Contacts of the helix formed by residues 166 - 178 (chain A) in PDB entry 2Q5E
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A SER* 1.3 76.4 - - - +
167A ALA* 1.3 62.0 + - - +
168A LYS* 4.2 31.6 - - + -
169A TYR* 3.0 12.3 + - + +
170A ALA* 2.8 22.5 + - - -
189A ARG* 3.6 45.2 - - + +
190A GLU* 5.5 5.4 - - + +
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Residues in contact with ALA 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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165A SER 3.8 2.0 + - - -
166A LEU* 1.3 72.3 - - - +
168A LYS* 1.3 58.2 + - - +
170A ALA 2.8 3.4 + - - +
171A ASP* 2.8 36.1 + - + +
188A PHE* 3.5 44.9 - - + +
190A GLU* 4.7 6.7 + - - +
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Residues in contact with LYS 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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129A ILE* 3.8 28.3 - - + +
130A GLU 4.1 12.0 + - - +
131A ILE* 3.4 32.0 - - - +
132A GLU 5.0 3.0 - - - +
166A LEU* 4.2 30.5 - - + +
167A ALA* 1.3 77.5 - - - +
169A TYR* 1.3 59.7 + - + +
171A ASP* 5.5 0.2 - - - -
172A PRO* 3.3 21.8 - - - +
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Residues in contact with TYR 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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108A LEU* 4.2 10.3 - - + -
109A ASP* 2.5 41.7 + - - -
113A VAL* 4.4 5.2 - - - +
115A SER* 2.6 33.3 + - - -
129A ILE* 3.8 26.2 - - + +
138A VAL* 3.9 13.7 - - + -
165A SER* 3.6 22.4 - - - -
166A LEU* 3.0 11.2 + - + +
167A ALA 3.3 0.2 - - - -
168A LYS* 1.3 84.2 - - + +
170A ALA* 1.3 63.7 + - - +
171A ASP 3.5 0.2 - - - -
172A PRO* 3.4 9.5 - - - +
173A VAL* 3.4 33.9 + - + +
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Residues in contact with ALA 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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108A LEU* 4.2 10.8 - - + -
163A THR* 4.0 7.9 - - + -
165A SER* 3.4 22.4 - - - +
166A LEU 2.8 11.4 + - - +
167A ALA 2.8 3.6 + - - -
169A TYR* 1.3 77.0 - - - +
171A ASP* 1.3 55.1 + - - +
173A VAL* 3.4 1.6 + - - +
174A THR* 2.9 35.9 + - - +
188A PHE* 3.3 30.3 - - + -
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Residues in contact with ASP 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 ALA* 2.8 23.8 + - + +
170A ALA* 1.3 71.6 - - - +
172A PRO* 1.3 66.5 - - + +
175A ASP* 2.9 27.8 + - - +
186A ARG* 3.0 31.5 + - - +
188A PHE* 3.0 27.0 - - + -
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Residues in contact with PRO 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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127A VAL* 4.2 23.3 - - + -
128A PRO 5.9 0.7 - - - +
129A ILE* 5.0 2.2 - - + -
167A ALA 3.6 1.1 - - - +
168A LYS* 3.3 27.6 - - - +
169A TYR 3.4 6.1 - - - +
171A ASP* 1.3 94.5 - - + +
173A VAL* 1.3 61.8 + - - +
175A ASP* 3.4 9.6 + - + +
176A LEU* 3.1 32.3 + - + +
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Residues in contact with VAL 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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108A LEU* 4.0 28.9 - - + -
113A VAL* 4.4 14.8 - - + -
125A PHE* 4.3 3.5 - - + -
127A VAL* 4.1 16.4 - - + -
138A VAL* 5.3 0.2 - - + -
140A VAL* 4.1 26.0 - - + -
169A TYR* 3.4 43.7 + - + +
170A ALA 3.4 3.3 + - - +
171A ASP 3.3 0.4 - - - -
172A PRO* 1.3 76.4 - - - +
174A THR* 1.3 52.1 + - - +
176A LEU* 3.2 6.7 + - - +
177A LEU* 2.7 36.7 + - + +
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Residues in contact with THR 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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108A LEU* 4.1 9.2 - - - +
161A LEU* 3.0 34.2 - - + +
170A ALA 2.9 20.9 + - - -
173A VAL* 1.3 71.3 - - - +
175A ASP* 1.3 58.7 + - - +
177A LEU* 4.1 8.5 - - + -
178A ASP* 2.7 32.9 + - + +
183A PHE* 3.8 25.6 - - + -
186A ARG* 3.7 27.1 - - - +
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Residues in contact with ASP 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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171A ASP* 2.9 25.1 + - - +
172A PRO* 3.5 11.1 - - + +
174A THR* 1.3 71.4 - - - +
176A LEU* 1.3 63.2 + - + +
178A ASP* 4.2 10.7 + - - +
179A ARG* 4.7 2.3 + - - -
186A ARG* 2.6 37.8 + - - +
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Residues in contact with LEU 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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125A PHE* 4.0 38.4 - - + -
126A ILE 5.1 2.7 - - - +
127A VAL* 4.1 27.1 - - + -
172A PRO* 3.1 19.3 + - + +
173A VAL 3.8 2.2 - - - +
175A ASP* 1.3 82.1 - - + +
177A LEU* 1.3 68.6 + - - +
179A ARG* 4.1 10.4 + - - +
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Residues in contact with LEU 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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108A LEU* 3.7 28.3 - - + -
112A LEU* 3.8 24.0 - - + -
113A VAL* 4.1 14.1 - - + -
125A PHE* 3.7 15.3 - - + -
142A LYS* 4.5 8.3 - - + -
146A VAL* 3.9 35.0 - - + -
147A ASP* 4.0 12.6 - - - +
150A LEU* 4.3 11.7 - - + +
173A VAL 2.7 22.5 + - - +
174A THR* 3.9 4.3 - - - +
176A LEU* 1.3 75.5 - - - +
178A ASP* 1.3 52.7 + - - +
179A ARG* 2.7 18.9 + - - +
183A PHE* 4.6 8.5 - - + -
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Residues in contact with ASP 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 LEU* 4.7 8.8 - - - +
174A THR* 2.7 23.9 + - + +
175A ASP* 4.4 6.4 - - - +
176A LEU 3.5 0.2 - - - -
177A LEU* 1.3 69.4 - - - +
179A ARG* 1.3 57.3 + - - +
180A CYS 2.9 10.0 + - - -
181A GLY* 3.1 12.4 + - - -
182A VAL* 3.1 28.2 + - - +
183A PHE* 2.9 57.1 + - + +
186A ARG* 5.0 5.8 + - - +
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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