Contacts of the helix formed by residues 165 - 172 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E THR* 1.3 80.2 + - - +
166E LEU* 1.3 65.9 + - - +
167E PHE 4.4 0.9 - - - +
168E GLY* 3.0 21.5 + - - +
169E SER 3.3 0.2 + - - -
170E VAL* 3.2 22.9 + - + +
171E PHE* 3.6 34.3 - + + -
204E ILE* 3.5 38.6 - - + -
206E PRO* 4.0 19.7 - - + -
207E THR 3.4 20.9 - - - -
208E SER 4.0 7.2 - - - +
209E GLU 3.1 11.5 + - - +
210E GLY* 3.5 17.0 - - - -
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Residues in contact with LEU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E LYS* 3.6 31.0 - - + +
163E ASN* 3.0 14.8 + - - +
164E THR 3.2 0.2 - - - -
165E PHE* 1.3 77.9 - - - +
167E PHE* 1.3 82.2 + - + +
169E SER* 2.8 37.9 + - - +
170E VAL* 4.4 3.6 - - + -
179E VAL* 4.1 9.5 - - + +
183E ALA* 3.6 17.9 - - + +
184E HIS* 3.4 41.1 - - + +
187E MET* 4.3 17.7 - - + -
209E GLU 4.2 0.2 + - - -
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Residues in contact with PHE 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E LYS* 3.8 33.9 - - + -
163E ASN* 3.9 22.9 - - + +
165E PHE* 3.3 2.6 - - - +
166E LEU* 1.3 92.3 - - + +
168E GLY* 1.3 57.3 + - - +
169E SER* 3.3 2.1 + - - -
179E VAL* 4.3 16.2 - - + -
208E SER 5.6 5.4 + - - -
209E GLU* 5.1 6.6 + - + +
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Residues in contact with GLY 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E PHE* 3.0 12.7 + - - +
167E PHE* 1.3 77.6 - - - +
169E SER* 1.3 58.3 + - - +
170E VAL 3.3 3.4 - - - -
171E PHE* 3.2 39.2 + - - +
172E ASP* 4.9 4.5 - - - +
208E SER 5.7 0.6 + - - -
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Residues in contact with SER 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E LEU* 2.8 39.8 + - - +
167E PHE 3.3 2.7 + - - -
168E GLY* 1.3 74.8 - - - +
170E VAL* 1.3 64.2 + - - +
171E PHE 3.2 4.2 + - - -
172E ASP* 3.4 14.4 + - - +
174E HIS 4.8 0.9 - - - +
176E THR* 4.4 14.8 - - - -
179E VAL* 3.6 24.6 - - - +
184E HIS* 3.0 24.0 + - - -
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Residues in contact with VAL 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E THR 3.4 19.7 - - - +
165E PHE* 3.2 23.4 + - + +
166E LEU* 4.4 3.6 - - + -
168E GLY 3.3 0.2 - - - -
169E SER* 1.3 80.3 + - - +
171E PHE* 1.3 73.3 + - + +
172E ASP 3.3 0.4 - - - -
184E HIS* 4.1 8.3 - - + +
187E MET* 3.9 7.9 - - + -
188E ARG* 2.9 60.5 + - + +
191E ASN* 3.7 21.8 - - + +
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Residues in contact with PHE 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E PHE* 3.6 49.8 - + + -
168E GLY* 3.2 30.7 - - - +
169E SER 3.2 1.0 - - - -
170E VAL* 1.3 87.0 - - + +
172E ASP* 1.3 64.8 + - - +
173E GLU 4.1 0.2 + - - -
188E ARG* 3.7 7.9 + - - +
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Residues in contact with ASP 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLY 4.9 5.4 - - - +
169E SER* 3.4 7.8 + - - +
170E VAL 3.3 0.4 - - - -
171E PHE* 1.3 84.1 - - - +
173E GLU* 1.3 60.9 + - - +
174E HIS* 3.6 39.4 + - + +
176E THR* 5.5 7.5 - - + +
184E HIS* 2.9 28.1 + - - -
188E ARG* 3.8 6.8 + - - -
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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