Contacts of the helix formed by residues 337 - 358 (chain B) in PDB entry 2OFV
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 THR 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B LYS 4.7 5.4 - - - +
336B LEU* 1.3 77.7 - - - +
338B ILE* 1.3 56.3 + - - +
339B ASN* 2.5 36.8 + - - +
340B LYS* 2.4 36.3 + - - +
341B LEU* 2.8 10.8 + - - -
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Residues in contact with ILE 338 (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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337B THR* 1.3 70.2 - - - +
339B ASN* 1.3 71.6 + - - +
341B LEU* 3.7 17.0 - - - +
342B LEU* 2.6 62.8 + - + +
434B VAL* 6.5 0.4 - - + -
466B PRO* 3.2 38.8 - - + -
469B LEU* 5.4 0.2 - - + -
497B PHE* 4.1 2.5 - - + -
498B PHE* 3.3 28.3 - - + -
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Residues in contact with ASN 339 (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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337B THR* 2.5 29.6 + - - +
338B ILE* 1.3 86.4 - - - +
340B LYS* 1.3 57.5 + - - +
342B LEU* 3.9 2.8 - - - +
343B ASP* 3.2 23.7 + - - +
498B PHE* 3.7 31.4 - - + +
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Residues in contact with LYS 340 (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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336B LEU* 3.5 25.1 - - + -
337B THR* 2.4 21.2 + - - +
339B ASN* 1.3 71.9 - - + +
341B LEU* 1.3 67.0 + - - +
342B LEU 2.9 1.3 - - - -
343B ASP* 2.9 30.2 + - + +
344B MET* 3.1 34.5 + - + +
347B GLN* 5.0 1.8 + - - +
375B THR 4.5 2.8 + - - -
376B LEU* 2.8 44.2 + - - +
377B SER* 5.0 0.8 - - - +
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Residues in contact with LEU 341 (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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328B LEU* 4.0 12.3 - - + -
334B ILE* 3.6 32.8 - - + -
336B LEU* 3.9 27.8 - - + +
337B THR 2.8 12.8 + - - +
338B ILE* 3.7 20.4 - - - +
340B LYS* 1.3 77.7 - - - +
342B LEU* 1.3 64.4 + - + +
344B MET* 3.6 10.2 - - - +
345B ALA* 3.3 14.0 + - - +
433B ILE* 3.6 40.3 - - + +
434B VAL* 4.6 10.5 - - + -
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Residues in contact with LEU 342 (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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338B ILE* 2.6 42.0 + - + +
339B ASN* 3.9 4.3 - - - +
341B LEU* 1.3 78.1 - - + +
343B ASP* 1.3 60.3 + - - +
344B MET 3.1 1.8 - - - -
345B ALA* 3.1 13.8 + - + +
346B ALA* 2.9 27.9 + - - +
430B LEU* 5.7 0.7 - - + -
433B ILE* 5.0 5.4 - - + -
434B VAL* 5.3 0.7 - - + -
469B LEU* 3.6 31.4 - - + -
494B LEU* 4.0 15.6 - - + +
497B PHE* 3.3 54.1 - - + -
498B PHE* 4.4 3.1 - - + -
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Residues in contact with ASP 343 (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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339B ASN 3.2 13.9 + - - +
340B LYS* 2.9 26.7 + - + +
342B LEU* 1.3 75.9 - - - +
344B MET* 1.3 57.5 + - - +
346B ALA* 3.3 9.4 + - - +
347B GLN* 2.9 48.3 + - - +
494B LEU 5.3 1.1 - - - -
495B GLU* 6.0 0.7 - - - +
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Residues in contact with MET 344 (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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324B LEU* 3.6 22.7 - - + -
327B PHE* 4.4 12.6 - - + -
328B LEU* 5.2 1.1 - - - -
336B LEU* 4.1 14.4 - - - -
340B LYS* 3.4 38.4 - - - +
341B LEU* 3.6 15.7 - - - +
342B LEU 3.1 0.2 - - - -
343B ASP* 1.3 75.3 - - - +
345B ALA* 1.3 65.3 + - - +
347B GLN* 3.1 14.6 + - - +
348B ILE* 3.0 29.6 + - - +
372B VAL* 4.1 9.4 - - + -
376B LEU 3.9 11.7 - - - +
378B CYS* 3.2 33.2 - - - +
433B ILE* 5.1 5.2 - - + -
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Residues in contact with ALA 345 (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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341B LEU 3.3 11.1 + - - +
342B LEU* 3.1 20.1 + - + +
344B MET* 1.3 79.7 - - - +
346B ALA* 1.3 56.8 + - - +
348B ILE* 3.3 4.8 + - - +
349B ALA 2.9 23.4 + - - -
426B PHE* 3.5 5.5 - - - -
430B LEU* 3.7 20.0 - - + -
433B ILE* 3.9 14.1 - - + +
494B LEU* 3.4 23.0 - - + +
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Residues in contact with ALA 346 (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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342B LEU 2.9 10.5 + - - +
343B ASP* 3.6 14.1 - - - +
344B MET 3.2 0.2 - - - -
345B ALA* 1.3 75.0 - - - +
347B GLN* 1.3 60.4 + - - +
349B ALA* 3.6 3.5 - - - +
350B GLU* 2.9 28.4 + - - +
491B ARG* 4.3 2.7 - - - +
494B LEU* 3.6 25.1 - - + +
495B GLU* 3.4 36.7 - - + +
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Residues in contact with GLN 347 (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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299B ARG* 3.3 46.8 - - - +
340B LYS* 5.4 1.0 - - - +
343B ASP* 2.9 39.1 + - - +
344B MET* 3.1 13.5 + - - +
346B ALA* 1.3 73.1 - - - +
348B ILE* 1.3 67.3 + - - +
350B GLU* 3.1 10.2 + - - +
351B GLY* 2.9 18.7 + - - -
376B LEU 4.1 3.4 + - - +
377B SER* 3.5 17.5 - - - +
378B CYS* 2.8 40.2 + - + +
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Residues in contact with ILE 348 (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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324B LEU* 4.1 17.7 - - + -
344B MET 3.0 16.6 - - - +
345B ALA* 3.5 4.9 - - - +
347B GLN* 1.3 76.0 - - - +
349B ALA* 1.3 57.8 + - - +
351B GLY* 2.9 3.5 + - - -
352B MET* 2.9 27.3 + - + +
365B LEU* 4.4 4.5 - - + -
370B ILE* 3.7 35.0 - - + -
378B CYS* 4.2 14.8 - - + +
380B ILE* 3.5 15.5 - - + +
426B PHE* 3.8 18.2 - - + -
429B LEU* 4.1 12.3 - - + -
433B ILE* 3.9 25.1 - - + -
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Residues in contact with ALA 349 (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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345B ALA 2.9 16.3 + - - +
346B ALA 3.6 6.1 - - - +
348B ILE* 1.3 76.2 - - - +
350B GLU* 1.3 58.1 + - - +
352B MET* 3.8 5.0 - - - +
353B ALA* 2.9 28.9 + - - +
426B PHE* 3.9 20.6 - - + -
487B PHE* 3.9 9.8 - - + +
490B LEU* 4.2 3.6 - - + -
491B ARG* 3.7 28.0 - - - +
494B LEU* 4.0 5.8 - - + -
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Residues in contact with GLU 350 (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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297B HIS* 4.0 14.2 + - + +
299B ARG* 2.3 53.1 + - + -
346B ALA 2.9 14.5 + - - +
347B GLN* 3.3 9.1 - - - +
349B ALA* 1.3 73.6 - - - +
351B GLY* 1.3 66.2 + - - +
353B ALA* 3.2 16.1 + - + +
354B PHE* 3.3 11.4 + - - +
491B ARG* 4.4 7.8 - - + +
495B GLU* 4.9 10.3 - - - +
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Residues in contact with GLY 351 (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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297B HIS* 5.1 0.2 - - - -
299B ARG* 3.6 20.6 - - - -
300B LEU* 4.0 6.9 - - - +
347B GLN 2.9 11.7 + - - -
348B ILE 2.9 3.6 + - - -
350B GLU* 1.3 77.3 - - - +
352B MET* 1.3 61.6 + - - +
354B PHE* 3.0 17.5 + - - +
355B ILE* 3.1 13.4 + - - +
380B ILE* 3.4 16.8 - - - -
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Residues in contact with MET 352 (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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348B ILE* 2.9 16.4 + - + +
349B ALA* 4.0 0.7 - - - +
351B GLY* 1.3 72.0 - - - +
353B ALA* 1.3 59.7 + - - +
355B ILE* 3.4 28.8 - - + +
356B GLU* 2.8 29.8 + - - +
362B HIS* 4.0 10.1 - - + -
365B LEU* 3.8 31.0 - - + -
380B ILE* 3.3 21.7 - - + +
419B ILE* 4.4 0.2 - - + -
422B ASP* 3.7 28.7 - - + +
426B PHE* 5.2 0.4 - - + -
487B PHE* 3.6 46.1 - - + -
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Residues in contact with ALA 353 (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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349B ALA 2.9 18.6 + - - +
350B GLU* 3.3 11.4 - - - +
351B GLY 3.1 0.4 - - - -
352B MET* 1.3 77.0 - - - +
354B PHE* 1.3 57.4 + - - +
356B GLU* 3.2 8.1 - - - +
357B GLU* 3.1 25.4 + - - +
487B PHE* 3.8 15.2 - - + +
488B ASP* 4.3 18.4 - - + +
491B ARG* 5.1 2.9 - - + -
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Residues in contact with PHE 354 (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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294B GLN 4.5 4.3 - - - -
295B LEU* 3.3 38.4 - - + -
296B GLN 3.8 12.1 - - - -
297B HIS* 3.5 37.5 - + + +
300B LEU* 4.8 4.7 - - + -
350B GLU 3.3 5.6 + - - +
351B GLY 3.0 9.3 + - - +
353B ALA* 1.3 75.6 - - - +
355B ILE* 1.3 66.4 + - - +
356B GLU 3.0 1.3 - - - -
357B GLU* 3.0 32.0 + - - +
358B ARG* 2.9 56.7 + - + +
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Residues in contact with ILE 355 (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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295B LEU* 4.7 5.4 - - + -
300B LEU* 4.6 14.4 - - + -
351B GLY 3.1 13.9 + - - +
352B MET* 3.4 46.0 - - + +
354B PHE* 1.3 77.9 - - + +
356B GLU* 1.3 62.9 + - - +
358B ARG* 3.3 3.7 + - - -
359B ASN 3.3 2.8 + - - -
360B TYR* 3.0 67.4 + - + +
361B ILE 4.4 0.7 - - - +
362B HIS* 4.4 5.2 - - + +
380B ILE* 4.2 12.6 - - + -
419B ILE* 4.5 2.7 - - + -
503B 242 3.9 23.3 - - - -
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Residues in contact with GLU 356 (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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352B MET 2.8 13.4 + - - +
353B ALA* 3.2 12.1 - - - +
354B PHE 3.0 0.2 - - - -
355B ILE* 1.3 77.3 - - - +
357B GLU* 1.3 62.6 + - - +
359B ASN* 3.0 16.8 + - - +
360B TYR 4.8 1.3 - - - -
419B ILE* 3.3 42.7 - - + +
420B LYS* 5.1 1.2 + - - -
423B VAL* 5.3 0.7 - - - +
486B THR* 3.6 23.8 - - - +
487B PHE* 3.1 33.5 + - - +
488B ASP* 3.7 7.1 + - - +
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Residues in contact with GLU 357 (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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353B ALA 3.1 10.9 + - - +
354B PHE* 3.0 33.1 + - + +
356B GLU* 1.3 80.6 - - - +
358B ARG* 1.3 82.6 + - + +
359B ASN* 3.0 17.3 - - - +
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Residues in contact with ARG 358 (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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294B GLN* 4.6 9.4 + - - -
295B LEU* 3.7 26.7 - - + -
354B PHE* 2.9 48.1 + - + +
355B ILE 4.0 2.0 - - - +
356B GLU 3.3 0.4 - - - -
357B GLU* 1.3 101.8 + - - +
359B ASN* 1.3 71.1 + - - +
360B TYR* 3.1 3.0 + - - +
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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