Contacts of the helix formed by residues 175 - 184 (chain A) in PDB entry 2OTD
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ARG* 2.8 53.5 + - - +
174A ASP* 1.3 73.0 + - + +
176A TRP* 1.3 62.9 - - - +
177A ARG* 3.1 4.5 + - - -
178A GLU* 3.1 20.9 + - + +
179A LEU* 2.9 24.0 + - - +
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Residues in contact with TRP 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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167A LEU* 5.4 1.6 - - - -
169A LEU* 4.8 6.1 - - + -
172A TRP* 3.3 31.9 - + + +
173A ARG* 3.0 30.7 + - + +
174A ASP* 3.8 10.9 + - - +
175A ASP* 1.3 78.9 + - - +
177A ARG* 1.3 93.8 + - + +
179A LEU* 4.4 6.7 - - - -
180A THR* 2.6 42.5 + - + +
188A ILE* 4.3 16.4 - - + -
202A GLN* 3.8 36.1 - - + +
203A LEU* 3.6 25.6 - - + -
206A ALA* 3.7 31.9 - - + -
208A LEU* 4.1 12.1 - - + -
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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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174A ASP 5.0 1.1 + - - +
175A ASP 3.1 1.5 - - - -
176A TRP* 1.3 116.2 - - + +
178A GLU* 1.3 67.2 + - - +
180A THR* 3.2 3.9 + - - -
181A ALA* 3.1 27.8 + - + +
202A GLN* 4.5 8.1 + - - +
205A ASP* 5.2 2.0 - - - +
206A ALA* 3.3 34.2 - - + +
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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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175A ASP* 3.1 25.4 + - + +
177A ARG* 1.3 80.7 - - - +
179A LEU* 1.3 70.7 + - + +
181A ALA* 3.5 4.8 - - - +
182A ARG* 3.0 36.9 + - - +
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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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150A ILE* 4.1 14.1 - - + -
167A LEU* 3.8 23.3 - - + -
173A ARG* 3.4 44.0 - - - +
175A ASP* 2.9 20.6 + - - +
176A TRP* 4.0 4.7 - - - +
178A GLU* 1.3 84.7 - - + +
180A THR* 1.3 63.6 + - - +
182A ARG* 3.4 29.9 + - - +
183A LEU* 3.0 40.6 + - + +
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Residues in contact with THR 180 (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 LEU* 4.0 23.8 - - + -
176A TRP 2.6 26.2 + - - +
177A ARG* 3.2 7.8 + - - -
179A LEU* 1.3 75.5 - - - +
181A ALA* 1.3 56.8 + - - +
183A LEU* 3.5 1.0 + - - -
184A GLY 2.9 23.4 + - - -
185A CYS* 3.0 38.2 + - + +
188A ILE* 4.3 12.6 - - + -
208A LEU* 3.8 31.1 - - + +
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Residues in contact with ALA 181 (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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177A ARG* 3.1 21.1 + - + +
178A GLU* 3.5 7.0 - - - +
180A THR* 1.3 76.8 + - - +
182A ARG* 1.3 58.2 - - - +
184A GLY* 3.0 19.5 + - - -
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Residues in contact with ARG 182 (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 ILE* 3.6 18.8 - - - +
154A GLU* 2.8 32.5 + - - +
157A GLN* 2.9 22.5 + - - +
178A GLU* 3.0 31.4 + - - +
179A LEU* 3.7 17.5 - - - +
181A ALA* 1.3 73.4 - - - +
183A LEU* 1.3 71.2 + - - +
184A GLY 3.2 0.7 + - - -
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Residues in contact with LEU 183 (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 ILE* 4.0 8.7 - - + -
153A LEU* 3.8 38.1 - - + -
154A GLU* 4.0 16.4 - - + +
157A GLN* 3.1 14.3 + - - +
165A ARG* 2.9 31.7 + - - +
167A LEU* 4.3 6.5 - - + -
179A LEU* 3.0 35.4 + - + +
182A ARG* 1.3 111.8 - - - +
184A GLY* 1.3 57.8 + - - +
185A CYS* 3.7 17.9 - - - -
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Residues in contact with GLY 184 (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 GLN* 4.4 2.5 - - - -
165A ARG* 3.3 19.8 + - - +
180A THR 2.9 4.6 + - - -
181A ALA* 3.0 15.7 + - - -
182A ARG 3.1 1.6 + - - -
183A LEU* 1.3 77.5 - - - +
185A CYS* 1.3 63.4 + - - +
186A VAL* 3.5 4.5 + - - +
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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