Contacts of the helix formed by residues 363 - 372 (chain B) in PDB entry 4BEJ
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 GLY 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B THR 2.8 7.7 + - - -
348B ILE* 3.0 29.1 + - - +
349B GLU 4.6 0.2 - - - -
350B GLY* 3.9 10.8 - - - -
361B CYS 3.3 0.8 + - - -
362B GLY* 1.3 65.9 + - - -
364B ALA* 1.3 59.4 + - - +
365B ARG 3.8 0.4 - - - -
366B ILE* 4.2 15.7 - - - +
367B CYS* 3.6 23.2 + - - -
442B ILE* 4.4 0.2 - - - +
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Residues in contact with ALA 364 (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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361B CYS 5.8 1.6 - - - +
362B GLY* 3.1 11.9 - - - +
363B GLY* 1.3 72.5 - - - -
365B ARG* 1.3 59.4 + - - +
366B ILE 2.9 1.3 - - - -
367B CYS* 3.6 7.5 - - + +
368B TYR* 2.6 36.3 + - - +
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Residues in contact with ARG 365 (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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361B CYS* 2.9 30.2 + - - +
364B ALA* 1.3 75.9 - - - +
366B ILE* 1.3 51.6 + - - +
368B TYR* 3.1 13.4 - - + +
369B ILE* 2.6 62.7 + - + +
434B LEU* 4.4 6.3 + - - +
437B GLU* 4.0 18.2 + - - -
438B GLU* 2.7 66.4 + - + +
441B ARG* 4.3 13.6 - - - +
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ILE* 4.7 11.2 - - + +
363B GLY 4.2 23.3 - - - +
364B ALA* 2.9 1.0 - - - +
365B ARG* 1.3 74.3 - - - +
367B CYS* 1.3 58.0 + - - +
368B TYR 3.0 0.9 - - - -
369B ILE* 2.9 8.6 + - - +
370B PHE* 2.6 44.4 + - + +
435B VAL* 4.6 10.8 - - + -
438B GLU* 3.9 20.4 - - + -
439B MET* 4.5 20.6 - - + -
442B ILE* 4.9 5.6 - - + -
645B MET* 3.4 29.2 - - + -
649B VAL* 4.5 17.7 - - + -
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Residues in contact with CYS 367 (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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493A TYR* 3.7 27.8 - - - +
363B GLY 3.6 15.9 - - - +
364B ALA* 3.2 10.4 + - + +
366B ILE* 1.3 81.6 - - - +
368B TYR* 1.3 55.6 + - - +
370B PHE* 2.8 7.8 + - - +
371B HIS* 2.4 41.9 + - + +
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Residues in contact with TYR 368 (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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364B ALA 2.6 23.6 + - - +
365B ARG* 3.1 15.9 - - - +
367B CYS* 1.3 71.5 - - - +
369B ILE* 1.3 63.8 + - + +
371B HIS* 5.5 0.4 - - - -
372B GLU* 2.4 73.7 + - + +
373B THR* 3.2 18.3 + - - -
376B ARG* 4.5 8.0 + - - -
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Residues in contact with ILE 369 (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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365B ARG* 2.6 71.5 + - + +
366B ILE* 2.9 6.3 + - + +
368B TYR* 1.3 78.4 - - + +
370B PHE* 1.3 67.6 + - + +
373B THR* 4.3 12.6 - - - +
374B PHE* 2.9 30.0 + - - +
431B CYS* 4.8 3.8 - - - +
434B LEU* 3.7 51.1 - - + +
435B VAL* 4.8 7.2 - - + +
438B GLU* 4.3 4.3 - - + -
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Residues in contact with PHE 370 (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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493A TYR* 4.7 11.7 - + - +
366B ILE* 2.6 21.3 + - + +
367B CYS* 2.8 7.7 + - - +
369B ILE* 1.3 80.4 - - - +
371B HIS* 1.3 71.1 + - - +
372B GLU 3.9 0.2 + - - -
374B PHE* 3.8 16.3 - - - +
375B GLY* 4.0 5.9 + - - -
431B CYS* 3.3 32.8 - - - -
435B VAL* 3.4 22.7 - - + -
637B GLN 5.6 0.7 - - - +
641B PRO* 3.3 46.1 - - + +
644B VAL* 3.4 28.3 - - + -
645B MET* 3.3 29.4 - - + -
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Residues in contact with HIS 371 (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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493A TYR* 3.9 22.5 + + - -
495A ASN* 3.8 31.6 - - + +
497A LYS* 3.3 45.9 + - + +
498A HIS* 5.5 0.4 - - - -
367B CYS* 2.4 26.1 + - + +
368B TYR* 5.1 0.4 - - - -
370B PHE* 1.3 79.2 - - + +
372B GLU* 1.3 65.8 + - - +
375B GLY* 5.0 6.9 - - - +
637B GLN 5.9 1.7 + - - -
641B PRO* 5.6 5.4 - - + -
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Residues in contact with GLU 372 (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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368B TYR* 2.4 65.5 + - + +
371B HIS* 1.3 76.5 - - - +
373B THR* 1.3 61.1 + - - +
376B ARG* 3.1 56.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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