Contacts of the helix formed by residues 226 - 231 (chain B) in PDB entry 4BEJ
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ALA* 5.1 5.4 + - - +
189B THR 4.6 0.4 + - - -
191B MET* 3.5 36.1 - - + +
214B ILE* 3.9 8.9 - - - +
220B MET* 4.9 2.8 - - - +
225B ASP* 1.3 72.6 + - - +
227B MET* 1.3 65.5 + - - +
228B ASP* 3.1 8.7 - - - +
229B VAL* 3.1 39.5 - - + +
230B LEU* 3.5 2.8 + - - +
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Residues in contact with MET 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B MET* 3.7 41.8 - - + +
221B ASP* 5.1 6.5 - - - +
222B ALA* 5.3 12.6 - - + -
224B THR 4.3 8.5 + - - +
225B ASP* 3.6 5.2 - - - +
226B ALA* 1.3 75.7 - - - +
228B ASP* 1.3 65.5 + - - +
230B LEU* 3.4 13.4 + - - +
231B MET* 3.5 22.4 + - + +
233B ARG* 4.5 18.4 - - - +
273B TYR* 6.0 4.0 - - + -
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Residues in contact with ASP 228 (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 ASP* 3.1 30.9 - - - +
226B ALA* 3.1 6.9 - - - +
227B MET* 1.3 82.5 - - - +
229B VAL* 1.3 60.6 + - - +
231B MET* 3.4 4.6 + - - +
232B GLY 3.1 6.4 + - - -
233B ARG* 2.7 66.7 + - + +
234B VAL* 3.6 9.1 + - - +
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Residues in contact with VAL 229 (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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191B MET* 4.6 5.2 - - + -
214B ILE* 3.7 16.2 - - + -
226B ALA* 3.1 34.1 - - + +
228B ASP* 1.3 77.9 + - - +
230B LEU* 1.3 64.4 + - - +
231B MET 3.0 2.0 - - - -
232B GLY* 2.6 23.1 + - - +
234B VAL 3.0 25.4 - - - +
235B ILE* 4.1 0.4 - - - -
236B PRO* 3.5 22.9 - - + -
241B ILE* 3.5 31.9 - - + +
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Residues in contact with LEU 230 (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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214B ILE* 4.4 14.6 - - + -
217B LEU* 3.7 30.3 - - + -
220B MET* 4.7 9.4 - - + -
226B ALA 4.2 5.4 - - - +
227B MET 3.4 10.0 + - - +
228B ASP 3.4 0.6 - - - -
229B VAL* 1.3 83.5 - - - +
231B MET* 1.3 60.6 + - + +
232B GLY 3.6 0.2 + - - -
241B ILE* 4.9 14.1 - - + +
243B GLY* 4.7 2.9 - - - +
276B LEU* 3.7 37.2 - - + -
279B ARG* 3.8 19.8 + - + +
280B ASN* 3.7 31.0 - - - +
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Residues in contact with MET 231 (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 MET* 3.5 20.1 + - + +
228B ASP 3.4 8.2 + - - +
229B VAL 3.0 0.8 - - - -
230B LEU* 1.3 80.2 - - + +
232B GLY* 1.3 57.5 + - - +
233B ARG* 3.2 39.4 + - - +
275B SER* 4.4 10.8 - - - +
276B LEU* 3.6 38.1 - - + -
279B ARG* 4.3 10.7 + - - +
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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