Contacts of the strand formed by residues 238 - 243 (chain B) in PDB entry 2FN9
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 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ALA* 3.7 31.9 - - + +
203B LEU* 4.0 13.7 - - + -
206B MET* 3.9 31.3 - - + -
219B ILE* 3.3 31.2 - - + +
221B GLY 5.1 0.2 - - - +
228B VAL* 3.9 18.8 - - + +
231B ALA* 4.5 12.1 - - + -
232B ILE* 3.5 35.9 - - + +
236B LYS 3.2 11.2 - - - +
237B GLN* 1.3 75.8 - - - +
239B VAL* 1.3 60.9 + - - +
240B ALA 4.0 8.1 - - - +
280B ARG* 5.2 0.3 + - - -
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Residues in contact with VAL 239 (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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116B TYR* 3.9 5.2 - - + -
120B PHE* 3.8 20.9 - - + -
218B TYR* 3.7 14.8 - - + -
219B ILE 2.9 11.9 + - - +
220B PHE* 3.5 38.6 - - + -
232B ILE* 4.0 8.1 - - - -
237B GLN 3.6 11.9 - - - +
238B ILE* 1.3 73.9 - - - +
240B ALA* 1.3 61.9 + - + +
279B THR* 3.5 2.8 - - - -
280B ARG* 3.5 62.1 + - - +
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Residues in contact with ALA 240 (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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113B ALA* 6.3 1.1 - - - -
116B TYR* 3.6 27.1 - - + -
219B ILE 3.9 1.0 + - - -
220B PHE* 3.7 17.2 - - + -
221B GLY 2.9 22.9 + - - -
232B ILE* 3.5 8.8 - - - +
238B ILE* 3.7 6.4 - - - +
239B VAL* 1.3 82.5 - - - +
241B THR* 1.3 63.0 - - - +
277B LEU* 4.5 7.9 - - + -
278B VAL 3.2 13.0 - - - +
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Residues in contact with THR 241 (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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199B ASP* 2.7 31.7 + - - -
221B GLY 3.5 8.1 - - - -
222B PHE 3.2 5.2 + - - -
223B ASP 3.3 3.1 + - - -
224B GLY* 4.1 8.1 - - - -
228B VAL* 3.8 10.1 - - + -
229B ILE* 3.8 24.2 - - + -
232B ILE* 3.6 16.6 - - + -
240B ALA* 1.3 76.0 - - - +
242B ILE* 1.3 75.0 + - - +
277B LEU* 3.6 2.6 - - - +
278B VAL* 2.9 35.6 + - + +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY* 3.4 25.4 - - - +
112B LEU* 3.8 12.8 - - + -
113B ALA* 3.8 17.7 - - + +
221B GLY 3.8 8.4 + - - +
222B PHE* 3.8 35.7 - - + +
223B ASP* 2.8 33.3 + - - +
224B GLY* 4.0 1.6 - - - -
241B THR* 1.3 87.4 + - - +
243B MET* 1.3 59.8 + - - +
244B GLN 3.6 0.2 + - - -
275B VAL* 3.5 37.0 - - + -
276B GLU 3.5 3.8 - - - +
277B LEU* 3.9 14.8 - - + -
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Residues in contact with MET 243 (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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223B ASP 3.9 4.0 - - - +
224B GLY* 4.2 9.4 - - - +
229B ILE* 4.8 9.6 - - + -
241B THR 4.1 1.0 - - - -
242B ILE* 1.3 69.9 - - - +
244B GLN* 1.3 73.1 + - - +
245B PHE* 3.8 27.2 - - + -
275B VAL* 3.3 10.2 - - - +
276B GLU* 2.7 46.4 + - + +
278B VAL* 3.3 27.5 - - + +
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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