Contacts of the helix formed by residues 170 - 195 (chain F) in PDB entry 4P9U
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 LEU 170 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F LYS* 3.7 49.6 - - + +
169F GLU* 1.3 81.7 - - + +
171F LYS* 1.3 65.0 + - + +
172F ARG 3.2 0.4 - - - -
173F GLN* 3.9 6.4 - - - +
174F GLU* 2.9 30.5 + - - +
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Residues in contact with LYS 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F LYS* 4.3 10.5 + - - +
163F GLU* 5.1 1.6 - - - +
165F SER 5.4 0.8 + - - -
167F LYS* 3.5 15.5 + - + +
168F ASP* 3.3 19.3 + - - +
169F GLU 4.3 0.2 - - - +
170F LEU* 1.3 80.6 - - + +
172F ARG* 1.3 103.5 + - - +
173F GLN 3.1 0.4 - - - -
174F GLU* 2.9 9.5 + - + +
175F ILE* 2.8 38.8 + - + +
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Residues in contact with ARG 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F GLN* 3.2 21.4 + - - +
160F HIS* 3.2 17.9 + - - -
162F LYS* 2.7 44.3 - - - +
168F ASP* 2.2 55.7 + - - +
169F GLU* 3.8 9.9 - - + +
171F LYS* 1.3 119.4 - - - +
173F GLN* 1.3 60.4 + - - +
175F ILE* 3.4 0.6 + - - +
176F LEU* 2.8 40.1 + - + +
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Residues in contact with GLN 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F PRO* 3.7 35.6 + - + +
143F SER* 3.8 23.6 - - - +
169F GLU* 2.6 37.7 + - - +
170F LEU* 4.2 7.6 - - + +
171F LYS 3.1 0.2 - - - -
172F ARG* 1.3 83.8 - - - +
174F GLU* 1.3 62.3 + - - +
176F LEU* 3.7 22.9 - - + +
177F ILE* 2.9 34.6 + - - +
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Residues in contact with GLU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F PRO* 5.1 7.3 - - - +
170F LEU* 2.9 26.0 - - - +
171F LYS* 2.9 12.2 + - + +
173F GLN* 1.3 81.1 - - - +
175F ILE* 1.3 62.4 + - + +
177F ILE* 3.1 21.4 + - - +
178F ALA* 2.9 25.6 + - - +
221F SER* 5.0 10.0 - - - +
226F ARG* 5.2 8.1 + - - -
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Residues in contact with ILE 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F GLN* 3.0 24.5 - - - +
160F HIS* 3.4 32.5 - - + +
171F LYS* 2.8 26.2 + - + +
172F ARG* 4.7 2.9 - - - +
174F GLU* 1.3 73.3 - - + +
176F LEU* 1.3 57.0 + - - +
178F ALA* 3.3 6.7 + - - +
179F LYS* 2.8 41.6 + - + +
217F SER* 4.8 9.9 - - - +
221F SER* 5.7 4.7 - - - -
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Residues in contact with LEU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F LYS* 5.2 5.4 - - + +
157F ILE* 4.7 6.3 - - - +
158F GLN* 3.2 38.4 - - + +
172F ARG* 2.8 30.6 + - + +
173F GLN* 3.7 27.8 - - + +
175F ILE* 1.3 75.6 - - - +
177F ILE* 1.3 59.1 + - + +
179F LYS* 3.7 11.9 - - + +
180F THR* 2.9 32.3 + - - +
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Residues in contact with ILE 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ALA* 4.7 21.1 - - + +
138F LEU* 5.4 7.0 - - + -
142F PRO* 4.6 29.2 - - + +
144F TRP* 6.1 1.6 - - + -
173F GLN 2.9 24.1 + - - +
174F GLU* 3.1 24.9 + - - +
176F LEU* 1.3 73.1 - - + +
178F ALA* 1.3 65.5 + - - +
180F THR* 3.1 12.1 - - + +
181F PHE* 3.0 24.4 + - + +
226F ARG* 3.4 39.9 - - - +
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Residues in contact with ALA 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F GLU 2.9 12.3 + - - +
175F ILE* 3.4 10.1 - - - +
176F LEU 3.3 0.2 - - - -
177F ILE* 1.3 77.4 - - - +
179F LYS* 1.3 56.8 + - - +
182F ASN* 2.9 31.6 + - - +
216F GLY 4.1 0.2 - - - +
217F SER* 3.2 26.7 - - - +
220F PHE* 3.2 35.4 + - - +
221F SER* 3.6 7.9 - - - +
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Residues in contact with LYS 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F GLU 5.4 4.0 - - - +
156F LYS* 5.8 6.3 - - - -
157F ILE 3.1 29.4 + - - +
158F GLN* 3.4 23.2 - - - +
160F HIS* 6.0 0.2 - - - +
175F ILE* 2.8 35.2 + - + +
176F LEU* 3.7 13.7 - - + +
178F ALA* 1.3 77.0 - - - +
180F THR* 1.3 57.2 + - - +
182F ASN* 3.6 5.6 + - - +
183F PHE* 2.9 26.9 + - - +
217F SER* 4.0 29.2 - - - +
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Residues in contact with THR 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ALA* 4.6 11.9 - - + -
144F TRP* 3.6 35.6 - - - +
153F TYR* 5.5 3.3 + - - -
156F LYS* 5.8 9.1 - - - +
176F LEU 2.9 17.8 + - - +
177F ILE* 3.1 22.4 - - + +
179F LYS* 1.3 73.6 - - - +
181F PHE* 1.3 66.0 + - + +
183F PHE* 3.2 9.7 + - - +
184F TYR* 3.0 35.9 + - - -
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Residues in contact with PHE 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F CYS* 3.7 20.4 - - - -
137F ALA* 6.3 0.7 - - + -
138F LEU* 3.7 26.5 - - + -
177F ILE* 3.0 18.6 + - + +
178F ALA 3.9 2.5 - - - +
180F THR* 1.3 79.0 - - + +
182F ASN* 1.3 58.1 + - - +
184F TYR* 3.3 6.0 + - - +
185F ASP* 2.9 24.3 + - - +
220F PHE* 3.4 37.9 - + + -
226F ARG* 3.0 48.5 - - + -
229F ALA* 3.5 12.6 - - + -
230F MET* 3.7 14.4 - - + -
233F TYR* 3.7 15.3 - + - -
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Residues in contact with ASN 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F ALA 2.9 19.0 + - - +
179F LYS* 3.7 6.5 + - - +
181F PHE* 1.3 74.3 - - - +
183F PHE* 1.3 68.0 + - - +
185F ASP* 3.2 1.2 + - - +
186F TYR* 2.9 22.9 + - - +
212F TYR* 3.1 20.8 - - - +
213F ASP* 3.1 37.1 + - - +
216F GLY* 3.1 37.2 - - - -
217F SER* 4.0 4.3 + - - +
220F PHE* 3.4 12.9 - - + -
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Residues in contact with PHE 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F TYR* 4.7 8.5 - + - -
155F GLU* 4.2 22.2 - - + -
156F LYS* 3.7 38.8 - - + -
179F LYS 2.9 15.3 + - - +
180F THR* 3.2 12.5 + - - +
182F ASN* 1.3 80.6 - - - +
184F TYR* 1.3 82.5 + + - +
186F TYR* 3.5 9.7 + + - +
187F MET* 2.9 60.1 + - + +
209F LYS* 5.7 6.1 - - - -
213F ASP* 5.4 1.1 - - - -
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Residues in contact with TYR 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ASN* 4.6 6.5 - - - -
131F VAL* 3.8 23.0 - - + +
134F SER* 3.3 46.4 + - - -
135F CYS* 3.8 25.1 - - - -
144F TRP* 4.2 7.6 - + - -
148F ILE* 4.4 5.7 - - - +
153F TYR* 2.7 27.2 + + - -
180F THR* 3.0 42.4 + - + +
181F PHE* 3.9 1.3 - - - +
183F PHE* 1.3 86.4 - + - +
185F ASP* 1.3 61.5 + - - +
187F MET* 3.5 26.8 - - - +
188F LEU* 2.9 28.9 + - - +
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Residues in contact with ASP 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ARG* 3.8 3.7 + - - -
181F PHE 2.9 16.5 + - - +
182F ASN 3.4 5.6 - - - +
184F TYR* 1.3 75.6 - - - +
186F TYR* 1.3 62.4 + - - +
188F LEU* 3.1 6.2 + - - +
189F PHE* 3.0 32.0 + - - -
212F TYR* 2.3 39.9 + - + -
220F PHE* 3.4 28.7 - - + -
233F TYR* 2.6 35.8 + - - +
255F TYR* 4.2 6.6 + - - -
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Residues in contact with TYR 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F ASN 2.9 15.9 + - - +
183F PHE* 3.7 10.3 - + - +
185F ASP* 1.3 73.9 + - - +
187F MET* 1.3 71.2 + - + +
189F PHE* 4.1 1.1 - - - +
190F GLN* 2.9 46.5 + - + +
205F PHE* 3.3 41.2 + + + -
206F ASN* 3.4 23.4 + - - -
209F LYS* 3.4 46.6 - - + +
212F TYR* 3.8 38.6 - + + -
213F ASP* 4.4 8.7 - - - +
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Residues in contact with MET 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F ILE* 5.6 1.3 - - + +
130F ASN* 4.2 18.4 - - - +
131F VAL* 4.4 12.6 - - + -
183F PHE* 2.9 50.8 + - + +
184F TYR* 3.5 19.7 - - + +
185F ASP 3.3 0.2 - - - -
186F TYR* 1.3 82.0 - - + +
188F LEU* 1.3 65.0 + - - +
190F GLN* 4.9 1.6 - - - -
191F ARG* 2.9 77.7 + - - +
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F MET* 4.4 1.6 - - + -
127F ILE* 5.9 2.7 - - - -
128F MET* 4.5 21.1 - - + +
131F VAL* 3.8 30.2 - - + +
184F TYR 2.9 13.9 + - - +
185F ASP* 3.3 9.9 - - - +
187F MET* 1.3 75.4 - - - +
189F PHE* 1.3 85.5 + - + +
191F ARG* 4.2 1.5 - - - +
192F LEU* 2.9 51.1 + - + +
233F TYR* 3.7 35.7 - - + -
236F LEU* 4.4 12.1 - - + -
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Residues in contact with PHE 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ARG* 3.6 34.3 - - + -
109F SER* 3.6 22.9 - - - -
112F PHE* 3.8 10.2 - + - -
113F MET* 3.7 19.3 - - + -
185F ASP* 3.0 32.8 + - - +
186F TYR 4.1 2.2 - - - +
188F LEU* 1.3 88.9 - - + +
190F GLN* 1.3 58.8 + - - +
192F LEU* 4.6 2.5 - - - -
193F ALA* 2.9 28.8 + - - +
205F PHE* 3.6 24.2 - + + -
212F TYR* 3.2 23.8 - - + +
232F PHE* 3.9 25.6 - + - -
233F TYR* 5.0 2.0 - + - -
255F TYR* 4.7 4.7 - + - -
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Residues in contact with GLN 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E GLU* 3.0 26.6 + - - +
186F TYR* 2.9 47.0 + - + +
187F MET* 4.2 1.8 - - - +
189F PHE* 1.3 75.5 - - - +
191F ARG* 1.3 83.5 + - - +
193F ALA* 2.9 21.7 + - - +
194F PHE* 3.0 26.8 + - + -
202F GLY 4.3 5.6 - - - +
205F PHE* 3.9 17.9 - - + -
206F ASN* 2.8 32.2 + - - +
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Residues in contact with ARG 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E GLU* 5.6 5.6 + - - +
127F ILE* 3.6 35.2 - - + +
131F VAL* 6.0 0.4 - - - -
187F MET* 2.9 64.0 + - - +
188F LEU* 4.2 0.9 - - - +
190F GLN* 1.3 90.1 + - - +
192F LEU* 1.3 61.5 + - - +
194F PHE* 3.3 5.1 + - - +
195F HIS* 2.8 38.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE* 3.6 14.5 - - + -
113F MET* 4.1 20.2 - - + -
116F ALA* 3.5 27.5 - - + +
117F PHE* 4.3 10.1 - - + -
124F ALA* 3.7 31.0 - - + -
127F ILE* 3.8 15.9 - - + -
128F MET* 4.0 26.0 - - + -
188F LEU* 2.9 42.8 + - + +
189F PHE* 3.9 3.4 - - - +
191F ARG* 1.3 77.1 - - - +
193F ALA* 1.3 61.4 + - - +
194F PHE 3.5 0.3 + - - -
195F HIS* 3.5 5.9 + - + +
196F SER* 3.8 1.2 + - - -
236F LEU* 4.9 0.9 - - + -
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Residues in contact with ALA 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE* 3.5 19.1 - - + -
189F PHE 2.9 19.0 + - - +
190F GLN 2.9 8.4 + - - +
192F LEU* 1.3 76.9 - - - +
194F PHE* 1.3 54.6 + - - +
196F SER* 2.7 21.3 + - - -
198F ASN 3.5 4.2 - - - +
201F TYR* 3.4 38.2 - - + +
202F GLY* 3.7 4.2 + - - +
205F PHE* 3.9 10.1 - - + -
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Residues in contact with PHE 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E MET* 3.1 32.5 - - + -
76E GLU* 4.1 8.3 - - - -
190F GLN* 3.0 34.2 + - - -
191F ARG* 3.3 8.5 + - - +
192F LEU 3.2 0.4 - - - -
193F ALA* 1.3 77.1 - - - +
195F HIS* 1.3 62.8 + - + +
196F SER* 3.0 10.3 + - - -
197F GLY* 3.6 10.2 + - - -
198F ASN 4.7 3.4 + - - +
199F GLN* 3.7 34.3 - - + -
202F GLY* 3.5 16.8 - - - -
203F LEU* 3.9 9.9 - - + -
206F ASN* 3.1 27.6 - - - -
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Residues in contact with HIS 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ALA* 3.3 23.6 - - + -
119F LEU* 4.7 0.7 - - - +
120F ASN* 3.5 38.3 + - + +
123F SER* 3.3 35.4 - - - -
124F ALA* 5.3 1.8 - - - +
127F ILE* 4.2 21.5 - - + +
191F ARG* 2.8 33.7 + - + +
192F LEU* 3.5 7.7 + - + +
194F PHE* 1.3 81.5 - - + +
196F SER* 1.3 59.4 + - - +
197F GLY 3.4 1.1 - - - -
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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
------------------------------------------------------------
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