Contacts of the helix formed by residues 190 - 195 (chain B) in PDB entry 2OUX
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 LEU 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A TYR* 4.2 3.6 - - + -
190A LEU* 3.6 33.7 - - + -
194A ILE* 4.5 10.8 - - + -
159B MSE 3.7 33.4 - - + -
162B LEU* 4.8 7.2 - - + -
172B ILE* 3.6 27.5 + - + +
173B TYR* 2.9 35.6 + - + +
175B VAL* 5.0 1.0 - - - +
188B ILE 4.0 0.6 + - - -
189B SER* 1.3 71.4 - - - +
191B ARG* 1.3 56.4 + - - +
193B LEU* 3.1 15.0 + - + +
194B ILE* 2.9 36.9 + - + +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TYR* 5.0 2.4 + - - -
166A ALA 2.9 26.4 + - - -
167A ASP* 3.6 15.2 + - - +
169A ALA* 2.8 29.7 + - - +
170A GLU 3.1 17.8 + - - -
171A THR* 4.2 3.2 - - - +
172A ILE* 4.0 34.3 - - + +
173A TYR* 3.1 29.6 + - + +
189B SER* 2.9 7.8 - - - +
190B LEU* 1.3 80.5 - - - +
192B ASP* 1.3 63.5 + - - +
194B ILE* 3.6 2.1 + - - +
195B VAL* 3.5 27.9 + - + +
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Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 3.8 17.1 - - + +
189B SER* 2.8 32.6 + - - +
191B ARG* 1.3 78.3 - - - +
193B LEU* 1.3 64.4 + - - +
195B VAL* 3.5 9.8 - - - +
196B ASN* 2.7 36.9 + - - +
205B ILE* 5.4 4.8 - - + +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL* 3.7 36.1 - - + +
158B ALA* 4.1 22.0 - - + -
159B MSE 4.2 17.3 - - - -
162B LEU* 4.4 15.5 - - + -
175B VAL* 4.4 13.9 - - + -
188B ILE* 3.7 26.4 - - + +
189B SER 3.1 11.5 + - - +
190B LEU* 3.1 27.5 + - + +
192B ASP* 1.3 77.5 - - - +
194B ILE* 1.3 64.0 + - - +
196B ASN* 3.1 20.5 + - - +
202B ILE* 5.3 4.7 - - + -
205B ILE* 4.6 0.4 - - + -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MSE 3.2 34.8 - - + -
162A LEU* 4.3 8.5 - - + +
163A LYS* 3.3 41.2 - - - +
172A ILE* 4.8 5.6 - - + -
190A LEU* 4.7 11.4 - - + -
194A ILE* 4.7 3.1 - - + -
159B MSE 4.1 25.8 - - + -
190B LEU* 2.9 31.6 + - + +
191B ARG* 3.9 5.8 - - - +
192B ASP 3.4 0.2 - - - -
193B LEU* 1.3 77.1 - - - +
195B VAL* 1.3 64.7 + - + +
196B ASN 3.4 3.0 + - - +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU 3.9 14.1 - - - +
163A LYS* 3.6 35.5 - - - +
166A ALA 6.3 1.1 - - - -
167A ASP* 6.6 0.7 - - - -
172A ILE* 6.0 1.1 - - + -
191B ARG* 3.5 21.5 + - + +
192B ASP* 3.5 18.8 - - - +
193B LEU 3.2 0.2 - - - -
194B ILE* 1.3 80.4 - - + +
196B ASN* 1.3 65.2 + - - +
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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