Contacts of the helix formed by residues 219 - 231 (chain F) in PDB entry 2OX4
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 219 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A GLU* 3.5 35.8 - - + +
311A THR* 4.6 6.2 - - - +
181F LEU 4.0 0.2 + - - -
182F GLU* 3.6 15.1 - - + +
183F GLY* 2.9 26.9 + - - -
218F THR* 1.3 75.0 - - - +
220F LEU* 1.3 61.3 + - - +
221F VAL* 3.1 8.6 + - - +
222F SER* 3.0 26.9 + - - -
223F ALA* 2.8 28.4 + - - +
241F ILE 3.8 5.4 - - - -
242F ASN* 3.8 4.0 - - - -
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Residues in contact with LEU 220 (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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280A ARG* 3.7 44.2 - - + +
283A ASP* 4.8 2.2 - - - +
308A PHE 4.0 2.5 - - - +
309A GLU* 2.9 19.7 + - + +
219F ASP* 1.3 73.9 - - - +
221F VAL* 1.3 61.1 + - + +
223F ALA* 3.7 5.7 - - - +
224F ILE* 3.0 55.0 + - + +
241F ILE* 5.7 0.2 - - - -
242F ASN* 3.9 6.3 - - - +
249F LEU* 3.8 36.8 - - + +
252F GLU* 4.6 5.8 - - + -
253F ALA* 4.3 23.3 - - + +
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Residues in contact with VAL 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO* 4.5 16.4 - - + -
280A ARG* 3.2 30.5 - - - +
283A ASP* 3.5 23.6 - - + +
309A GLU 3.9 8.5 - - - +
183F GLY* 4.5 4.3 - - - -
184F PRO* 3.9 35.2 - - + -
219F ASP* 3.1 7.7 + - - +
220F LEU* 1.3 80.8 - - + +
222F SER* 1.3 62.5 + - - +
224F ILE* 3.5 5.9 + - - +
225F GLN* 3.2 22.3 + - + +
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Residues in contact with SER 222 (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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181F LEU 2.7 27.5 + - - -
183F GLY 3.3 18.8 + - - -
185F LEU* 3.6 18.4 - - - +
218F THR* 3.3 7.0 - - - +
219F ASP* 3.0 25.9 + - - -
221F VAL* 1.3 74.6 - - - +
223F ALA* 1.3 58.7 + - - +
225F GLN* 3.6 8.2 - - - +
226F PHE* 2.9 31.9 + - - +
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Residues in contact with ALA 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F THR* 4.1 4.7 - - - +
219F ASP 2.8 19.5 + - - +
220F LEU* 3.7 4.5 - - - +
222F SER* 1.3 78.2 + - - +
224F ILE* 1.3 56.3 + - - +
227F ALA* 3.0 20.3 + - - +
238F TYR* 2.8 25.5 + - - +
241F ILE* 3.6 45.5 - - + +
257F ILE* 4.2 2.5 - - + -
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Residues in contact with ILE 224 (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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254A LYS* 6.3 1.1 - - - +
258A ASP* 5.4 7.9 - - + +
220F LEU* 3.0 41.4 + - + +
221F VAL* 3.8 5.4 - - - +
223F ALA* 1.3 72.3 - - - +
225F GLN* 1.3 66.9 + - - +
227F ALA* 3.3 2.8 + - - +
228F LYS* 3.1 25.0 + - + +
252F GLU 4.6 1.1 - - - +
253F ALA* 4.2 10.3 - - - +
256F LYS* 3.8 42.6 - - + +
257F ILE* 3.8 25.4 - - + -
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Residues in contact with GLN 225 (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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234A ASN* 4.7 15.9 + - - +
236A PHE* 6.0 1.4 - - - -
260A PRO* 6.5 1.6 - - + -
184F PRO* 3.7 9.9 - - - +
185F LEU* 2.8 50.6 + - - +
187F SER* 5.5 0.4 - - - +
190F ILE* 3.7 26.2 - - + +
221F VAL* 3.2 13.6 + - + +
222F SER* 3.6 5.5 - - - +
224F ILE* 1.3 81.8 - - - +
226F PHE* 1.3 60.6 + - - +
228F LYS* 3.5 8.7 - - - +
229F ALA* 3.4 17.5 + - - +
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Residues in contact with PHE 226 (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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167F VAL* 3.5 33.2 - - + -
168F LEU* 3.8 32.5 - - + -
185F LEU* 5.0 1.1 - - + -
190F ILE* 3.8 28.6 - - + +
193F GLY* 3.6 22.4 - - - -
194F VAL* 3.7 6.5 - - + -
197F VAL* 4.6 0.2 - - + -
212F VAL* 4.2 5.8 - - + -
214F ASN* 4.6 0.2 - - - -
222F SER 2.9 17.6 + - - +
223F ALA* 4.8 0.2 - - - -
225F GLN* 1.3 75.0 - - - +
227F ALA* 1.3 65.7 + - - +
229F ALA* 3.0 13.7 + - + +
230F ILE* 3.1 51.7 + - + +
238F TYR* 3.6 19.7 - + - +
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Residues in contact with ALA 227 (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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223F ALA 3.0 18.9 + - - +
224F ILE 3.3 5.1 + - - +
226F PHE* 1.3 75.0 - - - +
228F LYS* 1.3 56.9 - - - +
230F ILE* 3.8 9.6 - - - +
231F GLU* 2.9 36.3 + - - +
238F TYR* 3.7 18.9 + - + -
256F LYS 5.5 0.4 - - - +
257F ILE* 3.9 27.4 - - + -
258F ASP 5.7 0.2 - - - +
259F ILE* 4.0 7.4 - - + +
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Residues in contact with LYS 228 (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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231A GLU* 4.4 17.2 + - - +
258A ASP* 4.6 15.7 + - + +
224F ILE* 3.1 14.9 + - + +
225F GLN* 3.5 13.2 - - - +
227F ALA* 1.3 76.9 - - - +
229F ALA* 1.3 60.8 + - - +
230F ILE 3.6 0.2 + - - -
231F GLU* 4.0 21.9 + - - +
232F GLU* 5.0 3.8 + - - +
256F LYS 5.8 3.6 - - - +
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Residues in contact with ALA 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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190F ILE* 3.6 20.2 - - + -
194F VAL* 3.6 28.2 - - + +
225F GLN 3.4 6.0 + - - +
226F PHE* 3.0 11.2 + - + +
228F LYS* 1.3 80.2 - - - +
230F ILE* 1.3 59.8 + - - +
232F GLU* 3.6 17.7 - - - +
233F PHE* 3.9 8.7 - - - -
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Residues in contact with ILE 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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194F VAL* 4.1 10.5 - - + -
197F VAL* 4.1 14.8 - - + -
212F VAL* 4.0 28.0 - - + -
226F PHE* 3.1 59.4 + - + +
227F ALA* 3.8 7.4 - - - +
229F ALA* 1.3 82.6 - - - +
231F GLU* 1.3 66.3 + - - +
232F GLU 3.1 3.6 - - - -
233F PHE* 2.9 29.0 + - + +
235F ILE* 3.6 18.6 - - + +
238F TYR* 4.6 6.7 - - + -
259F ILE* 4.2 8.5 - - + -
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Residues in contact with GLU 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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228D LYS* 4.7 6.1 - - - -
227F ALA 2.9 17.3 + - - +
228F LYS* 4.0 21.1 + - - +
229F ALA 3.7 1.2 - - - -
230F ILE* 1.3 76.7 - - - +
232F GLU* 1.3 61.2 + - - +
233F PHE 3.1 1.4 + - - -
234F ASN* 3.3 12.8 + - - -
235F ILE* 4.6 1.7 + - - -
258F ASP* 3.5 37.9 + - + +
259F ILE* 4.2 24.0 - - + +
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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