.4 - - - -
388B LEU* 1.3 76.7 - - - +
390B GLY* 1.3 62.5 + - - +
392B LEU* 3.1 14.9 + - + +
393B ASP* 3.0 22.2 + - + +
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B VAL 3.2 8.5 + - - -
387B LEU 3.3 0.9 + - - -
389B THR* 1.3 79.8 - - - +
391B LEU* 1.3 57.8 + - - +
393B ASP* 3.2 9.1 + - - +
394B LEU* 3.0 31.2 + - - +
461B LEU* 3.5 30.2 - - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B LEU* 3.0 33.1 + - + +
388B LEU* 3.2 10.1 + - + +
390B GLY* 1.3 74.6 - - - +
392B LEU* 1.3 58.6 + - - +
394B LEU* 3.2 13.3 + - + +
395B GLN* 2.9 28.8 + - - +
402B ILE* 4.7 2.2 - - + +
405B VAL* 3.6 22.8 - - + +
412B CYS* 4.2 14.8 - - + -
413B SER 4.8 2.2 - - - +
414B PHE* 3.9 30.7 - - + -
446B PHE* 3.7 29.4 - - + -
460B PHE* 4.1 13.2 - - + -
461B LEU* 3.7 3.1 - - + +
464B PHE* 5.3 1.1 - - + -
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B LEU* 2.9 34.7 + - + +
389B THR* 3.4 12.6 - - + +
391B LEU* 1.3 75.7 - - - +
393B ASP* 1.3 61.4 + - - +
395B GLN* 3.3 24.7 + - - +
396B ALA* 3.1 22.3 + - - +
405B VAL* 3.7 24.7 - - + +
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B THR* 3.0 14.4 + - + +
390B GLY* 3.5 11.4 - - - +
392B LEU* 1.3 74.0 - - - +
394B LEU* 1.3 70.8 + - - +
396B ALA* 3.2 10.9 + - - +
397B ARG* 3.0 23.9 + - - +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B GLY 3.0 18.5 + - - +
391B LEU* 3.6 14.8 - - + +
393B ASP* 1.3 78.8 - - - +
395B GLN* 1.3 55.4 - - - +
397B ARG* 3.2 4.2 + - + -
398B TYR* 2.8 48.4 + - + +
402B ILE* 4.4 6.0 - - + +
461B LEU* 4.0 23.1 - - + +
464B PHE* 3.7 34.1 - - + -
465B SER* 4.0 29.6 - - - +
468B LEU* 4.1 14.4 - - + -
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Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B TYR* 6.3 0.4 - - - +
226B PRO* 5.8 6.7 - - - +
391B LEU 2.9 13.6 + - - +
392B LEU* 3.4 33.4 + - - +
393B ASP 3.2 0.2 - - - -
394B LEU* 1.3 76.3 - - - +
396B ALA* 1.3 62.5 + - - +
398B TYR 3.5 0.2 - - - -
399B PRO* 3.2 27.1 - - + +
402B ILE* 3.7 25.5 - - + +
403B SER* 3.1 3.7 - - - -
404B ARG* 2.9 15.6 + - - -
405B VAL* 2.9 35.3 + - + +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B LEU 3.1 9.6 + - - +
393B ASP* 3.2 14.1 + - - +
395B GLN* 1.3 81.9 - - - +
397B ARG* 1.3 58.6 + - - +
399B PRO* 3.6 9.4 - - - +
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Residues in contact with ARG 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ASP* 3.0 18.5 + - - +
394B LEU* 3.8 4.0 - - + +
396B ALA* 1.3 77.0 - - - +
398B TYR* 1.3 89.4 + - + +
399B PRO* 3.3 7.8 - - - +
400B GLN* 4.2 2.9 + - - +
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Residues in contact with TYR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B LEU* 2.8 24.9 + - + +
395B GLN 3.5 4.3 - - - -
397B ARG* 1.3 101.5 - - + +
399B PRO* 1.3 56.5 - - - +
400B GLN* 3.1 27.8 - - - -
401B PHE* 3.0 18.2 + + + -
402B ILE* 2.8 28.2 + - + +
465B SER* 4.2 6.3 + - - -
468B LEU* 3.6 47.3 - - + -
469B ALA* 3.3 31.3 + - - +
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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