Contacts of the helix formed by residues 433 - 453 (chain W) in PDB entry 4UJ3
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 ASP 433 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431W GLN 3.7 10.4 - - - +
432W GLN* 1.3 77.7 - - - +
434W VAL* 1.3 67.7 + - - +
435W ASP* 3.2 6.3 - - + +
436W GLN* 3.0 29.1 + - + +
437W MET* 3.1 11.5 + - - +
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Residues in contact with VAL 434 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302W TYR* 3.9 15.5 - - + +
305W PHE* 4.1 7.7 - - + -
306W ARG* 3.3 41.1 - - + +
309W LYS* 3.4 35.9 - - + -
432W GLN 4.0 0.4 + - - -
433W ASP* 1.3 73.1 - - - +
435W ASP* 1.3 62.8 + - - +
437W MET* 3.3 11.0 + - - +
438W PHE* 3.1 21.0 + - - +
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Residues in contact with ASP 435 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302W TYR* 2.6 36.3 + - - -
433W ASP* 3.2 5.2 - - + +
434W VAL* 1.3 77.4 - - - +
436W GLN* 1.3 64.3 - - + +
438W PHE* 3.2 6.7 + - - +
439W TRP* 3.1 34.3 + - + -
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Residues in contact with GLN 436 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431W GLN 4.0 2.8 - - - +
432W GLN* 3.4 27.7 + - + +
433W ASP* 3.0 37.1 + - + +
435W ASP* 1.3 78.0 - - + +
437W MET* 1.3 58.4 + - - +
439W TRP* 3.2 6.9 + - - +
440W GLU* 2.9 28.9 + - - +
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Residues in contact with MET 437 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305W PHE* 3.8 11.4 - - + -
309W LYS* 4.3 31.4 - - + +
420W TYR* 3.4 20.0 + - - +
424W ILE* 3.2 45.5 - - + -
429W VAL* 4.7 15.5 - - + +
432W GLN* 3.6 30.1 - - + +
433W ASP 3.1 12.2 + - - +
434W VAL* 3.6 6.3 - - - +
435W ASP 3.2 0.2 - - - -
436W GLN* 1.3 77.0 - - - +
438W PHE* 1.3 62.1 + - - +
440W GLU* 3.2 3.5 + - - +
441W VAL* 3.1 26.7 + - - +
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Residues in contact with PHE 438 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297W ALA* 3.4 26.7 - - + -
298W ASP 4.2 3.1 - - - -
301W LEU* 3.7 7.6 - - + -
302W TYR* 3.3 57.4 - + + -
305W PHE* 3.6 30.0 - + + -
434W VAL 3.1 12.9 + - - +
435W ASP 3.2 6.9 + - - +
437W MET* 1.3 75.7 - - - +
439W TRP* 1.3 77.7 + + - +
441W VAL* 3.2 7.3 + - + +
442W MET* 2.9 67.0 + - + +
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Residues in contact with TRP 439 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295W LYS* 3.9 57.0 + - + +
296W GLU* 3.8 10.3 - - - -
297W ALA* 3.4 40.1 - - + +
302W TYR* 6.4 0.2 - + - -
435W ASP* 3.1 29.2 + - + +
436W GLN* 3.2 6.0 + - - +
438W PHE* 1.3 91.4 - + - +
440W GLU* 1.3 60.4 + - - +
442W MET* 3.5 30.7 - - + +
443W GLN* 3.2 24.1 + - - +
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Residues in contact with GLU 440 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300V PG4 3.4 38.4 - - - +
420W TYR* 3.5 30.1 - - + +
432W GLN* 3.6 11.5 + - - +
436W GLN 2.9 12.7 + - - +
437W MET* 3.2 8.5 + - - +
439W TRP* 1.3 74.4 - - - +
441W VAL* 1.3 61.0 + - - +
443W GLN* 3.2 13.0 + - - +
444W LEU* 2.9 37.2 + - + +
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Residues in contact with VAL 441 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305W PHE* 3.7 23.3 - - + -
320W PHE* 4.2 22.4 - - + -
324W ILE* 4.6 0.2 - - + -
417W PHE* 4.2 16.4 - - + -
420W TYR* 3.9 19.7 - - + -
421W ILE* 4.5 7.9 - - + -
437W MET 3.1 14.9 + - - +
438W PHE* 3.4 9.0 - - + +
440W GLU* 1.3 72.8 - - - +
442W MET* 1.3 61.6 + - - +
444W LEU* 3.4 8.8 + - + +
445W ARG* 2.9 46.4 + - + +
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Residues in contact with MET 442 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298W ASP* 4.8 9.0 - - + +
301W LEU* 3.4 32.5 - - + -
438W PHE* 2.9 52.2 + - + +
439W TRP* 3.5 38.8 - - + +
440W GLU 3.3 0.2 - - - -
441W VAL* 1.3 81.0 - - - +
443W GLN* 1.3 56.7 + - - +
445W ARG* 3.3 16.7 + - - +
446W LYS* 2.9 29.5 + - - +
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Residues in contact with GLN 443 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439W TRP* 3.2 15.8 + - - +
440W GLU* 3.3 19.5 - - - +
442W MET* 1.3 75.4 - - - +
444W LEU* 1.3 60.9 + - + +
446W LYS* 2.8 53.9 + - - +
447W GLU* 3.0 43.1 + - + +
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Residues in contact with LEU 444 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300V PG4 5.6 2.0 - - - -
413W SER 4.5 3.4 - - - +
416W ASN* 3.6 33.0 - - + +
417W PHE* 3.7 26.9 - - + +
420W TYR* 3.8 39.5 - - + -
440W GLU* 2.9 33.2 + - + +
441W VAL* 3.6 7.9 - - - +
443W GLN* 1.3 77.5 - - + +
445W ARG* 1.3 61.4 + - - +
447W GLU* 3.4 11.1 + - + +
448W MET* 3.2 27.7 + - - +
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Residues in contact with ARG 445 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301W LEU* 4.0 33.7 - - - +
323W LYS* 4.8 4.4 - - - +
324W ILE* 3.7 31.3 - - + +
327W GLU* 3.0 31.7 + - - +
328W ASP* 2.4 41.2 + - - +
417W PHE* 5.0 1.8 - - + -
441W VAL* 2.9 30.6 + - + +
442W MET* 3.6 14.2 - - - +
444W LEU* 1.3 74.7 - - - +
446W LYS* 1.3 57.0 + - - +
448W MET* 3.3 16.5 + - + +
449W SER* 2.8 41.1 + - - +
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Residues in contact with LYS 446 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442W MET 2.9 12.9 + - - +
443W GLN* 2.8 41.4 + - - +
445W ARG* 1.3 74.9 - - - +
447W GLU* 1.3 70.0 + - - +
449W SER* 3.4 6.5 + - - -
450W LEU* 3.0 45.5 + - + +
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Residues in contact with GLU 447 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409W TYR* 2.3 42.5 + - - +
413W SER* 4.1 15.7 - - - +
443W GLN* 3.0 37.3 + - + +
444W LEU* 3.7 13.0 - - + +
445W ARG 3.2 0.2 - - - -
446W LYS* 1.3 80.5 + - - +
448W MET* 1.3 62.9 + - - +
450W LEU* 3.1 15.9 + - - +
451W ALA* 3.0 22.2 + - - +
457W LYS* 5.9 0.3 - - - +
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Residues in contact with MET 448 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324W ILE* 3.9 13.2 - - + -
328W ASP* 3.2 43.5 - - + +
329W ILE* 4.2 10.5 - - - -
332W CYS* 3.3 16.7 - - - -
413W SER* 3.7 24.0 - - - +
414W VAL* 4.0 29.8 - - + +
417W PHE* 4.1 17.0 - - + -
444W LEU 3.2 9.2 + - - +
445W ARG* 3.3 19.5 + - + +
447W GLU* 1.3 77.5 - - - +
449W SER* 1.3 56.9 + - - +
451W ALA* 3.2 1.1 + - - -
452W LYS* 2.8 29.4 + - - +
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Residues in contact with SER 449 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328W ASP* 3.6 17.1 + - - -
445W ARG* 2.8 24.9 + - - +
446W LYS* 3.7 8.3 - - - -
447W GLU 3.2 0.2 - - - -
448W MET* 1.3 72.9 - - - +
450W LEU* 1.3 61.5 + - - +
452W LYS* 3.4 32.9 + - - +
453W LEU* 3.6 17.5 + - - +
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Residues in contact with LEU 450 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409W TYR* 4.5 5.2 - - - +
446W LYS* 3.0 34.9 + - + +
447W GLU* 3.6 21.8 - - - +
449W SER* 1.3 76.1 - - - +
451W ALA* 1.3 64.5 + - - +
453W LEU* 3.0 13.5 + - + +
454W GLY 3.1 0.2 + - - -
455W TYR* 2.9 56.8 + - + +
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Residues in contact with ALA 451 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332W CYS* 3.8 8.3 - - - -
406W PHE* 4.1 1.1 - - - -
409W TYR* 3.8 17.5 - - + -
410W ARG* 3.5 46.0 + - + +
413W SER* 4.8 1.8 - - - +
447W GLU 3.0 13.2 + - - +
448W MET* 3.6 7.6 - - - +
450W LEU* 1.3 75.2 - - - +
452W LYS* 1.3 65.8 + - - +
454W GLY* 3.0 14.3 + - - +
455W TYR 3.6 8.8 + - - +
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Residues in contact with LYS 452 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327W GLU* 3.3 32.0 + - - +
328W ASP* 4.8 1.3 + - - +
331W PRO* 3.6 26.9 - - + +
332W CYS* 3.8 10.9 - - - +
410W ARG* 4.2 15.5 + - - +
448W MET 2.8 17.8 + - - +
449W SER* 3.4 30.2 + - - +
451W ALA* 1.3 72.5 - - - +
453W LEU* 1.3 76.5 + - + +
454W GLY 3.7 0.2 + - - -
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Residues in contact with LEU 453 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449W SER 3.6 14.1 + - - +
450W LEU* 3.0 10.1 + - + +
451W ALA 3.0 1.0 - - - -
452W LYS* 1.3 97.5 - - + +
454W GLY* 1.3 59.8 + - - +
455W TYR* 3.5 27.6 - - + -
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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