Contacts of the helix formed by residues 226 - 240 (chain F) in PDB entry 1PQ3
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 GLY 226 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222F ILE* 2.8 18.2 + - - -
223F ASP 4.6 1.7 + - - -
224F ARG 3.6 1.0 - - - -
225F LEU* 1.3 80.3 - - - +
227F ILE* 1.3 66.8 + - - -
228F GLN* 3.1 4.9 + - - -
229F LYS 3.1 1.6 + - - -
230F VAL* 3.1 22.7 + - - +
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Residues in contact with ILE 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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223D ASP* 5.9 5.4 - - + +
196F ILE* 4.7 0.2 - - + -
222F ILE* 4.2 27.0 - - + +
226F GLY* 1.3 71.9 - - - -
228F GLN* 1.3 67.1 + - + +
230F VAL* 3.3 18.8 + - + +
231F MET* 3.2 25.0 + - + +
271F LEU* 4.8 0.4 - - + -
275F GLU* 4.0 40.8 + - + +
278F TYR* 3.9 29.4 - - + -
279F ILE* 3.7 29.6 - - + -
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Residues in contact with GLN 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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223D ASP 5.7 4.9 - - - +
224D ARG* 4.0 24.5 - - + +
226F GLY 3.1 1.2 + - - -
227F ILE* 1.3 81.3 - - + +
229F LYS* 1.3 65.0 + - - +
231F MET* 3.4 5.8 + - - +
232F GLU* 2.9 62.7 + - - +
278F TYR* 3.6 37.0 - - + +
282F GLU* 6.2 1.6 - - - -
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Residues in contact with LYS 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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225F LEU* 3.1 40.8 + - + +
226F GLY 3.1 2.0 + - - +
228F GLN* 1.3 80.8 - - - +
230F VAL* 1.3 64.7 + - - +
232F GLU* 3.2 22.9 + - + +
233F ARG* 3.1 53.7 + - + +
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Residues in contact with VAL 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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196F ILE* 4.4 14.8 - - + -
217F PHE* 3.7 40.7 - - + -
221F ASP 4.4 4.7 - - - +
222F ILE* 4.0 28.5 - - + -
225F LEU* 4.5 5.6 - - + -
226F GLY 3.1 19.4 + - - +
227F ILE* 3.4 19.1 - - + +
228F GLN 3.2 0.2 - - - -
229F LYS* 1.3 76.6 - - - +
231F MET* 1.3 57.5 + - - +
233F ARG* 3.2 7.7 + - - +
234F THR* 2.9 35.4 + - + +
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Residues in contact with MET 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F VAL* 5.4 1.1 - - + -
196F ILE* 3.8 25.6 - - + -
227F ILE* 3.2 18.2 + - + +
228F GLN* 3.8 7.0 - - - +
229F LYS 3.3 0.2 - - - -
230F VAL* 1.3 76.7 - - - +
232F GLU* 1.3 65.5 + - - +
234F THR* 3.7 7.4 + - - +
235F PHE* 3.1 60.9 + - + -
278F TYR* 4.9 4.5 - - + -
279F ILE* 3.9 44.2 - - + +
282F GLU* 3.8 26.7 - - + -
283F ILE* 4.2 5.8 - - + -
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Residues in contact with GLU 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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228F GLN* 2.9 41.8 + - - +
229F LYS* 3.3 29.0 + - + +
231F MET* 1.3 77.4 - - - +
233F ARG* 1.3 60.6 + - + +
235F PHE* 3.6 5.8 + - - +
236F ASP* 3.1 34.1 + - - +
282F GLU* 5.8 0.2 - - - +
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Residues in contact with ARG 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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217F PHE* 3.6 26.0 - - + -
224F ARG* 4.2 0.4 - - - +
225F LEU* 3.6 25.6 - - - +
229F LYS* 3.1 34.9 + - + +
230F VAL 3.5 7.6 - - - +
231F MET 3.1 0.4 - - - -
232F GLU* 1.3 78.7 - - + +
234F THR* 1.3 66.9 + - - +
235F PHE 3.2 1.3 - - - -
236F ASP* 2.9 11.4 + - - +
237F LEU* 2.8 30.0 + - + +
3074F SO4 2.5 45.0 + - - -
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Residues in contact with THR 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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140F VAL* 4.9 7.2 - - - +
194F VAL* 3.8 17.7 - - + -
196F ILE* 3.8 21.2 - - + +
217F PHE* 3.5 22.9 - - + -
230F VAL 2.9 22.3 + - - +
231F MET* 3.4 12.3 + - - +
233F ARG* 1.3 73.8 - - - +
235F PHE* 1.3 72.9 + - - +
237F LEU* 3.1 11.6 + - - +
238F LEU* 2.9 33.7 + - - +
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Residues in contact with PHE 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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140F VAL* 4.9 8.5 - - + -
231F MET* 3.1 45.3 + - + +
232F GLU* 3.9 5.4 - - - +
234F THR* 1.3 88.2 + - - +
236F ASP* 1.3 61.0 + - - +
238F LEU* 4.4 5.2 - - + +
239F ILE* 2.8 55.1 + - + +
240F GLY* 3.2 3.5 + - - -
246F ILE* 4.2 11.0 - - + -
282F GLU* 3.8 20.2 - - + -
283F ILE* 3.7 21.8 - - + -
286F THR* 3.4 30.1 - - + -
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Residues in contact with ASP 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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232F GLU* 3.1 22.3 + - - +
233F ARG* 2.9 15.4 + - - +
235F PHE* 1.3 78.0 - - - +
237F LEU* 1.3 66.2 + - + +
240F GLY* 3.2 28.1 + - - -
241F LYS* 4.9 4.5 + - - -
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Residues in contact with LEU 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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191F ALA 4.6 8.1 - - - +
194F VAL* 4.2 13.0 - - + -
215F GLN* 4.0 33.2 - - + +
217F PHE* 4.3 16.8 - - + -
233F ARG* 2.8 36.6 + - + +
234F THR* 3.1 9.8 + - - +
236F ASP* 1.3 81.1 - - + +
238F LEU* 1.3 65.1 + - + +
241F LYS* 3.4 20.0 + - - +
244F ARG* 5.2 1.7 + - - -
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Residues in contact with LEU 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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138F CYS* 3.9 25.8 - - + -
139F VAL 3.9 11.9 - - - +
140F VAL* 3.7 29.6 - - + -
191F ALA 3.9 10.8 - - - +
192F SER* 3.7 30.1 - - - +
194F VAL* 3.8 22.9 - - + -
234F THR* 2.9 22.3 + - - +
235F PHE* 4.5 6.1 - - + +
237F LEU* 1.3 79.2 - - - +
239F ILE* 1.3 62.7 + - + +
240F GLY 3.5 1.2 + - - -
241F LYS* 5.0 5.1 + - - +
242F ARG* 4.5 2.3 + - - +
244F ARG* 3.3 27.4 + - - +
246F ILE* 6.0 0.4 - - + -
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Residues in contact with ILE 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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138F CYS* 4.3 9.6 - - - -
235F PHE* 2.8 48.3 + - + +
238F LEU* 1.3 78.0 - - + +
240F GLY* 1.3 64.2 + - - +
241F LYS 3.4 2.2 - - - -
242F ARG 3.4 26.5 + - - +
243F GLN* 4.4 10.4 + - - +
244F ARG* 3.9 17.9 - - + +
246F ILE* 4.5 3.8 - - + -
286F THR* 4.2 12.3 - - + -
288F LEU* 3.7 32.1 - - + -
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Residues in contact with GLY 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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235F PHE 3.2 3.5 + - - -
236F ASP* 3.2 31.6 + - - -
238F LEU 3.5 2.0 - - - -
239F ILE* 1.3 78.8 - - - +
241F LYS* 1.3 62.1 + - - +
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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