Contacts of the helix formed by residues 174 - 210 (chain R) in PDB entry 6XOX
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 CYS 174 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172R LEU 3.2 5.6 + - - -
173R HIS* 1.3 74.6 - - - +
175R THR* 1.3 60.2 + - - +
176R ARG* 3.5 24.0 - - - -
177R ASN* 3.2 39.6 - - - +
178R TYR* 3.1 35.4 + - - -
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Residues in contact with THR 175 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174R CYS* 1.3 75.2 - - - +
176R ARG* 1.3 57.7 + - - +
178R TYR* 3.2 8.9 + - - +
179R ILE* 3.0 28.4 + - - +
250R TYR* 3.4 30.1 - - + +
262R GLU* 4.4 30.5 + - + +
266R PHE* 3.7 33.5 - - + +
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Residues in contact with ARG 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN* 3.3 51.3 + - - +
391A TYR* 3.4 45.4 - - + +
174R CYS* 3.3 11.2 - - - -
175R THR* 1.3 78.7 - - - +
177R ASN* 1.3 84.3 + - - +
179R ILE* 3.3 2.9 + - - +
180R HIS* 3.0 42.5 + - - +
250R TYR* 3.3 19.5 + - + +
254R LEU* 5.4 0.4 - - + -
402R TYR* 5.9 0.2 - - - -
406R ASN* 4.3 13.7 - - - +
408R GLU* 3.6 24.7 + - - -
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Residues in contact with ASN 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166R LEU* 3.8 28.2 - - + +
172R LEU* 2.4 44.8 + - - +
173R HIS* 4.9 1.3 - - + -
174R CYS* 3.2 19.4 - - - +
176R ARG* 1.3 100.0 + - - +
178R TYR* 1.3 62.4 + - + +
180R HIS* 3.7 11.9 + - - +
181R LEU* 2.8 29.5 + - - +
402R TYR 5.1 2.1 - - - +
406R ASN* 5.1 5.4 + - - +
408R GLU* 5.1 1.0 + - - -
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Residues in contact with TYR 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167R LEU* 5.4 2.5 - - + -
170R ARG* 4.4 5.4 + - - -
173R HIS* 3.3 52.5 + + + +
174R CYS* 3.1 27.5 + - - +
175R THR* 3.2 6.7 + - - +
177R ASN* 1.3 79.3 - - + +
179R ILE* 1.3 62.4 + - - +
181R LEU* 3.4 20.4 - - + +
182R ASN* 2.8 31.1 + - - +
266R PHE* 3.7 32.1 - + + -
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Residues in contact with ILE 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175R THR 3.0 14.7 + - - +
176R ARG 3.7 7.0 - - - +
178R TYR* 1.3 75.7 - - - +
180R HIS* 1.3 59.8 + - + +
182R ASN* 2.9 16.2 - - - +
183R LEU* 3.0 13.3 + - - +
243R TRP* 4.0 24.8 - - + -
246R VAL* 4.3 4.9 - - + -
247R GLU* 3.3 34.8 - - - +
250R TYR* 4.2 25.8 - - + -
266R PHE* 3.6 27.6 - - + +
269R TYR* 4.1 21.5 - - + -
270R VAL* 5.1 0.2 - - + -
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Residues in contact with HIS 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR* 3.2 22.6 - + - -
166R LEU* 4.6 5.2 - - + -
176R ARG* 3.0 35.3 + - + +
177R ASN* 3.8 16.0 + - - +
179R ILE* 1.3 74.6 - - + +
181R LEU* 1.3 57.4 + - - +
183R LEU* 3.3 7.0 + - + +
184R PHE* 2.9 48.7 + + + -
247R GLU* 2.8 36.4 + - - -
359R LEU* 4.4 6.0 - - + +
402R TYR* 3.6 43.6 + + + +
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Residues in contact with LEU 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163R SER* 3.8 30.4 + - - +
166R LEU* 3.8 31.4 - - + +
167R LEU* 3.7 30.7 - - + -
177R ASN 2.8 17.8 + - - +
178R TYR* 3.1 25.9 + - + +
180R HIS* 1.3 76.5 - - - +
182R ASN* 1.3 61.0 + - - +
184R PHE* 3.2 10.2 + - + +
185R ALA* 3.0 22.9 + - - +
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Residues in contact with ASN 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R TYR* 2.8 19.6 + - - +
179R ILE* 2.9 12.7 - - - +
181R LEU* 1.3 73.2 - - - +
183R LEU* 1.3 58.5 + - - +
185R ALA* 3.5 10.0 - - + +
186R SER* 2.9 27.4 + - - -
243R TRP* 3.1 36.8 - - - -
266R PHE* 4.9 4.0 - - - -
270R VAL* 4.0 16.6 - - - +
274R TRP* 4.0 22.2 - - + +
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Residues in contact with LEU 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179R ILE 3.0 20.2 + - - +
180R HIS* 3.3 9.0 - - + +
182R ASN* 1.3 76.8 + - - +
184R PHE* 1.3 64.8 + - + +
186R SER* 3.1 6.6 + - - -
187R PHE* 3.0 48.0 + - + -
240R ASN* 4.6 1.8 - - - +
243R TRP* 3.6 43.4 - - + +
244R LEU* 3.7 15.9 - - + -
247R GLU* 3.7 22.0 - - + +
359R LEU* 3.9 26.7 - - + +
398R VAL* 5.4 1.6 - - + -
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Residues in contact with PHE 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R LEU* 3.5 24.3 - - + +
162R ALA* 3.6 21.8 - - + -
163R SER* 3.9 11.9 - - - +
166R LEU* 3.7 16.4 - - + -
180R HIS* 2.9 29.3 + + + -
181R LEU* 3.3 9.0 - - + +
183R LEU* 1.3 81.3 - - + +
185R ALA* 1.3 60.4 + - - +
187R PHE* 3.3 4.8 + - - +
188R ILE* 3.0 33.4 + - - +
359R LEU* 6.0 0.4 - - + -
398R VAL* 4.0 36.8 - - + -
399R ALA* 4.5 0.4 - - - -
402R TYR* 4.1 12.3 - + + -
403R CYS* 3.5 31.0 - - - -
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Residues in contact with ALA 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163R SER* 4.7 1.5 + - - +
181R LEU 3.0 13.1 + - - +
182R ASN* 3.5 16.6 - - + +
183R LEU 3.3 0.2 - - - -
184R PHE* 1.3 76.5 - - - +
186R SER* 1.3 56.7 + - - +
188R ILE* 3.3 15.0 + - + +
189R LEU* 2.9 28.8 + - - +
274R TRP* 4.7 9.0 - - + -
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Residues in contact with SER 186 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182R ASN 2.9 14.0 + - - -
183R LEU 3.1 9.4 + - - -
185R ALA* 1.3 75.0 - - - +
187R PHE* 1.3 59.8 + - - +
189R LEU* 3.2 5.4 + - - +
190R ARG* 2.9 29.5 + - - +
236R CYS 4.6 1.0 + - - +
239R ALA* 3.4 8.7 + - - +
240R ASN* 3.2 32.5 + - - +
243R TRP* 4.0 20.8 - - - -
274R TRP* 4.0 11.0 - - - -
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Residues in contact with PHE 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R TYR* 5.7 5.0 - + - -
155R SER* 5.4 1.0 + - - +
159R LEU* 3.7 17.9 - - + -
183R LEU* 3.0 50.5 + - + -
184R PHE* 3.3 8.9 + - - +
186R SER* 1.3 74.1 - - - +
188R ILE* 1.3 59.0 + - - +
190R ARG* 3.4 2.0 + - + +
191R ALA* 3.0 30.3 + - - +
240R ASN* 3.3 32.8 - - - +
244R LEU* 3.7 18.6 - - + -
358R PRO 4.9 0.9 - - - -
391R THR 5.5 3.4 - - - -
394R GLN* 3.9 33.0 - - + -
395R GLY* 3.9 15.3 - - - -
398R VAL* 3.9 22.7 - - + -
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Residues in contact with ILE 188 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R PHE* 3.6 37.1 - - + +
159R LEU* 3.6 37.5 - - + +
160R VAL* 4.0 13.2 - - + +
163R SER* 4.1 10.8 - - - +
184R PHE 3.0 19.0 + - - +
185R ALA* 3.5 13.9 - - - +
187R PHE* 1.3 75.8 - - - +
189R LEU* 1.3 61.8 + - + +
191R ALA* 3.4 3.0 + - - +
192R LEU* 2.9 34.1 + - + +
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Residues in contact with LEU 189 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185R ALA 2.9 17.0 + - - +
186R SER* 3.2 7.1 + - - +
188R ILE* 1.3 78.5 - - + +
190R ARG* 1.3 59.3 + - - +
192R LEU* 3.4 17.6 + - + +
193R SER* 2.9 26.3 + - - -
235R TYR* 5.2 7.9 - - + -
236R CYS* 3.7 28.0 - - + -
239R ALA* 5.8 0.2 - - + -
274R TRP* 4.1 26.5 - - + -
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Residues in contact with ARG 190 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R TYR* 4.0 17.1 + - + +
186R SER 2.9 16.7 + - - +
187R PHE* 3.9 3.6 - - + +
189R LEU* 1.3 74.4 - - - +
191R ALA* 1.3 64.2 + - - +
193R SER* 3.2 8.0 + - - -
194R VAL* 3.0 27.9 + - + +
236R CYS* 4.1 14.7 - - + +
237R VAL* 3.9 28.9 - - + +
240R ASN* 3.3 34.4 - - - +
241R TYR* 3.1 49.1 + - - -
244R LEU* 6.3 0.2 - - - +
391R THR* 3.7 24.7 - - - +
394R GLN* 5.7 1.4 + - - -
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Residues in contact with ALA 191 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R TYR* 3.8 46.4 - - + +
155R SER* 4.3 4.7 - - - +
156R PHE* 4.6 7.6 - - + +
187R PHE 3.0 18.5 + - - +
188R ILE* 3.9 3.8 - - - +
190R ARG* 1.3 76.7 - - - +
192R LEU* 1.3 58.7 + - - +
194R VAL* 3.3 2.9 + - - +
195R PHE* 2.9 40.3 + - + -
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Residues in contact with LEU 192 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R PHE* 5.3 15.6 - - + -
188R ILE* 2.9 21.7 + - + +
189R LEU* 3.7 18.8 - - + +
191R ALA* 1.3 75.0 - - - +
193R SER* 1.3 58.8 + - - +
195R PHE* 4.2 16.1 - - + -
196R ILE* 2.9 55.0 + - + +
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Residues in contact with SER 193 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189R LEU 2.9 14.9 + - - -
190R ARG* 3.2 11.4 + - - -
192R LEU* 1.3 76.1 - - - +
194R VAL* 1.3 60.7 + - - +
196R ILE* 3.5 2.6 + - - -
197R LYS* 3.0 30.5 + - - +
233R MET* 3.2 38.9 + - - +
236R CYS* 3.9 22.0 - - - -
237R VAL* 5.2 3.3 - - - +
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Residues in contact with VAL 194 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148R TYR* 3.5 34.3 - - + +
149R THR* 6.1 0.9 - - - +
152R TYR* 3.6 32.1 - - + +
190R ARG* 3.0 20.9 + - + +
191R ALA 3.3 6.7 + - - +
193R SER* 1.3 78.4 - - - +
195R PHE* 1.3 60.8 + - + +
197R LYS* 3.4 12.3 + - + +
198R ASP* 2.9 33.6 + - + +
237R VAL* 6.2 1.8 - - + -
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Residues in contact with PHE 195 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149R THR* 3.7 23.8 - - - -
152R TYR* 3.5 49.4 - + + -
153R ALA* 3.5 11.4 - - + -
156R PHE* 4.2 23.1 - + + -
191R ALA 2.9 22.5 + - - +
192R LEU* 3.6 18.8 - - + +
194R VAL* 1.3 78.4 - - + +
196R ILE* 1.3 61.6 + - + +
198R ASP* 2.8 19.8 - - - +
199R ALA* 2.9 22.2 + - - +
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Residues in contact with ILE 196 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192R LEU* 2.9 47.1 + - + +
193R SER* 4.0 4.9 - - - +
195R PHE* 1.3 75.8 - - + +
197R LYS* 1.3 57.0 + - - +
199R ALA* 4.8 2.2 - - - -
200R ALA* 2.9 39.0 + - + +
229R VAL* 5.1 6.1 - - + -
233R MET* 3.9 14.8 - - + -
501R V6G 5.7 0.2 - - + -
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Residues in contact with LYS 197 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148R TYR* 5.6 0.8 + - - -
193R SER* 3.0 19.7 + - - +
194R VAL* 3.5 13.2 - - + +
195R PHE 3.2 0.2 - - - -
196R ILE* 1.3 77.7 - - - +
198R ASP* 1.3 60.7 + - + +
200R ALA* 3.6 0.9 - - - +
201R LEU* 3.0 36.5 + - + +
230R PHE* 5.8 0.2 - - - -
233R MET* 3.6 25.5 - - + +
501R V6G 2.6 99.0 + - + -
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Residues in contact with ASP 198 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R TYR* 2.9 43.6 + - + -
148R TYR* 4.2 15.5 + - - +
149R THR* 4.0 13.0 + - - -
194R VAL* 2.9 17.5 + - + +
195R PHE* 2.8 32.6 - - - +
197R LYS* 1.3 77.5 - - + +
199R ALA* 1.3 61.1 + - - +
201R LEU* 3.4 6.8 + - - +
202R LYS* 2.9 26.5 + - - +
501R V6G 4.5 19.2 - - + -
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Residues in contact with ALA 199 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R TYR* 5.6 1.1 - - - -
195R PHE 2.9 16.2 + - - +
196R ILE* 4.3 2.9 - - - +
198R ASP* 1.3 82.0 + - - +
200R ALA* 1.3 61.8 + - - +
202R LYS* 3.2 9.8 + - + +
203R TRP* 2.9 28.4 + - - +
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Residues in contact with ALA 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196R ILE* 2.9 26.2 + - + +
197R LYS 3.6 3.8 - - - +
199R ALA* 1.3 75.6 - - - +
201R LEU* 1.3 58.9 + - - +
203R TRP* 3.3 9.9 + - + +
204R MET* 2.9 37.5 + - - +
220R TYR* 5.7 0.9 - - - +
501R V6G 4.2 20.9 - - + -
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Residues in contact with LEU 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R TRP* 4.8 11.2 - - + -
197R LYS* 3.0 30.5 + - + +
198R ASP* 3.9 2.0 - - - +
200R ALA* 1.3 75.9 - - - +
202R LYS* 1.3 58.9 + - - +
204R MET* 4.3 5.8 - - + +
205R TYR* 2.9 63.9 + - + +
501R V6G 3.5 95.6 - - + +
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Residues in contact with LYS 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R TYR* 5.5 5.6 - - - +
198R ASP 2.9 15.8 + - - +
199R ALA* 3.2 13.4 + - + +
201R LEU* 1.3 76.4 - - - +
203R TRP* 1.3 55.9 + - - +
205R TYR* 3.8 0.7 - - - +
206R SER* 2.8 46.9 + - - +
501R V6G 3.7 30.6 - - - +
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Residues in contact with TRP 203 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199R ALA 2.9 16.0 + - - +
200R ALA* 3.7 7.6 - - + +
202R LYS* 1.3 76.5 - - - +
204R MET* 1.3 78.5 + - + +
206R SER* 3.4 6.4 + - - -
207R THR* 2.9 44.9 + - + +
220R TYR* 6.6 0.4 - + - -
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Residues in contact with MET 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R TRP* 4.4 8.5 - - + -
200R ALA* 2.9 21.7 + - - +
201R LEU* 4.0 7.0 - - + +
203R TRP* 1.3 92.7 - - + +
205R TYR* 1.3 64.9 + - + +
207R THR* 3.3 12.1 - - + +
208R ALA* 2.9 30.7 + - - +
216R GLY 5.5 0.2 - - - -
217R LEU* 3.7 34.0 - - + +
220R TYR* 3.5 39.0 - - + -
221R GLN* 4.2 4.7 - - - +
501R V6G 4.0 24.9 - - - -
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Residues in contact with TYR 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R SER* 3.6 11.2 + - - -
32R LEU* 3.5 43.3 - - + -
33R TRP* 3.5 33.5 + + + +
138R GLU* 5.1 12.1 - - + -
201R LEU* 2.9 40.8 + - + +
202R LYS* 4.3 2.7 - - - +
204R MET* 1.3 79.1 - - + +
206R SER* 1.3 52.4 + - - +
208R ALA* 4.5 2.0 - - + +
209R ALA* 2.7 42.5 + - + +
217R LEU* 5.4 9.4 - - + -
501R V6G 3.5 45.7 - + - +
----------------------------------------------------------
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Residues in contact with SER 206 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202R LYS* 2.8 38.9 + - - +
203R TRP* 3.8 9.4 - - - -
204R MET 3.2 0.4 - - - -
205R TYR* 1.3 79.6 - - - +
207R THR* 1.3 57.7 + - - +
208R ALA 3.5 0.3 + - - -
209R ALA* 3.7 3.4 + - - -
210R GLN* 2.6 34.4 + - - +
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Residues in contact with THR 207 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203R TRP* 2.9 37.8 + - + +
204R MET* 3.3 22.4 - - + +
206R SER* 1.3 75.2 - - - +
208R ALA* 1.3 56.0 + - + +
210R GLN* 4.8 0.2 - - - +
211R GLN* 2.4 31.0 + - - +
217R LEU* 4.8 7.2 - - + -
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Residues in contact with ALA 208 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R LEU* 4.6 9.8 - - + +
204R MET 2.9 16.2 + - - +
205R TYR* 3.8 2.2 - - - -
207R THR* 1.3 77.3 - - - +
209R ALA* 1.3 61.0 + - - +
210R GLN 3.4 1.1 - - - -
211R GLN* 2.9 28.8 - - + +
214R TRP* 3.8 24.9 + - + -
217R LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 209 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R LEU* 5.1 9.0 - - + -
205R TYR* 2.7 22.0 + - + +
206R SER* 3.7 4.4 + - - +
207R THR 3.7 0.2 - - - -
208R ALA* 1.3 78.9 - - - +
210R GLN* 1.3 71.6 + - - +
211R GLN 3.2 5.4 + - - +
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Residues in contact with GLN 210 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206R SER* 2.6 30.9 + - - +
207R THR* 4.8 0.4 - - - +
208R ALA 3.4 0.2 - - - -
209R ALA* 1.3 84.1 - - - +
211R GLN* 1.3 78.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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