Contacts of the helix formed by residues 230 - 243 (chain F) in PDB entry 6C3P
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 TYR 230 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219F GLN* 3.8 19.9 + - - -
226F SER 2.5 19.5 + - - -
227F LYS 4.8 5.0 + - - -
228F GLY 3.9 16.8 - - - -
229F THR* 1.3 77.0 - - - +
231F TRP* 1.3 60.3 + - - +
232F TRP* 3.3 29.2 - + - +
233F MET* 3.6 13.9 - - + -
234F ASN 2.9 20.6 + - - -
374F GLN* 4.4 9.6 + - + -
375F ALA* 5.7 0.2 - - - -
378F TYR* 3.1 43.8 - + - +
1242F ALA* 4.3 10.1 - - - -
1245F ARG* 3.6 27.1 - - + +
1246F TRP* 3.1 21.8 - - + -
1249F VAL* 4.1 13.7 - - + -
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Residues in contact with TRP 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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226F SER* 3.9 17.5 - - - -
229F THR* 3.4 11.0 + - + -
230F TYR* 1.3 74.1 - - - +
232F TRP* 1.3 68.0 + - - +
234F ASN* 3.0 15.6 + - + +
235F ALA* 3.0 22.4 + - + +
1250F ARG* 3.6 23.3 - - - +
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Residues in contact with TRP 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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217F PHE* 3.3 42.4 - + - -
218F LEU* 4.7 18.6 - - - +
219F GLN* 3.8 32.7 - - + +
222F VAL* 3.8 29.4 - - + +
226F SER* 3.9 17.8 + - - -
230F TYR* 3.8 32.1 - + - +
231F TRP* 1.3 79.8 - - - +
233F MET* 1.3 78.0 + - + +
235F ALA* 3.2 9.8 + - - +
236F PHE* 2.9 27.1 + - + +
378F TYR* 5.6 5.2 - + - -
1242F ALA* 3.7 20.0 - - + -
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Residues in contact with MET 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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230F TYR* 3.3 24.6 + - + +
231F TRP 3.2 0.4 - - - -
232F TRP* 1.3 98.6 - - + +
234F ASN* 1.3 60.8 + - - +
236F PHE* 3.5 7.4 - - + +
237F ILE* 2.9 30.5 + - - +
1242F ALA* 4.1 25.1 - - + +
1243F ALA* 5.0 1.7 - - - +
1246F TRP* 4.4 6.1 - - + +
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Residues in contact with ASN 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F TYR 2.9 8.6 + - - +
231F TRP* 3.1 26.7 - - + +
233F MET* 1.3 76.0 - - - +
235F ALA* 1.3 60.9 + - - +
237F ILE* 3.2 3.7 + - - +
238F LYS* 2.9 21.4 + - - +
1180F TYR* 5.1 0.2 + - - -
1246F TRP* 3.2 42.9 - - + +
1250F ARG* 4.2 4.7 - - - +
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Residues in contact with ALA 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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231F TRP* 3.0 15.1 + - + +
232F TRP* 3.4 11.4 - - - +
234F ASN* 1.3 75.0 - - - +
236F PHE* 1.3 65.4 + - - +
238F LYS* 2.9 23.4 + - - +
239F THR* 3.8 4.2 + - - -
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Residues in contact with PHE 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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217F PHE* 4.1 25.1 - - + -
232F TRP* 2.9 14.2 + - + +
233F MET* 3.2 13.9 + - + +
235F ALA* 1.3 77.0 - - - +
237F ILE* 1.3 61.2 + - - +
238F LYS 3.4 0.2 + - - -
239F THR* 3.7 10.6 + - - -
240F ALA* 4.1 6.1 + - - +
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Residues in contact with ILE 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 MET 2.9 16.1 + - - +
234F ASN 3.8 4.0 - - - +
236F PHE* 1.3 75.8 - - - +
238F LYS* 1.3 66.4 + - - +
240F ALA* 2.8 24.7 + - - +
241F HIS 3.7 0.9 + - - -
1180F TYR* 2.9 17.0 + - + -
1181F PHE* 6.2 2.0 - - + -
1184F ALA* 4.9 12.1 - - + +
1243F ALA* 5.9 8.1 - - + -
1246F TRP* 4.4 23.1 - - + -
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Residues in contact with LYS 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 ASN 2.9 12.2 + - - +
235F ALA* 2.9 20.5 + - - +
237F ILE* 1.3 77.8 - - - +
239F THR* 1.3 59.2 + - - +
241F HIS* 3.7 9.5 + - - +
242F LYS* 4.2 4.7 + - - +
1180F TYR* 3.1 16.7 + - - -
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Residues in contact with THR 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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235F ALA 3.8 3.1 + - - -
236F PHE 3.7 8.1 + - - -
237F ILE 3.2 0.8 - - - -
238F LYS* 1.3 74.7 - - - +
240F ALA* 1.3 59.7 + - - +
241F HIS 3.0 6.4 + - - -
242F LYS* 3.1 7.4 + - - +
243F LYS* 2.9 34.8 + - - +
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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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236F PHE 4.1 3.6 + - - +
237F ILE* 2.8 19.4 + - - +
239F THR* 1.3 76.9 - - - +
241F HIS* 1.3 59.7 + - - +
243F LYS 3.4 16.4 - - - +
244F PRO* 4.9 2.1 - - - +
245F ILE* 5.4 12.5 + - + +
1183F VAL* 4.6 12.4 - - - +
1184F ALA* 4.1 27.8 - - + +
1187F ASP* 5.6 4.2 - - + +
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Residues in contact with HIS 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 ILE 3.7 2.0 + - - -
238F LYS 3.7 6.8 + - - +
239F THR 3.0 0.8 - - - -
240F ALA* 1.3 80.0 - - - +
242F LYS* 1.3 65.5 + - - +
243F LYS* 3.2 1.7 + - - -
244F PRO* 5.7 0.3 - - - +
1180F TYR* 3.4 34.5 - - + -
1183F VAL* 5.1 12.2 - - + +
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Residues in contact with LYS 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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238F LYS 4.2 4.6 + - - +
239F THR* 3.1 9.6 + - - +
241F HIS* 1.3 79.0 - - + +
243F LYS* 1.3 62.0 + - + +
244F PRO* 4.7 0.9 - - - +
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Residues in contact with LYS 243 (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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239F THR* 2.9 20.7 + - - +
240F ALA* 3.4 14.4 - - - +
241F HIS 3.2 2.7 + - - -
242F LYS* 1.3 82.0 - - + +
244F PRO* 1.3 76.8 - - + +
245F ILE* 3.4 3.3 + - - -
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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