Contacts of the helix formed by residues 230 - 239 (chain F) in PDB entry 1PV2
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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211F ASP* 3.4 36.8 - - + +
214F ASP* 4.2 3.5 + - + -
215F LYS* 3.4 50.5 - - + +
226F HIS* 4.2 14.9 + - - +
227F LEU* 3.8 47.6 + - + -
228F THR 5.3 0.7 - - - -
229F TRP* 1.3 80.2 - - - +
231F PHE* 1.3 66.3 + - - +
232F GLY 3.4 0.3 + - - -
233F GLU* 3.5 9.9 + - + +
234F GLU* 3.3 24.1 + - - +
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Residues in contact with PHE 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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158F LEU* 4.2 4.9 - - + +
185F CYS 3.4 24.5 - - - -
186F HIS* 3.5 34.1 - + - -
188F PRO* 4.4 1.3 - - + -
189F ALA* 3.7 28.7 - - + -
192F LEU* 3.8 4.0 - - + -
208F ALA* 4.1 12.8 - - + -
209F PHE* 3.2 29.2 - - + -
211F ASP* 3.9 7.2 - - - -
214F ASP* 4.4 5.4 - - - -
227F LEU* 6.1 2.9 - - + -
229F TRP* 3.5 27.8 + - + -
230F TYR* 1.3 70.7 - - - +
232F GLY* 1.3 63.4 + - - +
234F GLU* 3.1 2.4 + - - +
235F LEU* 2.7 56.9 + - + +
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Residues in contact with GLY 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F PHE 5.3 1.8 - - - -
211F ASP* 3.2 17.9 + - - -
231F PHE* 1.3 89.7 - - - +
233F GLU* 1.3 61.0 + - - +
235F LEU* 3.4 0.8 + - - -
236F LYS* 3.1 24.9 + - - +
242F ILE* 3.4 30.1 - - - +
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Residues in contact with GLU 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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211F ASP* 2.8 15.3 + - - +
230F TYR* 3.7 12.8 - - + +
232F GLY* 1.3 73.9 - - - +
234F GLU* 1.3 70.9 + - - +
236F LYS* 3.1 21.0 + - - +
237F LYS* 2.9 42.4 + - - +
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Residues in contact with GLU 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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192F LEU* 3.9 21.4 - - + +
195F ARG* 4.9 18.0 + - - +
229F TRP* 4.1 20.1 - - + +
230F TYR 3.3 16.6 + - - +
231F PHE 3.1 7.3 + - - +
233F GLU* 1.3 94.1 - - - +
235F LEU* 1.3 58.4 + - - +
237F LYS* 3.3 20.0 + - - +
238F MET* 2.9 27.7 + - - +
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Residues in contact with LEU 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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188F PRO* 3.4 40.4 - - + +
191F PHE* 3.8 6.7 - - + -
192F LEU* 3.6 21.8 - - + -
206F ILE* 4.3 10.8 - - + -
231F PHE* 2.7 44.4 + - + +
232F GLY 3.7 4.5 - - - +
234F GLU* 1.3 70.8 - - - +
236F LYS* 1.3 62.6 + - - +
238F MET* 3.2 4.7 + - + +
239F GLY 3.1 6.1 + - - -
240F MET* 3.1 57.8 + - + +
242F ILE* 4.4 9.0 - - + -
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Residues in contact with LYS 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 GLY 3.1 17.7 + - - +
233F GLU* 3.3 23.6 - - - +
235F LEU* 1.3 74.7 - - - +
237F LYS* 1.3 64.6 + - - +
239F GLY* 3.2 13.9 + - - -
240F MET 3.6 16.9 - - - +
241F ASN* 5.6 0.7 - - - -
242F ILE* 4.4 24.7 + - + +
7G LYS* 5.7 7.1 - - - +
24G TYR* 5.2 10.1 - - - +
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Residues in contact with LYS 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 GLU* 2.9 27.3 + - - +
234F GLU* 3.5 24.9 - - - +
236F LYS* 1.3 77.0 - - - +
238F MET* 1.3 60.3 + - - +
239F GLY* 3.6 0.5 + - - -
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Residues in contact with MET 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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191F PHE* 3.5 26.0 - - + +
192F LEU* 4.3 6.1 - - + -
195F ARG* 3.9 40.2 - - + +
199F ASN* 2.9 52.3 - - - +
201F LEU* 4.8 1.3 - - + -
202F ASN* 4.0 5.0 - - - +
234F GLU 2.9 16.2 + - - +
235F LEU* 3.5 10.5 - - + +
236F LYS 3.1 0.6 - - - -
237F LYS* 1.3 79.4 - - - +
239F GLY* 1.3 55.8 + - - +
240F MET* 3.7 34.1 - - + -
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Residues in contact with GLY 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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202F ASN* 3.3 18.0 - - - +
203F GLY* 3.1 23.7 + - - -
235F LEU 3.1 1.2 + - - -
236F LYS 3.2 9.2 + - - -
237F LYS 4.6 0.4 - - - -
238F MET* 1.3 79.8 - - - +
240F MET* 1.3 66.8 + - - +
241F ASN* 4.0 3.5 - - - +
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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