Contacts of the helix formed by residues 233 - 245 (chain F) in PDB entry 6D84
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 ASP 233 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232F LYS* 1.3 92.4 - - - +
234F ASP* 1.3 63.8 + - - +
235F ARG* 4.0 4.7 - - + +
236F GLU* 3.6 31.0 + - + +
237F ALA* 3.4 14.0 + - - +
269F MET* 3.4 21.3 - - - +
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Residues in contact with ASP 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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233F ASP* 1.3 73.9 - - - +
235F ARG* 1.3 58.6 + - - +
237F ALA* 3.7 2.1 + - - +
238F GLN* 3.1 29.9 + - - +
269F MET* 4.1 12.4 - - + +
270F LEU* 3.7 13.0 - - - +
271F SER* 3.4 31.0 + - - -
274F LEU* 3.3 28.8 - - - +
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Residues in contact with ARG 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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233F ASP* 4.0 4.1 - - + +
234F ASP* 1.3 77.9 - - - +
236F GLU* 1.3 57.0 + - - +
238F GLN* 3.9 7.0 - - + +
239F SER* 2.3 46.8 + - - +
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Residues in contact with GLU 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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201F PRO* 3.4 22.0 - - + +
229F TYR* 2.8 32.7 + - - -
231F PRO* 4.1 6.1 - - + -
232F LYS* 3.3 28.8 + - - +
233F ASP* 3.6 30.1 + - + +
235F ARG* 1.3 78.1 - - - +
237F ALA* 1.3 58.0 + - - +
239F SER* 3.2 4.5 + - - -
240F ILE* 3.0 39.9 + - + +
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Residues in contact with ALA 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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231F PRO* 3.7 24.0 - - + +
233F ASP 3.4 18.2 + - - +
234F ASP* 4.0 2.7 - - - +
236F GLU* 1.3 78.8 - - - +
238F GLN* 1.3 58.6 + - - +
240F ILE* 3.3 8.6 - - + +
241F CYS* 2.9 38.2 + - - -
266F PHE* 4.7 4.5 - - + +
269F MET* 3.8 16.2 - - + -
270F LEU* 4.6 9.0 - - + -
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Residues in contact with GLN 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 ASP* 3.1 22.8 + - - +
235F ARG* 4.1 5.5 - - - +
237F ALA* 1.3 76.2 - - - +
239F SER* 1.3 59.2 + - - +
242F GLU* 2.9 52.1 + - - +
270F LEU* 4.1 5.1 - - + +
274F LEU* 4.4 15.8 - - - +
276F TYR* 3.3 61.9 + - + +
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Residues in contact with SER 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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205F ASN* 5.9 1.1 - - - -
235F ARG* 2.3 39.0 + - - +
236F GLU* 3.2 7.2 + - - -
238F GLN* 1.3 78.6 - - - +
240F ILE* 1.3 63.6 + - - +
242F GLU* 3.9 18.8 + - - +
243F ARG* 4.2 16.9 + - - +
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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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201F PRO* 6.4 1.8 - - + -
204F ILE* 4.8 16.4 - - + -
205F ASN* 4.1 22.0 - - - +
208F LEU* 4.4 16.1 - - + +
226F LEU* 5.7 4.5 - - + -
229F TYR* 6.6 0.2 - - + -
231F PRO* 5.2 6.5 - - + -
236F GLU* 3.0 29.7 + - + +
237F ALA* 3.3 14.8 - - - +
239F SER* 1.3 80.6 - - - +
241F CYS* 1.3 73.1 + - - +
243F ARG* 3.3 6.3 + - - +
244F VAL* 3.0 32.1 + - + +
266F PHE* 3.6 37.5 - - + -
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Residues in contact with CYS 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 ALA 2.9 26.2 + - - +
238F GLN 3.3 0.6 + - - +
240F ILE* 1.3 83.3 - - - +
242F GLU* 1.3 55.0 + - - +
244F VAL* 3.7 8.1 - - - +
245F THR* 2.4 38.6 + - - -
263F LEU* 3.7 24.1 - - + +
266F PHE* 3.7 35.4 - - - -
270F LEU* 5.6 4.5 - - + -
276F TYR* 3.2 20.0 - - + +
280F LEU* 5.8 1.1 - - + -
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Residues in contact with GLU 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 GLN* 2.9 43.6 + - - +
239F SER* 4.1 11.8 - - - +
240F ILE 3.2 0.4 - - - -
241F CYS* 1.3 76.6 - - - +
243F ARG* 1.3 63.3 + - + +
245F THR* 3.8 6.7 - - - -
246F PRO* 3.5 13.9 - - - +
276F TYR* 3.1 21.3 + - + +
248P GLU* 4.7 7.1 - - - +
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Residues in contact with ARG 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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205F ASN* 3.0 33.5 + - - +
208F LEU* 3.6 49.1 + - + +
209F THR* 4.6 11.7 - - - +
211F LEU* 3.8 16.0 - - + +
212F ASN* 5.7 8.1 - - - +
239F SER 4.2 16.0 + - - +
240F ILE* 3.3 4.3 + - - +
241F CYS 3.2 0.2 - - - -
242F GLU* 1.3 79.8 - - + +
244F VAL* 1.3 65.0 + - - +
245F THR 3.2 0.7 - - - -
246F PRO* 3.3 17.9 - - + +
247F ARG* 3.9 2.8 + - - -
245P SER* 5.7 8.3 - - - -
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Residues in contact with VAL 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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208F LEU* 4.9 8.7 - - + -
211F LEU* 5.0 1.8 - - + -
223F LEU* 4.7 7.4 - - + -
226F LEU* 4.5 22.0 - - + -
240F ILE* 3.0 30.9 + - + +
241F CYS* 3.3 11.2 + - - +
243F ARG* 1.3 78.1 - - - +
245F THR* 1.3 62.6 + - - +
247F ARG* 3.2 24.8 + - - +
248F LEU* 4.5 1.4 + - - +
259F ALA* 4.4 8.8 - - + +
262F VAL* 3.8 25.6 - - + -
263F LEU* 3.8 23.1 - - + -
266F PHE* 5.5 0.9 - - + -
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Residues in contact with THR 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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241F CYS* 2.4 26.6 + - - +
242F GLU* 3.8 7.2 - - - -
244F VAL* 1.3 76.3 - - - +
246F PRO* 1.3 67.2 - - - +
247F ARG 3.0 1.6 + - - -
248F LEU* 3.3 25.9 + - + +
249F SER* 5.6 0.2 + - - -
263F LEU* 4.8 12.4 - - - +
276F TYR* 3.8 8.5 + - - -
280F LEU* 4.9 9.7 - - + +
283F LYS* 4.7 18.2 - - + +
248P GLU* 3.9 24.5 - - - +
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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