Contacts of the helix formed by residues 232 - 243 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236I LYS* 6.5 0.7 - - - -
88J TYR* 4.4 15.3 + - + -
89J ASP* 4.7 18.4 - - - +
146J LEU* 3.7 24.7 - - + +
230J GLU* 3.2 11.1 - - + +
231J ALA* 1.3 75.2 - - - +
233J ASP* 1.3 65.5 + - - +
234J ALA 3.2 0.2 - - - -
235J PRO* 3.3 8.7 - - - +
236J LYS* 3.3 22.4 + - + +
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Residues in contact with ASP 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228J GLY* 3.9 17.7 - - - -
229J GLU* 3.4 15.4 + - - +
230J GLU* 3.0 37.8 + - - +
232J ALA* 1.3 80.1 - - - +
234J ALA* 1.3 56.4 + - - +
236J LYS* 3.7 21.0 + - - +
237J ILE* 3.0 31.6 + - - +
255J PHE* 4.4 13.4 - - + -
258J HIS* 5.7 0.7 - - - -
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Residues in contact with ALA 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J VAL* 4.0 21.1 - - + -
147J LEU* 3.8 9.4 - - + +
177J MET* 4.2 2.8 - - - +
179J THR* 4.8 3.8 - - + -
208J ALA* 5.2 0.4 - - + -
230J GLU 4.2 0.8 + - - -
231J ALA 3.2 9.9 + - - +
233J ASP* 1.3 75.3 - - - +
235J PRO* 1.4 72.0 - - + +
237J ILE* 3.1 12.2 - - - +
238J ALA* 3.1 22.2 + - - +
500J B13 4.0 25.2 - - + +
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Residues in contact with PRO 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J VAL 5.5 0.2 - - - +
146J LEU* 3.4 35.2 - - + +
147J LEU* 3.5 18.4 - - + -
150J ASN* 3.7 32.1 - - + +
152J TYR* 5.0 1.6 - - + -
231J ALA 3.3 14.1 - - - +
232J ALA* 3.3 10.8 - - - +
234J ALA* 1.4 91.4 - - + +
236J LYS* 1.3 54.6 + - - +
238J ALA* 3.1 3.9 + - + +
239J ASP* 2.9 36.8 + - - -
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Residues in contact with LYS 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J ASP* 4.7 16.8 - - - +
232J ALA* 3.3 20.9 + - + +
233J ASP* 3.7 20.7 + - - +
235J PRO* 1.3 78.7 - - - +
237J ILE* 1.3 58.4 + - - +
239J ASP* 3.9 8.8 + - - +
240J ALA* 3.8 12.6 + - - +
255J PHE* 3.2 33.4 - - + -
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Residues in contact with ILE 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J MET* 3.5 22.4 - - + -
208J ALA* 4.3 10.3 - - + -
226J VAL* 3.6 31.4 - - + -
233J ASP 3.0 26.5 + - - +
234J ALA* 3.1 20.0 - - - +
236J LYS* 1.3 74.4 - - - +
238J ALA* 1.3 62.3 + - - +
239J ASP 3.3 0.4 - - - -
240J ALA* 3.4 7.8 + - - +
241J ILE* 3.2 16.8 + - - +
251J LEU* 3.6 25.1 - - + -
255J PHE* 3.4 37.2 - - + -
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Residues in contact with ALA 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J VAL* 4.7 2.9 - - + -
147J LEU* 4.4 6.5 - - + -
152J TYR* 3.2 30.2 + - + -
176J ILE* 4.0 7.1 - - + +
177J MET* 3.6 19.5 - - - -
234J ALA 3.1 17.1 + - - +
235J PRO* 3.1 7.6 + - + +
237J ILE* 1.3 75.9 - - - +
239J ASP* 1.3 64.8 + - - +
241J ILE* 3.3 7.6 + - - +
242J ILE* 3.2 19.9 + - - +
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Residues in contact with ASP 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J LYS* 3.4 15.0 + - - +
150J ASN* 4.5 10.3 - - - +
152J TYR* 2.5 36.5 + - - -
235J PRO 2.9 18.8 + - - +
236J LYS* 4.0 9.2 - - - +
238J ALA* 1.3 74.3 - - - +
240J ALA* 1.3 59.9 + - - +
242J ILE* 3.6 5.3 + - - +
243J ALA* 3.1 28.2 + - - +
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Residues in contact with ALA 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236J LYS 3.8 10.0 + - - +
237J ILE 3.4 11.4 + - - +
238J ALA 3.2 0.2 - - - -
239J ASP* 1.3 77.2 - - - +
241J ILE* 1.3 62.1 + - - +
243J ALA* 3.5 7.1 + - - +
244J GLY 3.3 5.2 + - - -
245J THR* 2.9 31.5 + - - +
251J LEU* 3.6 19.5 - - + -
254J LYS* 5.4 10.5 - - + +
255J PHE* 4.2 11.9 - - + -
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Residues in contact with ILE 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J ILE* 4.0 34.3 - - + +
177J MET* 3.6 22.0 - - + -
206J PRO* 3.7 8.7 - - + -
237J ILE 3.2 19.7 - - - +
238J ALA* 3.3 8.9 + - - +
240J ALA* 1.3 75.5 - - - +
242J ILE* 1.3 56.4 + - - +
244J GLY* 2.8 24.6 + - - -
245J THR 3.5 12.2 + - - +
246J THR* 4.5 19.1 + - + +
251J LEU* 3.4 32.1 - - + -
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Residues in contact with ILE 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J LYS* 2.9 44.6 - - + +
152J TYR* 3.2 27.1 - - + +
176J ILE* 3.8 28.3 - - + -
238J ALA 3.2 4.0 + - - +
239J ASP* 3.8 9.9 - - - +
241J ILE* 1.3 77.2 - - - +
243J ALA* 1.3 58.3 + - - +
244J GLY 3.3 1.0 + - - -
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Residues in contact with ALA 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239J ASP 3.1 17.6 + - - +
240J ALA* 3.7 8.3 - - - +
241J ILE 3.1 0.6 - - - -
242J ILE* 1.3 76.0 - - + +
244J GLY* 1.3 55.7 + - - +
245J THR* 3.9 2.0 + - - +
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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