Contacts of the helix formed by residues 233 - 239 (chain B) in PDB entry 5Y9F
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 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ILE* 3.0 22.9 + - + +
167B GLU* 4.0 25.7 - - + +
190B LEU* 5.8 1.0 - - - +
192B ASN* 2.7 35.4 + - - +
231B TYR 3.3 2.2 + - - -
232B PRO* 1.3 67.3 - - - +
234B TYR* 1.3 60.7 + - - +
235B LEU* 3.7 10.6 + - - +
236B GLN* 3.2 29.6 + - + +
237B MET* 2.9 32.2 + - - +
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Residues in contact with TYR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 4.2 11.1 - - + +
158B ILE* 4.2 6.1 - - + -
231B TYR* 3.2 41.2 + + - -
232B PRO* 3.0 46.1 + - + +
233B ASP* 1.3 72.3 - - - +
235B LEU* 1.3 65.5 + - + +
237B MET* 4.1 11.0 - - + -
238B SER* 2.9 35.3 + - - -
246B MET* 4.3 4.8 - - + +
249B CYS* 3.6 32.5 - - - -
251B ARG* 3.7 33.8 - - + +
253B GLU* 4.8 0.5 + - - -
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Residues in contact with LEU 235 (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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233B ASP* 3.2 9.7 + - - +
234B TYR* 1.3 85.9 - - + +
236B GLN* 1.3 59.9 + - - +
238B SER* 3.4 6.0 + - - -
239B ALA* 3.2 24.9 + - - +
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Residues in contact with GLN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 3.4 35.9 - - - +
192B ASN* 4.5 9.8 + - - +
233B ASP* 3.2 28.1 + - - +
235B LEU* 1.3 78.7 - - - +
237B MET* 1.3 71.1 + - - +
239B ALA* 3.3 6.6 + - - +
240B ASP* 3.1 23.2 + - - +
245B SER* 5.4 0.3 + - - -
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Residues in contact with MET 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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158B ILE* 3.7 25.1 - - + -
164B ALA* 3.9 11.7 - - - -
165B ILE* 3.3 39.9 - - + +
232B PRO* 4.3 0.2 - - + -
233B ASP 2.9 31.3 + - - +
234B TYR* 4.1 5.6 - - + +
236B GLN* 1.3 87.8 + - - +
238B SER* 1.3 60.9 + - - +
240B ASP* 3.3 20.5 - - - +
243B GLY* 5.0 0.9 - - - -
245B SER* 4.0 15.4 - - - -
246B MET* 3.8 36.4 - - + +
317B GLN* 3.6 12.0 + - - -
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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
----------------------------------------------------------
234B TYR* 2.9 20.5 + - - -
235B LEU* 3.4 7.3 + - - -
237B MET* 1.3 76.3 - - - +
239B ALA* 1.3 62.2 + - - +
240B ASP 3.2 7.2 + - - +
246B MET* 3.6 9.5 - - - +
317B GLN* 3.6 25.0 + - - +
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Residues in contact with ALA 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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235B LEU 3.2 17.4 + - - +
236B GLN* 3.3 6.7 + - - +
238B SER* 1.3 77.4 + - - +
240B ASP* 1.3 65.9 + - - +
241B ALA* 3.6 1.7 + - - -
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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