Contacts of the helix formed by residues 167 - 178 (chain A) in PDB entry 2UVU
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 ASP 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.8 22.4 - - + -
165A VAL* 3.7 6.6 + - + +
166A ILE* 1.3 73.5 - - - +
168A ASP* 1.3 56.5 + - - +
169A GLU* 2.7 18.5 + - - +
170A GLU* 2.5 64.8 + - - +
171A VAL* 2.9 10.9 + - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.4 25.9 + - - -
146A LYS* 3.3 30.2 + - - +
166A ILE 4.0 0.2 + - - -
167A ASP* 1.3 71.4 - - - +
169A GLU* 1.3 68.8 + - + +
171A VAL* 3.3 19.7 + - - +
172A LYS* 3.3 22.4 + - - +
231A ASP* 4.9 1.0 - - - +
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASP* 2.7 19.0 + - - +
168A ASP* 1.3 79.3 - - - +
170A GLU* 1.3 58.3 + - - +
172A LYS* 3.5 37.9 + - - +
173A ARG* 3.4 15.9 + - - +
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A MET* 5.2 4.2 - - - +
164A LYS* 3.0 34.1 + - - -
165A VAL 3.6 1.7 - - - +
166A ILE* 3.5 23.2 - - + -
167A ASP* 2.5 30.4 + - - +
169A GLU* 1.3 70.7 - - - +
171A VAL* 1.3 64.2 + - - +
173A ARG* 2.8 40.3 + - + +
174A LEU* 2.9 23.4 + - + +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER* 4.1 7.2 - - - +
146A LYS* 3.6 24.9 - - + -
150A PHE* 3.8 33.2 - - + -
166A ILE* 3.8 17.9 - - + +
167A ASP 2.9 19.9 + - - +
168A ASP* 3.3 9.2 + - - +
170A GLU* 1.3 75.8 - - - +
172A LYS* 1.3 63.6 + - - +
174A LEU* 2.9 17.7 + - - +
175A ILE* 2.9 21.6 + - + +
231A ASP* 3.5 22.4 - - - +
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 3.5 16.6 - - - +
169A GLU* 3.5 40.6 + - - +
171A VAL* 1.3 79.2 - - - +
173A ARG* 1.3 61.9 + - - +
175A ILE* 3.7 18.1 + - + +
176A ARG* 3.7 15.3 + - - +
231A ASP* 4.6 11.7 - - + +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A MET* 5.2 6.3 - - - +
169A GLU 3.4 6.5 + - - +
170A GLU* 2.8 33.4 + - - +
172A LYS* 1.3 79.9 - - - +
174A LEU* 1.3 71.9 + - - +
176A ARG* 3.2 25.3 + - - +
177A GLU* 2.6 70.1 + - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 4.4 17.5 - - + -
153A ILE* 4.7 2.5 - - + -
157A MET* 4.5 18.8 - - + -
166A ILE* 3.7 33.0 - - + -
170A GLU* 2.9 21.6 + - + +
171A VAL 2.9 7.2 + - - +
173A ARG* 1.3 101.6 - - - +
175A ILE* 1.3 61.8 + - - +
176A ARG 2.8 5.8 - - - -
177A GLU* 5.0 1.3 - - + -
178A LEU* 2.8 61.5 + - + +
202A LEU* 4.7 3.0 - - - +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 4.1 8.1 - - + -
171A VAL* 2.9 36.1 + - + +
172A LYS* 3.9 11.0 - - + +
173A ARG 3.4 0.2 - - - -
174A LEU* 1.3 75.5 - - - +
176A ARG* 1.3 58.3 + - + +
202A LEU* 3.5 24.8 + - + +
203A VAL* 2.9 38.4 + - + +
206A LEU* 5.4 0.2 - - + -
228A LEU 3.4 20.2 - - - +
229A ALA* 3.6 31.0 - - - +
231A ASP* 4.0 15.5 - - + +
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS 3.7 10.0 + - - +
173A ARG* 3.2 33.0 + - - +
174A LEU 2.8 1.4 - - - -
175A ILE* 1.3 82.9 - - + +
177A GLU* 1.3 83.6 + - + +
201A LYS* 3.6 22.8 - - - +
203A VAL* 4.4 17.2 - - + +
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 2.6 73.6 + - - +
174A LEU* 4.7 3.1 - - + -
176A ARG* 1.3 97.6 + - - +
178A LEU* 1.3 58.7 + - - +
179A ASP 3.4 0.5 + - - -
201A LYS* 2.8 25.9 + - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 5.0 3.6 - - + -
153A ILE* 3.7 40.8 - - + -
157A MET* 5.9 4.9 - - + -
174A LEU* 2.8 52.2 + - + +
177A GLU* 1.3 71.2 - - - +
179A ASP* 1.3 78.0 + - - +
180A ILE* 3.2 3.5 + - - -
182A ASP* 3.6 26.9 - - + +
183A VAL* 4.0 14.8 - - + -
201A LYS* 3.3 16.3 - - - +
202A LEU* 4.3 6.0 + - + +
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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