Contacts of the helix formed by residues 232 - 243 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88L TYR* 5.5 9.2 - - + -
89L ASP* 4.4 17.0 - - - +
146L LEU* 4.9 13.7 - - + +
230L GLU* 3.1 17.7 - - + +
231L ALA* 1.3 75.0 - - - +
233L ASP* 1.3 59.7 + - - +
234L ALA 3.1 9.8 + - - -
235L PRO* 3.2 14.7 - - - +
236L LYS* 4.0 9.9 + - - +
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Residues in contact with ASP 233 (chain L).
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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228L GLY* 4.3 16.2 - - - -
229L GLU* 3.7 13.3 + - - +
230L GLU* 3.2 36.2 + - - +
232L ALA* 1.3 79.7 - - - +
234L ALA* 1.3 55.9 + - - +
235L PRO 3.7 0.2 - - - -
236L LYS* 3.7 25.6 + - + +
237L ILE* 3.2 29.5 + - - +
255L PHE* 5.4 6.0 - - + -
258L HIS* 5.6 1.7 + - - -
500L B13 5.6 0.2 - - - -
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Residues in contact with ALA 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L VAL* 3.9 22.4 - - + -
147L LEU* 3.5 21.9 - - + +
177L MET* 4.3 2.9 - - - +
179L THR* 5.3 2.9 - - + -
230L GLU 4.2 1.0 + - - -
231L ALA 3.4 12.0 + - - +
232L ALA 3.1 1.4 - - - -
233L ASP* 1.3 76.3 - - - +
235L PRO* 1.4 69.5 - - + +
237L ILE* 2.9 25.2 - - - +
238L ALA* 3.5 7.6 + - - +
500L B13 4.5 13.0 - - + +
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Residues in contact with PRO 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L LEU* 3.2 36.3 - - + +
147L LEU* 3.5 8.0 - - + -
150L ASN* 3.3 36.6 - - + +
152L TYR* 4.9 4.0 - - + -
231L ALA 3.7 7.0 - - - +
232L ALA 3.2 14.4 - - - +
234L ALA* 1.4 92.6 - - + +
236L LYS* 1.3 63.3 + - - +
238L ALA* 3.0 16.2 + - + +
239L ASP* 3.0 21.7 + - - +
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Residues in contact with LYS 236 (chain L).
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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232L ALA 4.0 9.4 - - - +
233L ASP* 3.7 26.8 + - - +
234L ALA 3.3 0.2 - - - -
235L PRO* 1.3 79.9 - - - +
237L ILE* 1.3 59.7 + - - +
239L ASP* 4.0 13.9 + - - +
240L ALA* 4.1 4.5 + - - +
255L PHE* 3.8 26.3 - - + -
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Residues in contact with ILE 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L MET* 3.7 28.2 - - + +
206L PRO* 5.9 0.2 - - + -
208L ALA* 4.5 12.1 - - + -
226L VAL* 3.5 30.7 - - + -
227L TYR 5.9 1.1 - - - +
233L ASP 3.2 16.0 + - - +
234L ALA* 2.9 29.4 - - - +
236L LYS* 1.3 74.8 - - - +
238L ALA* 1.3 62.8 + - - +
239L ASP 3.4 0.2 - - - -
240L ALA* 3.4 16.4 - - - +
241L ILE* 3.8 5.8 - - + +
251L LEU* 4.7 9.2 - - + -
255L PHE* 3.5 43.5 - - + -
500L B13 6.4 0.4 - - + -
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Residues in contact with ALA 238 (chain L).
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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126L VAL* 4.9 5.6 - - + -
147L LEU* 6.0 1.3 - - + -
152L TYR* 3.3 27.4 - - + +
176L ILE* 4.3 6.6 - - + +
177L MET* 3.8 25.6 - - - -
234L ALA 3.5 5.1 + - - +
235L PRO* 3.0 9.0 + - + +
237L ILE* 1.3 76.3 - - - +
239L ASP* 1.3 63.8 + - - +
240L ALA 3.1 2.0 - - - -
241L ILE* 3.2 18.5 + - - +
242L ILE* 3.4 13.3 + - - +
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Residues in contact with ASP 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L LYS* 3.4 11.1 + - - -
150L ASN* 5.0 6.3 - - - +
152L TYR* 2.4 35.8 + - - -
235L PRO* 3.0 18.3 - - - +
236L LYS* 4.1 9.1 - - - +
237L ILE 3.4 0.2 - - - -
238L ALA* 1.3 76.2 - - - +
240L ALA* 1.3 57.4 + - - +
242L ILE* 3.2 11.8 + - + +
243L ALA* 3.0 24.8 + - - +
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Residues in contact with ALA 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L LYS 4.1 2.1 + - - +
237L ILE 3.4 15.3 + - - +
238L ALA 3.1 0.6 - - - -
239L ASP* 1.3 77.6 - - - +
241L ILE* 1.3 58.6 + - - +
243L ALA* 3.3 14.1 + - - +
245L THR* 3.1 31.9 + - - +
251L LEU* 3.5 20.9 - - + -
254L LYS* 6.1 2.0 - - + -
255L PHE* 4.1 19.5 - - + -
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Residues in contact with ILE 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L ILE* 4.0 41.5 - - + +
177L MET* 4.0 9.4 - - + -
206L PRO* 3.4 26.5 - - + -
237L ILE 3.8 14.8 - - - +
238L ALA* 3.2 18.8 + - - +
240L ALA* 1.3 77.2 - - - +
242L ILE* 1.3 57.5 + - - +
243L ALA 3.1 0.4 - - - -
244L GLY* 3.0 19.9 + - - -
245L THR 3.4 18.8 + - - +
246L THR* 4.1 25.1 + - + +
251L LEU* 3.8 7.2 - - + -
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Residues in contact with ILE 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L LYS* 3.2 43.5 - - + +
152L TYR* 3.4 17.5 - - + +
176L ILE* 4.1 12.6 - - + -
238L ALA 3.4 15.5 - - - +
239L ASP* 3.2 12.5 + - + +
241L ILE* 1.3 75.7 - - - +
243L ALA* 1.3 55.6 + - - +
244L GLY 3.2 2.9 + - - -
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Residues in contact with ALA 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239L ASP 3.0 11.8 + - - +
240L ALA* 3.5 14.8 - - - +
241L ILE 3.1 0.8 - - - -
242L ILE* 1.3 75.6 - - - +
244L GLY* 1.3 60.2 + - - +
245L THR* 3.5 8.0 + - - +
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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