Contacts of the helix formed by residues 209 - 244 (chain B) in PDB entry 6H25
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 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B PHE* 3.3 47.6 - + + -
167B GLY* 5.5 2.7 - - - -
205B LEU* 4.7 5.4 - - + -
206B HIS* 3.4 32.6 + - + +
207B GLU 3.1 1.0 - - - -
208B ASP* 1.3 85.4 - - + +
210B LEU* 1.3 63.8 + - - +
211B GLU 3.4 1.3 - - - -
212B ARG* 3.0 43.1 + - - +
213B VAL* 3.5 5.4 + - + +
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Residues in contact with LEU 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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231A ILE* 3.8 24.7 - - + -
234A ILE* 5.6 5.4 - - + -
247A VAL* 5.0 8.5 - - + +
248A LEU* 4.7 19.5 - - + -
251A SER* 4.5 14.6 - - - +
185B LEU* 4.6 18.8 - - + -
201B MET* 4.7 9.4 - - + -
205B LEU* 4.0 24.2 - - + -
206B HIS 3.8 1.4 + - - +
207B GLU* 3.1 20.6 + - + +
208B ASP 3.4 0.4 - - - -
209B HIS* 1.3 74.0 - - - +
211B GLU* 1.3 66.0 + - - +
213B VAL* 3.1 10.6 + - + +
214B LEU* 3.1 26.9 + - + +
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Residues in contact with GLU 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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244A LYS* 3.6 23.0 + - - +
248A LEU* 3.7 35.6 - - + +
207B GLU 4.8 0.4 + - - -
208B ASP 5.2 1.5 + - - +
209B HIS 3.3 0.6 + - - -
210B LEU* 1.3 76.7 - - - +
212B ARG* 1.3 64.1 + - - +
214B LEU* 3.1 5.1 + - - +
215B GLU* 2.9 28.7 + - + +
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Residues in contact with ARG 212 (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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164B PHE* 4.1 15.1 - - - -
167B GLY* 4.4 14.9 + - - -
168B THR* 5.7 0.2 - - - +
169B ALA* 5.0 12.6 - - + +
208B ASP 5.0 3.5 + - - -
209B HIS* 3.0 46.0 + - - +
211B GLU* 1.3 76.9 - - - +
213B VAL* 1.3 67.2 + - + +
215B GLU* 3.1 10.9 + - - +
216B ALA* 3.1 19.9 + - + +
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA* 4.3 6.3 - - + +
163B GLY 4.4 5.6 - - - +
164B PHE* 3.6 42.0 - - + -
169B ALA* 4.0 19.7 - - + -
185B LEU* 4.2 25.1 - - + -
205B LEU* 4.4 15.7 - - + -
209B HIS 4.1 7.6 - - - +
210B LEU* 3.1 19.9 + - - +
212B ARG* 1.3 77.1 - - + +
214B LEU* 1.3 51.4 + - - +
216B ALA* 3.1 2.4 + - - +
217B ALA* 2.7 36.7 + - - +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 6.4 0.7 - - + -
244A LYS* 3.7 37.0 - - + -
247A VAL* 4.1 18.8 - - + -
248A LEU* 4.1 9.4 - - + -
185B LEU* 4.0 25.4 - - + -
187B LEU* 4.6 10.3 - - + -
196B ILE* 5.5 4.5 - - + -
199B LEU* 4.2 20.0 - - + -
210B LEU* 3.1 19.2 + - + +
211B GLU* 3.1 8.7 + - - +
213B VAL* 1.3 79.0 - - + +
215B GLU* 1.3 57.4 + - - +
217B ALA* 3.1 5.1 + - - +
218B ALA* 2.8 30.2 + - + +
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Residues in contact with GLU 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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244A LYS* 3.2 35.1 + - - +
211B GLU* 2.9 22.3 + - + +
212B ARG* 3.4 10.3 - - - +
214B LEU* 1.3 75.4 - - - +
216B ALA* 1.3 50.9 + - - +
218B ALA* 3.1 9.1 + - - +
219B GLN* 2.7 38.1 + - - +
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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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162B ALA* 4.9 4.5 - - + -
169B ALA* 3.8 28.9 - - + +
170B LEU 5.6 2.5 - - - +
171B ALA* 4.9 4.7 - - + +
212B ARG* 3.1 10.0 + - + +
213B VAL 3.1 6.9 + - - +
215B GLU* 1.3 74.6 - - - +
217B ALA* 1.3 58.2 + - - +
219B GLN* 3.1 8.8 + - - +
220B ALA* 2.9 29.8 + - - +
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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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160B CYS* 4.7 1.4 - - - +
161B SER 5.1 2.0 - - - -
162B ALA* 3.7 23.1 - - + +
185B LEU* 4.1 16.2 - - + +
187B LEU* 3.7 27.9 - - + +
213B VAL 2.7 13.4 + - - +
214B LEU* 3.3 9.9 - - - +
216B ALA* 1.3 76.2 - - - +
218B ALA* 1.3 62.6 + - - +
220B ALA* 3.1 8.7 + - - +
221B ALA 3.0 17.3 + - - -
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Residues in contact with ALA 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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244A LYS* 5.8 6.3 - - + -
187B LEU* 4.2 11.8 - - + +
189B LEU* 4.0 15.2 - - + +
196B ILE* 5.9 4.0 - - + -
214B LEU* 2.8 14.0 + - + +
215B GLU* 3.6 12.1 - - - +
217B ALA* 1.3 75.1 - - - +
219B GLN* 1.3 63.5 + - - +
221B ALA* 3.0 10.9 + - - +
222B ARG* 2.9 38.1 + - - +
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Residues in contact with GLN 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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20B GLY 6.2 0.2 - - - +
215B GLU* 2.7 19.5 + - - +
216B ALA* 3.1 13.2 + - - +
218B ALA* 1.3 72.4 - - - +
220B ALA* 1.3 62.4 + - - +
222B ARG* 3.1 33.2 + - - +
223B ASP* 3.1 31.2 + - - +
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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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20B GLY 5.2 2.7 - - - +
22B LEU* 4.1 7.4 - - + +
160B CYS* 3.7 24.5 - - - -
161B SER 4.7 0.2 - - - +
171B ALA* 3.8 22.2 - - + -
216B ALA 2.9 12.8 + - - +
217B ALA* 3.4 9.9 - - - +
219B GLN* 1.3 74.8 - - - +
221B ALA* 1.3 62.7 + - - +
223B ASP* 3.0 22.2 + - - +
224B VAL* 3.1 18.7 + - - +
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Residues in contact with ALA 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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158B CYS* 3.9 15.4 - - + +
159B ALA 5.2 0.2 - - - -
160B CYS* 4.2 11.8 - - + +
187B LEU* 4.6 8.3 - - + -
189B LEU* 3.7 29.4 - - + -
191B PRO* 6.5 0.2 - - - -
217B ALA 3.0 10.2 + - - +
218B ALA* 3.0 11.8 + - - +
220B ALA* 1.3 77.4 - - - +
222B ARG* 1.3 60.9 + - - +
224B VAL* 3.0 10.5 + - - +
225B HIS* 3.0 20.1 + - - +
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Residues in contact with ARG 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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189B LEU* 4.5 14.8 - - + +
191B PRO* 4.3 29.0 + - + +
194B GLY* 4.5 17.8 + - - -
218B ALA* 2.9 29.6 + - - +
219B GLN* 3.1 27.6 + - - +
221B ALA* 1.3 76.0 - - - +
223B ASP* 1.3 59.4 + - - +
225B HIS* 3.0 10.4 + - - +
226B THR* 2.9 34.9 + - + +
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Residues in contact with ASP 223 (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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20B GLY 4.2 15.2 - - - +
21B GLU* 5.5 1.2 - - - -
22B LEU* 3.7 21.0 - - + +
219B GLN* 3.1 32.4 + - - +
220B ALA* 3.0 13.3 + - - +
222B ARG* 1.3 76.9 - - - +
224B VAL* 1.3 59.9 + - - +
226B THR* 2.7 26.7 + - - +
227B LEU* 3.2 12.1 + - - +
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.7 23.3 - - + -
25B ILE* 4.4 12.6 - - + -
43B GLN* 5.2 3.6 - - - +
140B ASN* 4.2 13.2 - - - +
158B CYS* 3.9 15.5 - - + -
159B ALA 4.5 9.4 - - - +
160B CYS* 4.7 4.3 - - + -
220B ALA 3.1 14.9 + - - +
221B ALA* 3.0 10.9 + - - +
223B ASP* 1.3 74.8 - - - +
225B HIS* 1.3 58.2 + - - +
227B LEU* 3.0 19.0 + - - +
228B LEU* 3.1 39.9 + - + +
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Residues in contact with HIS 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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155B ASP* 4.7 3.1 - - - -
156B PHE* 3.5 42.6 - + + -
158B CYS* 3.7 12.6 - - + -
191B PRO* 3.5 35.6 - - + +
221B ALA 3.0 11.4 + - - +
222B ARG* 3.0 12.3 + - - +
224B VAL* 1.3 76.9 - - - +
226B THR* 1.3 66.5 + - + +
229B ASP* 3.3 37.7 + - + +
29H PRO 5.5 1.6 - - - -
31H ASP* 5.7 2.8 + - - -
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Residues in contact with THR 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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222B ARG* 2.9 16.6 + - + +
223B ASP* 2.7 30.9 + - - +
225B HIS* 1.3 83.2 - - + +
227B LEU* 1.3 59.9 + - - +
229B ASP* 4.8 3.4 - - - -
230B ARG* 4.1 21.3 + - - +
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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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22B LEU* 5.4 8.1 - - + -
23B ARG 5.7 2.7 - - - +
25B ILE* 4.3 40.2 - - + +
223B ASP 3.2 11.3 + - - +
224B VAL* 3.0 8.0 + - - +
225B HIS 3.2 0.2 - - - -
226B THR* 1.3 79.6 - - - +
228B LEU* 1.3 68.5 + - + +
229B ASP 3.2 1.8 - - - -
230B ARG* 3.0 33.6 + - + +
231B VAL* 3.5 14.7 + - + +
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Residues in contact with LEU 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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25B ILE* 3.7 27.8 - - + -
27B ALA* 3.7 30.5 - - + +
41B ILE* 4.0 13.2 - - + -
140B ASN* 4.4 13.2 - - + +
143B THR* 6.5 0.4 - - - -
144B LEU* 3.9 13.6 - - + +
156B PHE* 3.9 24.9 - - + -
157B VAL 5.5 0.4 - - - +
158B CYS* 4.5 0.9 - - - -
224B VAL* 3.1 31.9 + - + +
227B LEU* 1.3 77.9 - - + +
229B ASP* 1.3 56.7 + - - +
231B VAL* 3.0 13.6 + - + +
232B VAL* 2.9 31.6 + - - +
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Residues in contact with ASP 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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156B PHE* 4.3 9.6 - - + -
225B HIS* 3.3 39.6 + - + +
226B THR* 5.0 2.5 - - - -
227B LEU 4.9 0.4 - - - -
228B LEU* 1.3 77.2 - - - +
230B ARG* 1.3 57.1 + - + +
232B VAL* 3.1 7.4 + - - +
233B ARG* 2.8 64.1 + - - +
28H VAL* 3.5 18.0 - - - +
31H ASP* 4.7 1.4 - - - +
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Residues in contact with ARG 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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226B THR 4.1 18.8 + - - +
227B LEU* 3.0 22.0 + - + +
229B ASP* 1.3 75.6 - - + +
231B VAL* 1.3 54.9 + - + +
233B ARG* 3.1 8.5 + - - +
234B GLN* 2.7 38.0 + - - +
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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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25B ILE 6.2 0.2 - - - +
26B GLN* 6.0 1.1 - - - -
27B ALA* 3.4 38.4 - - + +
29B MET* 5.4 9.9 - - + +
144B LEU* 5.9 1.8 - - + -
227B LEU* 4.1 19.3 - - + +
228B LEU* 3.0 17.4 + - + +
230B ARG* 1.3 73.9 - - + +
232B VAL* 1.3 56.1 + - + +
234B GLN* 3.1 12.2 + - - +
235B HIS* 2.7 36.6 + - + +
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Residues in contact with VAL 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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29B MET* 4.3 16.6 - - + -
144B LEU* 3.8 26.9 - - + -
147B LEU* 5.6 6.5 - - + -
156B PHE* 3.8 19.1 - - + -
228B LEU 2.9 17.5 + - - +
229B ASP* 3.1 8.5 + - - +
231B VAL* 1.3 74.5 - - + +
233B ARG* 1.3 59.4 + - - +
235B HIS* 3.1 9.4 + - - +
236B VAL* 2.8 29.7 + - + +
28H VAL* 3.8 22.2 - - + -
29H PRO* 5.8 0.4 - - + -
57H ALA* 4.4 15.7 - - + -
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Residues in contact with ARG 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 ASP* 2.8 39.5 + - - +
230B ARG* 3.7 5.6 - - - +
232B VAL* 1.3 74.8 - - - +
234B GLN* 1.3 53.3 + - - +
236B VAL* 3.1 11.9 + - + +
237B ARG* 2.7 46.6 + - - +
26H LEU* 4.8 9.0 + - + +
27H VAL* 5.6 1.4 - - - +
28H VAL* 3.5 28.6 - - + +
31H ASP* 2.4 32.5 + - - +
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Residues in contact with GLN 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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230B ARG 2.7 22.2 + - - +
231B VAL* 3.4 10.9 - - - +
233B ARG* 1.3 72.0 - - - +
235B HIS* 1.3 67.4 + - - +
237B ARG* 3.2 10.7 + - - +
238B GLU* 3.0 38.0 + - - +
13H PRO* 5.8 5.9 - - - +
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Residues in contact with HIS 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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28B ARG* 6.0 2.0 - - - -
29B MET* 3.8 58.5 + - + +
30B GLY* 5.4 1.4 - - - -
148B ASP* 5.0 7.4 + - - -
231B VAL* 2.7 18.7 + - + +
232B VAL* 3.3 9.6 + - - +
234B GLN* 1.3 76.7 + - - +
236B VAL* 1.3 68.0 + - - +
238B GLU* 3.1 29.9 + - - +
239B ALA* 3.1 18.3 + - + +
72H LEU* 4.3 24.7 - - + +
73H LYS* 6.5 0.2 - - + -
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Residues in contact with VAL 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 VAL* 2.8 19.9 + - + +
233B ARG* 3.3 21.8 - - + +
235B HIS* 1.3 80.5 - - - +
237B ARG* 1.3 62.1 + - - +
239B ALA* 3.1 19.1 + - + +
240B SER* 3.3 17.6 + - - +
26H LEU* 3.7 21.5 - - + +
27H VAL 5.3 0.4 - - - +
28H VAL* 5.1 7.9 - - + -
57H ALA* 4.6 6.1 - - + -
58H GLY* 3.9 32.8 - - - +
72H LEU* 4.6 17.5 - - + -
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Residues in contact with ARG 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 ARG* 2.7 25.5 + - - +
234B GLN* 3.2 8.0 + - - +
236B VAL* 1.3 78.6 - - - +
238B GLU* 1.3 56.9 + - - +
240B SER* 3.0 19.4 + - - -
241B ILE* 3.4 16.4 + - + +
20H ARG* 2.9 53.0 - - - +
22H THR* 5.2 8.0 - - + +
26H LEU* 3.9 17.1 - - + +
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Residues in contact with GLU 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 GLN* 3.0 30.3 + - - +
235B HIS* 3.3 31.9 + - - +
237B ARG* 1.3 73.8 - - + +
239B ALA* 1.3 63.3 + - - +
241B ILE* 4.6 10.3 - - + +
242B LEU* 3.9 22.7 - - - +
13H PRO 5.2 7.1 - - - +
15H SER 5.2 9.4 - - - +
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Residues in contact with ALA 239 (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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235B HIS* 3.1 7.8 + - + +
236B VAL* 3.1 16.6 + - + +
238B GLU* 1.3 78.9 - - - +
240B SER* 1.3 62.6 + - - +
241B ILE 3.3 0.2 - - - -
242B LEU* 3.0 24.6 + - - +
243B LEU* 3.4 18.0 + - + +
72H LEU* 3.8 32.1 - - + -
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Residues in contact with SER 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 VAL* 3.3 12.4 + - - +
237B ARG* 3.0 9.7 + - - -
239B ALA* 1.3 75.4 - - - +
241B ILE* 1.3 59.9 + - - +
243B LEU* 3.0 10.1 + - - +
244B GLY 3.0 30.0 + - - -
22H THR* 4.9 8.1 - - - -
24H LYS* 3.1 31.8 + - - +
26H LEU* 4.6 15.2 - - - +
59H SER* 5.0 8.0 + - - -
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Residues in contact with ILE 241 (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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237B ARG* 3.6 17.3 - - + +
238B GLU* 4.6 7.6 - - + -
239B ALA 3.3 0.4 - - - -
240B SER* 1.3 76.7 - - - +
242B LEU* 1.3 69.4 + - + +
243B LEU 3.5 0.5 + - - -
244B GLY 4.4 8.3 + - - -
15H SER 4.4 17.7 - - - +
19H GLY 4.2 5.2 - - - +
20H ARG* 2.2 81.6 - - + +
22H THR* 4.2 13.0 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 3.9 23.3 - - - +
239B ALA* 3.0 10.2 + - - +
241B ILE* 1.3 85.8 - - + +
243B LEU* 1.3 62.1 + - + +
247H GLN* 4.1 15.3 - - - +
248H ARG* 3.5 31.9 - - + +
249H MET* 4.4 9.2 - - - +
250H MET 5.3 0.3 + - - -
285H ARG* 3.8 34.8 + - - +
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Residues in contact with LEU 243 (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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239B ALA* 3.8 21.5 - - + +
240B SER* 3.0 11.0 + - - +
241B ILE 4.6 0.4 - - - -
242B LEU* 1.3 82.8 - - + +
244B GLY* 1.3 60.9 + - - +
24H LYS* 4.5 3.8 - - - +
70H LYS* 5.6 7.9 - - - +
72H LEU* 5.3 13.2 - - + +
177H SER 5.3 3.1 - - - +
178H LEU* 3.9 27.1 - - + -
248H ARG* 4.2 15.9 - - + +
250H MET* 4.5 31.6 - - + +
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Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B SER 3.0 12.1 + - - -
241B ILE* 4.7 6.5 - - - -
243B LEU* 1.3 81.1 - - - +
20H ARG 6.1 0.9 - - - -
21H ASP 5.7 1.6 - - - +
22H THR* 4.9 6.8 + - - -
24H LYS* 3.4 23.5 - - - +
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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
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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