Contacts of the helix formed by residues 232 - 239 (chain F) in PDB entry 2I2X
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 ALA 232 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88F TYR* 5.3 9.8 - - + -
89F ASP* 4.8 17.7 - - - +
146F LEU* 4.2 18.4 - - + +
230F GLU* 3.2 16.4 - - + +
231F ALA* 1.3 77.6 - - - +
233F ASP* 1.3 60.8 + - - +
234F ALA 3.2 1.3 - - - -
235F PRO* 3.2 18.6 - - - +
236F LYS* 3.7 14.0 + - + +
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Residues in contact with ASP 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F TYR 5.5 0.4 - - - +
228F GLY* 4.0 15.1 - - - -
229F GLU* 3.5 15.6 + - - +
230F GLU* 3.2 38.0 + - - +
231F ALA 3.0 1.4 - - - -
232F ALA* 1.3 79.8 - - - +
234F ALA* 1.3 57.5 + - - +
235F PRO 3.8 0.2 - - - -
236F LYS* 3.9 24.8 + - - +
237F ILE* 3.2 27.7 + - - +
255F PHE* 4.9 8.5 - - + -
258F HIS* 5.2 3.8 - - - -
500F B13 5.2 2.0 - - - -
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Residues in contact with ALA 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F VAL* 3.5 19.7 - - + -
147F LEU* 3.5 20.0 - - + +
177F MET* 4.3 3.1 - - - +
179F THR* 4.8 4.0 - - + -
230F GLU 4.3 0.8 + - - -
231F ALA 3.0 13.8 + - - +
233F ASP* 1.3 77.8 - - - +
235F PRO* 1.4 68.6 - - + +
236F LYS 3.3 0.2 - - - -
237F ILE* 3.2 10.9 - - - +
238F ALA* 3.1 21.1 + - - +
500F B13 4.4 17.0 - - + +
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Residues in contact with PRO 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F LEU* 3.7 30.7 - - + +
147F LEU* 3.4 18.4 - - + -
150F ASN* 3.5 32.3 - - + +
152F TYR* 4.8 1.8 - - + -
231F ALA 3.5 7.0 - - - +
232F ALA* 3.2 14.6 - - - +
234F ALA* 1.4 92.8 - - + +
236F LYS* 1.3 63.2 + - - +
238F ALA* 3.0 16.1 + - + +
239F ASP* 3.0 22.7 + - - +
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Residues in contact with LYS 236 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232F ALA 3.7 14.3 + - - +
233F ASP* 3.9 24.0 + - - +
235F PRO* 1.3 80.8 - - - +
237F ILE* 1.3 60.5 + - - +
239F ASP* 3.6 11.7 + - - +
240F ALA* 3.8 6.1 + - - +
255F PHE* 3.4 34.6 - - + -
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Residues in contact with ILE 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F MET* 3.5 28.8 - - + +
206F PRO* 5.6 0.9 - - + -
208F ALA* 4.1 12.3 - - + -
226F VAL* 3.6 33.2 - - + -
233F ASP 3.2 15.7 + - - +
234F ALA* 3.2 20.6 - - - +
236F LYS* 1.3 77.1 - - - +
238F ALA* 1.3 63.5 + - - +
240F ALA* 3.2 15.2 + - - +
241F ILE* 3.8 4.3 - - - +
251F LEU* 3.9 21.3 - - + -
255F PHE* 3.4 38.5 - - + -
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F VAL* 5.0 4.5 - - + -
147F LEU* 5.3 2.9 - - + -
152F TYR* 2.9 36.1 + - + -
176F ILE* 3.8 6.6 - - + +
177F MET* 3.7 18.6 - - - -
234F ALA 3.1 15.8 + - - +
235F PRO* 3.0 14.0 + - + +
237F ILE* 1.3 77.0 - - - +
239F ASP* 1.3 57.2 + - - +
240F ALA 3.3 1.0 + - - -
241F ILE* 3.6 12.0 + - - +
242F ILE* 3.6 11.1 - - - +
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Residues in contact with ASP 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F LYS* 3.1 24.4 + - - +
150F ASN* 4.1 10.4 - - - +
152F TYR* 2.7 29.1 + - - -
235F PRO 3.0 19.8 + - - +
236F LYS* 3.6 7.4 + - - +
237F ILE 3.2 0.4 - - - -
238F ALA* 1.3 74.3 - - - +
240F ALA* 1.3 59.2 + - - +
241F ILE 3.3 2.0 - - - -
242F ILE* 3.7 8.8 + - - +
243F ALA* 3.1 22.9 + - - +
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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