Contacts of the helix formed by residues 175 - 184 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C ARG* 2.8 48.0 + - - +
174C ASP* 1.3 78.5 + - + +
176C TRP* 1.3 65.9 + - - +
177C ARG 3.2 2.9 - - - -
178C GLU* 3.3 27.6 + - + +
179C LEU* 2.9 30.8 + - - +
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Residues in contact with TRP 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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167C LEU* 5.3 2.0 - - - -
169C LEU* 4.7 10.1 - - + -
172C TRP* 3.1 33.5 - + + +
173C ARG* 3.2 30.9 + - - +
174C ASP 4.4 7.7 + - - -
175C ASP* 1.3 77.5 + - - +
177C ARG* 1.3 100.6 + - + +
179C LEU* 3.7 4.2 - - - +
180C THR* 2.9 35.1 + - - +
188C ILE* 4.5 15.9 - - + -
202C GLN* 3.4 41.5 - - + +
203C LEU* 3.5 27.8 - - + -
206C ALA* 3.9 16.6 - - + -
208C LEU* 3.9 17.0 - - + -
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Residues in contact with ARG 177 (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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174C ASP 5.4 0.2 + - - -
175C ASP 3.2 0.8 - - - -
176C TRP* 1.3 112.7 - - + +
178C GLU* 1.3 68.1 + - + +
180C THR* 3.4 5.2 + - - +
181C ALA* 3.0 26.7 + - + +
202C GLN 5.2 2.0 + - - -
205C ASP* 4.2 8.1 + - - +
206C ALA* 3.6 38.4 + - + +
208C LEU* 5.5 0.4 - - + -
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Residues in contact with GLU 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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174C ASP 4.5 3.6 - - - +
175C ASP* 3.3 29.0 + - + +
177C ARG* 1.3 78.1 - - + +
179C LEU* 1.3 59.3 + - - +
181C ALA* 3.3 6.7 - - - +
182C ARG* 2.9 31.7 + - - +
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Residues in contact with LEU 179 (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 ILE* 3.6 20.2 - - + -
167C LEU* 4.2 12.3 - - + -
173C ARG* 3.2 48.2 - - - +
175C ASP* 2.9 19.9 + - - +
176C TRP* 3.7 4.5 - - - +
178C GLU* 1.3 74.9 - - - +
180C THR* 1.3 66.1 + - - +
182C ARG* 3.3 34.7 + - - +
183C LEU* 3.1 51.4 + - + +
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Residues in contact with THR 180 (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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167C LEU* 4.0 29.4 - - + -
176C TRP 2.9 21.8 + - - +
177C ARG* 3.4 11.3 + - - +
179C LEU* 1.3 71.5 - - - +
181C ALA* 1.3 67.1 + - - +
183C LEU* 3.4 0.6 + - - -
184C GLY* 3.0 17.2 + - - -
185C CYS* 3.1 24.6 + - + +
187C SER 4.8 0.2 - - - +
188C ILE* 4.4 16.2 - - + -
208C LEU* 3.8 35.7 - - + +
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Residues in contact with ALA 181 (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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177C ARG* 3.0 22.5 + - + +
178C GLU* 3.3 7.9 - - - +
180C THR* 1.3 77.8 + - - +
182C ARG* 1.3 57.6 + - - +
184C GLY* 3.0 19.8 + - - -
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Residues in contact with ARG 182 (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 ILE* 4.1 7.5 - - - +
154C GLU* 3.1 33.3 + - - +
157C GLN* 3.0 18.9 + - - +
178C GLU 2.9 17.3 + - - +
179C LEU* 3.3 32.6 + - - +
181C ALA* 1.3 76.7 - - - +
183C LEU* 1.3 66.4 + - - +
184C GLY 3.5 0.2 + - - -
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Residues in contact with LEU 183 (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 ILE* 4.8 5.6 - - + -
153C LEU* 4.3 18.8 - - + -
154C GLU* 3.9 32.1 - - + +
157C GLN* 2.9 21.3 + - - +
165C ARG* 2.7 38.2 + - - +
167C LEU* 4.3 17.3 - - + -
179C LEU* 3.1 44.8 + - + +
180C THR* 4.8 0.2 - - - -
182C ARG* 1.3 93.5 - - - +
184C GLY* 1.3 54.1 + - - +
185C CYS* 3.5 17.9 + - - -
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Residues in contact with GLY 184 (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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157C GLN* 3.8 1.8 - - - +
164C PRO* 5.9 0.3 - - - +
165C ARG* 3.1 21.4 + - - +
180C THR 3.0 1.5 + - - -
181C ALA 3.0 17.1 + - - -
182C ARG 3.2 1.0 + - - -
183C LEU* 1.3 76.9 - - - +
185C CYS* 1.3 62.6 + - - +
186C VAL* 3.8 3.1 + - - +
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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