Contacts of the helix formed by residues 174 - 189 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 2.9 28.6 + - - +
172B THR* 2.9 13.5 + - - +
173B THR* 1.3 77.8 + - - +
175B CYS* 1.3 57.4 + - - +
176B ALA* 3.9 6.9 + - - +
177B GLY* 3.2 20.4 + - - -
178B ASP* 2.9 25.3 + - - -
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Residues in contact with CYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B THR 4.1 0.2 + - - -
173B THR 3.2 8.6 + - - -
174B ASP* 1.3 68.0 + - - +
176B ALA* 1.3 67.9 + - - +
178B ASP* 3.0 5.4 + - - +
179B VAL* 2.9 28.5 + - - +
202B TRP* 3.4 47.8 - - + +
206B ASP* 3.9 28.7 - - + +
210B ALA* 4.5 13.5 - - + -
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASP* 3.5 6.8 + - - +
175B CYS* 1.3 78.8 - - - +
177B GLY* 1.3 61.2 + - - +
179B VAL* 3.4 8.4 + - - +
180B ALA* 3.1 21.1 + - - +
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 3.4 7.0 - - - -
147B LEU* 6.3 1.1 - - - -
174B ASP* 3.2 27.2 + - - -
175B CYS 3.2 0.4 - - - -
176B ALA* 1.3 76.6 - - - +
178B ASP* 1.3 66.4 + - - +
180B ALA* 3.1 8.8 + - - +
181B ILE* 2.9 27.3 + - - +
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Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 2.9 23.8 + - - +
169B LEU* 3.9 8.0 - - + +
170B LYS 4.9 0.5 - - - +
171B GLY* 3.5 8.5 - - - -
172B THR* 2.8 43.6 + - - +
174B ASP 2.9 13.9 + - - +
175B CYS 3.4 6.3 - - - +
177B GLY* 1.3 73.9 - - - +
179B VAL* 1.3 63.2 + - - +
181B ILE* 3.2 11.8 + - - +
182B LEU* 3.0 29.1 + - + +
196B VAL* 5.0 3.4 - - + -
202B TRP* 3.3 27.1 + - + -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B CYS 2.9 17.9 + - - +
176B ALA* 3.6 11.2 - - - +
178B ASP* 1.3 78.1 - - + +
180B ALA* 1.3 61.1 + - - +
182B LEU* 3.3 3.0 + - - +
183B ARG* 3.0 58.1 + - - +
202B TRP* 5.4 0.4 - - + -
210B ALA* 3.9 29.6 - - + +
213B ALA* 4.2 9.6 - - + -
214B LEU* 4.1 31.1 - - + +
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PRO* 3.5 26.1 - - + +
176B ALA 3.1 14.1 + - - +
177B GLY* 3.1 12.3 + - - +
179B VAL* 1.3 75.4 - - - +
181B ILE* 1.3 66.8 + - - +
183B ARG* 3.3 12.5 + - - +
184B ALA* 3.2 14.7 + - - +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ILE* 5.2 0.4 - - + -
136B ARG* 3.6 33.2 - - + +
147B LEU* 4.0 21.5 - - + -
148B PRO* 4.0 13.2 - - + -
151B MSE 3.7 34.5 - - + -
169B LEU* 3.7 26.7 - - + -
177B GLY 2.9 19.5 + - - +
178B ASP* 3.2 11.6 + - - +
180B ALA* 1.3 75.8 - - - +
182B LEU* 1.3 59.3 + - - +
184B ALA* 3.0 5.9 + - - +
185B VAL* 2.9 37.5 + - + +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 3.7 18.6 - - + -
178B ASP* 3.0 17.1 + - + +
179B VAL 3.3 4.7 + - - +
181B ILE* 1.3 78.5 - - + +
183B ARG* 1.3 63.0 + - - +
185B VAL* 3.8 5.9 - - + +
186B ARG* 2.9 26.2 + - - +
194B LEU* 3.8 31.8 - - + +
195B ARG 3.9 13.7 - - - +
196B VAL* 3.6 31.2 - - + -
214B LEU* 3.5 24.9 - - + -
217B LEU* 3.6 16.5 - - + +
219B LEU* 4.4 5.8 - - + -
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.0 43.4 + - + +
180B ALA* 3.6 9.5 - - - +
181B ILE 3.2 0.2 - - - -
182B LEU* 1.3 76.9 - - - +
184B ALA* 1.3 61.5 + - - +
186B ARG* 3.6 2.6 + - - +
187B GLU* 3.2 22.7 + - - +
213B ALA* 3.5 31.7 + - - +
216B GLU* 3.1 22.5 + - - +
217B LEU* 3.9 25.3 - - + +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PRO* 3.4 42.0 - - + +
149B LYS* 4.2 2.7 - - - +
152B ALA* 3.5 12.2 - - + +
180B ALA 3.2 1.4 + - - +
181B ILE 3.0 6.8 + - - +
183B ARG* 1.3 78.4 - - - +
185B VAL* 1.3 65.9 + - - +
187B GLU* 3.3 7.8 + - - +
188B ALA* 3.0 18.9 + - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 4.4 15.9 - - + -
151B MSE 4.5 0.7 - - - +
152B ALA* 3.9 24.7 - - - +
155B ALA* 4.0 18.8 - - + -
167B VAL* 5.0 2.0 - - + -
181B ILE* 2.9 36.1 + - + +
182B LEU* 3.3 9.6 + - + +
184B ALA* 1.3 76.6 - - - +
186B ARG* 1.3 57.7 + - - +
188B ALA* 3.3 2.6 + - - +
189B LEU* 2.9 35.2 + - + +
192B VAL* 5.4 1.8 - - + -
194B LEU* 3.9 26.0 - - + -
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Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LEU 2.9 17.7 + - - +
183B ARG 3.9 3.8 - - - +
185B VAL* 1.3 74.2 - - - +
187B GLU* 1.3 67.3 + - - +
189B LEU 3.2 17.6 + - - -
190B PRO* 2.9 49.2 + - - +
191B GLY 4.4 0.4 - - - -
192B VAL* 2.8 30.3 + - - +
193B ASN* 5.1 0.4 - - - +
194B LEU* 3.7 30.5 - - + +
216B GLU 5.6 0.4 - - - +
217B LEU* 2.8 49.7 + - + +
218B ASP* 3.1 18.1 + - - +
219B LEU* 4.3 0.4 - - - +
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ARG 3.2 12.8 + - - +
184B ALA* 3.5 11.9 - - - +
186B ARG* 1.3 82.7 - - - +
188B ALA* 1.3 61.9 + - - +
189B LEU 3.6 0.2 + - - -
190B PRO* 3.7 9.6 - - - +
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA* 4.1 14.6 - - + +
156B VAL* 3.7 25.7 - - + +
184B ALA 3.0 16.0 + - - +
185B VAL* 3.8 3.8 - - - +
187B GLU* 1.3 78.9 - - - +
189B LEU* 1.3 68.5 + - + +
190B PRO* 3.6 5.5 - - - +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA 4.8 0.4 - - - +
155B ALA* 3.7 39.9 - - + +
156B VAL* 3.9 20.9 - - + +
159B VAL* 4.1 26.2 - - + -
167B VAL* 5.0 1.8 - - + -
185B VAL* 2.9 18.6 + - + +
186B ARG* 3.0 22.5 + - - +
188B ALA* 1.3 86.0 - - - +
190B PRO* 1.3 65.2 - - - +
191B GLY 3.2 4.4 + - - -
192B VAL* 3.5 24.6 - - + +
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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