Contacts of the helix formed by residues 177 - 213 (chain F) in PDB entry 5VOT
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 GLY 177 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ASP* 3.1 30.3 - - - -
32F TYR 3.3 15.7 + - - -
33F TRP* 3.5 3.5 - - - +
34F LEU* 4.2 7.2 - - - -
176F TYR* 1.3 78.4 - - - +
178F TRP* 1.3 62.1 + - - +
180F PHE* 3.1 21.7 - - - +
181F TYR* 3.6 6.7 + - - -
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Residues in contact with TRP 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ASP* 3.3 9.6 + - + +
34F LEU* 4.9 16.4 - - + +
176F TYR 4.9 5.8 + - - -
177F GLY* 1.3 72.3 - - - -
179F SER* 1.3 59.6 + - - +
180F PHE 3.0 4.3 - - - -
181F TYR* 2.9 45.4 + + + +
182F PHE* 3.0 9.2 + - - +
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Residues in contact with SER 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ILE* 3.8 29.0 - - - +
27F ALA* 3.6 13.4 - - - +
30F THR* 3.2 27.1 + - - -
31F ASP* 2.9 13.3 + - - +
178F TRP* 1.3 75.3 - - - +
180F PHE* 1.3 59.2 + - - +
182F PHE* 3.1 13.8 + - - +
183F GLY 2.9 21.1 + - - -
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Residues in contact with PHE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A MET* 5.1 7.2 - - + -
531A PHE* 5.8 3.6 - + - -
27F ALA* 5.5 1.6 - - - -
31F ASP 2.8 7.3 + - - +
32F TYR* 3.8 25.3 - - + +
153F ILE* 3.6 31.6 - - + +
156F TYR* 4.8 11.7 - + - -
157F ILE* 3.9 26.5 - - + -
176F TYR* 3.7 27.8 - + + -
177F GLY 3.1 10.3 - - - +
179F SER* 1.3 73.5 - - - +
181F TYR* 1.3 94.6 + + - +
183F GLY* 2.7 22.5 + - - +
184F ALA* 3.0 15.9 + - + +
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Residues in contact with TYR 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A TYR* 4.1 22.2 + - - -
527A MET* 4.3 21.1 - - + +
176F TYR* 4.6 13.2 - - + +
177F GLY 3.6 4.9 + - - -
178F TRP* 2.9 36.9 + + + +
180F PHE* 1.3 104.0 - + - +
182F PHE* 1.3 56.9 + - - +
184F ALA* 3.9 7.8 - - + +
185F LEU* 2.9 32.8 + - - +
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Residues in contact with PHE 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 4.0 19.4 - - + +
26F ILE* 5.4 5.2 - - + -
27F ALA 5.4 0.4 - - - +
178F TRP 3.0 7.1 + - - +
179F SER* 3.1 25.6 - - - +
180F PHE 3.0 0.4 - - - -
181F TYR* 1.3 77.5 - - - +
183F GLY* 1.3 53.4 + - - +
185F LEU* 3.9 7.6 - - - +
186F SER* 2.9 28.9 + - - -
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Residues in contact with GLY 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU 4.7 0.4 - - - -
24F MET* 5.3 1.3 - - - -
27F ALA* 3.8 21.1 - - - +
149F ASN* 5.7 1.6 - - - +
153F ILE* 4.7 6.4 - - - +
179F SER 2.9 6.5 + - - -
180F PHE 2.7 14.9 + - - -
182F PHE* 1.3 69.9 - - - +
184F ALA* 1.3 64.1 + - - -
186F SER* 3.2 8.4 + - - -
187F PHE* 2.9 21.0 + - - +
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Residues in contact with ALA 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A PHE* 3.5 34.2 - - + -
153F ILE* 4.1 16.5 - - + +
180F PHE* 3.0 16.5 + - + +
181F TYR* 3.9 11.7 - - + +
183F GLY* 1.3 75.3 - - - +
185F LEU* 1.3 62.9 + - - +
187F PHE* 2.9 16.1 + - - +
188F ILE* 2.9 19.6 + - + +
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Residues in contact with LEU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F TYR 2.9 19.5 + - - +
182F PHE* 4.0 6.7 - - - +
184F ALA* 1.3 76.2 - - - +
186F SER* 1.3 63.0 + - - +
188F ILE* 3.1 19.9 + - + +
189F ILE* 2.9 43.2 + - + +
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Residues in contact with SER 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ALA* 3.3 26.1 - - - +
23F LEU* 3.5 23.6 - - - -
24F MET* 4.2 6.3 - - - -
115F LEU* 6.4 0.2 - - - -
182F PHE 2.9 20.6 + - - -
183F GLY* 3.3 9.9 - - - -
184F ALA 3.1 0.2 - - - -
185F LEU* 1.3 76.7 - - - +
187F PHE* 1.3 63.1 + - - +
189F ILE* 3.5 2.2 + - - -
190F ALA* 2.9 25.1 + - - +
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Residues in contact with PHE 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A PHE* 6.5 0.7 - - + -
146F GLY* 4.7 3.8 - - - +
149F ASN* 4.0 26.7 - - + -
150F ILE* 4.2 21.1 - - + -
153F ILE* 5.1 1.8 - - + -
183F GLY 2.9 11.0 + - - +
184F ALA* 2.9 13.2 + - - +
186F SER* 1.3 75.4 - - - +
188F ILE* 1.3 58.8 + - + +
190F ALA* 3.2 8.5 - - - +
191F GLU* 2.9 34.0 + - - +
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Residues in contact with ILE 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A VAL* 6.1 3.4 - - + -
531A PHE* 4.2 26.0 - - + -
534A ILE* 5.1 16.6 - - + -
150F ILE* 6.3 0.9 - - + -
184F ALA* 2.9 16.5 + - + +
185F LEU* 3.1 24.4 + - + +
187F PHE* 1.3 74.5 - - + +
189F ILE* 1.3 62.7 + - + +
191F GLU* 2.7 31.2 + - + +
192F MET* 3.0 20.9 + - + +
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Residues in contact with ILE 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL* 5.7 0.7 - - + -
16F GLY* 4.4 20.4 - - - +
19F ALA* 4.6 14.4 - - + -
20F ALA* 5.1 1.8 - - + +
185F LEU* 2.9 37.2 + - + +
186F SER* 4.1 4.0 - - - +
188F ILE* 1.3 79.0 - - + +
190F ALA* 1.3 62.2 + - - +
192F MET* 3.3 12.3 + - + +
193F VAL* 2.9 22.3 + - + +
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Residues in contact with ALA 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLY 5.4 0.4 - - - -
20F ALA* 3.9 13.4 - - + +
115F LEU* 4.7 7.0 - - + -
142F PHE* 2.9 49.4 - - + +
143F VAL* 6.2 0.4 - - - -
146F GLY* 5.2 6.3 - - - -
186F SER 2.9 19.8 + - - +
187F PHE* 3.2 10.1 - - - +
189F ILE* 1.3 77.5 - - - +
191F GLU* 1.3 66.0 + - + +
193F VAL* 3.0 2.5 + - - -
194F GLY 2.9 4.7 + - - -
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Residues in contact with GLU 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ILE* 3.9 27.8 - - + -
535A GLY* 4.8 6.5 - - - -
538A VAL* 4.3 18.8 - - + +
143F VAL* 3.5 29.5 - - - +
146F GLY* 3.0 38.2 - - - -
147F LEU* 3.8 2.8 + - - +
150F ILE* 4.7 6.6 - - + +
187F PHE 2.9 19.2 + - - +
188F ILE* 2.7 15.2 + - + +
190F ALA* 1.3 71.4 - - - +
192F MET* 1.3 64.3 + - + +
194F GLY* 3.0 4.5 + - - -
195F VAL* 2.9 25.9 + - - +
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Residues in contact with MET 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 6.2 1.6 - - - -
188F ILE* 3.0 23.2 + - + +
189F ILE* 3.7 15.0 - - + +
191F GLU* 1.3 76.8 - - + +
193F VAL* 1.3 63.4 + - - +
195F VAL* 2.9 29.7 + - + +
196F LEU* 2.9 14.7 + - - +
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 4.6 10.3 - - - +
13F THR* 5.0 11.1 + - + +
16F GLY* 4.3 19.5 - - - -
142F PHE* 3.5 19.3 - - + -
189F ILE* 2.9 14.9 + - + +
190F ALA* 3.0 8.7 + - - +
192F MET* 1.3 76.2 - - - +
194F GLY* 1.3 57.2 + - - +
196F LEU* 3.4 7.4 + - - +
197F ALA* 2.9 27.5 + - - +
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Residues in contact with GLY 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A VAL* 5.6 0.7 - - - -
139F GLY 5.2 0.7 - - - -
142F PHE* 3.2 21.4 - - - -
143F VAL* 3.8 17.3 - - - -
190F ALA 2.9 10.5 + - - -
191F GLU 3.0 4.0 + - - -
193F VAL* 1.3 74.8 - - - +
195F VAL* 1.3 64.4 + - - +
197F ALA* 3.0 6.4 + - - +
198F VAL* 2.9 30.0 + - - +
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Residues in contact with VAL 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 3.9 31.0 - - + -
541A PHE* 5.1 8.7 - - + -
573A ILE* 4.6 29.4 - - + -
191F GLU 2.9 14.5 + - - +
192F MET* 2.9 26.8 + - + +
194F GLY* 1.3 76.9 - - - +
196F LEU* 1.3 63.8 + - - +
198F VAL* 3.3 9.2 - - - +
199F HIS* 2.9 31.9 + - + +
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLN* 5.1 10.3 - - + +
12F LEU* 5.0 15.9 - - + -
13F THR* 5.3 7.6 - - - +
192F MET 2.9 11.1 + - - +
193F VAL* 3.7 10.1 - - - +
195F VAL* 1.3 76.9 - - - +
197F ALA* 1.3 57.7 + - - +
199F HIS* 3.7 6.6 - - - +
200F MET* 2.9 30.3 + - - +
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Residues in contact with ALA 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F THR* 5.5 10.1 - - + +
122F ILE* 6.0 5.4 - - + -
135F ILE* 5.3 8.1 - - - +
139F GLY* 4.4 17.7 - - - -
142F PHE* 5.4 2.2 - - + -
193F VAL 2.9 14.7 + - - +
194F GLY* 3.0 13.9 + - - +
196F LEU* 1.3 75.8 - - - +
198F VAL* 1.3 64.9 + - - +
200F MET* 2.9 18.1 + - - +
201F PHE* 2.9 12.5 + - - +
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Residues in contact with VAL 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A VAL* 6.2 2.9 - - + -
541A PHE* 4.3 21.3 - - + -
542A LEU* 3.8 34.8 - - + +
545A ARG* 5.9 3.1 - - + -
135F ILE 6.0 0.4 - - - -
136F LEU* 5.2 9.6 - - + +
139F GLY* 4.7 20.6 - - - +
140F ILE* 5.2 0.9 - - + +
143F VAL* 5.3 4.5 - - + -
194F GLY 2.9 20.8 + - - +
195F VAL* 3.3 16.4 - - - +
197F ALA* 1.3 71.7 - - - +
199F HIS* 1.3 66.8 + - - +
201F PHE* 3.0 9.7 + - - +
202F ILE* 2.9 29.8 + - + +
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Residues in contact with HIS 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PHE* 5.0 17.6 - + + -
573A ILE* 6.2 3.8 - - + -
195F VAL* 2.9 23.8 + - + +
196F LEU* 3.7 8.3 - - - +
198F VAL* 1.3 78.6 - - + +
200F MET* 1.3 57.4 + - - +
202F ILE* 3.1 31.8 - - + +
203F ASP* 2.8 42.5 + - - +
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Residues in contact with MET 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLN* 4.3 20.4 - - + -
10F MET* 5.5 6.1 - - + -
135F ILE* 6.5 0.7 - - + -
196F LEU 2.9 13.6 + - - +
197F ALA* 2.9 11.5 + - - +
199F HIS* 1.3 74.3 - - - +
201F PHE* 1.3 60.8 + - - +
203F ASP* 3.1 15.1 + - - +
204F ARG* 2.9 26.7 + - - +
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Residues in contact with PHE 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F HIS 5.7 0.2 - - - +
135F ILE* 4.6 12.2 - - + +
136F LEU* 3.4 42.6 - - + +
197F ALA 2.9 11.6 + - - +
198F VAL* 3.0 11.4 + - - +
200F MET* 1.3 76.1 - - - +
202F ILE* 1.3 58.4 + - - +
204F ARG* 2.9 25.0 + - - +
205F HIS* 2.9 18.7 + - + +
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Residues in contact with ILE 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PHE* 5.9 1.6 - - + -
545A ARG* 3.4 47.6 - - + +
546A PHE* 4.5 3.4 - - - +
548A PRO* 6.5 0.2 - - + -
571A PHE* 5.6 12.3 - - + -
136F LEU* 5.4 4.3 - - + -
198F VAL* 2.9 17.4 + - + +
199F HIS* 3.1 44.2 - - + +
201F PHE* 1.3 76.9 - - + +
203F ASP* 1.3 65.0 + - - +
205F HIS* 3.5 19.1 - - + +
206F LYS* 2.9 26.7 + - + +
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Residues in contact with ASP 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F HIS* 2.8 37.9 + - - +
200F MET* 3.1 20.4 + - - +
201F PHE 3.1 0.2 - - - -
202F ILE* 1.3 84.1 - - - +
204F ARG* 1.3 63.2 + - - +
206F LYS* 2.9 19.0 + - - +
207F GLN* 2.9 13.2 + - - +
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Residues in contact with ARG 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ARG* 4.5 16.8 - - + +
200F MET 2.9 9.9 + - - +
201F PHE* 2.9 12.6 + - - +
203F ASP* 1.3 75.0 - - - +
205F HIS* 1.3 63.2 + - + +
207F GLN* 3.0 9.7 + - - +
208F LEU* 2.9 32.8 + - + +
----------------------------------------------------------
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Residues in contact with HIS 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A PHE* 5.3 2.5 - + - -
548A PRO* 4.0 37.7 - - + +
132F HIS* 4.2 21.0 + - + +
136F LEU* 3.3 31.4 - - + +
201F PHE* 2.9 34.9 + - + +
202F ILE* 3.5 20.2 - - + +
203F ASP 3.2 0.2 - - - -
204F ARG* 1.3 76.0 - - + +
206F LYS* 1.3 58.9 + - - +
208F LEU* 3.8 10.4 - - + +
209F ARG* 2.9 36.7 + - + +
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Residues in contact with LYS 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F ILE* 2.9 14.6 + - + +
203F ASP* 2.9 16.3 + - - +
205F HIS* 1.3 76.8 - - - +
207F GLN* 1.3 49.2 + - - +
209F ARG* 5.2 1.6 - - - -
210F ALA* 2.5 41.9 + - - +
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Residues in contact with GLN 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F ASP 2.9 11.5 + - - +
204F ARG* 3.0 11.6 + - - +
206F LYS* 1.3 77.5 - - - +
208F LEU* 1.3 60.4 + - + +
210F ALA* 3.6 3.3 - - - +
211F THR* 2.9 32.1 + - - -
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Residues in contact with LEU 208 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ARG* 3.8 32.5 - - + -
132F HIS* 5.4 5.8 - - + -
204F ARG* 2.9 23.5 + - + +
205F HIS* 3.8 11.0 - - - +
207F GLN* 1.3 79.0 - - + +
209F ARG* 1.3 67.6 + - - +
210F ALA 3.1 0.3 + - - -
211F THR* 3.2 3.9 + - - -
212F ALA* 2.9 22.5 + - - +
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Residues in contact with ARG 209 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A PRO* 6.2 3.8 - - + -
205F HIS 2.9 18.5 + - - +
206F LYS* 4.8 1.8 - - - +
208F LEU* 1.3 74.0 - - - +
210F ALA* 1.3 63.8 + - - +
212F ALA* 3.2 21.1 - - - +
213F ARG* 4.1 2.8 + - - +
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Residues in contact with ALA 210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F LYS 2.5 25.8 + - - +
207F GLN* 3.6 5.6 - - - +
208F LEU 3.1 0.2 - - - -
209F ARG* 1.3 78.3 - - - +
211F THR* 1.3 59.3 + - - +
212F ALA 3.1 4.3 + - - -
213F ARG* 3.7 12.8 + - - +
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Residues in contact with THR 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F GLN 2.9 18.6 + - - -
208F LEU* 3.6 3.8 - - - -
210F ALA* 1.3 74.1 - - - +
212F ALA* 1.3 63.6 + - - +
213F ARG 3.3 5.9 + - - -
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Residues in contact with ALA 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F LEU 2.9 13.0 + - - +
209F ARG* 3.2 20.2 - - - +
210F ALA 3.0 1.0 - - - -
211F THR* 1.3 78.8 - - - +
213F ARG* 1.3 65.6 + - - +
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Residues in contact with ARG 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F ARG 4.1 2.1 + - - +
210F ALA 3.7 9.9 + - - +
211F THR 3.3 6.8 - - - -
212F ALA* 1.3 83.5 - - - +
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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