Contacts of the helix formed by residues 161 - 173 (chain A) in PDB entry 2UVQ
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ASP* 5.0 7.8 - - - +
160A THR* 1.3 77.3 - - - +
162A SER* 1.3 65.8 + - - +
163A ASP* 3.5 16.1 - - - +
164A VAL* 3.1 14.9 + - + +
165A ARG* 3.0 17.8 + - - +
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Residues in contact with SER 162 (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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160A THR 3.5 1.2 + - - -
161A ASP* 1.3 72.6 - - - +
163A ASP* 1.3 59.5 + - - +
165A ARG* 2.7 33.1 + - - +
166A LEU* 2.8 31.1 + - - +
187A TYR* 4.0 15.5 + - - -
192A LYS* 5.5 8.2 + - - -
195A PHE* 4.2 9.5 - - - -
196A GLU* 5.7 0.9 + - - -
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Residues in contact with ASP 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP* 3.5 17.8 - - - +
162A SER* 1.3 75.6 - - - +
164A VAL* 1.3 71.3 + - - +
166A LEU* 3.5 10.6 + - + +
167A SER* 3.2 22.5 + - - -
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Residues in contact with VAL 164 (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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160A THR* 3.5 21.3 - - + -
161A ASP* 3.1 17.7 + - + +
163A ASP* 1.3 92.2 + - - +
165A ARG* 1.3 59.7 + - - +
167A SER* 2.6 24.8 + - - +
168A ARG* 3.1 30.1 + - + +
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Residues in contact with ARG 165 (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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31A GLY* 3.8 11.2 - - - +
32A THR* 3.2 34.9 + - - +
33A ALA* 3.5 16.8 - - - +
34A SER* 3.6 20.0 - - - +
160A THR* 2.9 33.7 + - + -
161A ASP 3.0 12.2 + - - +
162A SER* 2.7 38.2 + - - +
164A VAL* 1.3 77.1 - - - +
166A LEU* 1.3 56.3 + - - +
168A ARG* 3.2 2.1 + - - +
169A ARG* 2.9 32.1 + - - +
187A TYR* 4.8 11.9 + - - +
191A VAL* 6.3 1.2 - - - +
195A PHE* 3.2 41.1 - - - +
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Residues in contact with LEU 166 (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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162A SER 2.8 20.0 + - - +
163A ASP* 3.8 9.0 - - - +
164A VAL 3.3 0.2 - - - -
165A ARG* 1.3 72.0 - - - +
167A SER* 1.3 58.6 + - - +
169A ARG* 3.7 11.1 - - - +
170A VAL* 2.9 52.3 + - + +
183A ILE* 5.9 1.8 - - + -
184A LEU* 4.3 16.2 - - + -
187A TYR* 3.8 53.6 + - + +
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Residues in contact with SER 167 (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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163A ASP 3.2 12.8 + - - -
164A VAL* 2.6 24.9 + - - +
166A LEU* 1.3 79.1 - - - +
168A ARG* 1.3 61.0 + - - +
170A VAL* 3.9 5.7 - - - +
171A LEU* 3.2 27.6 + - - +
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Residues in contact with ARG 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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33A ALA* 3.1 31.6 + - + -
34A SER 3.1 23.0 + - - -
160A THR* 3.4 9.7 + - - +
164A VAL* 3.1 35.6 + - + +
165A ARG 3.5 5.8 - - - +
167A SER* 1.3 84.1 + - - +
169A ARG* 1.3 57.6 + - - +
171A LEU* 3.5 4.5 + - - +
172A ARG* 2.9 32.7 + - - +
212A ARG* 3.8 11.9 + - - +
1236A ADP 3.1 75.2 + - + +
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Residues in contact with ARG 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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32A THR* 3.5 38.7 + - + +
33A ALA* 3.9 12.7 - - + +
87A ASP* 4.1 10.9 + - - -
165A ARG* 2.9 18.6 + - - +
166A LEU* 3.7 11.0 - - + +
168A ARG* 1.3 74.1 - - - +
170A VAL* 1.3 66.1 + - - +
172A ARG* 3.4 10.6 + - - +
173A ASP* 3.1 44.8 + - - +
183A ILE* 5.0 11.9 - - + +
186A GLN* 5.7 1.4 + - - -
187A TYR* 4.0 20.3 - - - -
191A VAL* 3.2 36.8 - - - +
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Residues in contact with VAL 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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166A LEU* 2.9 45.3 + - + +
167A SER* 3.9 6.3 - - - +
169A ARG* 1.3 76.5 - - + +
171A LEU* 1.3 57.3 + - + +
173A ASP* 2.8 34.5 + - - +
174A VAL* 3.6 8.0 - - + +
180A LEU* 4.2 20.6 - - + -
183A ILE* 4.8 14.4 - - + +
184A LEU* 4.1 17.0 - - + -
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Residues in contact with LEU 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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167A SER 3.2 16.0 + - - +
168A ARG* 3.8 4.3 - - - +
170A VAL* 1.3 82.9 - - + +
172A ARG* 1.3 59.2 + - - +
173A ASP 3.5 0.3 + - - -
174A VAL* 3.8 20.2 + - + +
175A ARG* 5.7 0.2 + - - -
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Residues in contact with ARG 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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32A THR* 4.1 18.0 - - - +
33A ALA* 4.2 4.0 - - - +
37A SER* 4.7 4.2 + - - -
168A ARG 2.9 17.9 + - - +
169A ARG* 3.6 11.5 - - - +
170A VAL 3.1 0.2 - - - -
171A LEU* 1.3 77.1 - - - +
173A ASP* 1.3 68.6 + - - +
174A VAL 3.6 0.9 - - - -
175A ARG* 3.2 30.0 + - - +
1236A ADP 3.3 73.1 + - - +
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Residues in contact with ASP 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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169A ARG* 3.1 33.8 + - - +
170A VAL* 2.8 9.4 + - - +
172A ARG* 1.3 92.5 - - - +
174A VAL* 1.3 57.6 + - - +
175A ARG* 3.4 9.8 + - - +
179A ASP 5.0 3.5 + - - -
183A ILE* 3.1 40.8 - - + +
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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