Contacts of the helix formed by residues 233 - 240 (chain C) in PDB entry 5UWS
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 ASN 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C PHE* 4.0 18.9 - - + -
202C GLU* 4.4 7.5 + - - +
232C THR* 1.3 73.9 - - - +
234C ILE* 1.3 63.1 + - - +
235C LEU* 3.3 3.4 - - - -
236C GLU* 3.0 39.0 + - - +
237C LEU* 3.3 20.1 + - - +
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Residues in contact with ILE 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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194C PHE* 3.9 25.1 - - + -
197C CYS* 6.4 0.9 - - + -
198C PHE* 3.6 19.4 - - + +
201C LEU* 4.2 17.9 - - + -
217C LEU* 3.9 27.4 - - + -
228C TYR 3.9 0.7 - - - +
229C ILE* 3.5 34.5 - - + +
232C THR* 3.3 18.2 - - - +
233C ASN* 1.3 77.2 - - - +
235C LEU* 1.3 65.3 + - - +
237C LEU* 3.2 8.3 + - + +
238C LEU* 3.0 39.1 + - + +
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Residues in contact with LEU 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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229C ILE* 3.6 40.3 + - + +
230C TYR* 3.9 32.8 - - + +
232C THR 5.6 1.6 - - - +
233C ASN 3.3 0.8 - - - -
234C ILE* 1.3 82.6 - - - +
236C GLU* 1.3 56.8 + - - +
238C LEU* 3.3 6.3 + - + +
239C SER* 2.8 36.3 + - - -
256C LEU* 4.2 16.8 - - + +
259C VAL* 3.7 21.8 - - + -
274C GLN* 4.6 17.0 - - + +
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Residues in contact with GLU 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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233C ASN* 3.0 36.3 + - - +
235C LEU* 1.3 78.3 - - - +
237C LEU* 1.3 57.3 + - + +
239C SER* 3.6 7.8 + - - -
240C THR* 2.5 49.2 + - - +
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Residues in contact with LEU 237 (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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198C PHE* 4.2 24.7 - - + -
201C LEU* 4.3 16.6 - - + -
202C GLU* 4.3 33.9 - - + +
233C ASN* 3.3 22.4 + - - +
234C ILE* 3.2 10.0 + - + +
236C GLU* 1.3 78.8 - - + +
238C LEU* 1.3 64.2 + - + +
240C THR* 4.3 0.7 - - - +
241C LYS* 3.1 29.9 + - + +
242C PHE* 3.0 38.1 + - + -
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Residues in contact with LEU 238 (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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201C LEU* 5.2 0.2 - - + -
214C LEU* 3.6 30.3 - - + -
217C LEU* 4.1 21.3 - - + -
221C LEU* 5.7 0.2 - - + -
229C ILE* 5.9 2.0 - - + -
234C ILE* 3.0 32.0 + - + +
235C LEU* 3.8 11.0 - - + +
237C LEU* 1.3 76.5 - - - +
239C SER* 1.3 62.1 + - - +
240C THR 3.2 1.8 + - - -
242C PHE* 4.0 7.6 - - + -
243C MET* 3.3 11.4 + - - +
252C THR* 3.0 38.0 - - + +
255C CYS* 4.5 13.7 - - + -
256C LEU* 3.8 23.6 - - + -
259C VAL* 4.8 7.2 - - + -
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Residues in contact with SER 239 (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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235C LEU* 2.8 28.1 + - - +
236C GLU* 3.6 10.6 + - - -
238C LEU* 1.3 73.3 - - - +
240C THR* 1.3 67.3 + - - +
243C MET* 4.2 11.4 - - - +
256C LEU* 4.2 19.1 - - - -
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Residues in contact with THR 240 (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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236C GLU* 2.5 39.4 + - - +
237C LEU* 4.3 0.5 - - - +
238C LEU 3.2 0.8 - - - -
239C SER* 1.3 91.8 - - - +
241C LYS* 1.3 77.4 + - - +
242C PHE 3.2 1.2 + - - -
243C MET* 3.3 11.3 + - - +
244C THR* 3.4 18.1 + - - +
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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