Contacts of the helix formed by residues 208 - 243 (chain B) in PDB entry 6D6Q
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 HIS 208 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE* 3.2 41.8 - + + -
166B GLY* 5.1 2.5 - - - -
204B LEU* 3.7 18.7 - - + +
205B HIS* 3.6 37.2 + + + +
206B GLU 2.9 1.8 + - - -
207B ASP* 1.3 81.2 - - + +
209B LEU* 1.3 56.9 + - - -
210B GLU 3.9 0.2 - - - -
211B ARG* 4.4 25.4 + - - +
212B VAL* 3.8 16.1 + - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ILE* 4.9 15.0 - - + -
234A ILE* 5.7 3.8 - - + -
247A VAL* 5.2 9.9 - - + +
248A LEU* 4.8 21.1 - - + -
251A SER* 4.9 18.4 - - - +
184B LEU* 4.3 15.3 - - + -
200B MET* 4.2 28.0 - - + -
204B LEU* 5.2 2.0 - - + -
205B HIS 4.9 1.8 - - - +
206B GLU* 2.8 20.7 + - + +
207B ASP 3.2 0.4 - - - -
208B HIS* 1.3 77.2 - - - +
210B GLU* 1.3 68.1 + - - +
211B ARG 3.1 2.1 + - - -
212B VAL* 3.2 7.7 - - + +
213B LEU* 2.9 34.0 + - + +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LYS* 3.6 25.5 + - + +
248A LEU* 4.9 17.5 - - + +
206B GLU 4.6 0.2 + - - -
207B ASP 4.5 5.9 + - - +
209B LEU* 1.3 79.2 - - - +
211B ARG* 1.3 65.6 + - + +
213B LEU* 3.6 9.7 - - - +
214B GLU* 2.6 61.2 + - - +
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE* 4.5 4.4 - - + -
166B GLY* 2.8 34.4 + - - -
167B THR* 3.9 14.7 - - - +
168B ALA* 4.4 10.6 - - + +
207B ASP 4.9 11.9 - - - +
208B HIS* 4.4 27.1 + - - +
209B LEU 3.1 0.8 - - - -
210B GLU* 1.3 86.6 - - + +
212B VAL* 1.3 66.1 + - + +
214B GLU* 3.1 15.2 - - - +
215B ALA* 2.9 23.3 + - - +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA* 3.7 9.2 - - + +
162B GLY* 3.7 25.6 - - - +
163B PHE* 3.9 25.8 - - + -
168B ALA* 4.1 12.6 - - + -
184B LEU* 4.3 23.3 - - + +
200B MET* 5.6 1.1 - - + -
204B LEU* 5.0 6.5 - - + -
208B HIS 3.8 16.6 - - - +
209B LEU* 3.2 16.3 - - + +
211B ARG* 1.3 73.7 - - + +
213B LEU* 1.3 61.3 + - - +
215B ALA* 3.6 0.9 - - - +
216B ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 3.6 35.2 - - + -
247A VAL* 4.0 20.2 - - + -
248A LEU* 4.2 7.4 - - + -
184B LEU* 4.3 14.8 - - + -
186B LEU* 4.8 9.0 - - + +
195B ILE* 4.8 9.6 - - + -
198B LEU* 4.0 30.1 - - + -
209B LEU* 2.9 26.2 + - + +
210B GLU* 3.6 5.8 - - - +
211B ARG 3.1 0.2 - - - -
212B VAL* 1.3 81.2 - - + +
214B GLU* 1.3 63.0 + - - +
216B ALA* 3.3 4.6 + - - +
217B ALA* 3.0 21.7 + - - +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LYS* 3.4 22.5 + - - +
210B GLU* 2.6 41.5 + - - +
211B ARG* 3.1 22.6 - - - +
213B LEU* 1.3 76.6 - - - +
215B ALA* 1.3 57.6 + - - +
217B ALA* 3.3 8.4 + - - +
218B GLN* 2.9 29.1 + - - +
221B ARG* 5.4 0.5 + - - -
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ALA* 4.7 5.8 - - + -
168B ALA* 3.9 22.9 - - + +
169B LEU 5.1 3.6 - - - +
170B ALA* 4.9 5.7 - - + +
211B ARG 2.9 18.4 + - - +
212B VAL* 3.6 4.5 - - - +
213B LEU 3.2 0.2 - - - -
214B GLU* 1.3 76.0 - - + +
216B ALA* 1.3 65.6 + - - +
218B GLN* 3.2 6.0 + - - +
219B ALA* 2.9 24.0 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B CYS* 4.7 1.8 - - - +
160B SER 4.6 2.5 - - - +
161B ALA* 3.6 24.1 - - + +
184B LEU* 4.2 9.2 - - + -
186B LEU* 3.2 31.1 - - + +
212B VAL 2.9 17.6 + - - +
213B LEU 3.7 3.4 - - - +
215B ALA* 1.3 75.8 - - - +
217B ALA* 1.3 62.7 + - - +
219B ALA* 3.3 7.7 + - - +
220B ALA* 2.9 23.2 + - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LYS* 6.0 2.9 - - - +
186B LEU* 4.5 7.3 - - + +
188B LEU* 4.6 13.9 - - + -
213B LEU 3.0 13.4 + - - +
214B GLU* 3.4 13.2 - - - +
216B ALA* 1.3 76.9 - - - +
218B GLN* 1.3 57.1 + - - +
220B ALA* 3.1 7.9 + - - +
221B ARG* 2.8 50.9 + - - +
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Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLU 2.9 17.0 + - - +
215B ALA* 3.8 6.1 - - - +
217B ALA* 1.3 75.0 - - - +
219B ALA* 1.3 64.0 + - - +
221B ARG* 3.1 31.0 + - - +
222B ASP* 3.0 41.8 + - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY 5.8 2.0 - - - +
21B LEU* 4.1 8.3 - - + +
159B CYS* 3.9 22.0 - - - -
170B ALA* 4.0 22.2 - - + -
215B ALA 2.9 13.4 + - - +
216B ALA* 3.5 10.5 - - - +
218B GLN* 1.3 75.3 - - - +
220B ALA* 1.3 58.7 + - - +
222B ASP* 3.2 11.8 + - - +
223B VAL* 2.9 33.3 + - - +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B CYS* 3.8 18.2 - - - +
158B ALA 4.6 7.2 - - - -
159B CYS* 4.3 5.8 - - + +
186B LEU* 5.3 1.8 - - + -
188B LEU* 3.2 34.1 - - + -
190B PRO* 5.9 0.7 - - - -
216B ALA 2.9 12.7 + - - +
217B ALA 3.4 4.7 - - - +
219B ALA* 1.3 74.2 - - - +
221B ARG* 1.3 61.1 + - - +
223B VAL* 3.3 9.0 + - - +
224B HIS* 2.9 27.6 + - - +
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 4.1 21.4 - - - +
190B PRO* 5.1 18.3 + - + +
193B GLY* 5.0 11.1 - - - -
214B GLU 5.4 0.6 + - - -
217B ALA* 2.8 45.4 + - - +
218B GLN* 3.1 38.4 + - - +
220B ALA* 1.3 78.1 - - - +
222B ASP* 1.3 63.6 + - - +
224B HIS* 3.0 12.0 + - - +
225B THR* 3.0 25.9 + - + +
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY 4.7 10.0 - - - +
20B GLU* 5.9 0.7 - - - -
21B LEU* 4.4 14.2 - - + +
218B GLN* 3.0 36.2 + - - +
219B ALA* 3.2 12.3 + - - +
221B ARG* 1.3 74.9 - - - +
223B VAL* 1.3 62.6 + - - +
225B THR* 2.2 33.9 + - - +
226B LEU* 2.8 17.3 - - + +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.1 19.3 - - + -
24B ILE* 4.6 9.6 - - + -
42B GLN* 4.9 10.1 - - - +
139B ASN* 3.8 24.7 - - - +
157B CYS* 4.8 3.6 - - + -
158B ALA 4.4 9.2 - - - +
159B CYS* 4.5 7.4 - - + -
219B ALA 2.9 20.1 + - - +
220B ALA* 3.5 11.4 - - - +
221B ARG 3.3 0.2 - - - -
222B ASP* 1.3 74.9 - - - +
224B HIS* 1.3 56.9 + - - +
226B LEU* 3.3 7.3 + - - +
227B LEU* 2.9 49.3 + - + +
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Residues in contact with HIS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ASP* 4.4 6.5 + - - -
155B PHE* 3.5 41.0 - + + +
157B CYS* 3.7 13.0 - - - -
190B PRO* 3.3 34.7 - - + +
191B ALA 5.4 0.4 - - - -
220B ALA 2.9 14.7 + - - +
221B ARG* 3.1 16.8 + - - +
223B VAL* 1.3 75.0 - - - +
225B THR* 1.3 65.6 + - + +
227B LEU* 3.8 1.2 - - - +
228B ASP* 2.9 32.8 + - + +
29H PRO 5.4 0.6 + - - -
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Residues in contact with THR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ARG* 3.0 13.9 + - + +
222B ASP* 2.2 36.2 + - - +
224B HIS* 1.3 78.3 - - + +
226B LEU* 1.3 70.1 + - - +
228B ASP* 2.3 34.8 - - - +
229B ARG* 3.0 15.1 + - - +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.9 12.8 - - + -
23B LYS* 5.2 3.4 - - - -
24B ILE* 3.5 47.3 - - + +
222B ASP* 2.8 33.5 + - + +
223B VAL* 3.8 4.5 - - - +
225B THR* 1.3 87.8 + - - +
227B LEU* 1.3 64.3 + - - +
229B ARG* 3.2 33.0 + - - +
230B VAL* 3.1 27.4 + - + +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.2 28.3 - - + -
26B ALA* 6.2 1.3 - - + -
40B ILE* 4.9 4.9 - - + -
139B ASN* 4.0 27.6 - - + +
142B THR* 5.2 3.4 - - + -
143B LEU* 3.4 35.4 - - + +
155B PHE* 4.8 13.9 - - + -
157B CYS* 4.4 12.8 - - - -
223B VAL* 2.9 34.5 + - + +
224B HIS* 3.8 3.8 - - - +
226B LEU* 1.3 76.1 - - - +
228B ASP* 1.3 58.4 + - - +
230B VAL* 3.1 10.0 + - - +
231B VAL* 2.9 32.5 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 4.3 16.3 - - + -
224B HIS* 2.9 32.5 + - + +
225B THR* 2.3 24.9 - - - +
227B LEU* 1.3 76.9 - - - +
229B ARG* 1.3 90.0 + - - +
231B VAL* 3.7 6.5 - - - +
232B ARG* 2.9 54.8 + - - +
28H VAL* 5.1 2.7 - - + -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B THR* 3.0 18.4 + - - +
226B LEU* 3.2 40.1 + - - +
228B ASP* 1.3 91.6 + - - +
230B VAL* 1.3 65.4 + - - +
232B ARG* 3.3 8.0 + - - +
233B GLN* 3.0 38.9 + - - +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 5.9 4.7 - - + +
26B ALA* 4.6 32.8 - - + +
27B ARG* 5.0 2.5 - - - +
28B MET* 4.5 19.1 - - + -
143B LEU* 5.0 3.8 - - + -
226B LEU* 3.1 16.8 + - + +
227B LEU* 3.4 10.5 - - - +
229B ARG* 1.3 78.6 - - + +
231B VAL* 1.3 63.5 + - - +
233B GLN* 3.2 16.1 + - - +
234B HIS* 3.0 21.0 + - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET* 3.9 34.1 - - + -
143B LEU* 4.8 6.7 - - + -
146B LEU* 4.4 6.7 - - + -
155B PHE* 3.7 28.3 - - + -
227B LEU 2.9 20.3 + - - +
228B ASP 3.7 4.0 - - - +
230B VAL* 1.3 76.9 - - + +
232B ARG* 1.3 57.4 + - - +
234B HIS* 3.2 2.5 + - + +
235B VAL* 2.9 42.3 + - + +
28H VAL* 3.7 25.8 - - + -
57H ALA* 4.7 7.4 - - + -
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ASP* 2.9 39.2 + - - +
229B ARG* 3.8 8.5 - - - +
231B VAL* 1.3 74.3 - - - +
233B GLN* 1.3 67.0 + - + +
235B VAL* 4.0 5.0 - - - +
236B ARG* 2.9 45.5 + - - +
26H LEU* 4.4 23.1 + - + +
27H VAL* 4.6 3.0 - - - +
28H VAL* 3.5 21.4 - - + +
31H ASP* 3.1 36.4 + - - -
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Residues in contact with GLN 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ARG* 3.0 29.2 + - - +
230B VAL* 3.2 12.6 + - - +
232B ARG* 1.3 75.5 - - - +
234B HIS* 1.3 64.2 + - - +
236B ARG* 3.4 17.5 + - - +
237B GLU* 3.0 39.2 + - + +
14H LEU* 5.4 13.9 - - + +
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Residues in contact with HIS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET* 3.4 50.1 + - + +
29B GLY* 5.3 0.8 - - - -
147B ASP* 4.4 18.5 + - - -
230B VAL* 3.0 13.7 + - + +
231B VAL* 3.2 11.9 + - - +
233B GLN* 1.3 77.6 - - - +
235B VAL* 1.3 69.4 + - - +
237B GLU* 3.3 10.3 + - + +
238B ALA* 3.0 26.0 + - + +
11H ARG* 5.9 3.6 - - - -
72H LEU* 4.2 22.6 - - + +
73H LYS* 5.8 1.6 - - + -
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B VAL* 2.9 35.5 + - + +
232B ARG* 4.0 3.6 - - - +
234B HIS* 1.3 82.4 - - - +
236B ARG* 1.3 63.8 + - - +
238B ALA* 3.3 5.1 + - - +
239B SER* 2.9 26.0 + - - -
26H LEU* 3.3 28.9 - - + -
27H VAL 5.1 0.9 - - - +
28H VAL* 4.9 4.9 - - + -
57H ALA* 4.1 18.4 - - + -
58H GLY* 4.1 22.2 - - - +
72H LEU* 4.8 11.8 - - + +
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Residues in contact with ARG 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ARG* 2.9 41.9 + - - +
233B GLN* 3.7 19.8 - - - +
235B VAL* 1.3 77.1 - - - +
237B GLU* 1.3 63.3 + - + +
239B SER* 2.8 21.8 + - - +
240B ILE* 2.9 34.9 + - + +
14H LEU* 6.3 3.4 - - - +
21H ASP* 6.6 0.4 - - - +
22H THR* 5.1 7.2 - - - +
26H LEU* 3.5 15.9 - - + +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B GLN* 3.0 28.2 + - - +
234B HIS* 3.8 10.0 - - - +
236B ARG* 1.3 77.9 - - + +
238B ALA* 1.3 63.6 + - - +
240B ILE* 3.4 10.2 + - + +
241B LEU* 3.0 31.1 + - + +
11H ARG* 4.8 10.7 + - - -
13H PRO* 3.3 15.6 - - - +
14H LEU* 2.7 54.5 + - + +
15H SER* 4.5 8.6 + - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B HIS* 3.0 18.4 + - + +
235B VAL 3.7 0.9 - - - +
237B GLU* 1.3 78.0 - - - +
239B SER* 1.3 62.8 + - - +
241B LEU* 3.1 12.3 + - - +
242B LEU* 3.0 27.5 + - + +
72H LEU* 3.2 36.1 - - + -
248H ARG* 5.1 11.5 - - + +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B VAL* 2.9 16.8 + - - -
236B ARG* 2.8 23.7 + - - -
238B ALA* 1.3 76.6 - - - +
240B ILE* 1.3 67.7 + - - +
242B LEU* 2.9 25.4 + - - +
243B GLY 3.2 16.9 + - - +
22H THR* 4.5 8.8 + - - +
24H LYS* 4.4 21.4 + - - +
26H LEU* 4.5 12.1 - - - +
59H SER* 6.0 2.9 - - - -
72H LEU* 6.1 0.4 - - - +
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ARG* 2.9 39.5 + - + +
237B GLU* 3.6 9.4 - - + +
239B SER* 1.3 82.2 + - - +
241B LEU* 1.3 63.7 + - - +
243B GLY* 3.8 6.1 + - - -
14H LEU 4.9 10.3 - - - +
15H SER* 4.6 9.4 - - - +
18H LEU* 4.1 19.6 - - + +
19H GLY 5.7 0.2 - - - +
20H ARG* 3.8 40.8 + - + +
21H ASP* 5.0 10.5 - - - +
22H THR* 3.5 28.0 - - + +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLU* 3.0 22.7 + - + +
238B ALA* 3.1 7.8 + - - +
240B ILE* 1.3 75.8 - - - +
242B LEU* 1.3 65.2 + - - +
11H ARG* 6.4 0.7 - - - +
15H SER* 3.4 29.6 - - - +
17H ARG* 3.6 14.6 - - - +
18H LEU* 4.0 5.2 - - + -
247H GLN* 3.6 17.5 - - - +
248H ARG* 3.1 34.0 - - + +
249H MET* 4.1 8.5 - - - +
285H ARG* 3.5 34.1 + - - +
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA* 3.0 20.4 + - + +
239B SER* 2.9 17.8 + - - +
241B LEU* 1.3 81.5 - - - +
243B GLY* 1.3 58.6 + - - +
24H LYS* 5.3 5.2 - - - +
70H LYS* 5.2 9.9 - - - +
72H LEU* 5.0 17.5 - - + -
177H SER* 4.5 3.6 - - - +
178H LEU* 3.7 30.7 - - + -
248H ARG* 3.7 11.4 + - + +
249H MET* 4.9 3.8 - - - +
250H MET* 4.1 40.7 + - + +
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Residues in contact with GLY 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER 3.2 6.9 + - - +
240B ILE* 4.3 6.9 - - - -
241B LEU 3.6 0.8 - - - -
242B LEU* 1.3 81.7 - - - +
20H ARG* 4.6 13.7 - - - -
22H THR* 5.5 4.2 - - - +
24H LYS* 3.2 30.5 + - - -
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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