Contacts of the helix formed by residues 239 - 248 (chain B) in PDB entry 1O94
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 ASP 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LEU* 5.3 2.7 - - + -
182B PRO* 4.8 3.6 - - - +
195B LEU* 3.9 23.1 - - + +
198B ARG* 2.8 43.6 + - - +
223B PHE* 5.2 0.4 - - - -
233B GLN 5.1 4.5 - - - +
234B ILE* 4.4 22.9 - - + +
235B GLU 3.2 5.1 + - - +
238B VAL* 1.3 91.7 - - - +
240B GLY* 1.3 58.8 + - - +
241B GLN 3.7 0.2 - - - -
242B LYS 3.3 1.6 + - - -
243B PHE* 2.7 32.8 + - - +
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.5 16.0 - - - -
225B VAL* 3.9 24.5 - - - -
234B ILE* 4.3 1.4 - - - +
235B GLU 3.1 12.4 + - - -
236B ALA 3.6 6.3 + - - -
238B VAL 3.5 0.8 - - - -
239B ASP* 1.3 76.7 - - - +
241B GLN* 1.3 61.7 + - - +
243B PHE 3.2 1.0 + - - -
244B VAL* 3.0 27.1 + - - +
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B VAL* 4.5 2.4 - - + +
236B ALA 3.0 20.2 + - - +
237B GLU* 4.0 26.7 - - - +
238B VAL 4.8 0.4 + - - -
240B GLY* 1.3 70.8 - - - +
242B LYS* 1.3 65.0 + - + +
244B VAL* 3.4 5.3 + - - +
245B GLU* 3.1 29.5 + - - +
285B LEU* 3.1 51.5 + - + +
286B VAL* 5.5 0.9 - - - +
288B GLN* 4.1 12.7 - - - +
289B VAL* 3.8 23.7 - - + +
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 3.5 25.4 - - + -
237B GLU 5.8 0.4 - - - +
238B VAL 3.7 15.7 + - - +
239B ASP 3.3 3.9 + - - +
240B GLY 3.1 0.8 - - - -
241B GLN* 1.3 83.5 - - + +
243B PHE* 1.3 62.9 + - - +
245B GLU* 3.4 18.6 + - - +
246B MET* 3.1 26.9 + - + +
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 4.0 16.6 - - + -
195B LEU* 4.2 3.6 - - + +
199B ALA* 3.7 36.8 - - + -
202B TRP* 3.4 52.5 - + + -
203B LEU* 3.8 16.4 - - + -
221B THR* 5.5 0.2 - - + -
223B PHE* 3.8 25.8 - + + -
239B ASP 2.7 21.4 + - - +
240B GLY 3.7 3.4 - - - +
242B LYS* 1.3 73.5 - - - +
244B VAL* 1.3 65.4 + - - +
246B MET* 3.0 9.2 + - + +
247B ALA* 3.0 29.7 + - + +
254B TRP* 3.9 20.2 - + - -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 4.1 17.5 - - + -
240B GLY 3.0 17.4 + - - +
241B GLN* 3.4 9.6 + - - +
243B PHE* 1.3 75.8 - - - +
245B GLU* 1.3 57.2 + - - +
247B ALA 3.3 0.3 + - - -
248B ASP* 2.8 30.7 + - - +
254B TRP* 3.6 24.1 - - + -
286B VAL* 4.1 26.7 - - + -
289B VAL* 3.8 13.7 - - + -
290B SER* 3.7 31.0 - - - -
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B GLN* 3.1 17.6 + - - +
242B LYS* 3.8 20.5 - - - +
244B VAL* 1.3 75.9 - - - +
246B MET* 1.3 63.5 + - + +
248B ASP* 3.7 13.6 + - - +
249B SER 5.1 1.0 + - - -
289B VAL* 3.8 35.3 - - + +
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Residues in contact with MET 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 3.7 33.9 - - + -
196B GLU* 4.1 19.1 - - + +
199B ALA* 4.0 24.7 - - - -
203B LEU* 3.9 24.9 - - + +
242B LYS* 3.1 16.6 + - + +
243B PHE* 3.0 12.1 + - - +
245B GLU* 1.3 77.3 - - + +
247B ALA* 1.3 59.7 + - - +
249B SER* 4.7 7.4 + - - -
250B LEU* 5.1 2.8 - - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B LEU* 3.7 19.5 - - + -
206B LEU* 4.2 10.3 - - + -
243B PHE* 3.0 24.1 + - + +
246B MET* 1.3 75.2 - - - +
248B ASP* 1.3 65.5 + - - +
249B SER 3.2 2.7 - - - -
250B LEU* 2.9 19.0 + - - +
251B VAL* 3.3 11.1 + - - +
254B TRP* 3.7 21.8 - - + -
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B VAL* 2.8 15.6 + - - +
245B GLU* 4.0 10.3 - - - +
246B MET 3.5 1.6 - - - -
247B ALA* 1.3 78.0 - - - +
249B SER* 1.3 58.9 - - - +
251B VAL* 3.3 14.5 - - - +
254B TRP* 2.9 14.0 + - - -
289B VAL 4.5 2.2 - - - +
290B SER* 2.6 30.5 + - - -
291B LYS* 2.8 33.7 + - - +
292B LYS* 2.8 32.5 + - - +
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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