Contacts of the helix formed by residues 233 - 270 (chain F) 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 LEU 233 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E GLY* 3.3 29.6 - - - +
235E VAL* 3.6 18.2 - - + +
236E VAL 4.3 0.7 - - - +
260E LYS* 5.5 2.7 - - + -
232F GLY* 1.3 74.3 - - - +
234F THR* 1.3 74.8 + - - +
235F GLU* 3.3 14.4 - - + +
236F SER* 2.4 35.2 + - - +
237F TRP* 3.0 14.8 - - - +
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Residues in contact with THR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E GLY 4.1 1.9 + - - -
236E VAL* 4.1 16.1 - - - +
253E PHE 5.6 1.1 - - - +
256E MET* 3.5 37.4 - - + +
257E GLU* 4.9 7.6 - - + +
260E LYS* 3.7 32.2 - - - +
233F LEU* 1.3 78.4 - - - +
235F GLU* 1.3 70.8 + - + +
237F TRP* 3.1 2.0 + - - -
238F ALA* 2.9 22.6 + - + +
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Residues in contact with GLU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F LEU* 3.3 12.8 - - + +
234F THR* 1.3 81.3 - - + +
236F SER* 1.3 62.6 + - - +
238F ALA* 3.2 7.8 + - - +
239F GLU* 3.0 34.8 + - + +
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Residues in contact with SER 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F LEU* 5.7 1.6 - - - -
195F TRP* 3.1 36.0 + - - +
232F GLY* 3.9 3.9 - - - -
233F LEU* 2.4 41.2 + - - +
235F GLU* 1.3 79.4 - - - +
237F TRP* 1.3 61.6 + - - +
239F GLU* 3.3 7.7 + - - +
240F ALA 2.9 24.3 + - - -
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Residues in contact with TRP 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E VAL* 2.9 41.7 + - + -
237E THR 3.2 13.9 - - - -
238E CYS* 5.0 1.3 - - - -
239E MET* 4.0 16.4 - - + -
256E MET* 3.9 17.9 - - + -
195F TRP* 4.3 9.9 - + - -
209F ALA* 4.8 5.6 - - + -
210F GLY 4.2 4.0 - - - -
211F LEU* 3.5 32.7 - - + +
227F GLY* 4.3 5.8 - - - -
228F SER 3.4 35.4 - - - -
231F GLY 4.2 11.7 - - - -
232F GLY* 3.7 4.9 - - - -
233F LEU 3.0 43.4 + - - +
234F THR 3.6 6.1 - - - +
236F SER* 1.3 82.9 + - - +
238F ALA* 1.3 57.3 + - - +
240F ALA* 3.3 6.5 + - - +
241F VAL* 2.9 33.9 + - - +
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E PHE* 4.3 31.0 - - + -
256E MET* 4.7 6.4 - - - -
234F THR* 2.9 15.0 + - + +
235F GLU* 3.5 11.0 - - - +
236F SER 3.2 0.2 - - - -
237F TRP* 1.3 74.1 - - - +
239F GLU* 1.3 66.6 + - + +
241F VAL* 3.1 10.3 + - - +
242F ARG* 3.0 30.2 + - - +
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Residues in contact with GLU 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F TRP* 4.4 16.8 + - + -
235F GLU* 3.0 24.0 + - + +
236F SER* 3.6 8.4 - - - +
238F ALA* 1.3 76.3 - - + +
240F ALA* 1.3 62.4 + - - +
242F ARG* 3.0 21.8 - - - +
243F LEU* 2.9 27.5 + - + +
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Residues in contact with ALA 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F LEU* 3.4 20.8 - - + +
195F TRP* 3.6 37.6 - - + +
211F LEU* 4.1 14.4 - - + +
236F SER 2.9 13.3 + - - +
237F TRP 3.3 9.4 - - - +
239F GLU* 1.3 76.3 - - - +
241F VAL* 1.3 63.4 + - - +
243F LEU* 3.3 2.6 + - - -
244F GLY* 2.9 19.9 + - - -
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Residues in contact with VAL 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E MET* 4.0 26.2 - - + -
249E PRO* 5.2 4.5 - - + +
252E ILE* 5.0 15.3 - - + -
253E PHE* 4.3 17.0 - - + -
256E MET* 5.5 0.9 - - + -
211F LEU* 4.7 4.0 - - + -
213F VAL* 4.5 15.2 - - + +
222F VAL* 5.7 3.1 - - + -
225F LEU* 5.1 6.1 - - + -
237F TRP 2.9 20.9 + - - +
238F ALA* 3.1 10.7 + - - +
240F ALA* 1.3 76.1 - - - +
242F ARG* 1.3 63.5 + - - +
244F GLY* 3.2 2.9 + - - -
245F LEU* 2.9 45.8 + - + +
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Residues in contact with ARG 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E PHE* 4.0 28.2 - - + -
238F ALA* 3.0 14.9 + - - +
239F GLU* 3.0 39.6 - - - +
241F VAL* 1.3 79.4 - - - +
243F LEU* 1.3 64.9 + - + +
245F LEU* 3.2 13.8 + - + +
246F GLU* 3.0 29.8 + - + +
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Residues in contact with LEU 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PRO* 5.9 0.7 - - + +
34F THR* 4.8 18.4 - - + -
185F LEU* 3.7 10.8 - - + -
195F TRP* 4.2 28.9 - - + +
197F LEU* 3.5 46.2 - - + +
239F GLU* 2.9 18.6 + - + +
240F ALA 3.5 4.7 - - - +
242F ARG* 1.3 80.3 - - + +
244F GLY* 1.3 56.2 + - - +
246F GLU* 3.2 9.1 + - + +
247F GLY* 2.9 24.4 + - - -
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Residues in contact with GLY 244 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F CYS* 3.9 6.3 - - - +
185F LEU* 3.9 15.9 - - - -
213F VAL* 3.7 21.5 - - - -
240F ALA 2.9 14.6 + - - -
241F VAL 3.7 2.9 - - - -
243F LEU* 1.3 76.7 - - - +
245F LEU* 1.3 62.5 + - - +
247F GLY* 3.3 0.9 + - - -
248F CYS* 3.0 29.1 + - - -
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Residues in contact with LEU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E PRO* 3.8 26.5 - - + -
213F VAL* 4.7 11.0 - - + -
215F LEU* 4.1 22.5 - - + +
220F ASN* 4.3 13.0 - - - +
222F VAL* 4.8 13.7 - - + -
241F VAL* 2.9 46.3 + - + +
242F ARG* 3.2 14.3 + - + +
244F GLY* 1.3 77.0 - - - +
246F GLU* 1.3 64.7 + - + +
248F CYS* 3.3 6.8 + - - +
249F GLN* 3.0 35.9 + - - +
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Residues in contact with GLU 246 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F ARG* 3.0 21.5 + - + +
243F LEU* 3.2 8.9 + - - +
245F LEU* 1.3 76.6 - - - +
247F GLY* 1.3 63.3 + - - +
249F GLN* 3.3 25.5 + - - +
250F ARG* 3.0 38.8 + - - +
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Residues in contact with GLY 247 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 4.2 7.8 - - - +
183F CYS* 4.7 9.0 - - - -
197F LEU* 4.6 9.0 - - - -
243F LEU 2.9 13.6 + - - -
244F GLY 3.7 2.9 - - - -
245F LEU 3.2 0.2 - - - -
246F GLU* 1.3 76.6 - - - +
248F CYS* 1.3 60.8 + - - +
250F ARG* 3.2 23.5 + - - +
251F LEU* 3.0 24.7 + - - +
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Residues in contact with CYS 248 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F VAL* 3.3 35.2 - - + +
182F GLY* 3.4 13.7 - - - -
183F CYS* 3.4 22.9 - - - -
213F VAL* 4.1 6.3 - - - -
215F LEU* 3.2 28.9 - - + -
217F PRO* 5.5 1.7 - - - +
244F GLY 3.0 20.2 + - - +
245F LEU 3.7 1.1 - - - +
247F GLY* 1.3 75.8 - - - +
249F GLN* 1.3 64.7 + - - +
251F LEU* 3.1 1.8 + - - -
252F TYR* 3.0 22.5 + - - +
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Residues in contact with GLN 249 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F LEU* 5.3 7.8 - - + +
217F PRO* 4.8 21.8 + - + +
220F ASN* 5.3 12.5 - - - +
245F LEU* 3.0 26.1 + - - +
246F GLU* 3.5 34.3 + - - +
247F GLY 3.3 0.2 - - - -
248F CYS* 1.3 78.3 - - - +
250F ARG* 1.3 64.2 + - + +
251F LEU 3.1 0.9 + - - -
252F TYR* 3.4 13.8 + - - +
253F PRO* 3.6 9.4 - - - +
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Residues in contact with ARG 250 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F THR* 4.5 21.6 + - - -
35F ARG* 5.4 0.2 - - - +
36F LEU* 3.3 36.7 - - + +
197F LEU* 3.6 28.7 - - - +
246F GLU* 3.0 29.5 + - - +
247F GLY* 3.2 8.3 + - - +
249F GLN* 1.3 76.3 - - + +
251F LEU* 1.3 59.1 + - - +
253F PRO* 3.7 10.3 - - - +
254F VAL* 5.4 0.7 - - - +
630J PRO* 3.3 27.6 - - + +
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Residues in contact with LEU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 5.1 15.0 - - + -
39F VAL* 4.7 25.1 - - + -
55F LEU* 6.5 1.1 - - + -
163F THR* 5.0 6.5 - - + +
181F VAL* 4.1 10.8 - - + -
182F GLY 4.7 13.0 - - - +
183F CYS* 6.3 1.3 - - + -
198F ASP* 5.8 2.7 - - - +
247F GLY 3.0 15.5 + - - +
248F CYS* 3.6 4.9 - - - +
249F GLN 3.1 0.4 - - - -
250F ARG* 1.3 75.8 - - - +
252F TYR* 1.3 65.7 + - - +
253F PRO* 3.1 6.3 - - - -
254F VAL* 3.2 19.8 + - + +
255F LEU* 3.8 30.5 - - + -
630J PRO* 4.6 9.6 - - + -
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Residues in contact with TYR 252 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F ASP* 3.8 11.6 + - - -
179F LEU* 3.6 33.2 - - + +
181F VAL* 3.9 18.8 - - + -
217F PRO* 3.5 32.8 - - + -
218F VAL* 3.9 14.1 - - + +
248F CYS 3.0 11.0 + - - +
249F GLN* 3.6 10.5 - - - +
251F LEU* 1.3 74.8 - - - +
253F PRO* 1.3 72.1 - - + +
255F LEU* 3.1 17.5 + - + +
256F GLN* 3.1 27.6 + - + +
9I ILE* 4.3 17.1 - - + +
11I GLY* 4.3 8.5 - - - -
12I GLU* 4.6 1.4 + - - +
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Residues in contact with PRO 253 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F GLN 3.6 11.0 - - - +
250F ARG* 3.7 9.6 - - - +
251F LEU 3.2 6.1 - - - +
252F TYR* 1.3 98.5 - - + +
254F VAL* 1.3 62.8 + - + +
256F GLN* 3.2 17.9 + - + +
257F GLN* 2.9 36.8 + - - +
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Residues in contact with VAL 254 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F VAL* 4.3 28.3 - - + +
41F ALA* 4.5 13.9 - - + +
250F ARG 5.4 0.7 - - - +
251F LEU* 3.2 15.0 + - + +
253F PRO* 1.3 76.6 - - + +
255F LEU* 1.3 60.5 + - + +
257F GLN* 3.2 9.5 + - - +
258F SER* 2.9 26.8 + - - -
630J PRO* 4.4 28.3 - - + +
631J VAL 6.1 0.2 - - - +
632J GLN* 3.6 32.3 + - + +
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Residues in contact with LEU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F VAL* 5.7 0.4 - - + -
41F ALA* 3.9 15.0 - - + -
55F LEU* 4.9 3.8 - - + -
163F THR* 3.4 36.3 - - + -
167F LEU* 3.7 30.4 - - + +
179F LEU* 4.7 12.8 - - + -
180F VAL 4.6 2.2 - - - +
181F VAL* 4.1 20.6 - - + -
251F LEU* 3.8 25.4 - - + -
252F TYR 3.1 8.2 + - - +
254F VAL* 1.3 74.5 - - + +
256F GLN* 1.3 66.9 + - - +
258F SER* 3.2 8.1 + - - -
259F LEU* 3.0 28.4 + - - +
9I ILE* 4.9 0.7 - - - -
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Residues in contact with GLN 256 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F LEU* 5.1 0.4 - - - +
252F TYR* 3.1 30.3 + - + +
253F PRO* 3.3 17.7 - - - +
255F LEU* 1.3 77.9 - - - +
257F GLN* 1.3 67.6 + - + +
259F LEU* 3.2 2.9 + - - +
260F VAL* 3.0 34.6 + - + +
9I ILE* 3.5 32.5 - - + +
12I GLU* 4.0 19.4 + - - +
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Residues in contact with GLN 257 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F PRO* 2.9 26.5 + - - +
254F VAL* 3.6 8.1 - - - +
256F GLN* 1.3 78.9 - - + +
258F SER* 1.3 63.3 + - - +
260F VAL* 3.3 8.8 + - - +
261F ARG* 2.9 25.5 + - - +
632J GLN* 4.2 16.3 + - - +
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Residues in contact with SER 258 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ALA* 2.8 33.6 + - - +
42F ARG* 3.3 14.6 - - - -
43F ALA* 3.5 7.7 + - - +
167F LEU* 5.2 3.7 - - - +
254F VAL* 2.9 14.0 + - - -
255F LEU* 3.2 13.2 + - - -
257F GLN* 1.3 75.5 - - - +
259F LEU* 1.3 64.5 + - - +
261F ARG* 3.2 18.0 + - - +
262F ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 259 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ALA* 3.9 22.9 - - + -
167F LEU* 4.0 32.3 - - + +
170F ALA* 4.0 24.0 - - + -
171F ASP* 4.6 9.2 - - + +
179F LEU* 4.4 7.0 - - + -
255F LEU 3.0 14.7 + - - +
256F GLN 3.8 5.2 - - - +
258F SER* 1.3 72.5 - - - +
260F VAL* 1.3 67.8 + - + +
262F ALA* 3.2 5.9 + - + +
263F ALA* 3.0 23.8 + - - +
266F ARG* 5.0 0.5 + - - -
8I CYS 5.8 1.6 - - - +
9I ILE* 3.8 31.2 - - + -
38I ALA* 4.6 15.3 - - + +
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Residues in contact with VAL 260 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F GLN* 3.0 26.4 + - + +
257F GLN* 3.6 10.5 - - - +
258F SER 3.3 0.2 - - - -
259F LEU* 1.3 75.4 - - + +
261F ARG* 1.3 62.8 + - - +
263F ALA* 3.2 7.7 + - - +
264F ARG* 2.9 58.3 + - + +
7I TYR* 4.3 30.1 - - + +
8I CYS 5.3 5.6 + - - +
9I ILE* 5.8 2.0 - - + -
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Residues in contact with ARG 261 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F TYR* 5.0 13.9 + - - -
41F ALA 3.0 26.8 + - - -
42F ARG* 3.2 25.9 - - - +
43F ALA 4.7 0.4 - - - +
257F GLN 2.9 14.2 + - - +
258F SER* 3.4 18.0 + - - +
260F VAL* 1.3 78.1 - - - +
262F ALA* 1.3 61.6 + - - +
264F ARG* 3.2 15.1 + - + +
265F ARG* 3.0 33.4 + - + +
632J GLN* 5.3 8.7 + - - +
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Residues in contact with ALA 262 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ALA* 3.2 36.6 - - + +
44F GLY* 5.0 1.1 - - - -
171F ASP* 4.3 0.7 - - - +
258F SER 3.0 12.2 + - - +
259F LEU* 3.7 7.4 - - + +
261F ARG* 1.3 77.5 - - - +
263F ALA* 1.3 62.6 + - - +
265F ARG* 3.2 13.4 + - - +
266F ARG* 3.0 42.2 + - - +
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Residues in contact with ALA 263 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F LEU 3.0 13.1 + - - +
260F VAL* 3.6 7.9 - - - +
262F ALA* 1.3 76.6 - - - +
264F ARG* 1.3 57.4 + - - +
266F ARG* 3.2 18.1 + - - +
267F GLY 2.9 23.4 + - - -
7I TYR* 3.6 38.6 + - + -
38I ALA* 5.5 4.9 - - + +
39I GLY* 5.2 9.6 - - - +
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Residues in contact with ARG 264 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F VAL* 2.9 41.8 + - - +
261F ARG* 3.4 14.0 - - + +
263F ALA* 1.3 76.4 - - - +
265F ARG* 1.3 57.5 + - + +
267F GLY* 3.2 2.3 + - - -
268F ALA* 2.9 27.5 + - - +
7I TYR* 3.6 27.2 + - + -
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Residues in contact with ARG 265 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ARG* 3.0 30.9 - - - +
43F ALA 5.6 2.6 + - - -
44F GLY 5.4 3.0 + - - -
261F ARG* 3.0 29.1 + - + +
262F ALA* 3.2 13.4 + - - +
264F ARG* 1.3 75.3 - - + +
266F ARG* 1.3 62.4 + - + +
268F ALA* 3.1 9.3 + - - +
269F ALA* 2.9 22.3 + - - +
640J ASP* 3.7 29.6 + - - -
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Residues in contact with ARG 266 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLY* 4.6 9.2 - - - -
171F ASP* 2.3 42.5 + - - +
259F LEU 5.0 0.4 + - - -
262F ALA* 3.0 45.1 + - - +
263F ALA* 3.4 15.6 - - - +
265F ARG* 1.3 77.1 - - + +
267F GLY* 1.3 64.2 + - - +
269F ALA* 3.1 18.1 + - - +
270F ALA* 3.5 9.7 + - - +
57I ARG* 3.8 25.4 - - - +
59I THR* 3.5 23.0 + - + +
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Residues in contact with GLY 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F ALA 2.9 15.2 + - - -
264F ARG 3.2 4.2 + - - -
266F ARG* 1.3 75.2 - - - +
268F ALA* 1.3 60.5 + - - +
270F ALA 3.4 21.0 - - - +
7I TYR* 4.2 12.3 - - - -
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Residues in contact with ALA 268 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F ARG 2.9 12.9 + - - +
265F ARG* 3.3 13.5 - - - +
267F GLY* 1.3 74.0 - - - +
269F ALA* 1.3 66.3 + - - +
270F ALA* 3.0 5.5 + - - +
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Residues in contact with ALA 269 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F ARG 2.9 11.7 + - - +
266F ARG* 3.1 13.2 + - - +
268F ALA* 1.3 75.3 - - - +
270F ALA* 1.3 62.1 + - + +
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Residues in contact with ALA 270 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F ARG 3.5 6.1 + - - +
267F GLY* 3.4 18.4 + - - +
268F ALA 3.0 3.5 + - - +
269F ALA* 1.3 84.0 - - + +
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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