Contacts of the helix formed by residues 174 - 189 (chain C) in PDB entry 2OQH
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 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C ARG* 3.1 27.0 + - - +
172C THR* 3.1 11.1 + - - +
173C THR* 1.3 77.5 + - - +
175C CYS* 1.3 62.5 + - - +
176C ALA* 3.7 6.9 + - - +
177C GLY* 3.1 19.9 + - - -
178C ASP* 3.1 23.4 + - - -
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Residues in contact with CYS 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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173C THR 3.1 16.0 + - - -
174C ASP* 1.3 71.6 + - - +
176C ALA* 1.3 64.1 + - - +
178C ASP* 3.1 4.9 + - - +
179C VAL* 3.0 28.8 + - - +
202C TRP* 3.4 46.6 - - + +
206C ASP* 3.8 30.1 - - + +
210C ALA* 4.6 12.1 - - + -
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Residues in contact with ALA 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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174C ASP* 3.4 6.0 + - - +
175C CYS* 1.3 77.5 - - - +
177C GLY* 1.3 58.0 + - - +
179C VAL* 3.2 9.6 + - - +
180C ALA* 2.8 29.2 + - - +
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Residues in contact with GLY 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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136C ARG* 3.3 7.9 - - - -
147C LEU* 6.1 1.3 - - - -
148C PRO* 5.1 0.2 - - - +
174C ASP* 3.1 28.8 + - - -
176C ALA* 1.3 74.5 - - - +
178C ASP* 1.3 60.6 + - - +
180C ALA* 3.3 6.9 + - - +
181C ILE* 2.9 34.5 + - - +
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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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136C ARG* 2.8 22.8 + - - +
169C LEU* 4.0 14.2 - - + +
170C LYS 4.7 1.2 - - - +
171C GLY* 3.6 9.8 - - - -
172C THR* 2.9 42.0 + - - +
174C ASP 3.1 13.0 + - - +
175C CYS 3.1 6.0 + - - +
177C GLY* 1.3 75.2 - - - +
179C VAL* 1.3 63.9 + - - +
181C ILE* 3.1 4.1 + - - +
182C LEU* 2.9 30.0 + - + +
196C VAL* 5.0 3.1 - - + -
202C TRP* 3.2 27.1 + - + -
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Residues in contact with VAL 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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175C CYS 3.0 16.2 + - - +
176C ALA* 3.5 9.2 - - - +
178C ASP* 1.3 78.5 - - + +
180C ALA* 1.3 57.5 + - - +
182C LEU* 3.3 3.2 + - - +
183C ARG* 2.9 58.9 + - - +
202C TRP* 5.4 0.7 - - + -
210C ALA* 4.0 32.3 - - + +
213C ALA* 4.0 16.2 - - + -
214C LEU* 4.2 25.1 - - + +
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Residues in contact with ALA 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PRO* 3.5 27.1 - - + +
176C ALA 2.8 16.9 + - - +
177C GLY* 3.6 9.0 - - - +
179C VAL* 1.3 76.7 - - - +
181C ILE* 1.3 63.3 + - - +
183C ARG* 3.5 14.8 + - - +
184C ALA* 3.3 15.9 + - - +
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Residues in contact with ILE 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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136C ARG* 3.6 32.1 - - + +
147C LEU* 3.8 20.9 - - + -
148C PRO* 4.1 20.9 - - + -
151C MSE 3.6 33.4 - - + -
169C LEU* 3.9 24.9 - - + -
177C GLY 2.9 22.1 + - - +
178C ASP* 3.5 6.5 - - - +
180C ALA* 1.3 74.1 - - - +
182C LEU* 1.3 67.1 + - - +
184C ALA* 3.1 4.5 + - - +
185C VAL* 2.9 28.2 + - + +
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Residues in contact with LEU 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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169C LEU* 3.9 16.4 - - + -
178C ASP* 2.9 21.6 + - + +
179C VAL 3.7 3.1 - - - +
181C ILE* 1.3 77.5 - - - +
183C ARG* 1.3 63.2 + - - +
185C VAL* 3.2 5.5 + - + +
186C ARG* 2.9 26.9 + - - +
194C LEU* 3.8 33.0 - - + +
195C ARG 4.1 15.3 - - - +
196C VAL* 3.5 34.3 - - + -
202C TRP* 5.8 0.2 - - + -
214C LEU* 3.4 24.5 - - + -
217C LEU* 3.7 14.9 - - + +
219C LEU* 4.5 4.5 - - + -
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Residues in contact with ARG 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C VAL* 2.9 35.6 + - + +
180C ALA* 3.6 12.3 - - - +
182C LEU* 1.3 77.4 - - - +
184C ALA* 1.3 60.3 + - - +
186C ARG* 3.5 2.3 + - - +
187C GLU* 3.1 24.4 + - - +
213C ALA* 3.7 29.3 + - - +
216C GLU* 3.3 26.9 + - - +
217C LEU* 4.0 20.8 - - + +
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Residues in contact with ALA 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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148C PRO* 3.3 43.3 - - + +
149C LYS* 4.2 2.9 - - - +
152C ALA* 3.5 12.2 - - + +
180C ALA 3.3 2.9 + - - +
181C ILE 3.1 7.0 + - - +
183C ARG* 1.3 77.0 - - - +
185C VAL* 1.3 65.1 + - - +
187C GLU* 3.3 9.2 + - - +
188C ALA* 3.1 18.4 + - - +
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Residues in contact with VAL 185 (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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134C ILE* 4.2 17.0 - - + -
151C MSE 4.4 0.4 - - - +
152C ALA* 3.9 25.4 - - - +
155C ALA* 4.2 16.6 - - + -
167C VAL* 5.2 1.1 - - + -
169C LEU* 6.5 0.2 - - + -
181C ILE* 2.9 33.0 + - + +
182C LEU* 3.2 9.2 + - + +
184C ALA* 1.3 75.9 - - - +
186C ARG* 1.3 52.2 + - - +
188C ALA* 3.1 3.5 + - - +
189C LEU* 2.7 43.8 + - + +
192C VAL* 5.4 0.2 - - + -
194C LEU* 3.7 27.6 - - + -
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Residues in contact with ARG 186 (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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182C LEU 2.9 16.1 + - - +
183C ARG 3.9 3.1 - - - +
185C VAL* 1.3 75.5 - - - +
187C GLU* 1.3 64.7 + - - +
189C LEU 3.0 40.5 + - - -
190C PRO* 3.0 27.3 + - - +
192C VAL* 2.8 32.7 + - - +
193C ASN* 5.1 0.2 - - - +
194C LEU* 3.7 31.7 - - + +
216C GLU 5.6 0.4 - - - +
217C LEU* 2.8 48.9 + - + +
218C ASP* 3.2 17.7 + - - +
219C LEU* 4.4 0.2 - - - +
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Residues in contact with GLU 187 (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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183C ARG 3.1 17.0 + - - +
184C ALA* 3.6 7.9 - - - +
186C ARG* 1.3 79.2 - - - +
188C ALA* 1.3 60.7 + - - +
190C PRO* 3.8 9.8 - - - +
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Residues in contact with ALA 188 (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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152C ALA* 3.9 15.0 - - + +
153C GLU* 4.6 6.5 - - - +
156C VAL* 3.7 26.0 - - + +
184C ALA 3.1 13.7 + - - +
185C VAL 3.5 7.2 - - - +
187C GLU* 1.3 78.3 - - - +
189C LEU* 1.3 66.7 + - + +
190C PRO* 3.4 7.0 - - - +
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Residues in contact with LEU 189 (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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155C ALA* 3.9 25.6 - - + +
156C VAL* 4.0 22.2 - - + +
159C VAL* 3.6 39.3 - - + -
160C GLU* 5.9 2.0 - - + -
167C VAL* 4.7 2.5 - - + -
185C VAL* 2.7 21.0 + - + +
186C ARG* 3.0 27.5 + - - +
188C ALA* 1.3 80.0 - - + +
190C PRO* 1.3 62.2 - - - +
191C GLY 3.2 3.8 + - - +
192C VAL* 3.4 25.0 - - + +
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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