Contacts of the helix formed by residues 199 - 237 (chain B) in PDB entry 4ZWJ
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 ASN 199 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLY 5.1 1.6 + - - -
175B TRP* 3.2 38.6 + - + +
176B SER 4.1 0.2 + - - -
195B LYS 3.0 8.9 + - - -
196B PRO* 2.8 32.4 - - - +
197B GLU 3.8 7.2 + - - +
198B VAL* 1.3 81.0 + - - +
200B ASN* 1.3 61.1 + - - +
201B GLU* 3.5 2.9 - - - +
202B SER* 3.5 10.4 + - - +
203B PHE* 3.7 2.3 - - - +
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Residues in contact with ASN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 3.4 14.8 + - - -
177B ARG 4.3 0.3 + - - -
190B ASP* 3.2 40.5 + - - +
191B TYR* 5.7 1.1 - - - -
193B THR 2.6 31.0 + - - +
194B LEU* 4.6 6.7 - - + -
195B LYS* 3.6 17.5 + - - +
196B PRO* 5.1 0.2 - - - +
198B VAL* 3.2 23.0 - - - +
199B ASN* 1.3 72.0 - - - +
201B GLU* 1.3 65.3 - - - +
203B PHE* 4.4 4.9 - - - -
204B VAL* 3.0 31.2 + - + +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 5.1 11.2 - - + +
199B ASN* 3.5 1.2 - - - -
200B ASN* 1.3 78.8 - - - +
202B SER* 1.3 63.5 + - - +
204B VAL* 4.0 2.4 - - - +
205B ILE* 3.1 37.9 + - + +
276B PHE* 3.9 35.1 - - + -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TRP* 2.8 34.7 + - - -
199B ASN* 3.5 11.5 + - - +
201B GLU* 1.3 80.1 - - - +
203B PHE* 1.3 55.5 + - - +
205B ILE* 3.5 11.5 + - - +
206B TYR* 2.8 29.8 + - - +
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B CYS* 3.5 23.3 - - - -
170B PRO* 4.1 9.4 - - + -
171B PRO* 3.7 17.7 - - + -
175B TRP* 3.5 51.1 - + - +
176B SER* 3.5 18.4 - - - -
189B ILE* 3.7 28.0 - - + -
199B ASN 3.7 10.5 + - - +
200B ASN* 3.4 4.2 + - - +
201B GLU 3.2 0.6 - - - -
202B SER* 1.3 78.5 + - - +
204B VAL* 1.3 60.6 + - + +
206B TYR* 3.3 10.5 + + - +
207B MET* 2.8 58.7 + - + +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE* 6.0 0.7 - - + -
190B ASP 4.3 4.7 - - - +
191B TYR* 3.6 45.8 - - + +
194B LEU* 6.5 0.9 - - + -
200B ASN* 3.0 23.2 + - + +
201B GLU* 4.0 3.8 - - - +
203B PHE* 1.3 78.6 - - + +
205B ILE* 1.3 59.0 + - + +
207B MET* 3.8 5.7 - - + +
208B PHE* 2.8 33.3 + - + +
272B ALA* 4.9 16.6 - - + +
276B PHE* 4.9 18.2 - - + -
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 3.1 39.1 + - + +
202B SER* 3.6 9.2 - - - +
204B VAL* 1.3 74.0 - - + +
206B TYR* 1.3 59.2 + - - +
208B PHE* 4.6 2.5 - - - -
209B VAL* 2.7 56.2 + - + +
276B PHE* 4.9 13.9 - - + -
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Residues in contact with TYR 206 (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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166B ALA* 3.7 26.3 + - - +
167B CYS* 3.9 22.4 - - + -
175B TRP* 3.7 34.1 - + + -
202B SER 2.8 21.7 + - - +
203B PHE* 3.3 15.0 + + - +
205B ILE* 1.3 73.8 - - - +
207B MET* 1.3 69.6 + - + +
209B VAL* 5.0 0.4 - - - -
210B VAL* 3.1 50.0 + - + +
211B HIS* 3.3 26.8 + + - -
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 5.7 0.2 - - + -
122B GLU* 3.8 22.4 - - - +
167B CYS* 4.2 20.0 - - - -
189B ILE* 3.7 28.3 - - + -
203B PHE* 2.8 46.1 + - + +
204B VAL* 3.8 7.2 - - + +
206B TYR* 1.3 79.2 - - + +
208B PHE* 1.3 63.3 + - - +
211B HIS* 3.0 36.1 + - + +
212B PHE* 3.4 2.6 + - - +
265B TRP* 6.6 0.4 - - + -
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 2.8 28.6 + - + +
205B ILE* 4.0 2.7 - - - +
207B MET* 1.3 72.7 - - - +
209B VAL* 1.3 77.3 + - + +
212B PHE* 2.8 41.1 + + + +
213B THR* 3.6 6.7 + - - -
216B MET* 6.4 0.7 - - + -
269B ALA* 4.1 39.7 - - + -
272B ALA* 6.1 2.9 - - + -
273B PHE* 4.6 25.1 - + + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 2.7 41.8 + - + +
206B TYR* 5.0 0.4 - - - -
208B PHE* 1.3 85.3 - - + +
210B VAL* 1.3 67.6 + - + +
213B THR* 2.7 36.9 + - - +
214B ILE* 4.1 1.4 + - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TRP* 5.1 6.5 - - + -
163B MET* 6.3 1.6 - - - -
206B TYR* 3.1 36.6 + - + +
209B VAL* 1.3 82.0 - - + +
211B HIS* 1.3 74.7 + - + +
214B ILE* 3.0 51.4 + - + +
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Residues in contact with HIS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU* 3.4 30.5 - - - +
125B LEU* 3.9 13.3 - - + +
126B TRP* 3.5 27.1 + + + -
163B MET* 3.6 9.6 + - - +
166B ALA* 5.7 0.4 - - + -
167B CYS* 3.1 26.8 - - + -
206B TYR* 3.3 39.5 + + - -
207B MET* 3.0 23.2 + - + +
210B VAL* 1.3 91.6 - - + +
212B PHE* 1.3 58.9 + - - +
215B PRO* 3.2 23.7 - - - +
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Residues in contact with PHE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 6.5 0.7 - - + -
207B MET 3.4 1.9 + - - +
208B PHE* 2.8 38.3 + + + +
211B HIS* 1.3 81.2 - - - +
213B THR* 1.3 64.0 + - - +
214B ILE 3.4 0.2 - - - -
215B PRO* 3.8 3.4 - - - +
216B MET* 3.1 65.0 + - + +
261B PHE* 4.9 7.6 - + - -
265B TRP* 3.3 50.3 - + + -
266B VAL* 3.9 16.4 - - + -
269B ALA* 3.4 31.2 - - + -
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Residues in contact with THR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 3.7 8.8 + - - -
209B VAL* 2.7 31.4 + - - +
212B PHE* 1.3 78.4 - - - +
214B ILE* 1.3 58.7 + - + +
216B MET* 3.6 17.6 - - + +
217B ILE* 2.8 52.2 + - + +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TRP* 4.1 15.5 - - + -
209B VAL 4.7 1.1 - - - +
210B VAL* 3.0 35.8 + - + +
213B THR* 1.3 77.5 - - + +
215B PRO* 1.4 66.6 - - + +
217B ILE* 3.4 11.0 + - + +
218B ILE* 2.8 57.0 + - + +
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Residues in contact with PRO 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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125B LEU* 4.3 11.7 - - + -
126B TRP* 4.0 13.7 - - + -
129B VAL* 3.7 31.4 - - + -
210B VAL 3.6 2.7 - - - +
211B HIS 3.2 27.4 - - - +
212B PHE 3.8 3.6 - - - +
214B ILE* 1.4 96.0 - - + +
216B MET* 1.3 54.7 + - - +
218B ILE* 4.5 2.2 - - + -
219B ILE* 2.7 45.6 + - + +
261B PHE* 4.2 11.2 - - + -
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 6.4 1.1 - - + -
212B PHE* 3.1 57.4 + - + +
213B THR* 3.6 21.3 - - + +
215B PRO* 1.3 73.8 - - - +
217B ILE* 1.3 64.4 + - + +
220B PHE* 3.1 43.8 + - + +
261B PHE* 3.8 24.6 - - + -
262B LEU* 5.3 9.2 - - - -
266B VAL* 6.1 0.2 - - - -
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B THR* 2.8 44.1 + - + +
214B ILE* 3.9 11.7 - - + +
216B MET* 1.3 74.4 - - + +
218B ILE* 1.3 62.6 + - + +
220B PHE* 4.2 1.6 - - - +
221B PHE* 2.9 36.1 + - + +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TRP* 5.1 1.6 - - + -
129B VAL* 3.9 22.9 - - + +
133B ILE* 3.7 34.1 - - + -
214B ILE* 2.8 46.2 + - + +
215B PRO 4.1 1.1 - - - +
217B ILE* 1.3 77.7 - - + +
219B ILE* 1.3 54.0 + - - +
221B PHE* 3.3 6.2 + - + +
222B CYS* 2.7 46.1 + - - -
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU 5.2 0.2 - - - +
128B LEU* 4.3 9.2 - - + +
129B VAL* 3.9 42.0 - - + +
132B ALA* 4.2 11.4 - - + -
215B PRO* 2.7 24.9 + - + +
216B MET* 4.6 0.9 - - - +
218B ILE* 1.3 72.5 - - + +
220B PHE* 1.3 68.3 + - + +
223B TYR* 3.0 54.4 + - + +
257B TYR* 6.1 2.0 - - + +
258B VAL* 5.8 5.4 - - + -
261B PHE* 4.0 35.9 - - + -
306B TYR* 6.0 0.7 - - - +
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B MET* 3.1 35.9 + - + +
217B ILE* 4.3 1.6 - - - +
219B ILE* 1.3 84.5 - - + +
221B PHE* 1.3 57.2 + - - +
223B TYR* 5.4 1.3 - - - -
224B GLY* 2.9 26.4 + - - +
258B VAL* 3.5 43.1 - - + -
261B PHE* 4.4 23.6 - + - -
262B LEU* 4.4 16.6 - - + -
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Residues in contact with PHE 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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136B TYR* 4.6 21.3 - + - -
217B ILE* 2.9 26.4 + - + +
218B ILE* 3.6 5.8 - - - +
220B PHE* 1.3 77.0 - - - +
222B CYS* 1.3 67.1 + - - +
225B GLN* 2.9 69.5 + - + +
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Residues in contact with CYS 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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132B ALA* 3.4 35.7 - - + +
133B ILE* 3.7 21.1 - - - -
136B TYR* 3.7 23.8 - - + +
218B ILE* 2.7 41.5 + - - +
219B ILE 3.4 0.6 + - - +
221B PHE* 1.3 83.0 - - - +
223B TYR* 1.3 59.0 + - - +
226B LEU* 2.9 27.6 + - - +
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Residues in contact with TYR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 4.3 3.6 + - - +
131B LEU* 4.0 9.2 - - - +
132B ALA* 3.5 40.9 + - + +
135B ARG* 3.9 31.8 + - + -
219B ILE* 3.0 35.5 + - + +
220B PHE* 5.4 0.9 - - - -
222B CYS* 1.3 77.3 - - - +
224B GLY* 1.3 60.5 + - - +
226B LEU* 3.6 17.2 - - + +
227B VAL* 3.0 33.6 + - - +
254B VAL* 3.8 30.7 - - + +
257B TYR* 4.5 30.1 - + + -
258B VAL* 5.7 5.4 - - + -
306B TYR* 4.2 10.2 - - - -
2078B LEU* 5.1 2.7 - - + -
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Residues in contact with GLY 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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220B PHE 2.9 23.2 + - - -
221B PHE 4.0 0.2 - - - -
223B TYR* 1.3 77.2 - - - +
225B GLN* 1.3 57.9 + - - +
227B VAL* 3.6 3.7 + - - +
228B PHE* 2.9 28.9 + - - +
254B VAL* 5.9 0.4 - - - -
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Residues in contact with GLN 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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136B TYR* 3.4 26.6 + - + +
221B PHE* 2.9 55.9 + - + +
224B GLY* 1.3 73.7 - - - +
226B LEU* 1.3 57.2 + - - +
228B PHE* 3.6 26.6 - - - +
229B THR* 2.6 39.9 + - - -
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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
----------------------------------------------------------
135B ARG* 3.6 42.8 - - + +
136B TYR* 4.0 10.7 - - + +
139B VAL* 5.0 7.2 - - + -
140B CYS* 4.6 9.4 - - - -
222B CYS 2.9 17.4 + - - +
223B TYR* 3.6 21.1 - - + +
224B GLY 3.2 0.2 - - - -
225B GLN* 1.3 77.2 - - - +
227B VAL* 1.3 60.4 + - + +
229B THR* 3.3 2.6 + - - -
230B VAL* 3.0 43.5 + - + +
250B VAL* 3.8 28.3 - - + -
254B VAL* 5.0 2.5 - - + -
2078B LEU* 4.3 13.2 - - + -
2079B THR* 5.5 4.3 - - + -
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Residues in contact with VAL 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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223B TYR 3.0 20.9 + - - +
224B GLY* 4.1 4.0 - - - +
226B LEU* 1.3 72.5 - - + +
228B PHE* 1.3 60.9 + - - +
230B VAL* 4.0 5.3 - - + +
231B LYS* 2.8 61.6 + - + +
250B VAL* 4.6 9.4 - - + -
251B THR* 4.1 15.7 - - + +
254B VAL* 3.6 36.1 - - + -
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Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLY 2.9 19.9 + - - +
225B GLN* 3.6 28.7 - - - +
226B LEU 3.3 0.2 - - - -
227B VAL* 1.3 76.7 - - - +
229B THR* 1.3 67.3 + - - +
231B LYS* 4.1 4.2 - - - +
232B GLU* 3.1 49.6 + - + +
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Residues in contact with THR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 4.9 1.9 - - - -
140B CYS* 3.7 31.9 - - + +
225B GLN* 2.6 24.1 + - - -
226B LEU 3.7 4.5 - - - -
228B PHE* 1.3 83.8 - - - +
230B VAL* 1.3 61.5 + - + +
232B GLU* 3.8 5.8 - - - +
233B ALA* 2.9 33.2 + - + +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 5.1 13.0 - - + -
140B CYS* 6.3 0.4 - - - -
226B LEU* 3.0 35.8 + - + +
227B VAL* 4.0 5.8 - - + +
229B THR* 1.3 78.0 - - + +
231B LYS* 1.3 55.7 + - - +
233B ALA* 3.7 5.7 - - + +
234B ALA* 2.8 33.9 + - + +
243B THR* 5.6 4.2 - - + +
246B ALA* 6.2 0.4 - - + -
247B GLU* 3.7 34.1 - - + +
250B VAL* 5.2 9.9 - - + -
2079B THR* 5.2 11.2 - - + +
2082B ARG* 6.4 0.2 - - - +
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 2.8 45.3 + - + +
228B PHE* 4.1 4.3 - - - +
230B VAL* 1.3 71.5 - - - +
232B GLU* 1.3 58.0 + - - +
234B ALA* 3.5 2.0 + - - +
235B ALA* 3.1 28.4 + - - +
247B GLU* 2.8 39.2 + - + +
251B THR* 3.8 17.8 + - - +
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Residues in contact with GLU 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 PHE* 3.1 45.4 + - + +
229B THR* 3.9 5.3 - - - +
231B LYS* 1.3 76.1 - - - +
233B ALA* 1.3 57.3 + - - +
235B ALA* 3.5 6.0 + - - +
236B GLN* 3.1 33.5 + - - +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B THR* 2.9 23.7 + - + +
230B VAL* 3.7 7.0 - - + +
231B LYS 3.3 0.2 - - - -
232B GLU* 1.3 75.6 - - - +
234B ALA* 1.3 63.3 + - - +
236B GLN* 3.2 19.4 + - - +
237B GLN 3.4 2.6 + - - -
2082B ARG* 2.7 44.2 + - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B VAL 2.8 22.0 + - - +
231B LYS 3.9 4.3 - - - +
232B GLU 3.4 0.2 - - - -
233B ALA* 1.3 73.4 - - - +
235B ALA* 1.3 60.8 + - - +
237B GLN 3.2 13.0 - - - +
238B GLN* 3.5 1.8 + - - +
243B THR* 4.3 14.8 - - + +
244B GLN* 3.0 37.2 + - - +
247B GLU* 3.9 26.9 - - + +
2082B ARG* 4.9 0.4 - - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS 3.1 18.1 + - - +
232B GLU* 3.8 7.0 - - - +
233B ALA 3.3 0.2 - - - -
234B ALA* 1.3 75.6 - - - +
236B GLN* 1.3 64.8 + - - +
237B GLN 3.3 0.2 - - - -
238B GLN* 3.5 28.5 - - - +
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Residues in contact with GLN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU* 3.1 21.5 + - - +
233B ALA* 3.2 16.1 + - - +
235B ALA* 1.3 79.5 - - - +
237B GLN* 1.3 60.7 + - + +
238B GLN 4.0 0.4 + - - -
2082B ARG* 4.9 2.0 - - - +
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA 3.4 2.1 + - - +
234B ALA* 3.2 9.9 - - - +
236B GLN* 1.3 78.4 - - + +
238B GLN* 1.3 62.9 + - - +
239B GLU* 3.3 19.9 + - + +
240B SER* 3.8 15.7 + - - +
243B THR* 3.6 18.6 + - + -
244B GLN* 3.6 5.9 + - - -
2082B ARG* 3.2 41.1 + - - +
2083B ASP 3.4 17.5 + - - +
2084B LEU* 3.4 25.7 + - - +
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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) + - + + + + + -
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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