Contacts of the helix formed by residues 259 - 263 (chain W) in PDB entry 1G3I
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 259 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54W LEU* 5.2 2.5 - - + -
83W ALA* 5.0 2.0 - - - -
256W ILE* 4.4 24.5 - - + +
257W ASP 4.3 0.7 - - - -
258W GLU* 1.3 71.0 - - - +
260W ASP* 1.3 73.0 + - - +
261W LYS 2.8 3.1 - - - -
262W ILE* 2.7 51.2 + - + +
263W CYS* 4.1 0.8 - - - -
282W LEU* 6.1 1.1 - - + -
307W ALA* 4.1 21.3 - - + -
308W SER 3.0 22.1 + - - +
309W GLY* 4.6 0.2 - - - -
311W PHE* 3.5 23.8 - - + -
319W LEU* 4.6 15.7 - - + -
323W LEU* 4.5 19.7 - - + -
327W LEU* 5.2 3.8 - - + -
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Residues in contact with ASP 260 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258W GLU* 3.9 7.1 - - - +
259W ILE* 1.3 80.5 + - - +
261W LYS* 1.3 72.2 + - - +
262W ILE 2.6 12.5 + - - -
263W CYS* 2.9 26.1 + - - +
309W GLY* 3.0 26.3 - - - -
310W ALA* 3.3 9.2 + - - +
311W PHE* 3.1 43.5 + - + +
312W GLN* 5.1 3.8 + - - -
313W VAL* 4.6 19.3 - - + +
314W ALA* 5.1 3.6 - - + +
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Residues in contact with LYS 261 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276V GLU* 5.4 5.1 + - - -
280V ARG* 3.6 33.4 - - - +
82W GLU* 5.2 0.9 - - - +
83W ALA* 5.5 4.9 - - + -
258W GLU* 4.0 31.6 - - + +
259W ILE 2.7 4.4 + - - -
260W ASP* 1.3 87.9 - - - +
262W ILE* 1.3 62.3 + - + +
263W CYS 3.6 0.9 - - - -
275W ARG* 3.7 26.8 + - - +
312W GLN* 5.3 9.0 - - - +
313W VAL* 6.5 1.3 - - + -
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Residues in contact with ILE 262 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83W ALA* 3.4 34.3 - - + -
256W ILE* 6.1 0.4 - - + -
259W ILE* 2.7 43.0 + - + +
260W ASP 2.6 5.7 + - - -
261W LYS* 1.3 78.9 - - + +
263W CYS* 1.3 59.5 + - - -
264W LYS 4.2 0.3 + - - -
275W ARG* 2.6 40.7 - - + +
276W GLU* 4.3 0.5 - - - -
278W VAL* 4.4 15.0 - - + -
279W GLN* 3.0 51.0 - - + +
282W LEU* 5.4 6.3 - - + -
323W LEU* 5.7 0.4 - - + -
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Residues in contact with CYS 263 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259W ILE 4.1 0.4 - - - -
260W ASP* 2.9 32.9 + - - +
261W LYS 3.6 0.4 - - - -
262W ILE* 1.3 82.0 - - - +
264W LYS* 1.3 65.6 + - - +
265W LYS 3.3 10.6 + - - +
269W SER* 4.6 0.3 + - - -
275W ARG* 4.4 15.3 + - - -
279W GLN* 4.1 2.0 - - - -
311W PHE* 4.4 7.6 - - - -
314W ALA* 3.9 23.1 - - + -
315W ARG 4.9 0.7 - - - -
318W ASP* 3.5 14.1 - - + +
319W LEU* 3.2 34.1 - - - -
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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