Contacts of the helix formed by residues 435 - 459 (chain B) in PDB entry 1GWX
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 LEU 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374B PHE* 4.6 2.2 - - + -
377B LEU* 3.2 31.4 - - + -
379B LEU* 3.8 20.9 - - + -
383B ASP* 5.6 0.2 - - + -
387B PHE* 3.1 38.7 - - + -
417B LEU* 4.1 16.8 - - + -
421B LEU* 3.7 25.6 - - + -
430B TYR* 3.0 21.0 + - + +
432B PHE* 3.0 15.2 + - - +
434B LYS* 1.3 76.5 - - - +
436B LEU* 1.3 60.2 + - + +
438B LYS* 3.2 3.4 + - - +
439B MET* 3.0 29.5 + - - +
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLN* 5.9 0.4 - - - +
414B LEU* 3.6 30.7 - - + -
417B LEU* 4.9 1.8 - - + -
432B PHE* 2.4 64.7 + - + +
433B PRO* 4.8 1.6 - - + -
435B LEU* 1.3 70.6 - - + +
437B GLN* 1.3 61.2 + - - +
439B MET* 3.2 39.4 + - + +
440B ALA* 3.4 7.4 + - - +
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Residues in contact with GLN 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PHE 3.4 2.2 + - - -
433B PRO 3.0 22.2 + - - +
434B LYS* 3.3 6.0 + - - +
435B LEU 3.2 0.8 - - - -
436B LEU* 1.3 78.9 - - - +
438B LYS* 1.3 60.5 + - + +
440B ALA* 3.0 16.9 + - - +
441B ASP* 2.8 42.8 + - - +
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Residues in contact with LYS 438 (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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370B PHE* 4.1 5.2 - - + -
373B LYS* 4.4 16.3 - - - +
374B PHE* 3.3 46.2 - - + +
377B LEU* 3.4 39.7 - - + -
387B PHE* 4.4 0.7 - - + -
434B LYS* 2.7 31.7 + - - +
435B LEU* 3.4 8.1 - - - +
437B GLN* 1.3 74.4 - - + +
439B MET* 1.3 58.6 + - - +
440B ALA 3.1 2.0 - - - -
441B ASP* 3.2 21.2 + - + +
442B LEU* 2.9 34.4 + - - +
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Residues in contact with MET 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLU* 4.2 7.1 - - - +
387B PHE* 3.4 38.6 - - + +
390B ALA* 3.3 34.3 - - + -
391B ILE* 4.3 13.0 - - + +
410B GLN* 5.3 6.7 - - - +
414B LEU* 4.2 9.2 - - + -
417B LEU* 4.8 2.7 - - + -
435B LEU 3.0 19.6 + - - +
436B LEU* 3.3 37.7 - - + +
437B GLN 3.1 0.6 - - - -
438B LYS* 1.3 78.4 - - - +
440B ALA* 1.3 60.6 + - - +
442B LEU* 3.7 8.0 + - - +
443B ARG* 3.4 18.4 + - - +
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Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU 3.4 5.7 + - - +
437B GLN* 3.0 26.2 + - - +
439B MET* 1.3 77.9 - - - +
441B ASP* 1.3 64.6 + - - +
442B LEU 3.0 2.0 - - - -
443B ARG* 3.0 21.8 + - - +
444B GLN* 3.4 8.8 + - - +
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Residues in contact with ASP 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B PHE* 3.9 17.6 - - + -
437B GLN* 2.8 35.4 + - - +
438B LYS* 3.2 37.0 + - - +
440B ALA* 1.3 76.1 - - - +
442B LEU* 1.3 57.0 + - - +
444B GLN* 3.5 13.7 + - - +
445B LEU* 3.2 25.1 + - - +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLU* 3.5 38.8 - - + +
327B PHE* 3.9 13.7 - - + -
328B ALA* 3.7 24.2 - - + +
370B PHE* 3.3 32.8 - - + -
387B PHE* 3.9 18.6 - - + -
391B ILE* 5.7 3.8 - - + -
438B LYS 2.9 20.3 + - - +
439B MET* 3.7 8.7 - - - +
440B ALA 3.0 0.2 - - - -
441B ASP* 1.3 74.9 - - - +
443B ARG* 1.3 53.9 + - - +
444B GLN 3.1 4.9 - - - -
445B LEU* 3.7 6.6 - - + +
446B VAL* 3.0 36.2 + - - +
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Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLU* 2.7 32.7 + - - +
394B CYS* 4.9 5.0 - - - -
396B ASP* 3.4 41.3 + - - +
397B ARG* 3.3 21.2 - - - +
398B PRO* 5.8 3.8 - - - +
439B MET 3.4 10.5 + - - +
440B ALA* 3.0 15.6 + - - +
442B LEU* 1.3 78.1 - - - +
444B GLN* 1.3 55.7 + - - +
446B VAL* 4.1 3.9 - - - +
447B THR* 2.9 23.4 + - - +
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Residues in contact with GLN 444 (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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440B ALA 3.4 8.1 + - - +
441B ASP* 3.8 14.3 + - - +
442B LEU 3.1 0.2 - - - -
443B ARG* 1.3 76.8 - - - +
445B LEU* 1.3 56.5 + - - +
446B VAL 3.0 1.3 - - - -
447B THR* 2.8 13.7 + - + -
448B GLU* 2.7 38.6 + - + +
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Residues in contact with LEU 445 (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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327B PHE* 3.4 39.5 - - + +
366B PRO* 4.5 9.9 - - + +
367B LYS* 3.4 43.7 - - + +
370B PHE* 4.7 13.7 - - + -
441B ASP 3.2 15.2 + - - +
442B LEU* 3.7 14.1 - - + +
444B GLN* 1.3 79.7 - - - +
446B VAL* 1.3 57.7 + - - +
448B GLU* 3.3 19.3 + - - +
449B HIS* 2.8 25.5 + - - +
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Residues in contact with VAL 446 (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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320B TYR 5.5 3.4 - - - +
323B HIS* 4.0 13.0 - - + -
324B GLU* 3.3 41.5 - - + +
327B PHE* 3.8 16.8 - - + -
442B LEU 3.0 20.9 + - - +
443B ARG 4.2 4.9 - - - +
445B LEU* 1.3 77.0 - - - +
447B THR* 1.3 52.6 + - - +
449B HIS* 3.1 7.9 + - + +
450B ALA* 2.7 35.0 + - + +
473B TYR* 5.3 3.6 - - + -
476B MET* 4.4 24.0 - - + -
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Residues in contact with THR 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ARG* 2.9 18.0 + - - +
444B GLN* 2.8 18.2 + - + +
446B VAL* 1.3 81.4 - - - +
448B GLU* 1.3 61.7 + - - +
450B ALA* 3.4 6.8 + - - +
451B GLN* 3.3 34.0 + - - +
476B MET* 6.3 1.3 - - - -
477B TYR* 3.1 27.5 + - - +
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Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B PRO* 3.2 34.7 - - - +
444B GLN* 2.7 21.2 + - + +
445B LEU* 3.6 15.3 - - - +
447B THR* 1.3 74.8 - - - +
449B HIS* 1.3 64.5 + - - +
451B GLN* 3.2 18.2 + - - +
452B MET* 3.2 45.1 + - + +
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Residues in contact with HIS 449 (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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2B 433 2.4 40.9 + + - -
323B HIS* 5.2 0.4 - + - -
327B PHE* 3.4 25.2 - + + -
363B ILE* 3.8 12.8 - - + +
367B LYS* 3.1 24.8 + - - +
445B LEU 2.8 18.9 + - - +
446B VAL* 3.4 5.2 - - + +
448B GLU* 1.3 79.7 - - - +
450B ALA* 1.3 63.2 + - - +
452B MET* 3.6 4.8 + - - +
453B MET* 3.1 53.6 + - + +
473B TYR* 2.9 23.5 + + - -
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Residues in contact with ALA 450 (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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446B VAL 2.7 19.4 + - - +
447B THR* 3.8 7.2 - - - +
448B GLU 3.3 0.2 - - - -
449B HIS* 1.3 74.2 - - - +
451B GLN* 1.3 58.8 + - + +
453B MET* 3.5 4.2 - - - +
454B GLN* 3.0 28.3 + - - +
473B TYR* 4.0 32.8 - - + +
476B MET* 4.3 24.2 - - + +
477B TYR* 5.5 1.8 - - - +
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Residues in contact with GLN 451 (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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447B THR* 3.3 31.1 + - - +
448B GLU* 3.2 18.2 + - - +
449B HIS 3.1 0.4 - - - -
450B ALA* 1.3 76.1 - - + +
452B MET* 1.3 68.4 + - - +
453B MET 3.0 0.9 - - - -
454B GLN* 2.9 26.2 + - - +
455B ARG* 2.8 21.1 + - - +
477B TYR* 4.1 12.6 - - - +
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Residues in contact with MET 452 (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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359B PRO 6.0 1.1 - - - +
362B ASP* 3.4 34.5 - - - +
363B ILE* 3.5 33.7 - - + -
366B PRO* 4.2 7.6 - - + -
367B LYS* 4.7 3.4 - - - +
448B GLU* 3.2 47.4 + - + +
449B HIS* 4.0 4.5 - - - +
451B GLN* 1.3 75.6 - - + +
453B MET* 1.3 53.6 + - - +
455B ARG* 2.9 9.2 + - - +
456B ILE* 2.7 42.7 + - + +
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Residues in contact with MET 453 (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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2B 433 3.1 43.1 - - + +
282B PHE* 3.5 22.4 - - + -
363B ILE* 3.0 32.3 - - + -
449B HIS* 3.1 29.2 + - + +
450B ALA* 3.5 8.1 - - - +
451B GLN 3.0 0.2 - - - -
452B MET* 1.3 80.4 - - - +
454B GLN* 1.3 56.1 + - - +
456B ILE* 3.3 6.3 + - - +
457B LYS* 2.9 30.0 + - - +
465B LEU* 5.1 10.0 - - + +
473B TYR* 4.0 25.1 - - + -
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Residues in contact with GLN 454 (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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450B ALA 3.0 12.5 + - - +
451B GLN* 2.9 37.3 + - - +
453B MET* 1.3 76.1 - - - +
455B ARG* 1.3 64.7 + - + +
457B LYS* 3.6 12.7 + - + +
458B LYS* 3.2 22.5 + - - +
476B MET 5.4 3.8 - - - +
477B TYR* 5.6 3.1 - - - -
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Residues in contact with ARG 455 (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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451B GLN 2.8 11.2 + - - +
452B MET* 3.4 11.7 - - - +
454B GLN* 1.3 77.1 - - + +
456B ILE* 1.3 63.7 + - + +
458B LYS* 3.0 6.2 + - - -
459B THR* 2.9 40.0 + - + +
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Residues in contact with ILE 456 (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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282B PHE* 4.2 31.0 - - + -
359B PRO* 4.9 17.9 - - + +
360B PHE* 4.4 15.9 - - + -
363B ILE* 3.9 28.0 - - + -
452B MET* 2.7 24.9 + - + +
453B MET* 3.6 7.9 - - - +
455B ARG* 1.3 72.6 - - + +
457B LYS* 1.3 58.5 + - - +
459B THR* 4.6 2.0 - - - -
460B GLU* 2.6 62.4 + - + +
463B THR* 4.6 4.5 - - + +
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Residues in contact with LYS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B MET 2.9 17.2 + - - +
454B GLN* 3.9 11.4 - - + +
456B ILE* 1.3 78.9 - - - +
458B LYS* 1.3 59.9 + - + +
460B GLU 4.8 1.8 + - - -
461B THR* 4.8 11.3 + - - +
463B THR 6.2 0.4 - - - -
465B LEU* 5.1 7.6 - - + -
470B GLN* 3.3 42.3 + - - +
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B GLN 3.2 15.9 + - - +
455B ARG* 3.0 9.4 + - - +
457B LYS* 1.3 81.8 - - + +
459B THR* 1.3 63.9 + - + +
461B THR* 4.7 8.5 - - - +
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Residues in contact with THR 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PRO* 5.3 4.9 - - - +
455B ARG* 2.9 19.8 + - + +
456B ILE* 4.6 0.7 - - - -
458B LYS* 1.3 85.0 - - + +
460B GLU* 1.3 74.2 + - - +
461B THR* 3.2 16.4 + - - -
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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
------------------------------------------------------------
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