Contacts of the helix formed by residues 182 - 194 (chain B) in PDB entry 2OKC
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B ASP* 5.9 0.4 - - - -
179B CYS* 2.9 20.6 + - - -
180B GLY 3.1 2.1 - - - -
181B THR* 1.3 78.5 - - - +
183B GLY* 1.3 53.2 + - - +
184B PHE 3.4 2.7 - - - -
185B LEU* 3.1 16.4 + - - +
186B LEU* 2.8 34.3 + - - +
223B ALA* 4.4 6.7 - - - -
226B ASN* 4.9 0.9 - - - -
227B LEU* 3.8 12.8 - - - +
239B ILE* 5.3 0.4 - - - -
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Residues in contact with GLY 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.5 22.0 - - - +
159B ILE* 3.4 8.5 - - - +
179B CYS 4.3 0.2 + - - -
181B THR 3.5 2.4 + - - -
182B GLY* 1.3 74.0 - - - +
184B PHE* 1.3 63.4 + - - +
186B LEU* 4.1 7.4 - - - +
187B THR* 2.7 32.2 + - - -
500B SAM 3.1 17.0 + - - -
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Residues in contact with PHE 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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154B THR* 4.1 6.7 - - + -
159B ILE* 3.7 31.8 - - + +
162B MSE 3.4 44.9 - - + -
163B VAL* 4.4 1.5 - - + +
176B ASP* 3.2 28.6 + - + +
182B GLY 3.4 0.4 - - - -
183B GLY* 1.3 75.5 - - - +
185B LEU* 1.3 59.8 + - + +
187B THR* 4.0 0.9 - - - -
188B ALA* 2.8 32.7 + - - +
257B LEU* 3.5 37.6 - - + +
258B ALA* 3.7 6.3 - - - -
259B ASN* 3.6 19.7 - - + -
500B SAM 3.3 28.0 + - - -
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Residues in contact with LEU 185 (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 VAL* 4.1 15.9 - - + +
176B ASP* 4.1 19.1 - - + +
179B CYS* 4.5 6.3 - - + -
182B GLY* 3.1 11.5 + - - +
184B PHE* 1.3 74.4 - - + +
186B LEU* 1.3 65.0 - - - +
188B ALA* 4.5 0.9 - - - -
189B TYR* 3.1 25.6 + - - +
210B LEU* 3.9 32.1 - - + +
211B HIS 3.6 18.2 - - - +
212B GLY* 3.6 31.6 - - - +
227B LEU* 4.5 11.9 - - + -
238B PRO* 5.2 0.7 - - + -
239B ILE* 3.7 20.4 - - + -
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Residues in contact with LEU 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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135B GLU* 4.1 20.9 - - + +
182B GLY 2.8 19.7 + - - +
183B GLY* 4.1 6.3 - - - +
185B LEU* 1.3 73.0 - - - +
187B THR* 1.3 66.6 + - - +
189B TYR* 3.4 3.3 + - - +
190B ASP* 3.1 45.2 + - - +
226B ASN* 4.1 6.7 - - - +
227B LEU* 4.1 8.9 - - + +
230B HIS* 3.5 57.9 - - + +
232B ILE* 3.5 20.4 - - + -
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Residues in contact with THR 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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156B ARG* 5.7 2.3 - - - +
159B ILE* 3.4 14.5 - - + +
160B GLN* 4.0 30.5 + - + +
163B VAL* 3.9 20.6 - - + -
183B GLY* 2.7 23.8 + - - -
184B PHE 4.0 0.7 - - - -
186B LEU* 1.3 79.5 - - - +
188B ALA* 1.3 62.9 + - - +
190B ASP* 3.6 5.7 + - - +
191B TYR* 3.1 22.3 + - + +
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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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163B VAL* 4.0 11.8 - - - +
168B PRO* 4.4 7.6 - - + +
174B VAL* 4.3 11.9 - - + -
184B PHE 2.8 19.6 + - - +
185B LEU* 4.0 4.0 - - - +
187B THR* 1.3 73.9 - - - +
189B TYR* 1.3 64.9 + - - +
191B TYR* 3.2 4.5 + - - +
192B MSE 3.0 39.7 + - + +
210B LEU* 4.9 0.9 - - + -
257B LEU* 4.0 20.4 - - + -
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Residues in contact with TYR 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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185B LEU 3.1 19.4 + - - +
186B LEU 3.5 4.3 - - - +
188B ALA* 1.3 77.3 - - - +
190B ASP* 1.3 65.9 + - - +
192B MSE 3.0 12.5 + - - +
193B LYS* 2.7 58.4 + - + +
205B LEU* 3.8 41.3 - - + +
206B ARG* 4.6 14.2 + - - +
210B LEU* 3.6 20.9 - - + -
230B HIS 5.7 0.9 - - - -
231B GLY 4.2 11.5 + - - -
232B ILE* 3.7 37.0 - - + -
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Residues in contact with ASP 190 (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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186B LEU* 3.1 36.1 + - - +
187B THR* 4.1 5.4 - - - +
189B TYR* 1.3 86.5 - - - +
191B TYR* 1.3 65.3 + - - +
193B LYS* 2.7 45.2 + - - +
194B GLY* 3.9 8.5 + - - -
230B HIS* 5.3 5.0 - - - +
232B ILE* 4.9 0.7 - - - +
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Residues in contact with TYR 191 (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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163B VAL* 3.8 16.8 - - + -
164B ASP* 3.4 37.3 + - - -
167B ASN* 2.5 40.2 + - - +
168B PRO* 3.5 32.3 - - + -
187B THR* 3.1 15.5 + - + +
188B ALA 3.3 9.4 - - - +
189B TYR 3.2 0.4 - - - -
190B ASP* 1.3 79.6 - - - +
192B MSE 1.3 59.3 + - - +
194B GLY* 4.2 4.2 + - - -
195B GLN* 3.5 20.3 + - - +
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Residues in contact with MSE 192 (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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168B PRO* 3.3 33.2 - - + +
169B GLN 3.4 28.5 - - - +
170B MSE 3.9 14.5 - - + +
172B GLU* 4.7 6.1 - - - +
174B VAL* 3.8 25.4 - - + -
188B ALA* 3.0 32.7 + - + +
189B TYR* 3.6 6.5 - - - +
191B TYR* 1.3 76.0 - - - +
193B LYS* 1.3 58.9 + - - +
194B GLY 3.2 2.7 - - - -
195B GLN* 3.0 32.1 + - - +
205B LEU* 3.9 30.1 - - + -
209B ALA* 4.9 2.5 - - + -
210B LEU* 4.3 8.1 - - + -
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Residues in contact with LYS 193 (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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119A GLU* 3.5 38.7 + - + +
170B MSE 5.1 5.0 - - - +
189B TYR* 2.7 43.1 + - + +
190B ASP* 2.7 39.9 + - - +
191B TYR 3.6 0.2 - - - -
192B MSE 1.3 72.3 - - - +
194B GLY* 1.3 60.6 + - - +
195B GLN 3.2 6.1 + - - +
205B LEU* 3.7 12.3 - - + +
230B HIS 5.4 4.8 + - - -
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Residues in contact with GLY 194 (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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190B ASP 3.9 9.4 + - - -
191B TYR 4.2 2.6 + - - -
192B MSE 3.2 1.4 - - - -
193B LYS* 1.3 79.8 - - - +
195B GLN* 1.3 65.3 + - - +
196B SER* 5.2 0.7 + - - -
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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