Contacts of the helix formed by residues 79 - 83 (chain E) in PDB entry 4PJ7
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 GLN 79 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E GLU* 4.8 5.4 - - - +
59E ARG* 3.2 37.7 + - - +
77E GLU* 3.4 14.2 + - - +
78E LEU* 1.3 74.3 - - - +
80E MET* 1.3 64.2 + - - +
81E LYS* 3.2 13.2 - - + +
82E ASP* 2.8 29.5 + - - +
107E ILE* 3.4 12.0 - - - +
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Residues in contact with MET 80 (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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14E GLU* 4.1 8.1 + - - +
79E GLN* 1.3 73.2 - - - +
81E LYS* 1.4 55.6 - - - +
82E ASP 3.1 0.2 - - - -
83E SER* 3.1 36.5 + - - +
107E ILE* 3.3 41.3 - - + +
109E PRO* 3.8 24.5 - - - -
158E VAL* 4.0 28.3 - - + -
167E LYS* 3.7 30.1 - - + -
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Residues in contact with LYS 81 (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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36E GLN* 4.6 1.6 + - - -
38E HIS* 3.4 25.6 + - - -
59E ARG* 5.8 1.1 - - - +
79E GLN* 3.2 12.9 - - + +
80E MET* 1.4 75.2 - - - +
82E ASP* 1.4 61.5 + - - +
83E SER 3.2 4.1 + - - +
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Residues in contact with ASP 82 (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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36E GLN* 4.7 3.1 + - - +
59E ARG* 2.7 46.1 + - - -
60E PHE* 3.9 9.4 - - - -
75E LEU* 4.1 15.9 - - + -
78E LEU* 3.6 5.1 - - + +
79E GLN* 2.8 29.3 + - - +
81E LYS* 1.4 76.6 - - - +
83E SER* 1.4 58.9 + - - +
84E ALA* 3.1 7.8 + - - -
86E TYR* 2.6 34.5 + - - +
105E LEU* 3.7 3.1 - - - +
107E ILE* 3.6 11.4 - - + -
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Residues in contact with SER 83 (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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38E HIS* 3.6 14.2 - - - +
39E ALA 5.6 0.3 + - - -
80E MET* 3.1 23.2 + - - +
81E LYS 4.0 1.4 - - - +
82E ASP* 1.4 72.3 - - - +
84E ALA* 1.3 61.0 + - - +
105E LEU 3.5 12.1 - - - -
106E ILE* 4.3 1.5 - - - +
107E ILE* 3.4 31.6 + - - +
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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
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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