Contacts of the helix formed by residues 168 - 179 (chain A) in PDB entry 2V4R
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A TYR* 3.6 32.1 - - + -
166A VAL* 3.4 11.8 + - + +
167A ILE* 1.3 73.1 - - - +
169A ASP* 1.3 64.3 + - - +
170A GLU* 3.0 42.2 + - - +
171A GLU* 3.3 11.0 + - - +
172A VAL* 2.9 26.5 + - - +
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Residues in contact with ASP 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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119A TYR* 3.3 25.4 + - - -
147A LYS* 2.9 32.8 + - - +
168A ASP* 1.3 72.8 - - - +
170A GLU* 1.3 67.2 + - - +
172A VAL* 3.8 10.7 + - - +
173A LYS* 3.2 27.2 + - - +
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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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168A ASP* 3.0 21.0 + - - +
169A ASP* 1.3 80.7 - - - +
171A GLU* 1.3 74.3 + - - +
173A LYS* 3.3 16.9 + - - +
174A ARG* 3.7 5.2 + - + +
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Residues in contact with GLU 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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158A MET* 4.2 5.9 - - - +
165A LYS* 4.0 22.7 + - - -
166A VAL 3.7 18.2 - - - +
167A ILE* 3.7 24.4 - - + +
168A ASP* 3.3 13.2 + - - +
170A GLU* 1.3 87.3 - - - +
172A VAL* 1.3 64.9 + - - +
174A ARG* 2.8 50.3 + - - +
175A LEU* 2.9 21.6 + - + +
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Residues in contact with VAL 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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146A SER* 4.1 3.6 - - - +
147A LYS* 3.4 37.2 - - + +
151A PHE* 3.5 31.4 - - + -
167A ILE* 3.8 20.0 - - + +
168A ASP 2.9 21.8 + - - +
169A ASP* 3.9 5.8 - - - +
170A GLU 3.3 0.2 - - - -
171A GLU* 1.3 74.3 - - - +
173A LYS* 1.3 59.1 + - - +
175A LEU* 3.1 6.1 + - - +
176A ILE* 3.0 42.7 + - + +
232A ASP* 4.6 6.3 - - - +
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Residues in contact with LYS 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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147A LYS* 3.0 19.2 - - - +
169A ASP* 3.2 23.6 + - - +
170A GLU* 3.3 7.2 + - - +
171A GLU 3.1 0.4 - - - -
172A VAL* 1.3 76.5 - - - +
174A ARG* 1.3 59.0 + - - +
176A ILE* 3.9 10.5 + - + +
177A ARG* 3.8 19.2 + - - +
232A ASP* 2.7 36.1 + - + +
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Residues in contact with ARG 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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170A GLU* 3.7 3.1 + - + +
171A GLU* 2.8 47.3 + - - +
173A LYS* 1.3 77.2 - - - +
175A LEU* 1.3 62.2 + - - +
177A ARG* 3.4 6.7 + - + +
178A GLU* 2.8 65.0 + - + +
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Residues in contact with LEU 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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151A PHE* 4.3 18.4 - - + -
154A ILE* 4.6 5.8 - - + -
158A MET* 4.7 12.8 - - - -
167A ILE* 3.3 48.0 - - + -
171A GLU* 2.9 24.3 + - + +
172A VAL* 3.6 6.7 - - - +
174A ARG* 1.3 82.3 - - - +
176A ILE* 1.3 57.9 + - - +
177A ARG 2.8 7.5 + - - -
178A GLU* 4.6 12.3 - - + +
179A LEU* 2.7 56.1 + - + +
203A LEU* 3.4 3.7 - - - +
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Residues in contact with ILE 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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151A PHE* 3.9 14.1 - - + -
172A VAL* 3.0 27.7 + - + +
173A LYS* 4.1 12.1 - - + +
174A ARG 3.4 0.2 - - - -
175A LEU* 1.3 75.7 - - - +
177A ARG* 1.3 57.1 + - - +
203A LEU* 3.8 15.2 - - + +
204A VAL* 2.9 36.5 + - + +
229A LEU 3.1 23.1 - - - +
230A ALA* 3.4 32.5 - - - +
232A ASP* 4.0 20.9 - - + -
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Residues in contact with ARG 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 LYS 3.8 13.1 + - - +
174A ARG* 3.5 10.5 - - + +
175A LEU 2.8 1.8 - - - -
176A ILE* 1.3 82.6 - - - +
178A GLU* 1.3 60.8 + - + +
179A LEU 3.8 0.2 - - - -
202A LYS* 3.7 21.8 - - - +
204A VAL* 3.6 35.0 - - - +
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Residues in contact with GLU 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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174A ARG* 2.8 48.7 + - + +
175A LEU* 4.5 7.0 - - + +
177A ARG* 1.3 76.9 - - + +
179A LEU* 1.3 72.7 + - - +
180A ASP 3.3 1.6 + - - -
202A LYS* 2.6 30.6 + - - +
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Residues in contact with LEU 179 (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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151A PHE* 5.6 0.2 - - + -
154A ILE* 3.4 45.3 - - + -
158A MET* 5.8 3.6 - - + -
175A LEU* 2.7 45.0 + - + +
178A GLU* 1.3 82.9 - - - +
180A ASP* 1.3 78.6 + - - +
181A ILE 3.2 3.1 + - - -
183A ASP* 3.7 27.8 - - + +
184A VAL* 4.5 9.9 - - + -
202A LYS* 3.5 10.3 - - - +
203A LEU* 3.3 22.7 - - + +
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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