Contacts of the helix formed by residues 166 - 178 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C SER* 1.3 79.2 - - - +
167C ALA* 1.3 67.3 + - - +
168C LYS* 3.1 29.4 - - + +
169C TYR* 3.0 16.5 + - + +
170C ALA 3.0 9.4 + - - -
188C PHE* 4.3 2.9 - - - -
189C ARG* 3.8 37.4 - - + +
190C GLU* 3.3 27.6 - - - +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LEU* 1.3 72.8 - - - +
168C LYS* 1.3 52.1 + - - +
169C TYR 2.9 6.1 + - - -
171C ASP* 2.7 46.3 + - - +
188C PHE* 3.5 47.1 - - + +
190C GLU* 5.6 1.5 + - - +
195E HIS* 4.2 7.6 - - + +
132F GLU 5.6 5.6 - - - +
133F GLY* 5.9 3.6 - - - -
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ILE* 3.5 26.5 - - + +
130C GLU* 3.0 32.7 + - + +
131C ILE* 4.3 15.0 - - - +
132C GLU 5.4 0.2 - - - +
166C LEU* 3.0 27.5 + - + +
167C ALA* 1.3 76.0 - - - +
169C TYR* 1.3 62.5 + - + +
171C ASP* 5.2 0.4 - - - -
172C PRO* 3.4 16.9 - - - +
130F GLU* 5.0 18.2 - - - +
132F GLU 6.3 0.2 - - - -
133F GLY* 5.3 7.8 - - - +
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Residues in contact with TYR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 3.9 12.7 - - + +
109C ASP* 2.7 40.2 + - - -
113C VAL* 4.3 9.0 - - - +
115C SER* 2.6 36.3 + - - -
117C PHE* 6.3 0.7 - + - -
129C ILE* 4.2 10.1 - - + -
138C VAL* 3.9 20.6 - - + -
165C SER* 3.5 22.4 - - - -
166C LEU* 3.0 8.3 + - + +
167C ALA 2.9 0.4 - - - -
168C LYS* 1.3 86.6 - - + +
170C ALA* 1.3 66.9 + - - +
171C ASP 3.3 0.9 - - - -
172C PRO* 3.3 9.1 - - - +
173C VAL* 3.0 43.1 - - + +
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Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 4.0 12.6 - - + -
161C LEU* 4.5 0.7 - - + -
163C THR* 4.0 8.1 - - + -
165C SER* 3.8 13.9 - - - +
166C LEU 3.0 8.7 + - - +
167C ALA 2.9 1.6 + - - -
169C TYR* 1.3 81.1 - - - +
171C ASP* 1.3 54.5 + - - +
173C VAL* 3.7 0.7 - - - +
174C THR* 2.5 43.8 + - - +
188C PHE* 3.4 32.1 - - + -
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Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ALA* 2.7 27.2 + - - +
168C LYS* 5.2 0.4 - - - -
170C ALA* 1.3 70.8 - - - +
172C PRO* 1.4 64.3 - - + +
173C VAL 3.1 0.2 + - - -
174C THR 3.1 0.7 + - - -
175C ASP* 2.7 37.3 + - - +
186C ARG* 2.9 22.1 + - - +
188C PHE* 3.1 20.5 - - - -
195E HIS* 2.5 34.1 + - - -
224E ILE* 4.2 8.3 - - + +
225E PHE* 3.9 12.9 - - + -
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Residues in contact with PRO 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C VAL* 4.1 24.9 - - + -
128C PRO* 5.5 1.8 - - + +
129C ILE* 4.1 2.7 - - + -
167C ALA 3.5 6.3 - - - +
168C LYS* 3.4 20.0 - - - +
169C TYR* 3.3 13.2 - - - +
171C ASP* 1.4 95.2 - - + +
173C VAL* 1.3 64.5 + - - +
175C ASP* 3.6 10.6 + - + +
176C LEU* 3.4 26.8 + - + +
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 4.0 26.5 - - + -
113C VAL* 4.3 17.3 - - + -
125C PHE* 5.1 3.9 - - + -
127C VAL* 4.4 13.0 - - + -
140C VAL* 4.3 27.1 - - + -
169C TYR* 3.0 46.4 + - + +
170C ALA 3.7 2.5 - - - +
171C ASP 3.1 0.6 - - - -
172C PRO* 1.3 79.6 - - - +
174C THR* 1.3 58.7 + - - +
176C LEU* 3.1 6.6 + - - +
177C LEU* 2.8 26.3 + - + +
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Residues in contact with THR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 4.2 9.5 - - + +
161C LEU* 3.5 20.5 - - + +
170C ALA 2.5 28.0 + - - -
173C VAL* 1.3 69.3 - - - +
175C ASP* 1.3 68.2 + - - +
177C LEU* 4.2 9.6 - - + +
178C ASP* 2.9 29.8 + - + +
183C PHE* 3.9 28.9 - - + -
186C ARG* 3.5 34.8 - - - +
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Residues in contact with ASP 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ASP* 2.7 26.6 + - - +
172C PRO* 3.8 9.5 - - + +
174C THR* 1.3 73.8 - - - +
176C LEU* 1.3 66.4 + - + +
178C ASP 4.1 10.3 + - - +
179C ARG* 5.2 1.7 - - - -
186C ARG* 2.8 27.6 + - - +
202E ASP* 4.9 3.1 - - - +
225E PHE* 3.9 35.0 - - - +
226E HIS* 6.1 1.6 - - - -
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 3.8 43.1 - - + -
126C ILE 4.9 2.7 - - - +
127C VAL* 3.9 23.8 - - + -
172C PRO* 3.4 15.0 + - + +
173C VAL 3.1 6.6 + - - +
175C ASP* 1.3 81.2 - - + +
177C LEU* 1.3 66.2 + - - +
178C ASP 3.6 0.2 + - - -
179C ARG* 4.5 11.4 + - - +
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 4.0 26.0 - - + -
112C LEU* 4.2 15.7 - - + -
113C VAL* 3.6 26.5 - - + -
125C PHE* 4.2 8.9 - - + -
142C LYS* 3.9 23.7 - - + +
146C VAL* 4.1 15.2 - - + +
147C ASP* 4.5 9.6 - - - +
150C LEU* 4.2 20.8 - - + +
173C VAL* 2.8 16.9 + - + +
174C THR* 4.0 5.6 - - + +
176C LEU* 1.3 79.5 - - - +
178C ASP* 1.3 58.8 + - + +
179C ARG* 3.1 11.8 + - - +
183C PHE* 5.4 3.6 - - + -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.5 9.7 - - + +
174C THR* 2.9 25.5 + - + +
175C ASP* 4.4 6.8 - - - +
176C LEU 3.5 0.6 - - - -
177C LEU* 1.3 72.1 - - + +
179C ARG* 1.3 60.8 + - - +
180C CYS* 4.1 2.1 + - - +
181C GLY* 3.2 12.3 + - - -
182C VAL* 2.9 41.5 + - - +
183C PHE* 3.3 41.1 + - + +
186C ARG* 5.1 3.6 + - - +
205E ARG* 4.6 2.8 + - - -
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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