Contacts of the helix formed by residues 436 - 457 (chain B) in PDB entry 3IW4
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 LYS 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B VAL* 5.8 5.8 - - + -
434B LYS* 5.8 1.6 - - - +
435B PHE* 1.3 74.6 - - - +
437B GLU* 1.3 57.2 + - - +
438B PRO* 4.1 12.3 - - + -
439B GLN* 3.0 21.2 + - + +
440B ALA* 2.7 33.2 + - - +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B PHE 3.7 2.2 + - - -
436B LYS* 1.3 70.0 - - - +
438B PRO* 1.4 77.3 - - + +
440B ALA* 2.7 8.9 + - - +
441B VAL* 2.6 38.1 + - + +
532B LEU* 4.4 10.2 - - + +
561B LEU* 5.2 1.0 - - - -
562B SER* 2.6 43.6 + - - -
564B GLU* 4.5 4.9 - - - +
565B ALA* 4.0 9.2 + - - +
596B PHE* 4.1 15.9 - - + +
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Residues in contact with PRO 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LYS* 3.6 14.4 - - + -
437B GLU* 1.4 95.1 - - + +
439B GLN* 1.3 58.9 + - - +
441B VAL* 3.4 11.5 - - + +
442B PHE* 3.3 18.4 + - - +
599B ARG* 6.3 5.6 - - - +
600B ILE* 5.9 0.3 - - - +
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 5.7 2.7 - - - +
435B PHE* 3.3 34.1 - - - +
436B LYS* 3.0 31.5 + - + +
437B GLU 2.8 1.0 + - - -
438B PRO* 1.3 76.9 - - - +
440B ALA* 1.3 60.4 + - - +
441B VAL 3.1 1.3 - - - -
442B PHE* 2.8 25.1 + - - +
443B TYR* 3.1 33.0 + - + -
613B PRO* 3.4 33.8 - - + +
614B PHE* 4.0 10.0 - - - +
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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
----------------------------------------------------------
435B PHE* 3.7 20.4 - - + +
436B LYS 2.7 18.8 + - - +
437B GLU 3.6 0.4 - - - +
439B GLN* 1.3 73.6 - - - +
441B VAL* 1.3 60.4 + - - +
442B PHE 3.3 0.2 - - - -
443B TYR 4.8 0.2 - - - +
444B ALA* 3.1 24.0 + - - +
528B LEU* 5.3 0.4 - - + +
531B MET* 3.3 24.1 - - + +
532B LEU* 3.5 29.4 - - + -
596B PHE* 4.8 3.1 - - - -
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLU* 2.6 37.4 + - + +
438B PRO* 3.4 12.1 - - + +
440B ALA* 1.3 72.0 - - - +
442B PHE* 1.3 54.5 + - - +
444B ALA* 3.4 2.1 + - - +
445B ALA* 2.7 32.9 + - - +
596B PHE* 3.7 37.5 - - + +
597B PHE* 3.8 19.2 - - + -
600B ILE* 3.4 34.3 - - + -
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Residues in contact with PHE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PRO 3.3 8.6 + - - +
439B GLN 2.8 11.2 + - - +
441B VAL* 1.3 76.8 - - - +
443B TYR* 1.3 74.3 + + - +
445B ALA* 2.9 7.0 + - - +
446B GLU* 2.6 61.5 + - - +
475B GLY 4.2 4.9 - - - -
476B HIS* 4.1 0.9 - - - -
600B ILE* 5.9 3.1 - - + -
605B LEU* 4.1 12.8 - - + -
610B ILE* 3.3 49.1 - - + -
611B GLN 4.1 2.7 - - - -
612B PRO* 3.5 26.5 - - + -
613B PRO* 3.2 27.4 - - + -
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Residues in contact with TYR 443 (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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425B LEU* 4.2 14.1 - - + -
435B PHE* 3.7 35.2 - + - -
439B GLN* 3.1 29.4 + - + +
442B PHE* 1.3 96.1 - + - +
444B ALA* 1.3 64.5 + - - +
446B GLU* 3.1 1.9 + - - +
447B ILE* 3.1 29.4 + - + +
471B LEU* 3.5 16.2 - - + +
475B GLY 3.6 21.1 + - - -
477B ILE* 4.0 23.3 - - + +
531B MET* 3.8 14.6 - - + -
613B PRO* 3.9 10.2 - - + +
614B PHE* 3.3 33.8 + + - -
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Residues in contact with ALA 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 3.1 19.5 + - - +
441B VAL* 3.4 7.4 - - - +
443B TYR* 1.3 78.6 - - - +
445B ALA* 1.3 60.9 + - - +
447B ILE* 3.5 3.3 + - - -
448B SER 3.2 13.0 + - - -
524B TYR* 2.7 36.8 + - - +
528B LEU* 3.8 17.0 - - + -
531B MET* 3.6 15.5 - - + +
596B PHE* 4.4 6.1 - - + -
597B PHE* 4.6 1.1 - - + -
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Residues in contact with ALA 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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441B VAL* 2.7 23.1 + - + +
442B PHE* 2.9 5.6 + - - +
444B ALA* 1.3 74.3 - - - +
446B GLU* 1.3 62.8 + - - +
448B SER* 2.2 30.9 + - - -
449B ILE 3.5 2.3 + - - -
597B PHE* 4.3 10.7 - - + -
600B ILE* 5.0 6.3 - - + -
602B TRP* 4.0 15.5 - - + -
605B LEU* 3.5 29.7 - - + +
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Residues in contact with GLU 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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399B PHE* 3.4 47.7 - - + +
442B PHE* 2.6 53.3 + - - +
443B TYR 3.9 0.9 - - - +
445B ALA* 1.3 75.7 - - - +
447B ILE* 1.3 62.5 + - - +
449B ILE* 3.6 5.6 + - - +
450B GLY 3.9 0.5 + - - -
476B HIS* 2.7 24.5 + - - -
477B ILE* 2.7 48.7 + - + +
605B LEU* 3.9 20.6 - - + +
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Residues in contact with ILE 447 (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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425B LEU* 5.0 4.5 - - + -
443B TYR* 3.1 19.3 + - + +
444B ALA* 3.6 9.2 - - - +
446B GLU* 1.3 74.2 - - - +
448B SER* 1.3 69.4 + - - +
449B ILE 3.0 1.8 - - - -
450B GLY* 2.8 15.9 + - - -
451B LEU* 3.3 10.9 + - + -
464B LEU* 4.3 14.6 - - + -
469B VAL* 4.4 20.9 - - + -
477B ILE* 3.8 20.4 - - + -
479B ILE* 4.2 19.4 - - + +
524B TYR* 3.7 22.7 - - + -
527B LEU* 4.2 25.4 - - + -
531B MET* 5.3 0.4 - - + -
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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
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444B ALA 3.2 9.9 + - - -
445B ALA 2.2 26.5 + - - -
447B ILE* 1.3 80.3 - - - +
449B ILE* 1.3 67.4 + - - +
451B LEU* 2.9 19.2 + - - +
452B PHE* 2.9 36.4 + - - -
521B TRP* 4.8 5.2 - - - -
524B TYR* 4.1 14.4 - - - -
591B VAL* 5.2 3.4 - - - -
602B TRP* 3.1 23.4 - - - -
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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
----------------------------------------------------------
397B PRO* 3.9 22.2 - - + -
398B PRO* 6.0 0.2 - - + -
399B PHE* 4.0 13.9 - - + -
445B ALA 3.7 11.9 - - - +
446B GLU 3.7 9.9 - - - +
447B ILE 2.9 0.6 + - - -
448B SER* 1.3 76.1 + - - +
450B GLY* 1.3 63.3 + - - +
452B PHE* 3.3 15.9 + - + +
453B PHE* 2.9 22.2 + - + +
592B ARG* 4.9 4.3 - - - +
602B TRP* 3.9 26.9 - - + -
605B LEU* 4.1 11.0 - - + -
606B GLU* 4.1 35.0 - - + +
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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
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397B PRO* 4.3 10.8 - - - +
399B PHE* 5.2 3.0 - - - -
400B LEU* 4.1 22.2 - - - -
446B GLU 3.9 2.8 + - - -
447B ILE 2.8 13.5 + - - -
449B ILE* 1.3 73.4 - - - +
451B LEU* 1.3 65.1 + - - -
453B PHE* 3.1 4.5 + - - +
454B LEU* 2.8 29.7 + - - +
479B ILE* 4.4 4.7 - - - -
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Residues in contact with LEU 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 ILE* 3.3 12.2 + - + +
448B SER* 2.9 10.8 + - - +
450B GLY* 1.3 72.7 - - - +
452B PHE* 1.3 54.8 + - - +
454B LEU* 3.1 16.1 + - + +
455B HIS* 2.7 60.2 + - + +
461B TYR* 4.5 17.9 - - + -
464B LEU* 3.8 25.6 - - + -
479B ILE* 5.0 7.0 - - + -
520B ASP* 4.3 13.7 - - + +
521B TRP* 3.9 28.7 - - + -
524B TYR* 4.1 12.8 - - + -
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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
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448B SER* 2.9 47.6 + - - -
449B ILE* 3.3 17.0 - - + +
451B LEU* 1.3 76.2 - - - +
453B PHE* 1.3 66.6 + - - +
455B HIS* 3.8 4.4 - - - +
456B LYS* 2.9 33.3 + - - +
521B TRP* 3.8 24.7 - + - -
588B GLU* 3.4 54.1 - - + +
591B VAL* 4.6 3.8 - - + -
592B ARG* 3.0 45.1 - - - +
602B TRP* 4.4 2.9 - + - -
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Residues in contact with PHE 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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393B LEU* 4.2 13.9 - - + -
394B LEU 3.4 8.7 - - - -
395B ASP* 3.4 22.9 - - + -
396B LYS* 3.5 23.3 - - + -
397B PRO* 3.2 26.0 - - + -
400B LEU* 4.3 4.0 - - + -
449B ILE* 2.9 10.4 + - + +
450B GLY 3.3 7.2 - - - +
452B PHE* 1.3 81.4 - - - +
454B LEU* 1.3 77.0 + - + +
456B LYS* 3.4 13.5 + - - +
457B ARG* 3.0 70.7 + - + +
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Residues in contact with LEU 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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390B VAL* 4.2 20.0 - - + +
393B LEU* 4.7 4.7 - - + -
400B LEU* 4.6 15.5 - - + -
450B GLY 2.8 21.7 + - - +
451B LEU* 3.5 16.2 - - + +
453B PHE* 1.3 89.0 - - + +
455B HIS* 1.3 59.1 + - + +
457B ARG* 3.1 14.8 + - - +
459B ILE* 3.0 50.2 + - + +
461B TYR* 4.2 26.7 - - + -
479B ILE* 5.9 1.1 - - + -
482B PHE* 4.4 17.3 - - + -
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Residues in contact with HIS 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 LEU* 2.7 47.1 + - + +
452B PHE* 3.8 4.4 + - - +
454B LEU* 1.3 70.0 - - + +
456B LYS* 1.3 62.3 + - - +
457B ARG 3.0 1.6 - - - -
458B GLY* 2.8 16.8 + - - -
459B ILE 3.0 28.9 - - - +
460B ILE* 4.5 0.2 - - - -
490B MET* 3.0 23.2 - - + +
517B LYS* 3.5 48.4 - - + +
520B ASP* 2.9 33.8 + - + +
521B TRP* 3.8 18.3 + + - -
588B GLU* 5.7 2.9 - - - +
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Residues in contact with LYS 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B PHE* 2.9 25.3 + - - +
453B PHE* 3.7 11.4 - - - +
455B HIS* 1.3 76.3 - - - +
457B ARG* 1.3 67.3 + - - +
458B GLY 3.2 3.1 + - - -
490B MET* 4.3 13.1 - - - +
588B GLU* 2.8 34.4 + - - +
592B ARG* 5.5 1.8 - - - +
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Residues in contact with ARG 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 3.6 28.8 - - + +
394B LEU* 2.6 31.7 + - - +
395B ASP* 3.6 12.9 + - - +
453B PHE* 3.0 50.6 + - + +
454B LEU* 3.1 8.0 + - - +
455B HIS 3.0 0.8 - - - -
456B LYS* 1.3 85.1 - - - +
458B GLY* 1.3 65.8 + - - +
459B ILE* 3.3 18.8 + - + +
488B HIS* 5.1 1.9 + - - -
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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