Contacts of the helix formed by residues 387 - 392 (chain E) in PDB entry 4B2Q
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 ILE 387 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E SER 5.2 2.2 - - - +
384E LEU* 3.7 37.2 - - + +
386E ASP* 1.3 78.0 - - + +
388E ILE* 1.3 63.4 + - + +
390E ILE* 4.0 6.3 - - - -
391E LEU* 3.1 33.7 + - + +
392E GLY 3.2 8.2 - - - +
395E GLU* 4.1 16.2 - - + +
396E LEU* 3.9 16.4 - - + -
234G ARG* 5.6 8.1 - - - +
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Residues in contact with ILE 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381E TYR* 6.1 0.7 - - + -
384E LEU* 2.9 30.3 - - + +
385E GLN* 4.8 10.5 - - - +
386E ASP 3.1 1.2 - - - -
387E ILE* 1.3 80.9 - - + +
389E ALA* 1.3 58.6 + - + +
390E ILE 3.2 4.9 - - - -
392E GLY* 3.3 25.7 + - - +
393E MET* 3.3 53.2 - - + +
395E GLU 5.5 0.7 - - - +
396E LEU* 3.5 37.5 - - + -
404E VAL* 5.5 1.6 - - + -
408E ARG* 4.8 4.7 - - - +
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Residues in contact with ALA 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E GLN 4.2 15.8 + - - +
386E ASP 3.4 5.0 + - - +
388E ILE* 1.3 80.2 - - + +
390E ILE* 1.3 63.5 + - + +
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Residues in contact with ILE 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E ASP* 3.2 27.8 + - + +
387E ILE* 4.4 2.7 - - - +
388E ILE 3.2 0.6 - - - -
389E ALA* 1.3 84.8 - - + +
391E LEU* 1.3 75.1 + - + +
392E GLY 3.4 3.3 + - - -
24G LYS* 6.3 2.7 - - - -
25G ILE* 4.8 27.8 - - + -
28G SER* 3.8 27.1 - - - +
234G ARG* 5.8 6.7 - - - +
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Residues in contact with LEU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E ILE* 3.1 17.3 + - + +
390E ILE* 1.3 96.7 - - + +
392E GLY* 1.3 60.4 + - - +
394E ASP* 3.2 8.0 - - - +
395E GLU* 3.1 45.1 - - + +
28G SER* 4.4 11.9 - - - +
31G LEU* 6.5 0.7 - - + -
32G SER* 6.2 3.8 - - - -
234G ARG* 5.7 7.0 - - - +
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Residues in contact with GLY 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E ILE 3.2 13.5 - - - +
388E ILE* 3.3 23.0 + - - +
390E ILE 3.4 3.0 + - - -
391E LEU* 1.3 82.2 - - - +
393E MET* 1.3 63.2 + - - -
394E ASP* 3.4 6.1 - - - -
395E GLU* 3.9 5.2 + - - +
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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