Contacts of the helix formed by residues 482 - 486 (chain G) in PDB entry 2JG7
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 482 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481G SER* 1.3 83.4 + - - +
483G SER* 1.3 62.5 + - - -
484G TRP* 3.1 16.3 + - - +
485G LYS* 3.0 46.5 + - - +
486G GLN* 5.6 0.7 - - - +
151H GLU* 5.8 0.2 - - - -
485H LYS* 2.6 34.5 + - - +
490H ARG* 2.9 40.3 + - - -
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Residues in contact with SER 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G ILE* 5.8 0.4 - - - -
466G ALA* 3.5 13.2 - - - +
477G ARG* 3.7 7.4 - - - +
478G GLU 3.5 22.7 + - - -
479G SER 3.7 12.8 - - - -
480G GLY 2.6 22.7 + - - -
481G SER* 3.3 1.4 + - - -
482G ASP* 1.3 76.6 + - - +
484G TRP* 1.3 63.3 + - - +
485G LYS 3.0 1.9 + - - -
486G GLN* 2.9 40.6 + - - +
487G TYR* 3.6 6.6 - - - -
490H ARG* 5.1 3.1 - - - +
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Residues in contact with TRP 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 4.3 21.5 - - + +
135G ILE* 3.7 23.1 - - + +
136G GLY 3.4 40.2 - - - -
153G TRP* 3.7 27.4 - + + -
178G ILE* 3.8 27.2 - - + +
182G CYS* 3.8 8.7 - - - -
479G SER 4.9 1.6 + - - -
481G SER 4.0 8.6 + - - -
482G ASP* 3.1 21.5 - - - +
483G SER* 1.3 78.5 - - - +
485G LYS* 1.3 87.0 + - + +
487G TYR* 2.8 28.2 + - - +
488G MET* 3.6 33.1 + - - +
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Residues in contact with LYS 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G GLY 5.3 1.6 - - - -
151G GLU* 5.6 1.5 + - - -
153G TRP* 3.6 39.4 - - + +
482G ASP* 3.0 42.7 + - + +
483G SER 3.0 0.8 + - - -
484G TRP* 1.3 111.5 - - + +
486G GLN* 1.3 58.0 + - + +
488G MET 2.9 26.0 + - - +
490G ARG* 5.1 1.8 - - - +
482H ASP* 2.6 30.2 + - - +
485H LYS* 3.6 2.8 - - - +
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Residues in contact with GLN 486 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G VAL* 4.5 5.0 - - - +
240G LEU* 3.5 21.2 - - + +
263G ARG* 4.6 5.7 - - - -
264G LYS 5.5 2.2 - - - +
265G LEU* 3.6 25.8 - - + +
475G GLY 4.7 1.0 - - - +
476G GLY* 3.6 5.4 - - - -
477G ARG* 2.7 54.4 + - - +
482G ASP 5.6 0.2 - - - +
483G SER* 2.9 31.0 + - - +
485G LYS* 1.3 77.9 - - + +
487G TYR* 1.3 59.2 + - + +
488G MET 3.3 4.3 + - - +
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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