Contacts of the strand formed by residues 232 - 236 (chain F) in PDB entry 1I43
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 LEU 232 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F LEU* 4.6 21.8 - - + -
202F ASN 3.1 18.8 + - - +
203F LEU* 3.1 15.3 - - + -
204F PHE* 2.5 35.7 + - - +
227F HIS* 5.3 0.9 - - + +
230F GLY 5.2 2.9 - - - +
231F ALA* 1.3 77.7 - - - +
233F VAL* 1.3 59.3 - - - +
253F ASP* 3.2 29.4 - - + +
254F LEU* 5.1 0.7 - - + -
280F LEU* 4.1 32.5 - - + -
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Residues in contact with VAL 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F LEU* 4.7 1.3 - - - -
204F PHE* 3.5 7.6 - - + +
219F ILE* 5.6 0.4 - - + -
222F VAL* 4.4 10.8 - - + -
223F SER* 3.9 25.8 - - - +
226F CYS* 3.5 35.0 - - + -
227F HIS* 4.4 5.4 - - - +
232F LEU* 1.3 77.6 - - - +
234F CYS* 1.3 63.6 + - - +
235F ILE* 4.0 26.7 - - + -
252F ALA* 4.1 5.6 - - - -
253F ASP* 2.7 42.5 + - - +
254F LEU* 3.1 9.1 + - - +
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Residues in contact with CYS 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F MET* 3.4 26.9 - - - -
203F LEU* 3.9 20.2 - - + -
204F PHE 3.0 7.9 + - - +
205F PHE* 3.5 23.5 - - + -
206F THR 3.1 26.0 + - - +
232F LEU 4.2 0.2 - - - -
233F VAL* 1.3 75.0 - - - +
235F ILE* 1.3 68.1 + - - +
254F LEU* 3.3 22.7 - - + +
256F LEU* 3.8 13.5 - - - -
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Residues in contact with ILE 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F PHE* 5.3 1.1 - - + -
206F THR* 3.1 32.1 - - + +
208F SER* 4.2 22.0 - - - +
217F VAL* 5.5 4.0 - - + -
219F ILE* 4.3 23.6 - - + -
222F VAL* 5.6 0.7 - - + -
233F VAL* 4.0 14.4 - - + -
234F CYS* 1.3 79.4 - - - +
236F ASP* 1.3 70.9 + - - +
237F GLY 3.6 3.5 + - - +
245F GLN* 4.6 6.5 - - - +
247F ALA* 4.2 20.0 - - + -
252F ALA* 3.9 21.3 - - + -
254F LEU 3.0 7.1 + - - +
255F VAL* 3.3 3.8 - - - +
256F LEU* 2.9 26.2 + - - +
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Residues in contact with ASP 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F SER* 5.6 0.5 + - - -
205F PHE* 4.4 15.3 - - + -
206F THR 2.9 10.4 + - - +
207F GLU* 3.3 25.5 - - + +
208F SER 3.4 17.2 + - - +
209F PRO 4.4 2.4 - - - +
235F ILE* 1.3 74.1 - - - +
237F GLY* 1.3 57.8 + - - +
238F THR* 2.5 34.1 + - - -
239F PHE* 5.7 0.3 - - - -
256F LEU* 3.1 27.4 - - + +
500F PLP 3.3 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