Contacts of the strand formed by residues 232 - 236 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 4.4 23.6 - - + +
202C ASN 3.0 17.9 + - - +
203C LEU* 3.7 14.6 - - + -
204C PHE* 2.5 35.7 + - - +
227C HIS* 5.1 1.1 - - + +
230C GLY 5.3 2.0 - - - +
231C ALA* 1.3 77.4 - - - +
233C VAL* 1.3 60.5 + - - +
253C ASP* 3.1 31.4 - - + +
254C LEU* 4.8 1.8 - - + -
280C LEU* 4.0 31.6 - - + -
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 5.0 0.9 - - - -
204C PHE* 3.4 8.5 - - + +
219C ILE* 5.7 0.2 - - + -
222C VAL* 4.1 18.2 - - + -
223C SER* 3.9 23.3 - - - +
226C CYS* 3.6 33.0 - - + -
227C HIS* 4.2 5.6 - - - +
232C LEU* 1.3 79.4 - - - +
234C CYS* 1.3 63.7 + - - +
235C ILE* 4.1 22.7 - - + -
252C ALA* 4.4 5.2 - - - -
253C ASP* 2.6 43.0 + - - +
254C LEU* 3.2 7.8 + - - +
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Residues in contact with CYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C MET* 3.4 26.5 - - - -
203C LEU* 4.1 19.1 - - + -
204C PHE 2.9 9.5 + - - +
205C PHE* 3.5 20.1 - - + -
206C THR 3.0 25.1 + - - +
232C LEU 4.2 0.2 - - - -
233C VAL* 1.3 75.0 - - - +
235C ILE* 1.3 66.4 + - - +
254C LEU* 3.4 24.0 - - + +
256C LEU* 3.8 16.8 - - - -
274C ILE* 6.2 0.9 - - - -
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Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C PHE* 5.0 1.6 - - + -
205C PHE* 5.2 0.2 - - - -
206C THR* 3.0 33.7 - - + +
208C SER* 4.2 22.4 - - - +
217C VAL* 5.2 4.0 - - + -
219C ILE* 4.1 26.9 - - + -
222C VAL* 5.4 0.4 - - + -
233C VAL* 4.1 13.2 - - + -
234C CYS* 1.3 79.5 - - - +
236C ASP* 1.3 70.3 + - - +
237C GLY* 3.6 5.1 + - - +
245C GLN* 4.8 0.7 - - - +
247C ALA* 4.1 19.5 - - + -
252C ALA* 3.9 20.2 - - + -
254C LEU 3.0 7.3 + - - +
255C VAL* 3.2 4.5 - - - +
256C LEU* 3.0 24.6 + - - +
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Residues in contact with ASP 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C PHE* 4.4 11.2 - - + -
206C THR 2.8 11.0 + - - +
207C GLU* 3.2 38.2 - - + +
208C SER 3.2 9.0 + - - +
209C PRO 4.4 1.2 - - - +
235C ILE* 1.3 72.2 - - - +
237C GLY* 1.3 57.1 + - - +
238C THR* 2.6 32.3 + - - -
239C PHE* 4.9 0.3 + - - -
256C LEU* 3.0 31.0 - - + +
500C PLP 3.4 32.6 + - - +
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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