Contacts of the helix formed by residues 166 - 192 (chain F) in PDB entry 4DEM
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 TYR 166 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PHE* 5.9 0.3 - - - -
98F ARG* 3.3 31.5 + - - -
161F CYS* 4.1 11.7 - - + -
164F GLN* 3.6 27.1 - - + -
165F PRO* 1.3 85.9 - - + +
167F TYR* 1.3 65.4 + - - +
168F LEU 3.4 2.0 - - - -
169F ASN* 3.2 14.3 + - + +
170F LEU* 3.0 42.1 + - + +
229F TYR* 3.5 27.6 - - + +
230F MET* 3.6 54.0 - - + +
232F GLY* 5.7 0.4 - - - -
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Residues in contact with TYR 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F TYR 4.9 1.2 + - - -
157F LEU* 3.4 29.8 - - + +
158F LYS* 3.6 25.3 + - - +
161F CYS* 3.4 32.1 - - + +
162F ARG* 3.7 36.1 + - + +
164F GLN 3.1 11.5 + - - +
165F PRO 3.3 1.0 - - - -
166F TYR* 1.3 81.3 - - - +
168F LEU* 1.3 61.4 + - + +
170F LEU* 3.1 6.2 + - + +
171F ILE* 2.9 58.8 + - + +
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Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F PRO 4.9 2.8 + - - +
166F TYR 3.4 0.4 - - - -
167F TYR* 1.3 79.9 - - + +
169F ASN* 1.3 68.3 + - - +
171F ILE* 3.3 16.1 + - + +
172F GLU* 2.9 52.5 + - + +
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Residues in contact with ASN 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F PRO 5.0 3.2 + - - -
166F TYR* 3.2 18.5 + - - +
168F LEU* 1.3 80.8 - - - +
170F LEU* 1.3 57.8 + - - +
172F GLU* 3.9 10.6 - - - +
173F LEU* 3.0 29.1 + - - +
229F TYR* 3.5 49.5 + - + -
234F ASP* 4.2 13.7 + - - +
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Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F VAL* 3.9 27.1 - - + -
157F LEU* 4.0 20.2 - - + -
161F CYS* 4.4 4.3 - - + -
166F TYR* 3.0 43.7 + - + +
167F TYR 3.1 6.7 + - - +
169F ASN* 1.3 74.8 - - - +
171F ILE* 1.3 67.6 + - - +
173F LEU* 3.3 7.2 + - + +
174F PHE* 3.0 33.5 + - + -
226F ALA* 3.7 42.8 - - + +
229F TYR* 4.2 11.2 - - + -
230F MET* 4.2 2.5 - - + -
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Residues in contact with ILE 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F TYR* 4.1 14.0 - - + -
157F LEU* 4.3 17.3 - - + -
167F TYR* 2.9 61.7 + - + +
168F LEU* 3.3 20.2 + - + +
170F LEU* 1.3 76.8 - - - +
172F GLU* 1.3 59.3 + - + +
174F PHE* 3.3 1.7 + - - +
175F LEU* 3.0 48.6 + - + +
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Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LEU* 2.9 51.8 + - + +
169F ASN* 4.1 10.4 - - - +
171F ILE* 1.3 77.1 - - + +
173F LEU* 1.3 58.5 + - - +
175F LEU* 3.8 9.0 - - + +
176F GLN* 2.8 33.3 + - - +
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Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F ASN 3.0 18.2 + - - +
170F LEU* 3.6 7.4 - - + +
172F GLU* 1.3 74.0 - - - +
174F PHE* 1.3 60.3 + - + +
176F GLN* 4.1 5.1 - - + +
177F SER* 2.7 44.0 + - - +
221F TYR* 3.6 32.3 - - + +
222F LEU* 3.6 19.3 - - + -
225F ALA* 3.8 8.7 - - + -
226F ALA* 3.5 38.1 - - + +
229F TYR* 4.0 15.9 - - + +
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Residues in contact with PHE 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F VAL* 4.0 18.2 - - + -
105F CYS* 3.6 29.6 - - + -
106F VAL* 3.7 38.1 - - + -
109F LEU* 4.6 7.0 - - + +
153F ILE* 3.8 18.6 - - + -
154F TYR* 3.5 19.5 - - + +
157F LEU* 4.1 15.9 - - + -
170F LEU* 3.0 31.3 + - + +
171F ILE 3.8 2.7 - - - +
173F LEU* 1.3 78.3 - - + +
175F LEU* 1.3 60.2 + - - +
177F SER* 3.4 2.5 + - - -
178F SER* 2.8 30.3 + - - -
222F LEU* 4.1 26.5 - - + -
226F ALA* 4.9 4.9 - - + -
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Residues in contact with LEU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F GLU* 5.7 2.9 - - - +
154F TYR* 3.3 29.2 - - + +
171F ILE* 3.0 39.3 + - + +
172F GLU* 3.8 10.1 - - + +
174F PHE* 1.3 73.7 - - - +
176F GLN* 1.3 64.5 + - - +
178F SER* 3.3 6.2 + - - -
179F TYR* 3.0 23.1 + - - +
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Residues in contact with GLN 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F GLU 2.8 23.4 + - - +
173F LEU* 4.1 6.1 - - + +
175F LEU* 1.3 75.5 - - - +
177F SER* 1.3 56.8 + - - +
179F TYR* 3.3 18.6 + - - +
180F GLN* 2.9 57.7 + - - +
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Residues in contact with SER 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LEU* 4.9 1.8 - - - -
113F PHE* 5.3 0.2 - - - -
173F LEU* 2.7 34.3 + - - +
174F PHE 3.9 3.1 - - - -
176F GLN* 1.3 77.4 - - - +
178F SER* 1.3 53.3 + - - +
180F GLN* 3.5 13.7 + - - +
181F THR* 2.7 39.3 + - - -
217F PHE* 4.7 3.7 + - - +
218F TYR* 4.5 10.5 - - - +
221F TYR* 5.2 2.1 - - - -
222F LEU* 3.8 37.3 + - - +
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Residues in contact with SER 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LEU* 3.3 25.3 - - - +
113F PHE* 4.2 11.2 - - - -
150F GLU* 4.6 11.5 + - - -
154F TYR* 4.2 5.3 + - - -
174F PHE 2.8 19.2 + - - -
175F LEU* 3.6 8.1 - - - -
177F SER* 1.3 71.9 - - - +
179F TYR* 1.3 67.3 + - - +
181F THR* 3.3 1.7 + - - -
182F GLU* 3.0 43.2 + - - +
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Residues in contact with TYR 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175F LEU 3.0 13.8 + - - +
176F GLN* 3.6 23.8 - - - +
178F SER* 1.3 77.8 - - - +
180F GLN* 1.3 69.3 + - + +
182F GLU* 3.3 12.1 + - + +
183F ILE* 2.9 56.0 + - + +
213F TYR* 6.5 0.9 - + - -
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Residues in contact with GLN 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176F GLN* 2.9 44.6 + - - +
177F SER* 3.6 12.3 + - - +
179F TYR* 1.3 81.1 - - + +
181F THR* 1.3 62.5 + - - +
183F ILE* 3.2 5.5 + - - +
184F GLY 3.0 18.2 + - - -
213F TYR* 3.2 25.0 - - + +
217F PHE* 3.3 65.0 - - + +
221F TYR* 5.8 1.2 - - - -
243F LYS* 5.2 4.9 - - - +
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Residues in contact with THR 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F PHE* 3.5 27.1 - - + -
177F SER 2.7 22.2 + - - -
178F SER 3.7 0.9 - - - -
180F GLN* 1.3 76.4 - - - +
182F GLU* 1.3 57.5 + - - +
184F GLY* 3.2 2.6 + - - -
185F GLN* 2.9 26.3 + - - +
213F TYR 3.2 10.7 + - - -
214F LYS* 3.5 16.6 - - - +
218F TYR* 3.4 26.1 + - + +
401F YS4 3.3 31.2 - - + -
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Residues in contact with GLU 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE* 3.9 18.4 - - - -
113F PHE* 4.4 2.5 - - + -
150F GLU* 4.6 3.3 - - - +
178F SER* 3.0 30.5 + - - +
179F TYR* 3.7 10.4 - - + +
181F THR* 1.3 75.2 - - - +
183F ILE* 1.3 64.0 + - - +
185F GLN* 3.4 8.0 + - - +
186F THR* 2.8 28.4 + - - -
401F YS4 3.7 35.8 - - + +
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Residues in contact with ILE 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F TYR* 2.9 56.1 + - + +
180F GLN* 3.4 8.7 - - - +
182F GLU* 1.3 77.5 - - - +
184F GLY* 1.3 63.1 + - - +
186F THR* 3.2 12.9 + - + +
187F LEU* 3.0 30.8 + - + +
213F TYR* 4.0 23.8 - - + -
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Residues in contact with GLY 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F GLN 3.0 11.3 + - - -
181F THR 3.2 3.8 + - - -
183F ILE* 1.3 76.7 - - - +
185F GLN* 1.3 56.1 + - - +
187F LEU* 3.2 8.9 + - - +
188F ASP* 2.8 28.2 + - - +
210F ILE* 4.1 5.5 - - - +
213F TYR* 3.4 22.7 - - - -
214F LYS* 3.6 16.2 - - - +
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Residues in contact with GLN 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ASP* 3.1 25.7 + - - +
120F MET* 3.7 20.6 - - + +
121F ASP* 5.1 0.2 + - - -
181F THR 2.9 8.0 + - - +
182F GLU* 3.6 7.4 - - - +
184F GLY* 1.3 75.1 - - - +
186F THR* 1.3 57.1 + - - +
188F ASP* 3.2 12.4 + - - +
189F LEU* 2.9 54.5 + - + +
214F LYS* 3.9 6.7 - - - +
401F YS4 3.6 58.2 - - + -
402F MG 4.1 6.1 - - - -
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Residues in contact with THR 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F GLU 2.8 19.9 + - - -
183F ILE* 3.3 17.4 - - + +
185F GLN* 1.3 75.7 - - - +
187F LEU* 1.3 59.3 + - + +
189F LEU* 3.3 8.7 + - - +
190F LEU* 2.8 55.3 + - + +
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F ILE* 3.0 24.5 + - + +
184F GLY* 3.5 9.6 - - - +
186F THR* 1.3 74.0 - - + +
188F ASP* 1.3 63.8 + - - +
190F LEU* 3.9 11.4 - - + -
191F THR* 2.7 32.4 + - - -
206F ARG* 4.0 27.8 - - - +
209F SER* 4.2 31.2 - - - +
210F ILE* 3.9 18.2 - - + -
213F TYR* 4.9 8.5 - - + -
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Residues in contact with ASP 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F GLY 2.8 16.8 + - - +
185F GLN* 3.2 20.4 + - - +
187F LEU* 1.3 76.5 - - - +
189F LEU* 1.3 69.6 + - - +
191F THR* 3.4 2.6 + - - -
192F ALA* 3.4 21.1 + - - +
210F ILE* 4.0 19.8 - - + +
214F LYS* 2.9 30.0 + - + -
280F LYS* 3.5 33.4 + - - +
281F CYS* 5.7 0.9 + - - +
401F YS4 4.4 0.9 + - - -
402F MG 4.2 5.3 - - - -
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Residues in contact with LEU 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F MET* 4.3 41.5 - - + +
121F ASP* 4.6 9.4 - - - +
185F GLN* 2.9 35.4 + - + +
186F THR* 3.9 6.1 - - - +
188F ASP* 1.3 84.0 - - - +
190F LEU* 1.3 66.8 + - + +
192F ALA* 3.2 23.1 + - - +
193F PRO* 3.8 3.6 - - - +
280F LYS* 5.1 4.9 - - - -
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Residues in contact with LEU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F THR* 2.8 49.2 + - + +
187F LEU* 3.9 14.1 - - + +
189F LEU* 1.3 76.2 - - + +
191F THR* 1.3 60.7 + - - +
192F ALA 3.2 1.2 + - - -
193F PRO* 3.6 8.3 - - - +
201F ARG* 3.4 19.4 + - - +
206F ARG* 4.5 9.4 - - - +
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Residues in contact with THR 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F LEU 2.7 22.1 + - - -
188F ASP 3.9 3.8 - - - -
189F LEU 3.3 0.2 - - - -
190F LEU* 1.3 73.7 - - - +
192F ALA* 1.3 57.8 + - - +
193F PRO* 3.3 10.6 - - - +
198F ASP* 3.6 5.4 - - - +
201F ARG* 3.8 33.6 - - + +
202F PHE* 3.4 17.9 - - + -
206F ARG* 2.8 33.8 + - + +
210F ILE* 3.9 6.7 - - - +
281F CYS* 3.8 25.1 - - + -
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Residues in contact with ALA 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F ASP 3.4 15.7 - - - +
189F LEU* 3.2 10.5 + - - +
190F LEU 3.2 0.8 - - - -
191F THR* 1.3 77.9 - - - +
193F PRO* 1.3 68.0 - - - +
194F GLN* 3.4 5.2 + - - +
278F ASP 3.8 11.6 - - - +
279F ASN* 3.1 32.1 - - - +
280F LYS* 3.9 19.0 - - + -
281F CYS 4.7 0.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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