Contacts of the helix formed by residues 167 - 178 (chain B) in PDB entry 2OQ4
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 GLY 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GLN* 2.7 34.7 + - - +
52B LYS* 3.8 0.2 - - - -
157B LEU 4.4 0.3 - - - +
158B LEU* 4.0 7.4 - - - +
166B LEU* 1.3 76.8 - - - +
168B ASN* 1.3 59.8 + - - -
169B TYR 3.3 0.7 - - - -
170B LEU* 3.5 1.4 + - - +
171B ARG* 3.0 26.7 + - - +
428F G 2.9 14.8 - - - -
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Residues in contact with ASN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLN* 3.1 0.8 - - - +
158B LEU* 3.9 4.7 - - + +
167B GLY* 1.3 71.2 - - - -
169B TYR* 1.3 63.0 + - - +
170B LEU 3.4 0.2 - - - -
171B ARG* 3.0 35.8 + - - +
172B VAL* 3.4 16.8 - - - +
230B PHE* 4.8 3.9 - - - -
252B ARG* 3.1 29.1 - - + +
253B PRO* 2.7 29.1 + - - +
254B PHE 5.4 0.4 + - - -
427F PED 3.3 22.3 + - - -
428F G 2.9 21.4 + - - +
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Residues in contact with TYR 169 (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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2B GLN* 2.9 26.6 + - - +
4B PRO* 3.7 4.9 - - - +
5B GLU* 2.4 41.3 + - - -
167B GLY 3.3 0.8 - - - -
168B ASN* 1.3 75.9 - - - +
170B LEU* 1.3 83.5 + - + +
172B VAL* 4.2 2.0 - - - +
173B GLU* 3.1 32.6 + - - +
208B SER* 3.6 18.2 - - - -
212B ARG* 3.2 19.9 + - - -
225B PHE* 3.9 12.1 - + - -
227B PHE* 3.3 24.0 - + - -
230B PHE* 3.7 38.5 - + + +
427F PED 3.7 14.6 - - + +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLN* 3.0 21.8 + - + +
4B PRO* 3.6 31.0 - - + -
165B GLY 4.1 6.7 - - - +
166B LEU* 4.2 22.4 - - + -
167B GLY 4.0 3.8 - - - +
169B TYR* 1.3 96.8 - - + +
171B ARG* 1.3 70.4 - - - +
173B GLU* 3.1 2.1 + - - -
174B ILE* 2.9 28.4 + - + +
204B ILE* 3.5 30.1 - - + -
205B PRO* 3.7 23.3 - - + -
208B SER* 3.9 2.7 - - - +
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Residues in contact with ARG 171 (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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153B PHE 4.7 0.2 + - - -
154B ALA* 2.7 36.0 + - - +
157B LEU* 3.5 38.2 - - + +
158B LEU* 3.7 15.9 - - + +
166B LEU* 5.3 2.4 - - - +
167B GLY 3.0 19.3 + - - +
168B ASN* 3.0 28.9 + - - +
170B LEU* 1.3 80.5 - - - +
172B VAL* 1.3 70.6 + - + +
174B ILE* 3.1 21.0 + - - +
175B LEU* 3.3 5.2 + - + +
249B LEU 3.3 24.4 + - - -
250B SER* 3.9 6.7 + - - -
252B ARG* 3.8 9.5 - - - +
253B PRO 3.4 14.1 + - - -
254B PHE* 3.4 26.4 - - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASN* 3.4 16.8 - - - +
169B TYR* 4.2 5.8 - - - +
171B ARG* 1.3 97.4 - - + +
173B GLU* 1.3 67.8 + - + +
174B ILE 3.2 1.8 - - - -
175B LEU* 3.8 11.9 - - + +
176B TRP* 3.3 22.0 + - - +
229B VAL* 4.1 13.5 - - + +
230B PHE* 4.9 10.1 - - + -
254B PHE* 2.9 53.6 - - + +
255B TYR* 3.7 11.1 - - - +
261B GLN* 4.8 0.7 - - - +
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Residues in contact with GLU 173 (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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169B TYR 3.1 23.5 + - - +
170B LEU* 3.1 6.3 + - - +
172B VAL* 1.3 77.3 - - + +
174B ILE* 1.3 64.6 + - + +
176B TRP* 3.6 7.7 + - - +
177B GLN* 3.3 21.8 + - - +
204B ILE* 3.8 12.1 - - + +
225B PHE* 4.3 11.2 - - + -
226B ARG 3.4 5.9 - - - +
227B PHE* 2.9 27.3 - - + -
228B LYS* 2.4 34.2 + - - +
229B VAL* 2.8 34.8 + - - +
230B PHE* 3.0 12.6 + - + -
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Residues in contact with ILE 174 (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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157B LEU* 4.5 5.6 - - + -
166B LEU* 5.5 2.2 - - + -
170B LEU* 2.9 33.8 + - + +
171B ARG* 3.2 12.8 - - - +
173B GLU* 1.3 77.8 - - - +
175B LEU* 1.3 65.1 + - + +
177B GLN* 3.2 11.1 + - - +
178B VAL* 3.2 17.2 + - + +
197B LEU* 4.2 13.2 - - + -
200B ALA* 3.6 25.7 - - + +
201B LEU* 3.8 28.3 - - + +
204B ILE* 3.2 44.4 - - + -
205B PRO* 4.3 2.7 - - + -
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Residues in contact with LEU 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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153B PHE* 4.5 15.3 - - + +
157B LEU* 3.9 26.2 - - + -
171B ARG 3.3 8.8 + - - +
172B VAL* 3.9 17.0 - - + +
173B GLU 3.4 0.2 - - - -
174B ILE* 1.3 78.9 - - + +
176B TRP* 1.3 59.5 + - - +
178B VAL* 3.2 8.5 + - + -
179B GLY 2.9 8.7 + - - -
180B LEU* 2.8 52.1 + - + +
181B THR 3.0 32.8 - - - +
182B GLY* 4.6 1.8 - - - -
197B LEU* 5.7 3.1 - - + -
254B PHE* 4.3 17.3 - - + -
261B GLN* 5.0 1.6 - - + +
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Residues in contact with TRP 176 (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 VAL 3.3 13.0 + - - +
173B GLU* 4.0 7.0 - - - +
175B LEU* 1.3 78.8 - - - +
177B GLN* 1.3 83.2 + - + +
178B VAL 3.5 0.5 + - - -
179B GLY 3.5 2.3 + - - -
228B LYS* 3.2 57.9 - - + +
229B VAL* 3.6 27.6 - - + +
237B CYS* 3.6 21.2 - - - -
238B GLU* 4.7 6.7 - - + -
239B ARG* 2.7 72.5 + - + +
257B CYS* 4.5 2.2 - - + -
260B CYS* 4.1 3.8 - - - -
261B GLN* 3.0 38.5 - - - +
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Residues in contact with GLN 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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173B GLU 3.3 11.8 + - - +
174B ILE 3.2 9.6 + - - +
175B LEU 3.1 1.0 - - - -
176B TRP* 1.3 105.8 - - + +
178B VAL* 1.3 65.2 + - + +
179B GLY 3.5 0.2 - - - -
196B ALA* 5.7 0.2 - - - +
200B ALA* 4.9 5.6 - - + -
204B ILE* 4.1 20.1 - - + +
228B LYS* 4.5 5.5 - - - +
239B ARG* 3.8 10.8 + - - +
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Residues in contact with VAL 178 (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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174B ILE* 3.2 16.2 - - + +
175B LEU* 3.5 13.7 - - + +
177B GLN* 1.3 83.5 - - + +
179B GLY* 1.3 62.0 + - - +
180B LEU* 3.2 27.7 + - + +
193B GLN* 5.3 10.7 + - + +
196B ALA* 3.7 45.3 - - + +
197B LEU* 3.8 12.6 - - + +
200B ALA* 3.7 14.4 - - + -
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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