Contacts of the helix formed by residues 236 - 245 (chain B) in PDB entry 4OG2
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 PHE 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B PHE* 3.6 39.9 - + + -
233B ASP* 3.5 36.1 - - + -
234B THR 4.1 6.5 - - - -
235B ASP* 1.3 74.9 - - - +
237B GLN* 1.3 65.1 + - - +
238B SER 3.3 2.6 + - - -
239B GLN* 3.4 14.5 + - + +
240B ALA* 3.0 23.7 + - - +
259B ASP* 3.8 32.5 - - + -
262B ASN* 4.0 11.9 - - + -
263B LEU* 3.6 38.6 - - + -
266B GLN* 2.9 30.6 + - + +
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Residues in contact with GLN 237 (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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235B ASP* 2.9 24.7 + - - +
236B PHE* 1.3 76.9 - - - +
238B SER* 1.3 58.4 + - - +
240B ALA* 3.8 0.5 - - - +
241B THR* 2.9 36.8 + - - +
266B GLN* 3.0 39.2 + - - +
269B GLU* 4.9 3.4 + - - +
270B LEU* 3.6 32.1 - - + +
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Residues in contact with SER 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASP* 4.7 0.6 + - - -
237B GLN* 1.3 78.5 - - - +
239B GLN* 1.3 71.3 + - - +
241B THR* 3.8 4.1 - - - -
242B ASN* 2.9 40.7 + - - +
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Residues in contact with GLN 239 (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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197B PHE* 3.7 25.5 - - + -
227B GLN* 3.4 27.3 - - + +
228B LYS 2.9 28.6 + - - +
229B PHE* 3.8 17.6 - - + +
233B ASP* 4.5 5.3 + - - -
235B ASP 4.2 4.1 + - - +
236B PHE* 3.5 26.4 - - + +
238B SER* 1.3 85.7 + - - +
240B ALA* 1.3 63.3 + - - +
242B ASN* 3.3 4.4 + - - +
243B ALA* 3.1 18.5 + - - +
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Residues in contact with ALA 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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197B PHE* 4.0 4.2 - - - -
236B PHE* 3.0 19.8 + - + +
239B GLN* 1.3 76.1 - - - +
241B THR* 1.3 58.2 + - - +
243B ALA* 3.3 3.3 + - - +
244B ILE* 2.9 36.2 + - + +
263B LEU* 4.8 4.7 - - + -
266B GLN 4.8 1.1 - - - -
267B LEU* 3.7 33.8 - - + +
270B LEU* 3.7 22.2 - - + -
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Residues in contact with THR 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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237B GLN* 2.9 19.9 + - - +
238B SER* 3.8 4.7 - - - -
240B ALA* 1.3 74.5 - - - +
242B ASN* 1.3 66.8 + - - +
244B ILE* 3.3 8.0 + - + +
245B ASN* 3.0 44.5 + - - +
270B LEU* 3.9 17.5 - - - +
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Residues in contact with ASN 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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227B GLN* 3.2 34.9 + - - +
238B SER* 2.9 28.2 + - - +
239B GLN* 3.4 7.9 - - - +
241B THR* 1.3 78.6 - - - +
243B ALA* 1.3 64.0 + - - +
245B ASN* 3.7 10.0 + - - +
246B LEU* 3.7 19.5 + - - +
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Residues in contact with ALA 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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195B ALA* 3.9 16.3 - - + +
197B PHE* 3.5 36.1 - - + -
225B THR* 4.1 15.7 - - + +
227B GLN* 4.8 0.2 - - + -
239B GLN 3.1 3.4 + - - +
240B ALA 3.7 3.1 - - - +
241B THR 3.2 0.2 - - - -
242B ASN* 1.3 79.0 - - - +
244B ILE* 1.3 65.7 + - - +
246B LEU* 3.0 15.1 + - - +
248B PRO* 3.1 18.9 - - + +
251B VAL* 5.3 0.9 - - + -
267B LEU* 5.0 3.4 - - + -
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Residues in contact with ILE 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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240B ALA 2.9 25.5 + - - +
241B THR* 3.3 7.2 + - + +
243B ALA* 1.3 76.0 - - - +
245B ASN* 1.3 66.7 + - - +
247B LYS* 2.9 30.6 + - + +
248B PRO* 4.2 5.8 - - + -
267B LEU* 3.8 21.8 - - + +
270B LEU* 3.6 42.6 - - + +
271B GLY 5.5 1.1 - - - -
272B TYR* 3.9 27.1 - - + +
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Residues in contact with ASN 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 THR* 3.0 39.0 + - - +
242B ASN* 4.1 5.9 - - - +
243B ALA 3.2 0.2 - - - -
244B ILE* 1.3 83.3 - - - +
246B LEU* 1.3 60.2 + - - +
247B LYS* 3.2 10.3 + - - +
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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