Contacts of the helix formed by residues 181 - 195 (chain V) in PDB entry 1O1F
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 ALA 181 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155V SER* 4.5 1.1 - - - +
156V GLY 3.3 14.8 - - - +
157V ASP 3.4 17.7 - - - +
158V GLY 3.7 13.5 - - - -
159V VAL 3.8 9.6 - - - +
160V THR* 4.3 2.9 - - - +
179V ASP 4.4 0.2 - - - -
180V LEU* 1.3 78.5 - - - +
182V GLY* 1.3 61.6 + - - +
183V ARG 3.2 2.7 + - - -
184V ASP* 3.2 10.1 + - - +
185V LEU* 3.0 33.4 + - - +
303V THR* 4.2 7.0 - - - -
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Residues in contact with GLY 182 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156V GLY 3.0 10.4 + - - -
157V ASP* 4.4 5.2 - - - -
181V ALA* 1.3 76.3 - - - +
183V ARG* 1.3 55.8 + - - +
185V LEU* 3.5 7.9 + - - +
186V THR* 3.0 17.5 + - - -
213V LYS* 2.8 31.2 + - - -
303V THR* 3.1 20.7 + - - -
306V TYR* 4.6 0.4 - - - -
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Residues in contact with ARG 183 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V SER* 2.8 35.6 + - - -
69V TYR* 3.5 28.6 + - - +
71V ILE 4.8 5.5 + - - -
72V GLU* 4.6 14.5 + - - +
73V HIS* 5.2 7.2 - - - +
157V ASP* 2.9 47.9 + - - +
158V GLY* 4.4 16.0 - - - -
181V ALA 3.2 0.4 - - - -
182V GLY* 1.3 70.1 - - - +
184V ASP* 1.3 70.4 + - - +
186V THR* 3.3 13.7 + - - -
187V ASP* 3.4 25.1 + - - +
206V ARG* 6.1 2.2 - - - +
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Residues in contact with ASP 184 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73V HIS* 5.4 3.3 - - - -
157V ASP 4.5 1.0 - - - +
158V GLY* 4.7 4.9 - - - +
179V ASP 3.9 12.1 - - - +
180V LEU* 3.8 11.3 - - + +
181V ALA* 3.2 28.5 + - - +
183V ARG* 1.3 80.9 - - - +
185V LEU* 1.3 63.1 + - + +
187V ASP* 3.2 9.1 + - - +
188V TYR* 3.1 27.1 + - - +
267V ILE* 5.0 12.7 - - + +
269V MET* 5.6 1.2 - - - +
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Residues in contact with LEU 185 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180V LEU* 3.9 24.0 - - + -
181V ALA 3.0 18.0 + - - +
182V GLY 3.5 6.5 - - - +
184V ASP* 1.3 76.7 - - + +
186V THR* 1.3 63.6 + - - +
188V TYR* 3.7 5.0 + - - +
189V LEU 3.3 8.3 + - - -
213V LYS* 4.1 2.9 - - + -
257V CYS* 3.2 39.4 - - - +
258V PRO* 5.1 0.4 - - + -
260V THR* 4.3 19.7 - - + -
261V LEU* 4.0 11.0 - - + -
303V THR* 3.8 17.9 - - + -
306V TYR* 3.0 40.8 - - + +
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Residues in contact with THR 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182V GLY 3.0 7.6 + - - -
183V ARG* 3.3 6.8 + - - -
185V LEU* 1.3 75.7 - - - +
187V ASP* 1.3 67.2 + - - +
189V LEU* 3.4 5.1 + - - +
190V MET* 3.1 26.0 + - - +
206V ARG* 4.6 10.1 - - - +
209V VAL* 3.6 26.0 - - + +
210V ARG* 3.7 26.5 - - + +
213V LYS* 2.7 37.3 + - - +
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Residues in contact with ASP 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183V ARG* 3.4 17.8 + - - +
184V ASP* 3.2 10.9 + - - +
186V THR* 1.3 79.3 - - - +
188V TYR* 1.3 63.9 + - - +
190V MET* 3.1 19.7 - - - +
191V LYS* 3.3 9.5 + - - +
206V ARG* 3.4 35.1 + - - -
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Residues in contact with TYR 188 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184V ASP 3.1 14.3 + - - +
185V LEU* 4.1 6.3 - - - +
187V ASP* 1.3 76.9 - - - +
189V LEU* 1.3 65.8 + - - +
191V LYS* 3.2 39.5 + - + +
192V ILE* 3.0 45.1 + - + +
256V ARG* 3.3 20.5 + - - +
257V CYS* 3.9 11.2 - - + -
260V THR* 3.2 25.4 - - + +
266V PHE* 3.1 41.7 + + - +
267V ILE* 3.5 25.4 - - + -
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Residues in contact with LEU 189 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185V LEU 3.3 13.0 + - - +
186V THR 3.7 6.5 - - - +
187V ASP 3.4 0.2 - - - -
188V TYR* 1.3 77.2 - - - +
190V MET* 1.3 55.7 - - - +
192V ILE* 3.0 25.5 + - + +
193V LEU* 2.8 52.4 + - + +
209V VAL* 3.5 33.0 - - + +
212V ILE* 3.7 11.4 - - + -
213V LYS* 3.5 29.2 - - + +
217V CYS* 4.6 6.7 - - - -
250V ILE* 5.5 2.9 - - + -
253V GLU* 4.6 16.2 - - + +
254V ARG 5.3 0.7 - - - +
257V CYS* 3.8 9.2 - - + -
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Residues in contact with MET 190 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186V THR 3.1 9.0 + - - +
187V ASP* 3.1 17.7 - - - +
189V LEU* 1.3 78.4 - - - +
191V LYS* 1.3 58.2 + - - +
193V LEU* 3.3 3.1 + - - +
194V THR* 2.9 36.8 + - + +
200V PHE* 3.7 29.1 - - + +
206V ARG* 3.7 43.3 - - + +
209V VAL* 3.2 36.3 - - + -
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Residues in contact with LYS 191 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187V ASP 3.3 5.5 + - - +
188V TYR* 3.2 48.0 + - + +
190V MET* 1.3 78.1 - - - +
192V ILE* 1.3 64.6 + - - +
193V LEU 2.8 7.6 + - - -
194V THR* 2.9 10.7 + - - -
195V GLU* 2.8 54.2 + - + +
266V PHE 5.0 3.6 + - - -
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Residues in contact with ILE 192 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188V TYR* 3.0 50.4 + - + +
189V LEU* 3.0 22.8 + - + +
191V LYS* 1.3 90.2 - - - +
193V LEU* 1.3 56.1 + - - +
195V GLU* 3.5 24.5 - - - +
196V ARG* 3.2 20.6 + - - +
253V GLU* 3.6 38.7 - - + +
256V ARG* 3.6 33.6 + - + +
257V CYS* 4.0 4.0 - - + +
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Residues in contact with LEU 193 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189V LEU* 2.8 35.6 + - + +
190V MET 3.6 4.3 - - - +
191V LYS 2.8 0.8 + - - -
192V ILE* 1.3 78.6 - - - +
194V THR* 1.3 61.8 + - - +
195V GLU 3.2 1.1 - - - -
196V ARG* 3.3 7.1 + - + -
198V TYR* 2.8 40.7 - - + +
200V PHE* 3.6 27.6 - - + -
209V VAL* 4.1 10.3 - - + -
212V ILE* 4.2 18.4 - - + -
249V THR 4.5 0.4 - - - +
250V ILE* 3.3 34.1 - - + -
253V GLU* 4.1 13.5 - - + -
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Residues in contact with THR 194 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190V MET* 2.9 27.0 + - + +
191V LYS* 3.0 14.5 + - - +
193V LEU* 1.3 77.1 - - - +
195V GLU* 1.3 59.0 + - - +
197V GLY* 2.9 9.7 + - - -
198V TYR 2.9 37.7 + - - +
199V SER* 4.9 0.7 - - - -
200V PHE* 3.5 25.6 - - + +
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Residues in contact with GLU 195 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128 PRO* 5.3 19.3 - - + +
191V LYS* 2.8 46.4 + - + +
192V ILE* 3.5 24.3 - - - +
194V THR* 1.3 77.4 + - - +
196V ARG* 1.3 55.2 + - - +
197V GLY* 3.0 8.9 + - - -
256V ARG* 3.7 15.1 + - - -
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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