Contacts of the helix formed by residues 232 - 243 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88P TYR* 5.9 7.1 - - + -
89P ASP* 4.4 16.8 - - - +
146P LEU* 4.5 17.8 - - + +
230P GLU* 3.2 15.0 - - + +
231P ALA* 1.3 76.9 - - - +
233P ASP* 1.3 59.8 + - - +
234P ALA 3.2 0.7 - - - -
235P PRO* 3.2 20.7 - - - +
236P LYS* 3.5 14.8 + - - +
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Residues in contact with ASP 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227P TYR 5.1 1.0 - - - +
228P GLY* 4.0 16.7 - - - -
229P GLU* 3.4 23.7 + - - +
230P GLU* 2.8 28.6 + - - +
232P ALA* 1.3 78.1 - - - +
234P ALA* 1.3 52.8 + - - +
236P LYS* 3.8 17.3 + - - +
237P ILE* 2.5 40.9 + - - +
255P PHE* 4.9 11.0 - - + -
258P HIS* 5.4 3.8 + - - -
500P B13 5.0 0.7 - - - -
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Residues in contact with ALA 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P VAL* 3.8 24.5 - - + +
147P LEU* 3.7 17.4 - - + +
177P MET* 4.1 3.8 - - - +
179P THR* 4.5 3.6 - - + -
230P GLU 4.1 0.8 + - - -
231P ALA 2.9 11.7 + - - +
233P ASP* 1.3 77.7 - - - +
235P PRO* 1.4 57.6 - - + +
237P ILE* 3.1 11.4 - - - +
238P ALA* 2.8 33.8 + - - +
500P B13 4.1 14.6 - - + +
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Residues in contact with PRO 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P LEU* 3.3 31.9 - - + +
147P LEU* 3.4 14.1 - - + -
150P ASN* 3.6 33.2 - - + +
152P TYR* 4.7 0.7 - - + -
231P ALA 3.4 7.6 - - - +
232P ALA 3.2 14.8 - - - +
234P ALA* 1.4 92.5 - - + +
236P LYS* 1.3 58.2 + - - +
238P ALA* 3.8 4.3 - - + -
239P ASP* 2.8 37.9 + - - +
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Residues in contact with LYS 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232P ALA 3.5 15.4 + - - +
233P ASP* 3.8 17.4 + - - +
234P ALA 3.3 0.4 - - - -
235P PRO* 1.3 79.3 - - - +
237P ILE* 1.3 62.2 + - - +
239P ASP* 3.6 5.3 + - - +
240P ALA* 3.4 15.9 + - - +
254P LYS* 5.6 8.3 - - - +
255P PHE* 3.5 31.4 - - + -
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Residues in contact with ILE 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177P MET* 3.2 17.9 - - + -
206P PRO* 5.0 0.4 - - + -
208P ALA* 4.3 12.6 - - + -
226P VAL* 3.8 33.2 - - + -
228P GLY* 5.9 3.6 - - - -
233P ASP* 2.5 38.8 + - + +
234P ALA* 3.1 15.7 - - - +
236P LYS* 1.3 74.7 - - - +
238P ALA* 1.3 63.6 + - - +
240P ALA* 3.3 9.4 + - - +
241P ILE* 3.4 14.0 - - + +
251P LEU* 3.8 35.2 - - + -
255P PHE* 3.7 21.7 - - + -
500P B13 5.2 1.1 - - + +
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Residues in contact with ALA 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P VAL* 5.0 2.5 - - + -
147P LEU* 4.6 4.0 - - + -
152P TYR* 3.1 34.8 + - + -
176P ILE* 4.0 6.6 - - + +
177P MET* 3.5 19.7 - - - +
234P ALA 2.8 21.2 + - - +
235P PRO* 3.3 8.7 + - + +
237P ILE* 1.3 73.0 - - - +
239P ASP* 1.3 61.3 + - - +
241P ILE* 3.3 17.9 + - - +
242P ILE* 3.5 8.3 + - - +
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Residues in contact with ASP 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P LYS* 3.3 18.0 + - - -
150P ASN* 4.5 6.1 - - - +
152P TYR* 2.5 35.1 + - - -
235P PRO* 2.8 27.4 + - - +
236P LYS* 3.6 6.7 + - - +
238P ALA* 1.3 75.1 - - - +
240P ALA* 1.3 56.9 + - - +
242P ILE* 3.2 8.8 + - + +
243P ALA* 3.1 28.1 + - - +
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Residues in contact with ALA 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236P LYS 3.4 11.5 + - - +
237P ILE 3.3 11.6 + - - +
238P ALA 3.2 0.8 - - - -
239P ASP* 1.3 79.4 - - - +
241P ILE* 1.3 57.2 + - - +
243P ALA* 3.8 6.5 + - - +
244P GLY 3.7 3.1 + - - -
245P THR* 3.2 31.6 + - - +
251P LEU* 3.8 18.4 - - + -
254P LYS* 5.6 5.2 - - + -
255P PHE* 4.0 14.6 - - + -
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Residues in contact with ILE 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176P ILE* 4.1 33.0 - - + +
177P MET* 4.0 13.7 - - + -
206P PRO* 3.5 29.4 - - + -
237P ILE* 3.4 17.7 - - + +
238P ALA* 3.3 14.8 - - - +
240P ALA* 1.3 75.0 - - - +
242P ILE* 1.3 62.2 + - - +
244P GLY* 2.9 20.8 + - - -
245P THR 3.3 14.6 - - - +
246P THR* 3.7 23.2 + - + +
251P LEU* 4.0 10.1 - - + -
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Residues in contact with ILE 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P LYS* 3.2 39.0 - - + +
152P TYR* 3.2 26.2 - - + +
176P ILE* 3.8 23.1 - - + -
238P ALA 3.6 2.7 - - - +
239P ASP* 3.2 11.2 - - + +
241P ILE* 1.3 79.5 - - - +
243P ALA* 1.3 58.0 + - - +
244P GLY* 3.1 5.9 + - - -
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Residues in contact with ALA 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239P ASP 3.1 14.3 + - - +
240P ALA* 4.1 8.7 - - - +
241P ILE 3.3 0.4 - - - -
242P ILE* 1.3 76.3 - - - +
244P GLY* 1.3 55.9 + - - +
245P THR* 3.7 5.9 + - - +
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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