Contacts of the strand formed by residues 246 - 251 (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 ILE 246 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130F HIS* 4.5 2.5 - - - -
138F CYS* 3.6 21.3 - - - +
140F VAL* 4.2 20.0 - - + -
235F PHE* 4.2 18.4 - - + -
238F LEU* 6.4 0.4 - - + -
239F ILE* 4.5 4.7 - - + -
244F ARG 3.8 2.2 - - - +
245F PRO* 1.3 73.9 - - - +
247F HIS* 1.3 69.4 + - - +
248F LEU 4.3 0.7 - - - +
283F ILE* 4.6 11.9 - - + +
286F THR* 3.5 29.6 - - - +
288F LEU* 2.7 35.1 + - + +
289F LEU* 3.7 15.5 - - + +
290F SER* 3.0 23.6 + - - +
291F ALA 3.6 4.3 + - - -
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Residues in contact with HIS 247 (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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126F THR* 3.7 19.5 + - - -
127F ILE* 3.3 35.8 - - + +
130F HIS* 3.0 27.2 + - + +
137F LEU* 4.5 5.2 - - + -
138F CYS 2.8 16.1 + - - +
139F VAL* 3.4 11.3 - - + +
140F VAL 2.9 25.3 + - - +
246F ILE* 1.3 74.5 - - - +
248F LEU* 1.3 60.7 + - - +
249F SER* 3.7 9.2 + - - -
291F ALA* 3.4 22.2 + - + +
293F ASP* 2.6 34.5 + - - -
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Residues in contact with LEU 248 (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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140F VAL* 3.4 19.3 - - + +
142F VAL* 3.7 24.2 - - + -
246F ILE* 3.9 1.4 + - + -
247F HIS* 1.3 72.6 - - - +
249F SER* 1.3 59.0 + - - +
250F PHE* 3.6 20.2 + - + -
279F ILE* 5.2 1.6 - - + -
280F ALA* 5.3 4.3 - - - -
283F ILE* 3.4 37.9 - - + -
289F LEU* 3.8 16.2 - - + -
291F ALA 3.0 10.0 + - - +
292F LEU* 3.2 15.8 - - + +
293F ASP 2.8 25.1 + - - +
318F VAL* 5.5 0.4 - - + -
322F SER* 3.9 21.5 - - - +
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Residues in contact with SER 249 (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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120F HIS* 2.7 29.8 + - - -
123F ALA* 4.0 1.2 - - - +
139F VAL* 4.8 1.1 - - - -
140F VAL 3.0 9.3 + - - +
141F TRP* 3.6 30.7 - - - -
142F VAL 3.0 26.9 + - - +
247F HIS* 3.7 9.2 + - - -
248F LEU* 1.3 72.7 - - - +
250F PHE* 1.3 58.0 + - - +
251F ASP 3.9 0.6 + - - -
293F ASP* 3.2 23.4 + - - +
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Residues in contact with PHE 250 (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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120F HIS* 4.9 0.2 + - - -
142F VAL* 3.6 38.6 - - + -
248F LEU* 3.6 18.8 + - + -
249F SER* 1.3 71.1 + - - +
251F ASP* 1.3 80.0 + - - +
252F ILE* 3.6 2.3 + - + -
254F ALA* 4.5 2.0 - - + -
255F PHE* 3.5 43.3 - + - -
271F LEU* 4.7 5.4 - - + -
276F GLY* 4.7 11.9 - - - -
279F ILE* 4.7 7.9 - - + -
280F ALA* 5.6 0.9 - - + -
292F LEU* 5.2 1.8 - - + -
293F ASP* 2.7 18.1 + - - +
294F LEU* 3.5 18.4 - - + +
295F VAL* 3.2 25.5 + - - -
318F VAL* 3.8 23.8 - - + -
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Residues in contact with ASP 251 (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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120F HIS* 3.4 5.0 + - - +
142F VAL 2.9 7.3 + - - +
143F ASP* 3.1 22.9 - - + +
249F SER 3.9 1.6 + - - -
250F PHE* 1.3 76.1 - - - +
252F ILE* 1.3 64.8 + - - +
253F ASP* 2.8 34.2 + - - +
254F ALA* 3.1 18.9 + - - +
295F VAL* 3.9 7.2 - - - -
296F GLU* 3.4 17.4 - - - +
510F MN 2.6 8.2 + - - -
511F MN 2.2 32.6 + - - +
556F S2C 2.7 6.7 + - - -
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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
------------------------------------------------------------
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