Contacts of the helix formed by residues 228 - 241 (chain F) in PDB entry 6F0X
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 228 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122F ALA* 3.7 30.5 - - + -
212F ILE* 6.1 0.2 - - + -
213F ASN 5.9 3.4 - - - +
215F HIS 5.4 7.6 - - - +
216F SER* 5.8 9.6 - - - -
227F LYS* 1.3 87.9 - - + +
229F VAL* 1.3 56.1 + - + +
231F LYS* 4.0 2.0 - - - +
232F MET* 2.7 64.0 + - + +
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Residues in contact with VAL 229 (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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216F SER* 5.8 3.1 - - - -
227F LYS* 3.1 6.1 - - + -
228F LEU* 1.3 82.8 - - + +
230F THR* 1.3 65.0 + - + +
232F MET* 3.9 11.4 - - + -
233F PHE* 2.9 55.6 + - + -
276F VAL* 3.5 39.5 - - + -
279F ALA* 3.8 24.7 - - + -
280F VAL* 3.6 13.9 - - + -
283F GLN* 5.4 0.2 - - + -
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Residues in contact with THR 230 (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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227F LYS* 2.7 34.2 + - + +
229F VAL* 1.3 81.5 - - + +
231F LYS* 1.3 72.1 + - - +
233F PHE* 3.3 2.9 + - - +
234F GLN* 3.0 24.9 + - - +
275F ARG* 5.1 16.8 - - - +
279F ALA* 5.8 4.7 - - + -
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Residues in contact with LYS 231 (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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227F LYS 3.7 5.9 + - - +
228F LEU* 4.7 1.3 - - - +
230F THR* 1.3 87.3 + - - +
232F MET* 1.3 56.1 + - - +
234F GLN* 3.4 12.1 - - + +
235F LYS* 2.9 45.7 + - - +
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Residues in contact with MET 232 (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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122F ALA* 5.2 1.8 - - - -
210F ILE* 4.7 9.4 - - + -
211F GLU 4.9 2.0 - - - +
212F ILE* 3.5 46.9 - - + -
228F LEU* 2.7 44.6 + - + +
229F VAL* 3.3 16.6 - - + +
230F THR 3.1 0.2 - - - -
231F LYS* 1.3 76.9 - - - +
233F PHE* 1.3 91.3 + - + +
235F LYS* 3.1 13.8 + - - +
236F ILE* 2.9 35.0 + - + +
280F VAL* 4.6 0.9 - - + -
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Residues in contact with PHE 233 (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 ILE* 4.4 8.7 - - + -
229F VAL* 2.9 46.5 + - + +
230F THR* 4.1 2.5 - - - +
232F MET* 1.3 91.7 - - + +
234F GLN* 1.3 60.0 + - - +
236F ILE* 3.2 26.3 + - + +
237F GLN* 2.9 26.2 + - - +
249F VAL* 5.1 6.1 - - + -
280F VAL* 3.5 37.9 - - + -
283F GLN* 3.3 48.6 - - + +
284F ILE* 4.7 5.8 - - + -
287F ILE* 4.5 14.6 - - + +
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Residues in contact with GLN 234 (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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230F THR 3.0 14.2 + - - +
231F LYS* 3.4 17.5 - - + +
232F MET 3.1 0.2 - - - -
233F PHE* 1.3 74.1 - - - +
235F LYS* 1.3 66.5 + - + +
237F GLN* 3.0 22.9 + - - +
238F ASP* 3.0 32.1 + - - +
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Residues in contact with LYS 235 (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 ILE* 6.1 4.3 - - + -
231F LYS* 2.9 34.7 + - + +
232F MET* 3.4 10.8 - - - +
234F GLN* 1.3 73.6 - - + +
236F ILE* 1.3 58.3 + - + +
238F ASP* 3.1 18.6 + - + +
239F LEU* 2.9 36.0 + - + +
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Residues in contact with ILE 236 (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 ILE* 4.5 13.0 - - + -
212F ILE* 4.2 17.3 - - + -
232F MET* 2.9 24.2 + - + +
233F PHE* 3.4 37.9 - - + +
234F GLN 3.1 0.2 - - - -
235F LYS* 1.3 74.7 - - + +
237F GLN* 1.3 60.6 + - - +
239F LEU* 3.1 18.6 + - + +
240F ILE* 2.9 37.1 + - + +
247F VAL* 4.3 15.3 - - + -
248F PHE 5.8 0.9 - - - +
249F VAL* 4.9 8.5 - - + -
287F ILE* 3.7 26.9 - - + -
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Residues in contact with GLN 237 (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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233F PHE 2.9 13.2 + - - +
234F GLN* 3.0 26.4 + - - +
236F ILE* 1.3 75.8 - - - +
238F ASP* 1.3 63.9 + - - +
240F ILE* 3.0 19.0 + - - +
241F ASP* 2.9 48.1 + - - +
287F ILE* 5.1 5.6 - - + +
290F HIS* 3.8 29.0 + - - -
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Residues in contact with ASP 238 (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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234F GLN* 3.0 29.5 + - - +
235F LYS* 3.1 20.2 + - - +
237F GLN* 1.3 74.8 - - - +
239F LEU* 1.3 67.7 + - + +
241F ASP* 3.0 32.6 + - - +
242F ASP* 4.5 1.4 + - - +
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Residues in contact with LEU 239 (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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124F HIS* 5.0 7.0 - - + +
206F TYR* 6.4 0.2 - - - -
208F GLN* 3.4 47.6 - - + +
210F ILE* 3.7 31.2 - - + -
235F LYS* 2.9 24.1 + - + +
236F ILE* 3.1 20.8 + - + +
238F ASP* 1.3 80.4 - - + +
240F ILE* 1.3 62.8 + - - +
241F ASP 3.3 0.7 + - - -
242F ASP* 3.7 1.4 + - - +
245F ALA* 3.1 27.8 - - - +
247F VAL* 3.5 18.8 - - + +
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Residues in contact with ILE 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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236F ILE* 2.9 31.0 + - + +
237F GLN* 3.0 24.7 + - - +
239F LEU* 1.3 72.0 - - - +
241F ASP* 1.3 53.6 + - - +
242F ASP 2.7 14.3 + - - +
247F VAL* 3.6 9.0 - - + -
287F ILE* 4.1 10.3 - - + -
290F HIS* 3.3 43.5 - - + +
292F ASN* 2.5 37.0 + - - +
293F VAL* 3.6 27.4 - - + -
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Residues in contact with ASP 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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237F GLN* 2.9 39.4 + - - +
238F ASP* 3.0 37.4 + - - +
240F ILE* 1.3 75.9 - - - +
242F ASP* 1.3 56.9 + - + +
243F LYS* 4.3 1.4 + - - +
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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