Contacts of the strand formed by residues 239 - 246 (chain F) in PDB entry 6IWQ
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 239 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F SER* 3.9 7.2 - - - +
211F VAL* 4.0 16.8 - - + -
230F VAL* 4.8 1.1 - - + +
231F ILE* 4.6 11.0 - - + -
234F THR* 3.3 33.4 - - + +
235F PRO 3.6 1.7 + - - +
236F ARG* 3.3 19.8 + - - +
237F LYS 4.6 1.8 - - - +
238F TYR* 1.3 74.1 - - - +
240F ALA* 1.3 64.4 + - - +
241F GLU 3.5 21.8 - - - +
242F ILE* 3.8 30.5 - - + -
268F LEU* 3.9 27.8 - - + +
311F TYR* 5.9 1.3 - - + -
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Residues in contact with ALA 240 (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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208F THR* 4.4 7.9 - - - -
209F SER 2.8 24.2 + - - +
237F LYS 5.4 1.3 - - - -
238F TYR 3.3 1.0 + - - -
239F LEU* 1.3 74.0 - - - +
241F GLU* 1.3 61.9 + - - +
268F LEU* 3.6 11.1 - - - +
293F LEU* 3.8 19.8 - - + +
294F GLY* 3.8 28.5 - - - +
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Residues in contact with GLU 241 (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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210F SER* 3.1 28.3 + - - +
211F VAL 3.2 20.8 + - - -
239F LEU* 3.5 8.8 - - - +
240F ALA* 1.3 79.8 - - - +
242F ILE* 1.3 64.4 + - - +
243F VAL* 3.5 23.9 - - + +
268F LEU* 3.5 18.4 - - - +
270F LYS* 5.3 7.5 + - + +
272F PHE* 6.1 0.3 - - - -
290F LYS 4.7 1.6 - - - +
291F ALA* 3.2 15.8 - - - +
292F LYS 4.7 0.5 + - - -
293F LEU* 3.1 40.9 + - + +
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Residues in contact with ILE 242 (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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211F VAL* 3.4 26.9 - - + +
213F ILE* 4.2 7.2 - - + -
227F VAL* 4.4 14.1 - - + +
230F VAL* 2.9 35.4 - - + -
231F ILE* 4.5 5.8 - - + +
239F LEU* 3.8 20.0 - - + -
241F GLU* 1.3 76.2 - - - +
243F VAL* 1.3 61.7 + - - +
244F LEU* 4.0 17.3 - - + -
268F LEU* 3.2 19.1 + - + -
269F VAL* 3.3 23.1 - - + +
270F LYS 2.9 27.5 + - - +
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Residues in contact with VAL 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F VAL 2.8 12.0 + - - +
212F VAL* 3.2 6.8 - - + -
213F ILE 3.0 24.3 + - - -
241F GLU* 3.5 36.3 - - + +
242F ILE* 1.3 70.6 - - - +
244F LEU* 1.3 62.9 + - - +
245F ILE* 2.7 38.0 - - + +
270F LYS* 3.4 13.2 - - + +
272F PHE* 4.4 17.3 - - + -
287F GLY 4.7 1.3 - - - +
290F LYS* 4.3 6.1 - - + +
291F ALA* 3.5 25.1 - - + -
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Residues in contact with LEU 244 (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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213F ILE* 3.4 40.8 - - + +
215F PHE* 4.6 8.1 - - + -
223F LEU* 4.9 14.1 - - + -
224F MET* 5.3 1.3 - - + -
227F VAL* 4.0 15.3 - - + -
242F ILE* 4.0 9.0 - - + -
243F VAL* 1.3 73.2 - - - +
245F ILE* 1.3 66.8 + - - +
246F ASP 4.0 0.2 + - - -
258F LEU* 4.7 22.0 - - + -
262F ILE* 4.9 4.7 - - + -
269F VAL* 4.3 17.0 - - + -
270F LYS 2.7 17.2 + - - +
271F VAL* 3.4 16.2 - - + +
272F PHE 2.9 26.9 + - - -
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Residues in contact with ILE 245 (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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212F VAL* 4.8 3.4 - - + -
213F ILE 3.0 7.2 + - - +
214F VAL* 4.3 20.6 - - + -
215F PHE* 2.7 35.3 + - - -
243F VAL* 2.7 45.8 - - + +
244F LEU* 1.3 74.4 - - - +
246F ASP* 1.3 66.7 + - - +
247F ASP 3.6 0.6 + - - +
272F PHE* 3.9 10.1 - - + +
274F ASN* 4.2 19.7 - - - +
283F ALA* 3.9 17.0 - - + +
286F ILE* 4.9 6.7 - - + -
287F GLY* 3.7 25.4 - - - +
290F LYS* 5.1 1.3 - - + -
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Residues in contact with ASP 246 (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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215F PHE* 2.9 34.0 - - + -
244F LEU 4.0 0.6 + - - -
245F ILE* 1.3 73.6 - - - +
247F ASP* 1.3 76.7 + - - +
248F PHE* 4.2 2.3 - - - -
249F SER* 2.5 31.8 + - - -
271F VAL* 4.9 3.6 - - + -
272F PHE 3.0 16.5 + - - +
273F ARG* 3.6 25.7 - - + +
274F ASN* 2.9 30.7 + - - +
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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
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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