Contacts of the strand formed by residues 232 - 236 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A GLN* 2.9 24.7 - - - +
191A LEU* 3.2 20.0 - - + +
193A ILE* 4.6 1.0 - - - +
227A PHE* 3.5 23.8 - - + +
228A ASP 2.7 21.4 + - - +
229A ILE 4.1 0.9 - - - +
230A ASN 3.7 1.0 - - - -
231A LYS* 1.3 77.3 - - - +
233A PHE* 1.3 55.1 + - - +
234A ILE* 4.0 9.7 - - - +
460A PHE* 3.3 24.4 - - - -
464A ARG* 2.8 27.5 + - - -
466A LEU* 3.7 4.4 - - - +
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Residues in contact with PHE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU 2.9 11.3 + - - +
192A VAL* 3.5 8.2 - - + -
193A ILE* 2.9 24.8 + - - +
232A THR* 1.3 71.6 - - - +
234A ILE* 1.3 69.9 + - - +
235A PHE* 3.4 33.8 + + + -
240A TYR* 3.7 26.7 - + - -
293A PHE* 3.7 30.1 - + - -
295A GLN* 3.9 6.1 - - - -
296A ILE* 5.0 4.5 - - + -
460A PHE 3.6 9.2 - - - -
461A MET 3.9 9.6 - - - -
462A THR 3.8 10.1 - - - -
463A PRO* 3.5 28.7 - - + -
464A ARG* 4.1 7.6 - - + +
466A LEU* 4.3 13.6 - - + +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE* 3.4 22.2 - - + +
195A MET* 3.7 30.1 - - + -
219A ALA* 4.4 15.3 - - + +
222A ILE* 4.1 17.9 - - + -
223A ILE* 3.6 32.5 - - + -
227A PHE* 5.6 1.3 - - + -
232A THR* 4.0 11.7 - - - +
233A PHE* 1.3 76.1 - - - +
235A PHE* 1.3 64.1 + - - +
460A PHE* 3.1 24.3 + - + +
461A MET* 2.9 37.8 - - + +
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 3.3 28.0 - - + -
193A ILE 3.0 15.5 + - - -
194A GLN* 3.4 24.7 - - + -
195A MET* 2.7 38.3 + - - +
233A PHE* 3.4 39.0 - + + -
234A ILE* 1.3 74.9 - - - +
236A SER* 1.3 61.5 + - - +
237A ASP* 3.6 21.1 - - - -
240A TYR* 3.8 31.9 - + + -
247A PHE* 4.2 4.9 - + - -
287A PRO* 4.2 7.4 - - + -
293A PHE* 3.6 17.5 - + - -
461A MET* 5.0 5.6 - - - +
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 3.6 9.4 - - - -
197A ASP* 2.4 27.2 + - - -
212A TYR* 3.5 23.5 - - - -
215A ALA* 4.8 6.3 - - - -
235A PHE* 1.3 74.5 - - - +
237A ASP* 1.3 64.1 + - - +
238A LEU* 3.2 0.5 + - - +
239A ASP* 3.2 22.5 + - - +
240A TYR* 2.9 24.8 + - - +
461A MET* 5.1 9.5 - - - +
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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