Contacts of the helix formed by residues 172 - 205 (chain C) in PDB entry 3L73
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 ASP 172 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 3.8 16.7 + - - +
136C TRP* 4.5 7.2 - - - -
170C SER* 2.8 20.1 + - - +
171C VAL* 1.3 75.6 - - - +
173C ASN* 1.3 73.7 + - - +
174C PRO* 3.2 13.9 - - + -
175C THR* 2.7 28.0 + - - -
176C LEU* 3.1 8.7 + - - +
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Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ASP* 3.0 24.1 + - - +
60C THR* 2.7 47.0 + - + +
172C ASP* 1.3 86.2 + - - +
174C PRO* 1.3 68.1 - - + +
175C THR 3.0 0.2 + - - -
176C LEU* 3.1 3.3 + - - +
177C THR* 3.0 41.1 + - - +
57P THR* 5.0 2.4 + - - -
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Residues in contact with PRO 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C TRP 3.7 10.5 - - - +
167C GLY* 3.7 27.4 - - - +
168C GLY* 5.2 2.0 - - - -
170C SER 5.3 0.9 - - - +
172C ASP* 3.3 14.6 - - + -
173C ASN* 1.3 96.1 - - + +
175C THR* 1.3 58.3 - - - +
177C THR* 3.3 15.5 + - - +
178C ARG* 2.9 28.9 + - - +
54P MET 4.6 1.1 - - - +
55P HIS* 5.8 6.5 - - + -
68R VAL* 5.2 11.0 - - + -
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Residues in contact with THR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL* 6.3 0.4 - - + -
165C ALA 4.2 1.3 - - - +
166C TRP* 2.6 47.4 + - + -
170C SER 3.7 0.2 + - - -
171C VAL* 3.6 16.8 - - + -
172C ASP 2.7 28.8 + - - -
174C PRO* 1.3 71.0 - - - +
176C LEU* 1.3 67.2 + - - +
177C THR 3.3 0.2 - - - -
178C ARG* 3.2 8.1 - - - +
179C PHE* 2.9 55.4 + - + +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TYR* 3.5 19.5 - - - +
58C ALA* 4.0 4.5 - - + -
59C ASP* 3.5 17.0 - - - +
60C THR* 3.3 37.5 - - + +
63C ALA* 4.1 9.6 - - + -
133C VAL* 4.1 14.1 - - + +
134C LEU* 4.1 8.3 - - + +
136C TRP* 3.6 32.5 - - + -
172C ASP 3.1 6.3 + - - +
173C ASN* 3.1 10.4 + - - +
175C THR* 1.3 79.0 - - - +
177C THR* 1.3 63.7 + - - +
179C PHE* 3.0 7.5 + - - +
180C PHE* 3.0 22.3 + - - +
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Residues in contact with THR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ALA* 3.2 33.4 - - + +
173C ASN* 3.0 31.1 + - - +
174C PRO* 3.3 10.4 + - - +
176C LEU* 1.3 78.4 - - - +
178C ARG* 1.3 61.2 + - - +
180C PHE* 3.6 4.5 + - - +
181C ALA* 3.3 19.2 + - - +
53P ALA 4.2 6.5 - - - +
54P MET 3.1 26.9 + - - -
55P HIS* 4.7 4.1 - - - -
56P TYR 4.0 17.5 - - - +
57P THR* 4.5 3.1 - - - +
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Residues in contact with ARG 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TRP 2.6 30.5 + - - -
165C ALA* 3.0 23.0 + - - +
167C GLY* 3.3 18.7 + - - +
174C PRO* 2.9 20.4 + - - +
175C THR* 3.2 16.8 - - - +
177C THR* 1.3 78.9 + - - +
179C PHE* 1.3 69.6 + - + +
181C ALA* 3.4 2.6 + - - +
182C LEU* 3.0 33.3 + - + +
54P MET* 4.1 32.6 + - + +
55P HIS* 4.2 13.7 + - - -
62R LEU* 3.1 42.4 + - - +
63R SER 5.0 1.0 + - - -
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Residues in contact with PHE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C PHE* 4.4 14.1 - + - -
130C VAL* 4.0 29.7 - - + +
133C VAL* 3.8 40.4 - - + -
134C LEU* 4.4 5.2 - - + -
144C ALA* 4.8 6.1 - - + -
148C THR* 4.5 17.9 - - + -
165C ALA* 4.9 7.9 - - + -
166C TRP* 6.0 0.4 - + - -
175C THR* 2.9 44.1 + - + +
176C LEU* 3.0 6.7 + - - +
178C ARG* 1.3 84.5 - - + +
180C PHE* 1.3 56.4 + - - +
182C LEU* 3.2 14.8 + - + +
183C HIS* 2.7 37.4 + - - +
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Residues in contact with PHE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ALA* 4.0 34.5 - - + -
56C TYR* 3.8 32.3 - + - -
58C ALA* 3.9 22.2 - - + -
134C LEU* 3.6 25.7 - - + +
176C LEU 3.0 9.4 + - - +
177C THR 3.7 8.7 - - - +
178C ARG 3.3 0.2 - - - -
179C PHE* 1.3 76.1 - - - +
181C ALA* 1.3 65.6 + - - +
183C HIS* 3.1 3.8 + - + +
184C PHE* 2.9 38.4 + + + +
501C HEM 4.3 11.0 - + + -
180P PHE* 3.7 33.4 - + - -
184P PHE* 6.0 1.1 - + - -
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Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C THR 3.3 10.6 + - - +
178C ARG 3.6 8.1 - - - +
180C PHE* 1.3 80.7 - - - +
182C LEU* 1.3 63.8 + - - +
184C PHE* 3.1 4.3 + - - +
185C LEU* 2.9 24.8 + - - +
50P LEU* 5.1 3.6 - - + +
53P ALA* 4.6 9.9 - - + +
54P MET* 4.0 28.3 - - + -
184P PHE* 3.6 24.1 - - + -
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Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL* 4.4 18.8 - - + -
178C ARG* 3.0 21.0 + - + +
179C PHE* 3.5 17.5 - - + +
181C ALA* 1.3 77.5 - - - +
183C HIS* 1.3 59.4 + - - +
185C LEU* 3.1 14.2 + - + +
186C LEU* 3.0 57.5 + - + +
54P MET* 4.8 13.0 - - + -
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Residues in contact with HIS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C THR* 2.9 28.1 + - + +
130C VAL* 3.3 14.3 - - + +
131C GLY* 3.2 16.9 - - - -
134C LEU* 3.7 16.8 - - + -
179C PHE 2.7 18.0 + - - +
180C PHE* 3.1 5.1 + + - +
182C LEU* 1.3 73.3 - - - +
184C PHE* 1.3 56.3 + - - +
187C PRO* 3.0 27.5 - - - +
501C HEM 2.0 93.6 + + + -
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Residues in contact with PHE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.6 20.9 - - + -
53C ALA* 4.4 8.5 - - + -
180C PHE* 2.9 33.7 + + + +
181C ALA 3.4 8.5 - - - +
183C HIS* 1.3 80.4 - - - +
185C LEU* 1.3 57.2 + - - +
187C PRO* 3.6 4.9 - - - +
188C PHE* 3.0 42.2 - + - -
501C HEM 3.3 29.9 - - + +
180P PHE* 6.0 1.3 - + - -
181P ALA* 3.5 33.0 - - - -
184P PHE* 3.4 47.6 - + + -
185P LEU* 4.2 6.3 - - - -
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ALA 2.9 16.5 + - - +
182C LEU* 3.7 17.0 - - + +
184C PHE* 1.3 77.6 - - - +
186C LEU* 1.3 73.2 + - + +
188C PHE* 3.0 25.0 + - + +
189C ALA* 3.5 7.4 + - + +
50P LEU* 3.9 28.0 - - + -
54P MET* 6.2 2.5 - - + -
184P PHE* 4.5 8.3 - - + -
188P PHE* 3.9 31.0 - - + -
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C THR* 4.0 13.9 - - + +
126C ALA* 4.0 15.7 - - + +
127C THR* 3.1 39.5 - - + +
130C VAL* 5.0 3.6 - - + -
182C LEU* 3.0 43.2 + - + +
185C LEU* 1.3 77.5 - - + +
187C PRO* 1.3 67.5 - - + +
189C ALA* 2.9 14.3 + - + +
190C ILE* 2.8 25.6 + - - +
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Residues in contact with PRO 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.3 4.3 - - + +
46C ILE* 4.0 16.3 - - + +
127C THR* 3.8 12.8 - - + -
183C HIS 3.0 28.7 - - - +
184C PHE 3.6 3.6 - - - +
185C LEU 3.4 3.8 - - - -
186C LEU* 1.3 87.8 - - + +
188C PHE* 1.3 59.0 + - + +
190C ILE* 3.0 15.5 + - + +
191C ALA* 2.9 26.7 + - - +
501C HEM 3.7 46.0 - - + -
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Residues in contact with PHE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 4.3 32.1 - - + -
50C LEU* 5.0 3.4 - - + -
184C PHE* 3.0 50.7 - + - -
185C LEU* 3.0 15.8 + - + +
187C PRO* 1.3 75.6 - - - +
189C ALA* 1.3 66.2 + - - +
191C ALA* 3.0 9.0 + - + +
192C GLY* 2.8 21.1 + - - -
501C HEM 4.9 6.5 - - + -
185P LEU* 4.0 27.1 - - + -
188P PHE* 4.5 30.3 - + + -
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C THR* 4.7 8.7 - - + -
185C LEU* 3.5 8.3 + - + +
186C LEU* 2.9 21.9 + - + +
188C PHE* 1.3 79.0 - - - +
190C ILE* 1.3 58.7 + - - +
192C GLY* 3.3 1.7 + - - +
193C ILE* 2.8 44.1 + - + +
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 4.0 20.4 - - + -
91C PHE* 5.0 1.3 - - + -
120C LEU* 3.6 21.9 - - + +
123C THR* 3.3 18.6 - - + -
124C LEU* 3.8 25.1 - - + +
127C THR* 3.6 22.0 - - - +
186C LEU 2.8 16.5 + - - +
187C PRO* 3.2 8.5 - - + +
188C PHE 3.0 0.2 - - - -
189C ALA* 1.3 77.6 - - - +
191C ALA* 1.3 50.7 + - - +
193C ILE* 3.6 1.6 - - - -
194C THR* 2.7 41.6 + - - +
501C HEM 4.0 19.7 - - + -
502C HEM 4.1 11.7 - - + -
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 3.7 19.9 - - + +
46C ILE* 5.0 7.0 - - + -
187C PRO 2.9 12.2 + - - +
188C PHE* 3.0 13.0 + - + +
190C ILE* 1.3 76.0 - - - +
192C GLY* 1.3 66.4 + - - +
194C THR* 3.1 13.0 + - - -
195C ILE* 3.2 18.6 + - + +
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Residues in contact with GLY 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C PHE 2.8 17.9 + - - -
189C ALA* 3.6 3.4 - - - -
191C ALA* 1.3 71.9 - - - +
193C ILE* 1.3 53.7 + - - +
195C ILE* 2.7 39.3 + - - +
196C ILE* 3.3 7.9 + - - +
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Residues in contact with ILE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C THR* 4.4 14.6 - - + +
119C ILE* 3.6 33.0 - - + -
120C LEU* 3.9 22.7 - - + -
123C THR* 4.3 11.0 - - - +
189C ALA* 2.8 33.2 + - + +
190C ILE* 3.7 3.1 - - - +
192C GLY* 1.3 71.4 - - - -
194C THR* 1.3 56.0 + - - +
196C ILE* 3.1 14.8 + - + +
197C HIS* 2.8 24.6 + - - +
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Residues in contact with THR 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 5.5 6.3 - - + -
42C LEU* 4.4 4.9 - - + +
120C LEU* 3.8 13.2 - - - +
190C ILE* 2.7 32.4 + - - +
191C ALA* 3.3 12.9 - - - -
192C GLY 3.0 0.2 + - - -
193C ILE* 1.3 70.4 - - - +
195C ILE* 1.3 69.3 + - + +
197C HIS* 3.0 7.9 + - + +
198C LEU* 2.9 38.2 + - + +
502C HEM 3.8 31.9 - - + +
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Residues in contact with ILE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ALA 3.2 13.8 + - - +
192C GLY* 2.7 22.2 + - - +
194C THR* 1.3 74.6 - - + +
196C ILE* 1.3 66.7 + - + +
198C LEU* 3.4 9.4 + - + +
199C THR* 3.0 31.9 + - - +
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Residues in contact with ILE 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C THR* 3.9 11.0 - - + -
192C GLY 4.0 11.0 - - - +
193C ILE* 3.1 16.7 + - + +
195C ILE* 1.3 78.4 - - + +
197C HIS* 1.3 67.7 + - - +
199C THR* 3.0 17.2 + - - +
200C PHE* 3.0 41.0 + - + -
11P LEU* 3.8 32.8 - - + -
14P MET* 6.3 0.4 - - - -
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Residues in contact with HIS 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C THR* 2.9 28.2 + - + +
116C THR* 2.7 28.5 + - - +
117C GLY* 3.5 8.8 + - - -
120C LEU* 3.9 8.1 - - + -
193C ILE 2.8 13.8 + - - +
194C THR* 3.3 13.5 - - - +
196C ILE* 1.3 79.1 - - - +
198C LEU* 1.3 63.6 + - + +
200C PHE* 3.4 3.5 + - - +
201C LEU* 3.0 19.8 + - - +
502C HEM 2.0 90.2 + + + -
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 6.3 0.7 - - + -
194C THR* 2.9 29.4 + - + +
195C ILE* 4.0 8.1 - - + +
197C HIS* 1.3 72.8 - - + +
199C THR* 1.3 59.0 + - - +
201C LEU* 3.7 14.6 - - + -
202C HIS* 2.9 44.0 + - + +
502C HEM 3.4 46.2 - - + -
2002C UQ 3.9 36.8 - - + +
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C ILE* 3.0 21.4 + - - +
196C ILE* 3.0 14.5 + - - +
198C LEU* 1.3 74.7 - - - +
200C PHE* 1.3 72.5 + - + +
202C HIS* 3.2 15.5 + - - +
203C GLU* 3.6 14.2 + - - +
10P PRO* 4.5 23.1 - - + +
11P LEU* 5.2 9.2 - - + -
14P MET* 5.0 16.0 - - + +
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Residues in contact with PHE 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLU* 3.2 44.4 - - + -
113C THR* 3.5 18.4 + - - +
116C THR* 3.9 16.2 - - + -
196C ILE* 3.0 43.9 + - + -
197C HIS 3.8 4.0 - - - +
199C THR* 1.3 77.1 - - + +
201C LEU* 1.3 66.5 + - - +
203C GLU* 2.9 26.9 + - + +
204C SER* 4.0 2.3 + - - -
9P HIS* 4.3 11.4 - + - -
10P PRO* 3.3 28.5 - - + -
11P LEU* 4.2 24.2 - - + -
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 4.3 8.1 - - + -
113C THR* 3.2 17.2 + - + +
197C HIS* 3.0 15.8 + - + +
198C LEU* 3.5 16.2 - - + +
199C THR 3.2 0.2 - - - -
200C PHE* 1.3 78.3 - - - +
202C HIS* 1.3 61.0 + - + +
203C GLU 2.9 6.1 + - - -
204C SER* 3.1 6.6 + - - -
205C GLY* 2.9 38.3 + - - +
206C SER* 4.5 6.1 - - - +
502C HEM 3.7 58.6 - - + -
2002C UQ 4.0 23.6 - - - +
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Residues in contact with HIS 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASN 4.4 5.0 + - - +
18C SER* 3.3 37.2 - - - -
22C LEU* 4.3 17.2 - - + +
198C LEU* 2.9 31.3 + - + +
199C THR* 3.2 8.2 + - - +
200C PHE 3.2 0.2 + - - -
201C LEU* 1.3 81.5 - - + +
203C GLU* 1.3 63.9 + - - +
204C SER 3.3 0.6 - - - -
205C GLY* 4.0 10.0 + - - +
2002C UQ 2.6 37.7 + - + +
3G HIS* 4.1 16.6 + - - -
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Residues in contact with GLU 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C THR* 3.6 12.8 + - - +
200C PHE* 2.9 23.5 + - + +
202C HIS* 1.3 80.5 - - - +
204C SER* 1.3 61.0 + - - +
3G HIS* 4.8 11.3 + - - -
8P SER 5.1 2.8 - - - +
10P PRO* 4.0 32.0 - - + +
13P LYS* 5.4 7.4 + - - -
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.2 41.3 + - - -
113C THR* 5.3 0.2 + - - -
200C PHE 4.6 1.3 + - - -
201C LEU* 3.1 8.2 + - - +
202C HIS 4.5 0.4 - - - -
203C GLU* 1.3 81.8 - - - +
205C GLY* 1.3 69.3 + - - +
206C SER 5.1 0.3 - - - +
218C LYS* 5.8 3.5 + - - -
3G HIS* 6.1 2.3 - - - -
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Residues in contact with GLY 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 5.9 4.0 - - - -
23C PRO 5.1 7.2 - - - -
110C TYR* 3.1 13.7 + - - -
201C LEU* 2.9 18.5 + - - +
202C HIS* 4.0 9.2 - - - -
203C GLU 3.7 1.0 - - - -
204C SER* 1.3 92.5 + - - +
206C SER* 1.3 61.9 + - - -
218C LYS* 6.0 4.5 - - - -
2002C UQ 5.6 2.7 - - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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