Contacts of the helix formed by residues 432 - 462 (chain B) in PDB entry 2BG9
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 ALA 432 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PRO* 5.5 7.0 - - + -
307B ARG* 5.7 2.0 - - - +
430B TYR 3.7 1.8 + - - -
431B VAL* 1.3 87.1 - - - +
433B MET* 1.3 55.6 + - - +
434B VAL* 3.4 2.6 - - - +
435B ALA* 4.1 13.7 - - + +
436B ASP* 2.4 53.4 + - - +
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Residues in contact with MET 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B VAL* 3.3 22.0 - - + +
432B ALA* 1.3 79.3 - - - +
434B VAL* 1.3 68.0 + - + +
436B ASP* 3.4 12.1 + - + +
437B ARG* 3.0 48.6 + - + +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.8 18.6 - - + -
307B ARG* 2.9 35.9 - - - +
431B VAL* 6.2 0.9 - - + -
432B ALA* 6.0 0.4 - - - -
433B MET* 1.3 79.9 - - + +
435B ALA* 1.3 58.6 + - - +
437B ARG* 3.1 5.2 + - - -
438B LEU* 2.5 63.9 + - + +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 4.5 12.3 - - + -
243B PRO* 4.3 22.4 - - + -
304B LEU* 4.4 19.0 - - + +
432B ALA* 4.0 12.9 + - + +
433B MET 3.4 0.2 - - - -
434B VAL* 1.3 77.4 - - - +
436B ASP* 1.3 60.1 + - - +
439B PHE* 2.5 45.9 + - - +
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Residues in contact with ASP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PRO* 4.5 10.4 - - - +
432B ALA* 2.4 42.9 - - - +
433B MET* 3.6 14.9 - - + +
434B VAL 3.2 0.2 - - - -
435B ALA* 1.3 74.9 - - - +
437B ARG* 1.3 62.1 + - - +
439B PHE* 3.7 7.2 - - - -
440B LEU* 2.7 47.5 + - + +
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B MET* 3.0 35.4 + - + +
434B VAL* 3.6 5.2 - - - +
436B ASP* 1.3 84.0 - - - +
438B LEU* 1.3 63.6 + - + +
440B LEU* 3.3 8.4 + - - +
441B TYR* 2.7 22.5 + - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 4.2 15.3 - - + -
434B VAL* 2.5 43.8 + - + +
437B ARG* 1.3 74.3 - - + +
439B PHE* 1.3 48.1 + - - +
440B LEU 2.9 5.6 - - - -
441B TYR* 3.0 41.7 - - + -
442B ILE* 2.3 50.9 + - + +
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Residues in contact with PHE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 4.8 16.8 - - + -
239B PHE* 3.6 24.2 - - + +
240B TYR* 4.6 30.1 - + - -
243B PRO* 4.3 18.2 - - + -
304B LEU* 5.6 0.4 - - - +
435B ALA* 2.5 34.2 + - - +
436B ASP* 3.8 3.8 - - - +
438B LEU* 1.3 72.4 - - - +
440B LEU* 1.3 78.5 + - + +
442B ILE* 2.6 35.7 - - + +
443B PHE* 2.9 4.4 + - + +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ASP* 2.7 37.2 + - + +
437B ARG* 3.4 6.5 - - - +
438B LEU 2.9 0.4 - - - -
439B PHE* 1.3 100.1 - - + +
441B TYR* 1.3 49.9 + - - +
442B ILE 2.8 5.4 - - - -
443B PHE* 2.6 49.6 - - + +
444B ILE* 2.7 15.2 + - - +
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Residues in contact with TYR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 4.7 12.9 - - + +
300B VAL* 5.5 8.5 - - + -
437B ARG 2.7 9.6 + - - +
438B LEU* 2.9 49.3 + - + -
440B LEU* 1.3 76.2 - - - +
442B ILE* 1.3 58.4 + - + +
444B ILE* 2.7 19.9 - - + +
445B THR* 2.4 65.0 + - - +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 5.5 2.0 - - + -
239B PHE* 3.9 24.0 - - + -
297B LEU* 3.9 18.4 - - + -
301B VAL* 3.8 25.6 - - + -
304B LEU* 5.1 3.8 - - + -
438B LEU* 2.3 55.6 + - + +
439B PHE* 2.6 40.2 - - + +
441B TYR* 1.3 76.8 - - + +
443B PHE* 1.3 52.8 + - - +
445B THR* 4.3 4.9 - - - -
446B MET* 2.7 58.3 + - - +
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Residues in contact with PHE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B PHE* 2.9 9.4 + - + +
440B LEU* 2.6 47.6 - - + +
442B ILE* 1.3 77.0 - - - +
444B ILE* 1.3 58.8 + - + -
447B CYS* 2.2 54.3 - - + +
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B LEU 2.7 11.1 + - - +
441B TYR* 2.7 52.7 - - + +
443B PHE* 1.3 77.4 - - + +
445B THR* 1.3 59.1 + - - +
447B CYS* 5.1 0.2 - - - -
448B SER* 2.4 56.4 + - - +
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Residues in contact with THR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PHE* 5.8 0.9 - - + -
297B LEU* 3.1 32.8 - - + -
441B TYR* 2.4 61.3 + - - +
442B ILE 4.0 0.9 - - - -
444B ILE* 1.3 75.5 - - - +
446B MET* 1.3 58.1 + - - +
448B SER* 4.5 2.5 - - - -
449B ILE* 2.6 58.0 + - + +
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Residues in contact with MET 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B SER* 4.8 16.6 - - - +
235B ALA* 5.9 0.2 - - - -
236B ILE* 3.7 43.5 - - + -
239B PHE* 4.4 9.4 - - + -
297B LEU* 5.5 4.0 - - + -
442B ILE* 2.7 44.6 + - - +
443B PHE* 4.7 0.2 - - - -
445B THR* 1.3 79.7 - - + +
447B CYS* 1.3 69.2 + - - +
449B ILE* 3.7 12.8 - - + +
450B GLY* 3.0 23.4 + - - -
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Residues in contact with CYS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B PHE* 2.2 56.7 + - + +
446B MET* 1.3 92.4 - - - +
448B SER* 1.3 61.2 + - - +
450B GLY* 3.8 0.9 - - - -
451B THR* 2.8 30.8 + - - +
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Residues in contact with SER 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ILE* 2.4 51.2 + - - +
445B THR* 3.5 2.9 - - - -
447B CYS* 1.3 69.6 - - - +
449B ILE* 1.3 65.5 + - - +
450B GLY 2.8 4.4 + - - -
451B THR* 3.0 10.9 + - - +
452B PHE* 2.8 46.1 - - - -
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 3.9 10.9 - - + +
293B PHE* 3.5 59.0 - - + -
294B SER 5.3 0.7 - - - +
297B LEU* 5.3 1.1 - - + -
445B THR* 2.6 55.3 + - + +
446B MET* 3.7 9.6 - - + +
448B SER* 1.3 72.0 - - - +
450B GLY* 1.3 61.3 + - - +
452B PHE* 3.1 19.8 - - + +
453B SER* 3.3 24.3 + - - -
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Residues in contact with GLY 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 4.8 5.4 - - - -
446B MET 3.0 23.1 + - - -
447B CYS* 4.7 0.2 - - - -
448B SER 2.8 2.6 + - - -
449B ILE* 1.3 76.6 - - - +
451B THR* 1.3 50.9 + - - -
452B PHE 3.0 4.7 + - - -
453B SER* 3.7 3.8 + - - -
454B ILE* 2.6 45.7 + - - +
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Residues in contact with THR 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B CYS 2.8 26.7 + - - +
448B SER* 3.1 10.8 - - - +
450B GLY* 1.3 72.7 - - - +
452B PHE* 1.3 70.3 + - + +
454B ILE* 3.4 23.7 - - - +
455B PHE* 3.0 27.0 + - - +
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Residues in contact with PHE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PHE* 6.1 0.2 - + - -
448B SER* 2.8 46.4 - - - -
449B ILE* 3.1 25.1 - - + +
450B GLY 3.0 2.2 - - - -
451B THR* 1.3 89.3 - - + +
453B SER* 1.3 54.6 + - - +
454B ILE 3.0 0.9 - - - -
455B PHE* 2.8 8.9 + - + +
456B LEU* 2.5 45.4 + - + +
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Residues in contact with SER 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 3.3 18.8 - - - -
290B LEU* 2.8 52.4 - - - +
449B ILE 3.3 4.1 + - - -
450B GLY 3.9 1.7 + - - -
452B PHE* 1.3 76.1 - - - +
454B ILE* 1.3 60.1 + - - +
456B LEU* 3.8 10.7 - - - +
457B ASP* 2.3 43.5 + - - +
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B GLY* 2.6 29.0 + - - +
451B THR* 3.4 24.9 - - - +
453B SER* 1.3 75.1 + - - +
455B PHE* 1.3 55.8 + - + +
457B ASP* 3.7 5.6 - - - +
458B ALA* 2.7 35.7 + - + +
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Residues in contact with PHE 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B THR* 3.0 16.1 + - - +
452B PHE* 2.8 15.5 + - + +
454B ILE* 1.3 80.7 - - + +
456B LEU* 1.3 60.8 + - + -
458B ALA* 2.7 12.4 + - + +
459B SER* 2.4 51.3 + - - -
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B MET* 6.0 4.0 - - + -
286B PHE* 4.4 14.4 - - + -
452B PHE* 2.5 33.0 + - + +
453B SER* 3.7 9.9 - - - +
455B PHE* 1.3 78.6 - - + +
457B ASP* 1.3 53.9 + - - +
459B SER* 2.5 12.9 + - - +
460B HIS* 2.4 64.7 + - + +
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Residues in contact with ASP 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TYR* 4.7 11.8 - - - +
286B PHE* 2.7 41.3 - - - -
287B ILE* 5.3 0.2 - - - +
453B SER* 2.3 43.4 + - - +
454B ILE* 3.7 6.0 - - - +
456B LEU* 1.3 72.7 - - - +
458B ALA* 1.3 57.9 + - - +
460B HIS* 3.2 7.9 + - - -
461B ASN* 2.8 40.8 + - - +
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ILE* 2.7 24.1 + - + +
455B PHE* 2.7 28.3 + - + +
457B ASP* 1.3 71.7 - - - +
459B SER* 1.3 53.2 + - - +
461B ASN* 3.4 6.3 + - - +
462B VAL* 2.5 36.9 - - + +
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Residues in contact with SER 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PHE* 2.4 40.1 + - - -
456B LEU* 2.5 36.4 + - - +
458B ALA* 1.3 67.2 - - - +
460B HIS* 1.3 57.5 + - - +
463B PRO* 2.4 54.6 - - - +
464B PRO* 2.7 3.3 - - - +
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Residues in contact with HIS 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE* 3.0 22.7 - - + +
282B SER* 3.3 34.3 + - - +
285B MET* 5.2 6.2 - - + +
286B PHE* 3.7 15.9 - + - -
456B LEU* 2.4 67.4 + - + +
457B ASP* 3.2 11.6 + - - +
459B SER* 1.3 71.1 + - - +
461B ASN* 1.3 62.0 + - - +
464B PRO* 2.4 34.4 - - - +
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Residues in contact with ASN 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE* 2.6 50.4 - - + -
457B ASP* 2.8 29.1 + - - +
458B ALA* 4.1 6.6 + - - +
459B SER 3.3 0.2 - - - -
460B HIS* 1.3 76.5 - - - +
462B VAL* 1.3 63.9 - - + +
465B ASP* 3.3 19.3 - - - +
----------------------------------------------------------
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ALA* 2.5 29.4 - - + +
461B ASN* 1.3 83.5 - - + +
463B PRO* 1.3 65.7 - - + +
465B ASP* 2.2 38.8 - - - +
466B ASN* 4.7 0.3 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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