Contacts of the strand formed by residues 289 - 295 (chain F) in PDB entry 1PQ3
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 289 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F HIS* 5.4 2.1 + - - -
112F SER* 3.1 16.5 + - - -
246F ILE* 3.7 19.7 - - + +
248F LEU* 3.8 20.9 - - + -
283F ILE* 3.9 23.3 + - + +
284F HIS* 5.7 1.3 - - - -
286F THR* 4.5 2.4 + - - -
287F GLY 3.6 2.9 - - - +
288F LEU* 1.3 76.0 - - - +
290F SER* 1.3 58.6 + - - +
291F ALA 3.7 18.4 - - - +
292F LEU* 4.2 5.2 - - + -
322F SER* 3.6 37.2 - - - +
323F PHE* 3.7 31.1 - - + -
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Residues in contact with SER 290 (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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107F VAL* 4.8 4.7 - - - +
111F TYR 3.9 3.2 - - - +
112F SER* 2.9 13.4 - - - +
113F CYS* 2.7 28.6 + - - +
130F HIS* 2.9 32.4 + - - -
134F CYS* 4.7 4.5 - - - -
245F PRO* 3.4 24.6 - - - +
246F ILE 3.0 7.1 + - - -
288F LEU 3.3 1.8 + - - -
289F LEU* 1.3 74.5 + - - +
291F ALA* 1.3 54.0 + - - +
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Residues in contact with ALA 291 (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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103F VAL* 5.4 2.5 - - + -
107F VAL* 5.0 0.2 - - + -
112F SER* 5.5 0.4 - - - -
113F CYS* 2.9 22.7 - - + +
126F THR* 6.1 0.2 - - - -
130F HIS* 3.5 15.5 - - + +
246F ILE 3.6 3.7 + - - +
247F HIS* 3.4 30.7 + - + +
248F LEU 3.0 23.6 + - - -
289F LEU* 3.7 5.1 - - - +
290F SER* 1.3 81.0 - - - +
292F LEU* 1.3 61.9 + - - +
293F ASP* 5.7 0.2 - - - +
323F PHE* 6.2 0.4 - - - -
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Residues in contact with LEU 292 (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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113F CYS 2.6 11.6 + - - +
114F VAL* 3.3 16.5 - - + -
115F THR 2.7 32.4 + - - -
248F LEU* 3.2 24.9 - - + +
250F PHE* 5.2 1.6 - - + -
289F LEU* 4.2 13.0 - - + -
291F ALA* 1.3 74.9 - - - +
293F ASP* 1.3 78.2 + - - +
294F LEU* 3.9 16.4 - - + +
318F VAL* 4.8 2.9 - - + +
319F ILE* 4.2 17.9 - - + -
322F SER* 3.5 36.8 - - - +
323F PHE* 4.5 7.8 - - + -
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Residues in contact with ASP 293 (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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115F THR* 3.6 9.8 + - - +
120F HIS* 5.2 0.4 - - - +
123F ALA* 4.4 5.7 - - - +
126F THR* 3.1 35.8 + - - +
247F HIS* 2.6 29.5 + - - -
248F LEU 2.8 8.3 + - - -
249F SER* 3.2 25.1 + - - +
250F PHE* 2.7 33.9 + - - +
291F ALA* 5.7 0.2 - - - +
292F LEU* 1.3 79.8 - - - +
294F LEU* 1.3 60.0 + - - +
295F VAL* 3.8 16.6 - - + -
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Residues in contact with LEU 294 (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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49F ILE* 3.9 10.5 - - + +
115F THR 3.0 11.5 + - - +
116F LEU* 3.8 5.4 - - + -
117F GLY 2.9 21.8 + - - +
250F PHE* 3.5 29.2 - - + +
252F ILE* 4.4 6.7 - - + -
292F LEU* 3.9 5.8 - - + +
293F ASP* 1.3 71.7 - - - +
295F VAL* 1.3 63.7 + - - +
297F VAL* 3.9 12.9 - - + +
315F ALA* 3.6 32.3 - - + +
318F VAL* 4.2 22.0 - - + -
319F ILE* 4.0 29.4 - - + -
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Residues in contact with VAL 295 (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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115F THR* 5.0 2.5 - - + +
117F GLY* 4.1 9.4 - - - +
118F GLY 3.3 14.8 - - - +
119F ASP 4.4 5.6 - - - +
120F HIS* 3.4 48.7 - - + +
122F LEU* 5.0 6.3 - - + -
123F ALA 5.9 0.7 - - - +
250F PHE 3.2 6.7 + - - +
251F ASP* 3.9 10.3 - - - -
252F ILE* 3.2 24.4 + - - +
293F ASP* 4.2 14.8 - - + -
294F LEU* 1.3 86.6 - - - +
296F GLU* 1.3 74.0 + - + +
297F VAL 3.3 4.4 + - - -
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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