Contacts of the helix formed by residues 165 - 172 (chain F) in PDB entry 4OA5
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 PHE 165 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLN* 3.5 31.6 - - + -
12A TYR* 5.5 0.2 - + - -
13A LEU* 4.1 17.0 - - + -
322A EDO 3.7 14.6 - - - -
164F THR* 1.3 82.4 + - - +
166F LEU* 1.3 66.0 + - - +
167F PHE 4.4 1.1 - - - +
168F GLY* 3.0 18.7 + - - +
170F VAL* 3.2 21.9 + - + +
171F PHE* 3.6 29.2 - + + -
204F ILE* 3.4 34.1 - - + -
206F PRO* 4.1 9.6 - - + -
207F THR 3.4 18.2 - - - -
208F SER 3.9 3.1 - - - +
209F GLU 3.1 12.0 + - - +
210F GLY* 3.5 16.2 - - - -
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Residues in contact with LEU 166 (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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139F LYS* 4.0 30.1 - - + -
163F ASN* 2.9 14.9 + - - +
164F THR 3.2 0.4 - - - -
165F PHE* 1.3 77.6 - - - +
167F PHE* 1.3 88.4 + - + +
169F SER* 2.8 38.9 + - - +
170F VAL* 4.4 3.6 - - + -
179F VAL* 4.1 9.8 - - + +
183F ALA* 3.7 11.0 - - + +
184F HIS* 3.4 40.2 - - + +
187F MET* 4.3 18.2 - - + -
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Residues in contact with PHE 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F LYS* 4.4 17.3 - - + -
163F ASN* 3.8 24.4 + - + +
165F PHE* 3.3 2.9 - - - +
166F LEU* 1.3 100.8 - - + +
168F GLY* 1.3 56.9 + - - +
169F SER* 3.3 1.9 + - - -
179F VAL* 4.3 15.7 - - + -
208F SER 5.6 4.9 + - - -
209F GLU* 5.1 8.4 + - + +
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Residues in contact with GLY 168 (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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165F PHE* 3.0 13.4 + - - +
167F PHE* 1.3 78.2 - - - +
169F SER* 1.3 58.2 + - - +
170F VAL 3.4 2.5 - - - -
171F PHE* 3.2 40.6 + - - +
172F ASP* 5.1 3.8 - - - +
208F SER 5.8 0.6 + - - -
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Residues in contact with SER 169 (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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166F LEU* 2.8 39.8 + - - +
167F PHE 3.3 2.7 + - - -
168F GLY* 1.3 75.3 - - - +
170F VAL* 1.3 62.3 + - - +
171F PHE 3.2 4.4 + - - -
172F ASP* 3.4 14.1 + - - +
174F HIS 4.8 1.4 - - - +
176F THR* 4.5 14.4 - - - -
179F VAL* 3.6 25.0 - - - +
184F HIS* 3.0 23.3 + - - -
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Residues in contact with VAL 170 (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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12A TYR* 3.6 12.0 - - + +
164F THR 3.4 20.9 - - - +
165F PHE* 3.2 23.3 + - + +
166F LEU* 4.4 3.6 - - + -
169F SER* 1.3 82.1 + - - +
171F PHE* 1.3 73.8 + - + +
172F ASP 3.3 0.2 - - - -
184F HIS* 4.1 6.1 - - + +
187F MET* 4.1 8.1 - - + -
188F ARG* 2.9 55.5 + - + +
191F ASN* 3.7 21.5 - - - +
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Residues in contact with PHE 171 (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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8A LYS* 4.1 25.6 - - + +
9A GLN* 3.5 53.6 - - + -
12A TYR* 3.6 39.0 - + + +
320A IOD 4.1 11.2 - - + -
165F PHE* 3.6 36.1 - + + -
168F GLY* 3.2 32.1 - - - +
169F SER 3.2 1.0 - - - -
170F VAL* 1.3 84.0 - - + +
172F ASP* 1.3 62.5 + - - +
173F GLU 4.2 0.5 + - - -
188F ARG* 3.6 7.1 + - - -
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Residues in contact with ASP 172 (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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8A LYS* 5.4 5.6 - - - +
168F GLY 5.1 4.5 - - - +
169F SER* 3.4 8.0 + - - +
170F VAL 3.3 0.6 - - - -
171F PHE* 1.3 84.2 - - - +
173F GLU* 1.3 59.8 + - - +
174F HIS* 3.6 26.7 + - + +
176F THR* 5.6 5.7 - - - +
184F HIS* 2.9 28.1 + - - -
188F ARG* 3.8 6.3 + - - -
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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