Contacts of the helix formed by residues 422 - 444 (chain B) in PDB entry 2WSF
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 422 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B ILE* 2.9 27.2 + - + +
419B ILE* 4.1 2.5 - - - +
420B SER 2.8 3.8 - - - +
421B HIS* 1.3 77.0 - - - +
423B SER* 1.3 59.4 + - - +
424B TRP 3.2 1.1 - - - -
425B ALA* 3.0 26.9 + - - +
426B SER* 3.4 8.0 + - - -
528B HIS* 3.8 15.7 - - - +
531B THR* 3.4 24.9 - - - +
532B LEU* 4.0 13.0 - - + +
535B VAL* 3.2 36.1 - - + -
839B CLA 3.5 43.3 - - + -
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A LEU* 5.0 0.9 - - - -
707A ILE* 3.8 8.5 - - - +
851A CLA 3.9 19.5 - - - -
419B ILE* 4.9 1.8 - - - -
420B SER* 2.9 17.7 + - - +
422B LEU* 1.3 76.7 - - - +
424B TRP* 1.3 65.9 + - - +
426B SER* 3.4 2.9 + - - +
427B LEU* 3.1 23.9 + - - +
532B LEU* 4.4 20.6 - - - +
806B CLA 2.7 31.9 + - - -
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Residues in contact with TRP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B SER 2.4 31.8 + - - +
421B HIS* 4.4 7.9 - - + -
423B SER* 1.3 67.8 + - - +
425B ALA* 1.3 89.8 + - + +
427B LEU* 4.6 1.9 - - - +
428B PHE* 3.2 34.7 + + - +
806B CLA 2.8 54.0 + - + +
832B CLA 2.6 32.8 + - + -
838B CLA 3.9 17.9 - - + -
839B CLA 3.3 38.1 - + + -
201F CLA 3.1 54.4 - + + +
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B HIS 4.7 3.1 - - - +
422B LEU* 3.0 17.0 + - - +
424B TRP* 1.3 99.9 - - + +
426B SER* 1.3 51.5 + - - +
428B PHE* 3.4 3.3 - - - +
429B LEU* 2.7 41.6 + - + +
528B HIS* 3.8 33.9 - - + +
838B CLA 6.0 3.4 - - + -
839B CLA 4.8 5.6 - - + -
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A CLA 3.7 18.6 - - - -
422B LEU 3.4 3.3 + - - -
423B SER 3.4 7.5 + - - -
425B ALA* 1.3 77.1 - - - +
427B LEU* 1.3 52.7 + - - +
429B LEU* 2.9 8.3 + - - -
430B GLY* 2.3 37.8 + - - -
525B LEU* 3.9 3.4 - - - +
528B HIS* 3.5 9.6 + - - +
529B THR* 3.0 42.7 + - - -
532B LEU* 3.9 8.6 - - - +
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A CLA 3.5 47.5 - - + +
423B SER 3.1 10.8 + - - +
424B TRP* 4.6 2.0 - - - +
426B SER* 1.3 76.8 - - - +
428B PHE* 1.3 61.8 + - - +
431B PHE* 3.1 60.8 + - + -
806B CLA 3.3 52.9 - - + +
832B CLA 3.2 10.8 - - - -
203F BCR 4.2 20.6 - - + -
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Residues in contact with PHE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TRP* 3.2 34.7 + + + +
425B ALA* 3.4 3.4 - - - +
426B SER 3.1 0.6 - - - -
427B LEU* 1.3 75.0 - - - +
429B LEU* 1.3 67.7 + - + +
430B GLY 2.8 13.5 + - - -
432B HIS* 3.2 46.5 + + + +
832B CLA 2.8 75.4 - + + +
838B CLA 3.8 55.6 - - + -
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ALA* 2.7 23.7 + - + +
426B SER* 3.1 4.0 - - - +
428B PHE* 1.3 79.7 - - + +
430B GLY* 1.3 61.8 + - - +
432B HIS* 5.1 1.8 - - + -
433B THR* 3.1 22.0 + - - +
521B HIS* 4.1 19.3 - - + +
524B ALA* 3.5 36.1 - - + +
525B LEU* 3.5 23.5 - - + +
528B HIS* 3.9 9.2 - - + -
838B CLA 3.5 52.3 - - + -
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Residues in contact with GLY 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A CLA 3.1 38.7 - - - +
426B SER 2.3 16.9 + - - -
427B LEU 3.6 0.4 - - - -
428B PHE 2.8 1.8 + - - -
429B LEU* 1.3 68.6 - - - +
431B PHE* 1.3 54.4 + - - -
432B HIS 2.7 15.7 + - - -
433B THR* 2.9 15.2 + - - -
434B LEU* 3.2 8.0 + - - +
525B LEU* 4.3 4.5 - - - -
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A BCR 4.6 9.3 - - + +
851A CLA 3.2 61.9 - - + +
427B LEU* 3.1 38.7 + - + -
428B PHE 5.0 0.4 - - - -
430B GLY* 1.3 69.8 - - - +
432B HIS* 1.3 53.2 + + - +
433B THR 3.5 0.2 - - - -
434B LEU* 3.5 6.2 - - - -
435B GLY* 2.7 30.7 + - - -
806B CLA 4.5 4.7 - - + -
832B CLA 3.0 63.7 - + + -
833B CLA 4.0 5.6 - - + +
203F BCR 3.6 29.2 - - + -
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Residues in contact with HIS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU 5.1 0.4 - - - -
428B PHE* 3.2 51.1 + + + +
429B LEU* 5.1 1.6 - - + -
430B GLY 2.7 6.7 + - - -
431B PHE* 1.3 72.3 - - - +
433B THR* 1.3 62.2 + - - +
436B LEU* 3.6 32.2 + - + +
832B CLA 2.4 98.6 + + + +
833B CLA 4.5 7.7 - - - +
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Residues in contact with THR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 3.1 23.8 + - - +
430B GLY 2.9 3.3 + - - -
432B HIS* 1.3 77.3 - - - +
434B LEU* 1.3 56.9 + - - +
436B LEU* 2.3 35.3 - - - +
437B TYR* 3.7 11.3 - - + +
518B LEU* 4.3 16.3 - - + +
521B HIS* 3.7 22.7 + - - +
522B ALA* 4.2 9.6 - - + -
525B LEU* 5.7 0.9 - - - -
850B CLA 3.8 34.1 - - + -
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A PHE* 3.6 35.0 - - + -
845A BCR 3.9 18.6 - - + -
850A CLA 5.0 13.2 - - + +
851A CLA 3.8 34.5 - - + -
430B GLY 3.2 8.9 + - - +
431B PHE* 3.5 9.2 - - - +
433B THR* 1.3 76.8 - - - +
435B GLY* 1.3 62.3 + - - +
436B LEU 4.4 0.7 - - - -
437B TYR* 4.8 0.7 - - - -
438B VAL* 3.1 44.7 + - + +
616B LEU* 5.3 4.3 - - + -
833B CLA 3.9 3.5 - - - +
850B CLA 4.5 19.7 - - + -
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Residues in contact with GLY 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A BCR 4.9 1.6 - - - -
431B PHE 2.7 15.1 + - - -
432B HIS 3.9 0.4 + - - -
433B THR 3.3 0.6 - - - -
434B LEU* 1.3 72.5 - - - +
436B LEU* 1.3 61.1 + - - +
437B TYR 3.1 1.2 + - - -
439B HIS* 3.0 33.8 + - - +
833B CLA 3.4 46.0 - - - +
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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
----------------------------------------------------------
432B HIS* 3.6 17.4 + - - +
433B THR* 2.3 23.9 + - - +
435B GLY* 1.3 74.2 - - - +
437B TYR* 1.3 70.3 + - - +
440B ASN* 4.6 2.5 - - - -
453B ILE* 4.1 35.7 - - + +
455B ILE* 4.3 26.0 - - + -
517B PHE* 4.9 5.6 - - + -
518B LEU* 3.4 25.6 - - + +
833B CLA 4.0 30.1 - - + -
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Residues in contact with TYR 437 (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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433B THR* 3.7 12.1 - - + +
434B LEU* 4.8 2.7 - - + -
435B GLY 3.1 2.0 + - - -
436B LEU* 1.3 77.8 - - - +
438B VAL* 1.3 62.4 + - + +
440B ASN* 3.8 13.1 - - - +
441B ASP* 3.3 23.1 + - - +
518B LEU* 3.4 33.5 - - + +
519B VAL* 3.9 18.1 + - - +
613B SER 3.1 28.3 + - - -
614B THR 3.6 17.5 - - - -
615B TYR 3.4 21.5 - - - -
616B LEU* 3.0 33.4 + - + +
619B TRP* 4.1 4.7 + + - -
850B CLA 3.6 45.1 - - + +
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Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A BCR 4.5 8.5 - - + -
850A CLA 3.7 38.1 - - + -
434B LEU* 3.1 37.2 + - + +
435B GLY 3.5 1.4 + - - -
437B TYR* 1.3 76.8 - - - +
439B HIS* 1.3 51.1 + - - +
441B ASP* 2.4 27.4 + - - -
442B VAL* 2.4 20.9 + - + +
833B CLA 2.8 52.9 - - + -
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Residues in contact with HIS 439 (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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435B GLY 3.0 17.1 + - - +
438B VAL* 1.3 80.7 - - - +
440B ASN* 1.3 55.3 + - - +
442B VAL* 3.8 8.7 - - - -
443B MET* 2.9 51.0 + - + +
451B LYS 3.2 10.5 + - - -
453B ILE* 3.3 34.1 + - + +
833B CLA 2.4 88.6 + + + -
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Residues in contact with ASN 440 (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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436B LEU 5.2 0.4 - - - -
437B TYR* 3.8 19.1 - - - +
439B HIS* 1.3 81.4 - - - +
441B ASP* 1.3 56.8 + - - +
443B MET 4.3 0.4 - - - -
444B LEU* 3.1 15.8 + - - +
452B GLN* 2.6 54.3 + - - +
453B ILE* 2.4 36.6 + - - +
518B LEU* 4.9 4.8 - - - +
614B THR* 2.6 41.3 + - - +
615B TYR* 3.4 6.4 - - + +
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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
----------------------------------------------------------
668A TYR* 2.0 51.9 + - - -
677A LEU* 3.0 22.3 - - + +
680A LEU* 4.0 0.5 - - - +
850A CLA 4.0 11.5 - - + +
437B TYR 3.3 16.4 + - - +
438B VAL* 2.4 23.4 + - - +
440B ASN* 1.3 68.9 - - - +
442B VAL* 1.3 54.0 + - - -
443B MET 3.3 1.1 - - - -
444B LEU 2.7 21.2 - - - +
615B TYR* 3.3 20.8 - - + -
617B MET* 3.0 24.1 + - - +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A LEU* 3.8 16.1 - - + +
809A CLA 3.6 32.1 - - + -
850A CLA 4.8 3.1 - - + -
438B VAL* 2.4 36.1 + - + +
439B HIS* 3.8 5.6 - - - +
441B ASP* 1.3 68.4 - - - +
443B MET* 1.3 59.9 + - + +
444B LEU 2.8 11.4 - - - +
445B ALA* 4.5 0.5 - - - +
446B PHE* 3.0 35.4 + - + +
833B CLA 3.2 49.8 - - + -
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Residues in contact with MET 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY* 6.4 0.2 - - - -
439B HIS* 2.9 52.6 + - - +
441B ASP 3.3 0.2 - - - -
442B VAL* 1.3 75.9 - - + +
444B LEU* 1.3 62.3 + - - +
446B PHE* 3.5 7.6 - - + +
448B THR* 3.1 41.6 + - + +
451B LYS* 3.3 41.3 - - + +
452B GLN* 4.2 12.6 - - - +
833B CLA 3.4 57.7 - - + +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A TYR* 3.5 20.2 - - + -
440B ASN 3.1 26.1 + - - +
441B ASP 2.7 12.5 - - - +
442B VAL 2.8 9.2 - - - +
443B MET* 1.3 72.4 - - - +
445B ALA* 1.3 68.9 + - - +
446B PHE 2.9 5.6 - - - -
447B GLY 4.6 1.6 - - - +
448B THR 4.8 0.4 - - - +
449B PRO* 3.6 40.2 - - + -
452B GLN* 3.1 26.0 - - - +
611B GLU 5.7 0.7 - - - +
615B TYR* 3.5 29.4 - - + +
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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