Contacts of the helix formed by residues 172 - 205 (chain P) in PDB entry 3H1J
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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60P THR* 3.9 18.8 + - - +
136P TRP* 4.3 4.6 - - - -
141P PHE* 5.4 0.2 - - - -
170P SER* 3.2 12.6 + - - +
171P VAL* 1.3 80.2 - - - +
173P ASN* 1.3 74.4 + - - +
174P PRO* 3.3 15.0 - - + -
175P THR* 2.8 34.1 + - - -
176P LEU* 3.1 4.5 + - - +
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Residues in contact with ASN 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C THR* 4.7 4.0 + - - -
58P ALA 4.1 0.4 + - - -
59P ASP* 3.0 25.1 + - - +
60P THR* 2.5 46.9 + - + +
172P ASP* 1.3 86.1 + - - +
174P PRO* 1.3 68.8 - - + +
175P THR 2.8 1.6 + - - -
176P LEU* 2.9 12.9 + - - +
177P THR* 2.9 35.1 + - - +
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Residues in contact with PRO 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C MET 4.3 1.9 - - - +
55C HIS* 5.7 6.3 - - + -
65E SER* 5.9 2.5 - - - +
68E VAL* 6.1 2.9 - - + -
166P TRP 3.5 16.6 - - - +
167P GLY 3.9 19.5 - - - +
168P GLY* 4.8 3.6 - - - +
170P SER 5.3 0.4 - - - +
172P ASP* 3.3 16.8 - - + -
173P ASN* 1.3 92.9 - - + +
175P THR* 1.3 57.6 + - - +
177P THR* 3.3 14.7 + - - +
178P ARG* 3.0 33.4 + - - +
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Residues in contact with THR 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P VAL* 6.3 0.4 - - + -
136P TRP* 5.2 1.6 - - + -
144P ALA* 5.7 0.9 - - + -
165P ALA 3.3 22.4 - - - +
166P TRP* 2.7 39.4 + - + +
171P VAL* 3.7 10.2 - - + -
172P ASP 2.8 27.0 + - - -
174P PRO* 1.3 76.5 - - - +
176P LEU* 1.3 60.0 + - - -
178P ARG* 3.2 4.8 + - - +
179P PHE* 2.8 55.2 + - + -
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Residues in contact with LEU 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P TYR* 3.4 19.5 - - + +
58P ALA* 4.3 2.0 - - - -
59P ASP 3.5 15.5 - - - +
60P THR* 3.4 31.4 - - - +
63P ALA* 3.6 17.9 - - + -
133P VAL* 4.1 5.2 - - + +
134P LEU* 3.8 13.2 - - + +
136P TRP* 3.9 36.3 - - + -
172P ASP 3.1 2.6 + - - +
173P ASN* 2.9 15.5 + - - +
175P THR* 1.3 78.5 - - - +
177P THR* 1.3 57.2 + - - +
179P PHE* 3.2 4.5 + - + +
180P PHE* 2.9 26.3 + - - +
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Residues in contact with THR 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ALA 4.1 6.3 - - - +
54C MET 2.7 25.6 + - - -
55C HIS* 4.4 3.5 - - - -
56C TYR 3.7 21.8 - - - +
57C THR* 4.3 2.0 - - - +
58P ALA* 3.0 37.9 - - + +
173P ASN* 2.9 27.8 + - - +
174P PRO* 3.3 12.6 + - - +
176P LEU* 1.3 75.3 - - - +
178P ARG* 1.3 62.3 + - - +
180P PHE* 3.4 4.7 + - - +
181P ALA* 3.3 19.4 + - - +
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Residues in contact with ARG 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C MET* 4.1 36.5 + - + +
55C HIS* 3.8 24.3 + - - -
62E LEU* 2.8 48.4 + - - +
63E SER 4.8 1.2 + - - -
164P TRP 2.7 26.3 + - - -
165P ALA* 3.7 18.6 - - - +
167P GLY* 3.1 18.0 + - - -
174P PRO* 3.0 24.4 + - - +
175P THR* 3.2 13.2 + - - +
177P THR* 1.3 81.1 + - - +
179P PHE* 1.3 65.8 + - + +
181P ALA* 3.3 4.9 + - - +
182P LEU* 2.9 30.7 + - + +
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Residues in contact with PHE 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PHE* 3.9 23.1 - + - -
130P VAL* 3.9 17.8 - - + +
133P VAL* 3.9 29.8 - - + -
134P LEU* 4.2 9.2 - - + -
144P ALA* 4.5 4.9 - - + -
148P THR* 3.7 26.2 - - + -
165P ALA 3.4 20.9 - - - -
175P THR* 2.8 32.8 + - + +
176P LEU* 3.5 6.7 - - + +
178P ARG* 1.3 80.8 - - + +
180P PHE* 1.3 60.2 + - - +
182P LEU* 3.5 6.3 - - + +
183P HIS* 2.7 32.4 + - - +
3001P SMA 3.6 25.1 - - + -
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Residues in contact with PHE 180 (chain P).
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 6.1 0.7 - - - -
180C PHE* 3.7 34.3 - + - -
181C ALA* 6.3 0.4 - - + -
184C PHE* 5.7 0.4 - + - -
53P ALA* 3.9 35.0 - - + -
56P TYR* 3.7 24.2 - + + -
58P ALA* 3.9 22.7 - - + -
134P LEU* 3.5 33.3 - - + +
176P LEU 2.9 15.7 + - - +
177P THR 3.8 5.6 - - - +
178P ARG 3.3 0.2 - - - -
179P PHE* 1.3 76.6 - - - +
181P ALA* 1.3 65.0 + - + +
183P HIS* 3.7 0.9 - - + +
184P PHE* 3.0 39.9 + + + +
501P HEM 4.3 8.7 - + + -
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Residues in contact with ALA 181 (chain P).
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* 5.1 4.7 - - + +
53C ALA* 4.5 18.8 - - + +
54C MET* 4.7 12.6 - - + +
180C PHE* 6.3 0.7 - - + -
184C PHE* 3.6 24.7 - - + -
177P THR 3.3 10.2 + - - +
178P ARG* 3.4 11.0 - - - +
179P PHE 3.1 0.2 - - - -
180P PHE* 1.3 80.9 - - - +
182P LEU* 1.3 64.5 + - - +
184P PHE* 3.0 4.9 + - - +
185P LEU* 2.9 24.8 + - - +
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Residues in contact with LEU 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C MET* 5.4 13.2 - - + +
130P VAL* 4.8 6.5 - - + -
178P ARG* 2.9 19.7 + - + +
179P PHE* 3.5 9.9 - - + +
181P ALA* 1.3 77.9 - - - +
183P HIS* 1.3 56.6 + - - +
185P LEU* 3.4 14.3 + - + -
186P LEU* 3.1 62.2 + - + +
3001P SMA 3.7 32.3 - - + -
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Residues in contact with HIS 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P THR* 3.0 27.0 + - + +
130P VAL* 3.6 11.6 - - + +
131P GLY* 3.1 26.2 - - - +
134P LEU* 3.8 9.6 - - + -
179P PHE 2.7 20.6 + - - +
180P PHE* 3.7 4.9 - + - +
182P LEU* 1.3 70.4 - - - +
184P PHE* 1.3 57.8 + - - +
186P LEU* 5.1 1.6 - - - -
187P PRO* 2.8 34.1 - - - +
501P HEM 2.0 90.0 + + + -
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Residues in contact with PHE 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 5.9 0.4 - + - -
181C ALA* 3.6 39.3 - - + -
184C PHE* 3.3 44.4 - + + -
185C LEU* 4.3 7.4 - - - -
188C PHE* 6.0 0.2 - + - -
50P LEU* 3.6 16.8 - - + -
53P ALA* 4.2 6.7 - - + -
180P PHE* 3.0 35.9 + + + +
181P ALA* 3.3 8.7 - - - +
183P HIS* 1.3 77.7 - - - +
185P LEU* 1.3 59.6 + - - +
187P PRO* 3.6 3.1 - - - +
188P PHE* 3.1 32.2 - + - -
501P HEM 3.3 34.0 - - + +
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Residues in contact with LEU 185 (chain P).
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* 3.9 29.4 - - + -
184C PHE* 4.4 7.2 - - + -
188C PHE* 3.4 39.5 - - + -
181P ALA 2.9 15.1 + - - +
182P LEU* 3.7 17.9 - - + +
184P PHE* 1.3 77.7 - - - +
186P LEU* 1.3 71.8 + - + +
188P PHE* 3.0 28.3 + - + +
189P ALA* 3.6 6.2 + - + +
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Residues in contact with LEU 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P THR* 4.5 13.7 - - + +
126P ALA* 4.5 11.9 - - + -
127P THR* 3.2 38.6 - - + +
130P VAL* 4.8 3.8 - - + -
182P LEU* 3.1 41.4 + - + +
185P LEU* 1.3 75.2 - - + +
187P PRO* 1.3 72.9 - - + +
189P ALA* 2.8 16.3 + - + +
190P ILE* 2.7 25.3 + - - +
3001P SMA 6.5 0.7 - - + -
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Residues in contact with PRO 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P LEU* 3.9 4.7 - - + +
46P ILE* 3.8 17.7 - - + +
127P THR* 4.1 3.6 - - + -
183P HIS 2.8 25.1 - - - +
184P PHE 3.6 1.8 - - - +
185P LEU 3.3 3.8 - - - -
186P LEU* 1.3 86.7 - - + +
188P PHE* 1.3 58.6 + - + +
190P ILE* 3.0 11.0 + - + +
191P ALA* 2.8 26.5 + - - +
501P HEM 3.2 64.2 - - + -
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Residues in contact with PHE 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.4 31.9 - - + -
188C PHE* 5.4 26.7 - + + -
46P ILE* 4.1 31.2 - - + -
50P LEU* 4.8 3.6 - - + -
184P PHE* 3.1 40.8 - + - -
185P LEU* 3.0 12.9 + - + +
187P PRO* 1.3 73.4 - - + +
189P ALA* 1.3 60.9 + - - +
190P ILE 2.9 1.6 - - - -
191P ALA* 3.6 8.3 - - + +
192P GLY* 2.7 28.2 + - - -
501P HEM 4.3 10.8 - - + -
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Residues in contact with ALA 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P THR* 5.1 3.8 - - + -
185P LEU* 3.6 6.2 + - + +
186P LEU* 2.8 29.9 + - + +
188P PHE* 1.3 75.6 - - - +
190P ILE* 1.3 60.7 + - - +
192P GLY* 4.9 1.1 - - - -
193P ILE* 2.9 41.3 + - + +
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Residues in contact with ILE 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P LEU* 3.3 24.0 - - + -
91P PHE* 4.9 1.1 - - + -
120P LEU* 3.7 22.4 - - + +
123P THR* 3.4 23.1 - - + -
124P LEU* 3.9 21.8 - - + +
127P THR* 3.5 21.8 - - - +
186P LEU 2.7 9.7 + - - +
187P PRO* 3.1 7.0 - - + +
188P PHE 2.9 0.2 - - - -
189P ALA* 1.3 75.7 - - - +
191P ALA* 1.3 67.0 + - - +
193P ILE* 3.0 6.5 + - - +
194P THR* 2.8 23.6 + - - -
501P HEM 3.7 24.0 - - + -
502P HEM 3.8 11.0 - - + -
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Residues in contact with ALA 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P LEU* 3.4 21.6 - - + +
43P MET* 5.5 6.1 - - - -
46P ILE* 4.6 9.2 - - + -
187P PRO 2.8 13.8 + - - +
188P PHE* 3.6 12.8 - - + +
190P ILE* 1.3 73.6 - - - +
192P GLY* 1.3 64.7 + - - +
194P THR* 3.3 11.0 + - - -
195P ILE* 3.3 18.3 + - - +
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Residues in contact with GLY 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188P PHE 2.7 20.0 + - - -
189P ALA* 3.9 1.8 - - - -
191P ALA* 1.3 74.0 - - - +
193P ILE* 1.3 57.1 + - - +
195P ILE* 2.8 32.4 + - - +
196P ILE* 3.3 8.7 + - - +
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Residues in contact with ILE 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P THR* 4.4 18.6 - - + +
119P ILE* 4.0 25.1 - - + +
120P LEU* 3.9 23.3 - - + -
123P THR* 4.5 10.8 - - + +
189P ALA* 2.9 24.9 - - + +
190P ILE* 3.0 6.4 + - - +
192P GLY* 1.3 75.0 - - - +
194P THR* 1.3 57.2 + - - +
196P ILE* 2.9 19.2 + - + +
197P HIS* 2.8 25.3 + - - +
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Residues in contact with THR 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P ALA* 5.4 6.7 - - + -
42P LEU* 4.0 7.9 - - + +
120P LEU* 3.5 15.7 - - - +
190P ILE 2.8 17.4 + - - -
191P ALA* 3.4 12.8 - - - -
192P GLY 3.1 0.2 - - - -
193P ILE* 1.3 77.3 - - - +
195P ILE* 1.3 60.1 + - + +
197P HIS* 3.2 7.8 - - + +
198P LEU* 3.0 43.6 + - + +
502P HEM 3.9 33.5 - - + +
3002P UQ 5.8 2.7 - - + -
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Residues in contact with ILE 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191P ALA 3.4 15.3 - - - +
192P GLY* 2.8 13.6 + - - +
194P THR* 1.3 78.7 - - + +
196P ILE* 1.3 67.4 + - + +
198P LEU* 3.5 6.3 + - + +
199P THR* 2.9 34.8 + - - +
2015P UNL 4.6 7.9 - - - +
3002P UQ 5.6 10.3 - - + -
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Residues in contact with ILE 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.3 28.0 - - + -
116P THR* 4.3 7.9 - - + -
192P GLY 4.0 10.8 - - - +
193P ILE* 2.9 21.8 + - + +
195P ILE* 1.3 80.0 - - + +
197P HIS* 1.3 62.3 + - - +
199P THR* 3.1 7.0 + - - -
200P PHE* 2.9 51.5 + - + -
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Residues in contact with HIS 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P THR* 2.9 27.9 + - + +
116P THR* 2.8 27.6 + - - +
117P GLY* 3.6 7.5 + - - -
120P LEU* 3.9 6.0 - - + +
193P ILE 2.8 12.3 + - - +
194P THR* 3.2 15.0 - - - +
196P ILE* 1.3 78.5 - - - +
198P LEU* 1.3 61.6 + - + +
200P PHE* 3.1 3.6 + - - +
201P LEU* 2.9 26.4 + - - +
502P HEM 2.0 90.8 + + + -
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Residues in contact with LEU 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P THR* 3.0 25.2 + - + +
195P ILE* 4.1 7.6 - - + +
197P HIS* 1.3 80.4 - - + +
199P THR* 1.3 57.8 + - - +
201P LEU* 3.4 13.3 - - + +
202P HIS* 2.8 47.7 + - + -
502P HEM 3.4 43.3 - - + -
2015P UNL 4.3 4.7 - - - +
3002P UQ 3.7 53.8 - - + +
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Residues in contact with THR 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PRO* 4.8 18.2 - - + +
11C LEU* 5.1 12.1 - - + -
14C MET* 6.2 2.7 - - - -
195P ILE* 2.9 30.6 + - - +
196P ILE* 3.1 9.1 + - - +
198P LEU* 1.3 75.0 - - - +
200P PHE* 1.3 69.0 + - + +
202P HIS* 3.4 14.1 + - - +
203P GLU* 3.5 15.2 + - + +
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Residues in contact with PHE 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C HIS* 4.6 8.7 - + - -
10C PRO* 4.1 32.5 - - + -
11C LEU* 4.0 22.2 - - + -
112P GLU* 3.3 44.0 - - + -
113P THR* 3.5 15.5 + - - +
116P THR* 3.9 19.3 - - + -
196P ILE* 2.9 44.2 + - + -
197P HIS 3.6 4.9 - - - +
199P THR* 1.3 78.2 - - + +
201P LEU* 1.3 65.0 + - - +
203P GLU* 3.1 24.8 + - + +
204P SER* 3.9 2.9 + - - -
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Residues in contact with LEU 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P TYR* 4.0 11.4 - - + -
113P THR* 3.3 14.3 + - + -
197P HIS 2.9 13.6 + - - +
198P LEU* 3.4 14.1 - - + +
200P PHE* 1.3 77.1 - - - +
202P HIS* 1.3 54.9 + - + +
204P SER* 2.9 9.7 + - - -
205P GLY 2.7 48.5 + - - +
206P SER* 4.6 4.7 - - - +
502P HEM 3.7 64.4 - - + +
3002P UQ 4.2 21.5 - - - +
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Residues in contact with HIS 202 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ASN 5.3 1.0 + - - -
18P SER* 3.5 30.7 - - - -
22P LEU* 3.3 25.9 - - + +
198P LEU* 2.8 29.0 + - + +
199P THR* 3.8 8.1 - - - +
200P PHE 3.3 0.6 - - - -
201P LEU* 1.3 75.3 - - + +
203P GLU* 1.3 64.9 + - - +
204P SER 3.1 1.3 + - - -
205P GLY* 3.8 10.6 + - - +
2015P UNL 4.1 14.1 + - - -
3002P UQ 2.5 41.3 + - + +
3T HIS* 3.9 18.2 + - - -
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Residues in contact with GLU 203 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PRO* 3.7 33.8 - - + +
13C LYS* 5.8 2.7 + - - -
199P THR* 3.5 13.7 + - + +
200P PHE* 3.1 20.1 + - + +
201P LEU 3.0 0.8 + - - -
202P HIS* 1.3 79.5 - - - +
204P SER* 1.3 58.1 + - - +
3T HIS* 4.8 10.4 - - - -
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Residues in contact with SER 204 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P TYR* 3.4 46.4 + - - +
113P THR* 5.1 0.3 + - - -
200P PHE 4.2 2.6 + - - -
201P LEU* 2.9 14.0 + - - -
202P HIS 4.3 0.9 - - - -
203P GLU* 1.3 82.1 - - - +
205P GLY* 1.3 58.3 + - - +
206P SER 5.0 0.5 - - - +
218P LYS* 4.8 7.3 + - - -
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Residues in contact with GLY 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P LEU* 5.8 4.7 - - - -
23P PRO 5.2 6.3 - - - -
110P TYR* 2.9 30.0 + - - -
201P LEU* 2.7 23.8 + - - +
202P HIS* 3.8 11.3 + - - -
204P SER* 1.3 74.0 + - - +
206P SER* 1.3 61.7 + - - -
218P LYS* 5.0 6.5 - - - -
3002P UQ 5.9 1.1 - - - -
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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
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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