Contacts of the helix formed by residues 171 - 196 (chain V) in PDB entry 6QY3
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 ASN 171 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169V SER* 3.3 13.3 - - - -
170V ASP* 1.3 82.4 - - - +
172V ASP* 1.3 63.7 + - - +
173V ILE* 3.0 14.2 + - + +
174V ASN* 3.1 6.2 + - - +
175V ALA* 3.1 16.6 + - - +
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Residues in contact with ASP 172 (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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170V ASP 3.8 0.6 + - - -
171V ASN* 1.3 73.3 - - - +
173V ILE* 1.3 57.4 + - - +
175V ALA* 3.7 12.4 - - + +
176V ALA* 2.9 29.8 + - - +
238V PHE* 4.4 24.2 - - + +
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Residues in contact with ILE 173 (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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161V PHE* 6.2 4.3 - - + -
171V ASN* 3.0 8.1 + - + +
172V ASP* 1.3 77.5 - - - +
174V ASN* 1.3 57.9 + - - +
176V ALA* 3.3 6.2 + - - +
177V LEU* 2.9 27.4 + - - +
230V VAL* 5.5 6.3 - - + +
234V ARG* 5.8 9.2 - - + -
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Residues in contact with ASN 174 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166V THR 4.9 4.9 - - - +
167V ARG* 4.2 17.7 - - - +
169V SER* 3.4 27.1 - - - +
171V ASN* 3.1 6.8 + - + +
173V ILE* 1.3 75.8 - - - +
175V ALA* 1.3 61.3 + - - +
177V LEU* 3.6 8.6 - - - +
178V ASP* 2.9 29.8 + - - +
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Residues in contact with ALA 175 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170V ASP 5.1 3.6 - - - +
171V ASN 3.1 13.4 + - - +
172V ASP* 3.7 13.9 - - + +
174V ASN* 1.3 77.0 - - - +
176V ALA* 1.3 57.4 + - - +
178V ASP* 3.4 5.7 + - - +
179V TYR* 2.9 27.9 + - - +
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Residues in contact with ALA 176 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172V ASP 2.9 17.4 + - - +
173V ILE* 3.8 4.9 - - - +
175V ALA* 1.3 72.5 - - - +
177V LEU* 1.3 60.3 + - - +
179V TYR* 3.6 7.6 - - - +
180V GLY* 2.9 26.0 + - - -
226V ILE* 6.1 0.3 - - - +
230V VAL* 5.3 11.2 - - + -
238V PHE* 6.2 2.2 - - + +
241V ILE* 4.9 19.1 - - + +
242V LYS* 6.5 0.4 - - - -
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Residues in contact with LEU 177 (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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173V ILE 2.9 17.4 + - - +
174V ASN* 3.6 9.0 - - - +
176V ALA* 1.3 78.0 - - - +
178V ASP* 1.3 58.3 + - - +
180V GLY* 3.9 0.9 - - - -
181V TYR* 2.9 29.9 + - - +
226V ILE* 5.9 4.8 - - - +
230V VAL* 5.7 6.7 - - + +
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Residues in contact with ASP 178 (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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174V ASN 2.9 18.0 + - - +
175V ALA* 3.9 5.6 - - - +
177V LEU* 1.3 75.1 - - - +
179V TYR* 1.3 57.9 + - - +
181V TYR* 3.8 6.9 - - - +
182V THR* 2.9 29.3 + - - -
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Residues in contact with TYR 179 (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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175V ALA 2.9 17.7 + - - +
176V ALA* 3.6 9.0 - - - +
177V LEU 3.2 0.4 - - - -
178V ASP* 1.3 75.4 - - - +
180V GLY* 1.3 60.4 + - - +
182V THR* 3.1 7.8 + - - -
183V LEU* 2.9 28.2 + - - +
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Residues in contact with GLY 180 (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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176V ALA 2.9 15.2 + - - -
177V LEU 4.0 1.1 - - - -
179V TYR* 1.3 76.1 - - - +
181V TYR* 1.3 56.3 + - - +
183V LEU* 3.9 5.4 - - - +
184V LEU* 2.9 32.7 + - - +
226V ILE* 5.0 16.8 - - - -
245V LEU* 5.7 9.0 - - - -
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Residues in contact with TYR 181 (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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177V LEU 2.9 19.2 + - - +
178V ASP* 3.9 8.3 - - - +
180V GLY* 1.3 76.3 - - - +
182V THR* 1.3 57.6 + - - +
184V LEU* 4.4 3.8 - - - +
185V LEU* 2.8 31.5 + - - +
226V ILE* 5.7 0.4 - - - +
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Residues in contact with THR 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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81U TYR* 6.2 3.8 - - - -
74V PRO* 5.2 15.3 - - - -
178V ASP 2.9 19.9 + - - -
179V TYR* 3.1 8.0 + - - -
181V TYR* 1.3 75.9 - - - +
183V LEU* 1.3 59.7 + - - +
185V LEU* 3.7 5.0 - - - +
186V SER* 2.9 27.7 + - - -
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Residues in contact with LEU 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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179V TYR 2.9 14.7 + - - +
180V GLY* 3.9 6.3 - - - +
182V THR* 1.3 74.3 - - - +
184V LEU* 1.3 59.2 + - - +
186V SER* 3.0 8.4 + - - -
187V MET* 2.9 28.1 + - - +
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Residues in contact with LEU 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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180V GLY 2.9 17.2 + - - +
181V TYR* 4.4 4.0 - - - +
183V LEU* 1.3 76.5 - - - +
185V LEU* 1.3 56.6 + - - +
187V MET* 3.5 6.4 + - - +
188V PHE* 2.9 31.7 + - - +
219V MET* 4.5 12.5 - - + +
222V PHE* 5.9 7.9 - - + -
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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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181V TYR 2.8 23.7 + - - +
182V THR* 3.8 6.3 - - - +
184V LEU* 1.3 76.3 - - - +
186V SER* 1.3 57.9 + - - +
188V PHE* 3.9 3.8 - - - -
189V ALA* 2.9 30.5 + - - +
212V PHE* 5.5 10.7 - - + +
215V ALA* 4.1 11.4 - - + +
216V SER* 5.8 4.3 - - - +
219V MET* 5.1 6.2 - - + +
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Residues in contact with SER 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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77V PHE* 5.4 13.0 - - - -
182V THR 2.9 18.3 + - - -
183V LEU* 3.0 8.5 + - - -
185V LEU* 1.3 75.0 - - - +
187V MET* 1.3 60.2 + - - +
189V ALA* 3.4 5.5 + - - +
190V ARG* 2.9 29.3 + - - +
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Residues in contact with MET 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 LEU 2.9 14.8 + - - +
184V LEU* 3.9 6.5 - - - +
186V SER* 1.3 77.7 - - - +
188V PHE* 1.3 57.4 + - - +
190V ARG* 3.2 8.1 + - - +
191V GLU* 2.9 26.9 + - - +
266V VAL* 5.8 7.9 - - + -
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Residues in contact with PHE 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 LEU 2.9 19.2 + - - +
185V LEU* 4.2 0.7 - - - +
187V MET* 1.3 75.8 - - - +
189V ALA* 1.3 58.4 + - - +
191V GLU* 3.3 8.9 + - - +
192V VAL* 2.9 27.4 + - - +
215V ALA* 3.8 28.8 - - + +
218V ILE* 5.1 6.0 - - + +
219V MET* 4.2 10.5 - - + +
266V VAL* 5.8 6.5 - - + +
270V THR* 5.9 0.2 - - - -
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Residues in contact with ALA 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 2.9 21.2 + - - +
186V SER* 3.7 6.7 - - - +
187V MET 3.2 0.2 - - - -
188V PHE* 1.3 73.9 - - - +
190V ARG* 1.3 58.5 + - - +
192V VAL* 3.3 6.7 + - - +
193V VAL* 2.9 27.2 + - - +
199V THR* 5.6 7.5 - - - -
212V PHE* 6.1 4.0 - - + -
215V ALA* 3.7 16.3 - - + +
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Residues in contact with ARG 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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64V LEU* 4.3 22.7 - - + -
186V SER 2.9 18.2 + - - +
187V MET* 3.2 7.6 + - - +
189V ALA* 1.3 73.0 - - - +
191V GLU* 1.3 60.9 + - - +
193V VAL* 3.2 9.9 + - - +
194V VAL* 2.9 26.5 + - - +
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Residues in contact with GLU 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 MET 2.9 13.3 + - - +
188V PHE* 3.3 11.6 + - - +
190V ARG* 1.3 77.5 - - - +
192V VAL* 1.3 57.0 + - - +
194V VAL* 3.0 10.0 + - - +
195V CYS* 2.9 26.7 + - - +
266V VAL* 4.7 10.3 - - + +
267V SER* 5.0 8.5 - - - +
270V THR* 4.2 23.9 - - - -
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Residues in contact with VAL 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 PHE 2.9 17.1 + - - +
189V ALA* 3.6 8.7 - - - +
191V GLU* 1.3 75.7 - - - +
193V VAL* 1.3 58.0 + - - +
195V CYS* 3.3 8.8 + - - +
196V GLY 3.0 21.7 + - - -
197V CYS* 3.7 16.4 + - + +
199V THR* 4.9 17.7 - - - -
214V LEU* 5.8 3.1 - - + -
215V ALA* 5.2 8.7 - - + +
270V THR* 5.4 2.4 - - - -
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Residues in contact with VAL 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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79V THR* 6.0 5.2 - - - -
80V PRO* 5.2 15.0 - - + +
83V ALA* 3.3 20.4 + - + +
189V ALA 2.9 14.0 + - - +
190V ARG* 3.2 13.4 + - - +
192V VAL* 1.3 76.2 - - - +
194V VAL* 1.3 61.7 + - - +
196V GLY* 3.4 11.7 + - - +
197V CYS 5.3 1.6 - - - -
199V THR* 6.1 0.2 - - - -
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Residues in contact with VAL 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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62V ASN* 6.5 0.7 - - + -
83V ALA* 4.2 14.0 - - + +
84V ARG* 4.9 9.7 - - - +
190V ARG 2.9 13.8 + - - +
191V GLU* 3.0 12.5 + - - +
193V VAL* 1.3 75.9 - - - +
195V CYS* 1.3 62.9 + - - +
196V GLY* 3.5 0.7 + - - -
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Residues in contact with CYS 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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86V ASP* 4.9 4.9 - - - +
87V SER* 4.7 3.1 + - - -
90V GLN* 4.5 10.7 - - - +
191V GLU 2.9 12.9 + - - +
192V VAL* 3.6 11.7 - - - +
193V VAL 3.3 0.4 - - - -
194V VAL* 1.3 77.8 - - - +
196V GLY* 1.3 57.9 + - - +
197V CYS* 3.4 9.4 + - + +
270V THR* 5.6 6.1 - - - +
271V LYS* 6.4 0.7 - - - -
274V ILE* 4.7 20.2 - - + -
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Residues in contact with GLY 196 (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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83V ALA* 6.0 0.4 - - - -
87V SER* 3.6 39.1 - - - +
90V GLN* 4.8 1.6 - - - -
91V ILE* 5.4 1.9 + - - +
192V VAL 3.0 6.8 + - - -
193V VAL* 3.4 10.3 + - - -
194V VAL 3.3 2.6 - - - -
195V CYS* 1.3 77.0 - - - +
197V CYS* 1.3 65.2 + - - +
198V MET 3.8 0.2 + - - -
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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