Contacts of the strand formed by residues 232 - 236 (chain B) in PDB entry 2QUH
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 THR 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B GLN* 3.4 14.6 - - - +
191B LEU* 3.2 20.9 - - - -
193B ILE* 4.5 3.1 - - - +
227B PHE* 3.5 24.7 - - + +
228B ASP 2.7 24.4 + - - +
229B ILE 4.2 0.3 - - - +
230B ASN 3.7 0.8 - - - -
231B LYS* 1.3 82.3 - - - +
233B PHE* 1.3 60.6 + - - +
234B ILE* 3.9 11.3 - - - +
460B PHE* 3.8 22.1 - - + -
464B ARG* 3.3 22.3 + - - -
466B LEU* 4.0 4.8 - - - +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU 2.9 10.0 + - - +
192B VAL* 3.5 4.3 - - + -
193B ILE 2.8 25.7 + - - +
232B THR* 1.3 71.8 - - - +
234B ILE* 1.3 61.8 + - - +
235B PHE* 3.5 37.4 + + + -
240B TYR* 3.6 31.0 - + - -
293B PHE* 3.8 15.7 - + - -
295B GLN* 5.7 0.7 - - + -
296B ILE* 3.8 33.2 - - + -
460B PHE 3.7 9.0 - - - -
461B MET 4.0 8.1 - - - -
462B THR 3.6 11.9 - - - -
463B PRO* 3.3 34.5 - - + -
464B ARG* 3.9 4.7 - - - +
466B LEU* 4.2 5.3 - - + +
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Residues in contact with ILE 234 (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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193B ILE* 3.4 20.9 - - + +
195B MET* 3.8 28.9 - - + -
219B ALA* 4.1 17.7 - - + +
222B ILE* 4.2 18.8 - - + -
223B ILE* 3.6 33.0 - - + -
227B PHE* 5.5 1.1 - - + -
232B THR* 3.9 13.7 - - - +
233B PHE* 1.3 74.1 - - - +
235B PHE* 1.3 60.3 + - - +
460B PHE* 3.0 24.7 + - + +
461B MET* 3.0 35.3 - - + +
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Residues in contact with PHE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL* 3.5 26.2 - - + -
193B ILE 2.9 13.9 + - - -
194B GLN* 3.3 31.9 - - + -
195B MET* 2.7 38.3 + - - +
233B PHE* 3.5 41.3 - + + -
234B ILE* 1.3 75.3 - - - +
236B SER* 1.3 57.8 + - - +
237B ASP* 3.6 21.3 - - - -
240B TYR* 3.8 29.8 - + + -
247B PHE* 4.3 6.7 - + - -
287B PRO* 4.2 8.5 - - + -
293B PHE* 3.5 18.2 - + - -
461B MET* 5.2 3.6 - - - +
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Residues in contact with SER 236 (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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195B MET* 3.6 8.5 - - - -
197B ASP* 2.5 27.7 + - - -
212B TYR* 3.7 20.0 - - - -
215B ALA* 4.5 8.3 - - - -
235B PHE* 1.3 75.6 - - - +
237B ASP* 1.3 57.0 + - - +
238B LEU* 3.6 0.9 - - - +
239B ASP* 3.1 21.4 + - - +
240B TYR* 2.9 30.5 + - - +
461B MET* 5.2 10.0 - - - +
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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