Contacts of the helix formed by residues 190 - 224 (chain c) in PDB entry 5W97
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 ASP 190 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118c PRO* 6.0 0.2 - - - +
121c ILE* 4.0 13.9 - - + +
185c PRO 4.3 2.1 - - - +
186c PHE* 3.1 13.2 - - + +
187c THR* 2.8 46.7 + - - +
188c ILE 3.2 1.4 - - - -
189c SER* 1.3 73.0 - - - +
191c GLY* 1.3 64.2 + - - +
193c TYR* 4.1 2.8 + - - +
194c GLY* 3.5 10.8 + - - -
53g LEU* 3.6 28.7 - - + +
54g ARG* 3.0 45.5 + - - +
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Residues in contact with GLY 191 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218a THR* 3.0 18.6 - - - +
224a GLY* 3.7 6.1 - - - -
112c LEU* 5.6 1.3 - - - -
188c ILE 4.0 1.2 - - - +
189c SER 3.0 9.3 + - - -
190c ASP* 1.3 77.8 - - - +
192c VAL* 1.3 57.3 + - - -
195c SER* 2.7 32.4 + - - -
52g HIS 3.5 19.2 + - - -
53g LEU* 5.1 0.2 - - - -
55g ILE* 4.1 2.8 - - - +
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Residues in contact with VAL 192 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218a THR* 3.1 19.7 + - - +
219a PHE* 4.6 9.2 - - + -
224a GLY 2.9 22.6 + - - +
225a GLY 4.0 11.4 - - - +
226a GLY* 4.5 2.9 - - - +
104c SER* 3.3 28.7 - - - +
112c LEU* 3.9 17.6 - - + +
116c TRP* 3.8 22.0 - - + -
191c GLY* 1.3 69.8 - - - -
193c TYR* 1.3 65.2 + - - +
195c SER* 3.9 4.0 - - - -
196c THR* 2.9 35.6 + - + +
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Residues in contact with TYR 193 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101c PHE* 5.6 2.7 - + - -
116c TRP* 3.4 31.6 - + + -
117c PRO* 4.3 5.8 - - + -
118c PRO* 3.8 30.2 - - + +
121c ILE* 3.7 35.7 - - + -
123c PRO* 3.6 20.6 - - + +
124c LEU 4.9 0.5 + - - -
186c PHE* 3.9 28.7 - + - -
190c ASP 4.1 3.1 + - - +
191c GLY 3.3 0.6 - - - -
192c VAL* 1.3 81.6 - - - +
194c GLY* 1.3 64.9 + - - +
196c THR* 3.0 14.5 + - - -
197c PHE* 3.1 27.9 + + + +
256c ILE* 4.7 10.4 + - + +
257c TYR* 5.9 0.5 - - - -
260c GLY 3.9 20.7 + - - -
261c SER* 5.4 0.3 - - - -
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Residues in contact with GLY 194 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186c PHE* 4.9 1.6 - - - -
187c THR 3.4 21.1 - - - -
188c ILE* 3.8 6.9 - - - -
190c ASP* 3.5 7.4 + - - -
191c GLY 3.2 6.0 + - - -
193c TYR* 1.3 84.5 - - - +
195c SER* 1.3 59.7 + - - +
197c PHE* 4.4 1.1 - - - -
198c PHE* 3.0 42.1 + - - +
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Residues in contact with SER 195 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217a THR* 3.3 29.1 - - - -
218a THR 3.1 21.5 + - - -
219a PHE* 3.5 15.2 - - - -
188c ILE* 3.5 8.2 + - - -
191c GLY 2.7 23.2 + - - -
192c VAL* 3.8 6.1 - - - -
193c TYR 3.3 0.2 - - - -
194c GLY* 1.3 77.9 - - - +
196c THR* 1.3 57.0 + - - +
199c VAL* 3.1 36.2 + - - +
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Residues in contact with THR 196 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219a PHE* 3.6 27.4 - - + -
97c PHE 5.2 2.2 - - - +
100c ALA* 4.4 4.5 - - + +
101c PHE* 4.1 46.4 - - + +
104c SER* 4.7 2.0 - - - +
116c TRP* 4.7 1.8 - - + -
192c VAL* 2.9 27.3 + - + +
193c TYR* 3.0 9.7 + - - -
195c SER* 1.3 73.1 - - - +
197c PHE* 1.3 69.0 + - - +
199c VAL* 5.1 0.2 - - - -
200c ALA* 3.1 30.5 + - - +
256c ILE* 4.4 2.9 - - - +
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Residues in contact with PHE 197 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101c PHE* 5.9 0.2 - - - -
124c LEU* 4.4 14.4 - - + -
180c GLU* 6.6 0.2 - - + -
181c TYR* 4.3 7.2 - + - -
186c PHE* 4.0 19.5 - + - -
193c TYR* 3.1 31.9 + + + +
194c GLY* 3.8 4.9 - - - +
195c SER 3.3 0.2 - - - -
196c THR* 1.3 82.0 + - - +
198c PHE* 1.3 87.7 + + - +
201c THR* 2.5 52.3 + - + +
256c ILE* 3.6 30.1 - - + -
257c TYR* 3.5 43.5 - + - -
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Residues in contact with PHE 198 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181c TYR* 3.8 33.6 + + - -
184c ALA* 4.2 5.2 - - + -
186c PHE* 3.6 43.5 - + - -
187c THR* 3.5 20.4 - - - -
188c ILE* 3.4 24.0 - - + -
194c GLY 3.0 27.2 + - - +
197c PHE* 1.3 91.2 - + - +
199c VAL* 1.3 61.1 + - - +
201c THR* 3.5 1.1 - - - -
202c GLY* 2.7 27.4 + - - -
102g PEK 3.3 49.4 - - - +
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Residues in contact with VAL 199 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207a THR* 5.4 0.9 - - + -
208a MET* 5.4 0.4 - - + -
211a THR* 4.5 11.7 - - + +
217a THR* 4.4 4.3 - - + -
219a PHE* 3.9 22.2 - - + -
97c PHE* 3.7 24.2 - - + -
188c ILE* 4.3 19.3 - - + -
195c SER 3.1 20.7 + - - +
196c THR 4.6 0.4 - - - +
198c PHE* 1.3 77.7 - - - +
200c ALA* 1.3 54.0 + - - +
203c PHE* 2.7 58.7 + - + +
102g PEK 4.1 11.2 - - + +
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Residues in contact with ALA 200 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94c PHE* 3.9 10.7 - - + -
97c PHE* 4.4 27.3 - - + +
98c PHE* 6.2 1.1 - - + -
101c PHE* 6.5 0.7 - - + -
196c THR* 3.1 20.1 + - - +
199c VAL* 1.3 74.2 - - - +
201c THR* 1.3 64.8 + - - +
203c PHE* 5.0 1.1 - - - -
204c HIS* 3.2 21.5 + - - +
252c LEU* 3.6 24.2 - - + +
256c ILE* 3.9 8.5 - - + -
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Residues in contact with THR 201 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177c GLN* 4.1 15.5 + - - +
181c TYR* 2.5 30.7 + - - -
197c PHE* 2.5 37.1 + - + +
198c PHE* 3.5 1.4 - - - -
200c ALA* 1.3 77.5 - - - +
202c GLY* 1.3 60.5 + - - +
204c HIS* 3.2 3.4 + - - +
205c GLY* 2.7 27.4 + - - -
252c LEU* 4.1 15.7 - - + -
256c ILE* 4.8 8.3 - - + -
257c TYR* 3.7 33.2 - - + +
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Residues in contact with GLY 202 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181c TYR* 3.0 13.0 + - - -
198c PHE 2.7 26.9 + - - -
201c THR* 1.3 74.0 - - - +
203c PHE* 1.3 61.1 + - - +
205c GLY* 3.0 3.5 + - - -
206c LEU* 2.9 21.8 + - - +
102g PEK 3.9 27.6 - - - +
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Residues in contact with PHE 203 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207a THR* 3.9 14.8 - - + -
211a THR* 6.2 0.2 - - + -
93c PHE* 3.7 30.5 - + + -
94c PHE* 3.9 17.3 - - + -
97c PHE* 3.9 21.5 - + + -
199c VAL* 2.7 41.0 + - + +
200c ALA* 4.2 0.7 - - - +
202c GLY* 1.3 70.5 - - - +
204c HIS* 1.3 56.9 + - - +
206c LEU* 3.4 19.8 + - + +
207c HIS* 2.7 40.6 + + - -
304c PGV 4.6 8.1 - - + -
102g PEK 3.9 57.9 - - + +
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Residues in contact with HIS 204 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94c PHE* 3.8 11.5 - + + -
137c LEU* 4.1 3.4 - - + -
173c PHE* 3.7 17.6 - + - -
177c GLN* 5.5 0.8 + - - -
200c ALA 3.2 15.8 + - - +
201c THR 3.4 8.4 + - - +
202c GLY 3.1 0.6 - - - -
203c PHE* 1.3 73.4 - - - +
205c GLY* 1.3 56.0 + - - +
207c HIS* 2.9 8.5 + - + +
208c VAL* 2.8 56.3 + - + +
245c VAL* 2.8 34.6 + - + +
248c VAL* 3.7 23.8 - - + -
249c TRP* 3.5 29.8 - + + +
252c LEU* 3.6 13.7 - - + +
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Residues in contact with GLY 205 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173c PHE* 5.0 6.3 - - - -
174c THR* 5.3 0.3 + - - -
177c GLN* 5.6 2.5 - - - -
201c THR 2.7 17.0 + - - -
202c GLY 3.0 4.7 + - - -
204c HIS* 1.3 74.4 + - - +
206c LEU* 1.3 60.3 + - - +
208c VAL* 3.2 13.8 + - - +
209c ILE* 3.2 23.6 + - - +
102g PEK 4.3 25.0 - - - +
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Residues in contact with LEU 206 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202c GLY 2.9 11.6 + - - +
203c PHE* 3.4 24.0 - - + +
205c GLY* 1.3 75.7 - - - +
207c HIS* 1.3 57.5 + - - +
209c ILE* 3.3 14.4 + - + +
210c ILE* 3.0 45.6 + - + +
304c PGV 4.5 40.4 - - + -
305c CDL 4.6 16.4 - - + -
102g PEK 3.5 40.6 - - + +
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Residues in contact with HIS 207 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90c GLU* 2.6 29.6 + - - -
93c PHE* 4.9 2.2 - + - -
94c PHE* 3.7 21.1 - + + -
203c PHE* 2.7 33.7 + + - +
204c HIS* 2.9 14.8 + - + +
206c LEU* 1.3 71.7 - - + +
208c VAL* 1.3 56.4 + - - +
210c ILE* 3.7 7.8 - - + +
211c GLY* 2.8 32.1 + - - -
241c TYR* 2.9 28.1 - + - +
244c PHE* 4.2 9.6 - + + -
245c VAL* 3.7 22.5 - - + +
304c PGV 4.0 27.4 - - + +
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Residues in contact with VAL 208 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137c LEU* 5.0 2.9 - - + -
170c GLY* 3.8 13.2 - - - +
173c PHE* 3.6 22.9 - - + -
174c THR* 3.5 22.2 - - - +
204c HIS* 2.8 44.9 + - + +
205c GLY* 3.4 7.9 - - - +
207c HIS* 1.3 75.1 - - - +
209c ILE* 1.3 54.6 + - - +
211c GLY* 3.3 1.6 + - - -
212c SER* 2.7 40.8 + - - +
242c TRP* 3.7 12.0 - - + -
245c VAL* 4.1 15.0 - - + +
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Residues in contact with ILE 209 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174c THR* 4.4 16.8 - - + +
205c GLY 3.2 15.3 + - - +
206c LEU* 3.6 15.3 - - + +
207c HIS 3.3 0.2 - - - -
208c VAL* 1.3 73.6 - - - +
210c ILE* 1.3 58.6 + - + +
212c SER* 3.8 5.4 - - - -
213c THR* 2.7 47.3 + - - +
305c CDL 4.2 59.0 - - + -
102g PEK 4.2 33.7 - - + -
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Residues in contact with ILE 210 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206c LEU* 3.0 44.7 + - + +
207c HIS* 3.7 9.9 - - + +
209c ILE* 1.3 77.2 - - + +
211c GLY* 1.3 62.3 + - - +
213c THR* 3.5 6.5 + - - -
214c PHE* 3.0 23.4 + - + +
241c TYR* 3.8 19.1 - - + +
304c PGV 3.9 88.4 - - + +
305c CDL 5.7 0.4 - - + -
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Residues in contact with GLY 211 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207c HIS 2.8 16.8 + - - -
208c VAL 3.6 1.3 - - - -
210c ILE* 1.3 78.5 - - - +
212c SER* 1.3 56.0 + - - +
214c PHE* 3.2 7.1 + - - +
215c LEU* 2.9 29.8 + - - +
238c ALA 5.5 2.3 - - - +
241c TYR* 3.9 19.7 - - - -
242c TRP* 3.8 17.9 - - - -
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Residues in contact with SER 212 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167c ILE* 4.8 6.0 - - - +
170c GLY* 4.1 10.6 - - - -
171c VAL* 5.3 6.5 - - - -
174c THR* 5.1 1.0 + - - -
208c VAL* 2.7 27.3 + - - +
209c ILE* 3.8 6.0 - - - -
211c GLY* 1.3 72.7 - - - +
213c THR* 1.3 56.8 + - - +
215c LEU* 2.9 11.7 + - - +
216c ILE* 2.7 46.0 + - - +
242c TRP* 3.6 19.1 - - - -
305c CDL 5.1 10.5 - - - -
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Residues in contact with THR 213 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209c ILE* 2.7 34.6 + - - +
210c ILE* 3.6 6.1 - - - -
212c SER* 1.3 76.3 - - - +
214c PHE* 1.3 54.4 + - - -
216c ILE* 3.3 14.0 + - - +
217c VAL* 2.9 29.3 + - + +
304c PGV 3.6 27.8 - - + -
305c CDL 3.8 54.3 - - + +
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Residues in contact with PHE 214 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83c MET* 4.7 4.7 - - + -
210c ILE* 3.0 18.3 + - + +
211c GLY 3.3 6.5 - - - +
212c SER 3.1 0.2 - - - -
213c THR* 1.3 77.8 - - - +
215c LEU* 1.3 57.0 + - - +
217c VAL* 3.2 4.3 + - + +
218c CYS* 3.0 28.7 + - - -
234c GLY 3.6 25.6 - - - -
237c ALA* 4.0 9.9 - - + -
238c ALA* 3.6 28.3 - - + -
241c TYR* 4.6 15.3 - + + -
304c PGV 3.6 90.4 - - + -
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Residues in contact with LEU 215 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144c ILE* 3.4 27.4 - - + -
163c LEU* 3.9 16.9 - - + +
166c THR* 4.1 16.8 - - + -
167c ILE* 3.8 23.8 - - + +
211c GLY 2.9 12.8 + - - +
212c SER* 2.9 10.8 + - - +
214c PHE* 1.3 73.1 - - - +
216c ILE* 1.3 61.0 + - - +
218c CYS* 3.2 6.0 + - - +
219c PHE* 2.9 28.4 + - - +
235c PHE* 4.9 3.8 - - + -
238c ALA* 4.2 19.7 - - + +
242c TRP* 3.8 37.7 - - + -
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Residues in contact with ILE 216 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167c ILE* 4.0 27.8 - - + -
171c VAL* 5.7 1.8 - - + -
212c SER* 2.7 31.0 + - - +
213c THR* 3.5 6.5 - - - +
215c LEU* 1.3 72.2 - - - +
217c VAL* 1.4 63.8 + - - +
219c PHE* 3.0 18.3 + - + +
220c PHE* 3.1 44.7 + - + -
305c CDL 3.9 50.3 - - + -
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Residues in contact with VAL 217 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213c THR* 2.9 20.3 + - + +
214c PHE* 3.5 10.5 - - + +
215c LEU 3.2 0.2 - - - -
216c ILE* 1.4 76.3 - - - +
218c CYS* 1.3 63.4 + - - +
220c PHE* 3.5 2.1 + - - +
221c ARG* 3.0 37.8 + - - +
304c PGV 4.3 29.2 - - + -
305c CDL 3.7 68.1 - - + +
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Residues in contact with CYS 218 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163c LEU* 4.2 5.2 - - + -
214c PHE* 3.0 25.2 + - - -
215c LEU* 3.2 8.9 + - - +
217c VAL* 1.3 77.9 - - - +
219c PHE* 1.3 56.5 + - - +
221c ARG* 3.3 1.7 + - - +
222c GLN* 2.8 31.5 + - - +
227c PHE* 3.5 17.4 - - + -
234c GLY* 3.6 26.9 - - - -
235c PHE* 3.9 25.8 - - + -
238c ALA* 3.7 15.3 - - - -
304c PGV 5.9 0.7 - - - -
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Residues in contact with PHE 219 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160c LEU* 3.7 41.8 - - + +
163c LEU* 3.9 23.3 - - + +
164c PHE* 4.0 20.2 - + + -
167c ILE* 4.1 16.8 - - + -
215c LEU 2.9 12.4 + - - +
216c ILE* 3.2 11.0 - - + +
218c CYS* 1.3 75.8 - - - +
220c PHE* 1.3 75.7 + + - +
222c GLN* 3.1 5.9 + - - +
223c LEU* 2.8 48.1 + - + +
306c CHD 4.3 21.1 - - + -
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Residues in contact with PHE 220 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216c ILE* 3.1 44.1 + - + +
217c VAL 4.1 0.7 - - - +
219c PHE* 1.3 88.5 - + - +
221c ARG* 1.3 63.1 + - - +
223c LEU* 3.1 27.2 + - + +
224c LYS* 3.0 38.6 + - - +
305c CDL 3.6 38.8 - - + +
1j PHE* 6.3 1.3 - + - -
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Residues in contact with ARG 221 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62c ILE* 3.7 29.8 - - - +
66c THR* 3.0 26.9 + - - -
217c VAL* 3.0 33.5 + - + +
218c CYS* 3.7 6.0 - - - +
220c PHE* 1.3 75.8 - - - +
222c GLN* 1.3 59.8 + - - +
224c LYS* 3.5 2.4 + - - +
225c PHE 3.3 3.1 + - - -
226c HIS* 3.0 63.1 + - + +
227c PHE* 3.4 25.7 - - + -
234c GLY* 4.5 0.6 - - - -
304c PGV 2.9 56.1 + - - -
305c CDL 3.9 15.3 - - - -
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Residues in contact with GLN 222 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151c LEU* 4.1 3.6 - - - +
156c ARG* 2.7 52.5 + - - +
159c MET* 3.7 37.1 - - + +
160c LEU* 3.6 20.9 - - + -
218c CYS 2.8 17.1 + - - +
219c PHE* 3.1 5.8 + - - +
221c ARG* 1.3 73.8 - - - +
223c LEU* 1.3 58.3 + - - +
224c LYS 3.2 0.2 - - - -
225c PHE* 3.1 8.3 + - - -
226c HIS 5.0 0.2 - - - +
227c PHE* 3.6 30.1 + - + +
6f VAL* 3.9 23.9 - - - +
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Residues in contact with LEU 223 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156c ARG* 2.8 36.8 + - - +
160c LEU* 4.2 19.3 - - + -
219c PHE* 2.8 33.7 + - + +
220c PHE* 3.1 29.1 + - + +
222c GLN* 1.3 77.1 - - - +
224c LYS* 1.3 58.6 + - + +
225c PHE* 3.1 12.7 - - - -
306c CHD 4.4 18.6 - - + -
1j PHE* 4.0 48.9 - - + +
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Residues in contact with LYS 224 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220c PHE* 3.0 25.7 + - - +
221c ARG 4.0 0.4 - - - +
222c GLN 3.2 0.4 - - - -
223c LEU* 1.3 75.7 - - + +
225c PHE* 1.3 72.4 + - - +
226c HIS* 3.4 18.6 + - + +
305c CDL 3.3 80.7 + - - +
1j PHE* 5.1 15.5 - - + -
2j GLU 5.1 3.8 - - - +
3j ASN* 4.5 0.5 - - - +
4j ARG 5.0 4.0 + - - -
5j VAL* 3.5 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
------------------------------------------------------------
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