Contacts of the helix formed by residues 177 - 213 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ASP* 3.1 28.9 - - - -
32H TYR 3.3 16.0 + - - -
33H TRP* 3.5 3.1 - - - +
34H LEU* 4.2 7.9 - - - -
176H TYR* 1.3 78.0 - - - +
178H TRP* 1.3 64.1 + - - +
180H PHE* 3.1 17.8 - - - +
181H TYR* 3.6 6.5 + - - -
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Residues in contact with TRP 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ASP* 3.3 10.3 + - + +
34H LEU* 4.9 16.4 - - + +
176H TYR 4.9 4.9 + - - -
177H GLY* 1.3 71.7 - - - -
179H SER* 1.3 58.6 + - - +
180H PHE 3.0 4.3 - - - -
181H TYR* 2.9 46.6 + + + +
182H PHE* 3.0 9.1 + - - +
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Residues in contact with SER 179 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ILE* 3.8 27.7 + - - +
27H ALA* 3.6 13.8 - - - +
30H THR* 3.2 26.2 + - - -
31H ASP* 2.9 13.3 + - - +
178H TRP* 1.3 74.3 - - - +
180H PHE* 1.3 60.1 + - - +
182H PHE* 3.1 14.9 + - - +
183H GLY 2.9 21.5 + - - -
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Residues in contact with PHE 180 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C MET* 5.1 7.0 - - + -
531C PHE* 5.8 3.4 - + - -
27H ALA* 5.5 2.2 - - - -
31H ASP 2.8 7.6 + - - +
32H TYR* 3.8 26.4 - - + +
153H ILE* 3.6 31.2 - - + -
156H TYR* 4.8 11.2 - + - -
157H ILE* 3.9 26.7 - - + -
176H TYR* 3.7 29.2 - + + -
177H GLY 3.1 9.9 - - - +
179H SER* 1.3 72.7 - - - +
181H TYR* 1.3 93.8 + + - +
183H GLY* 2.7 22.2 + - - -
184H ALA* 3.0 17.5 + - + +
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Residues in contact with TYR 181 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C TYR* 4.1 22.0 + - - -
527C MET* 4.3 21.4 - - + +
176H TYR* 4.6 12.1 - + + +
177H GLY 3.6 5.1 + - - -
178H TRP* 2.9 36.9 + + + +
180H PHE* 1.3 103.0 - + - +
182H PHE* 1.3 57.0 + - - +
184H ALA* 3.9 7.2 - - + +
185H LEU* 2.9 33.6 + - - +
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Residues in contact with PHE 182 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LEU* 4.0 20.4 - - + +
26H ILE* 5.4 4.9 - - + -
178H TRP 3.0 6.9 + - - +
179H SER* 3.1 26.0 - - - +
180H PHE 3.0 0.4 - - - -
181H TYR* 1.3 77.7 - - - +
183H GLY* 1.3 55.0 + - - +
185H LEU* 4.0 8.1 - - - +
186H SER* 2.9 28.6 + - - -
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Residues in contact with GLY 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H MET* 5.3 1.1 - - - -
27H ALA* 3.8 20.8 - - - +
149H ASN* 5.7 1.6 - - - +
153H ILE* 4.7 6.4 - - - +
179H SER 2.9 6.5 + - - -
180H PHE 2.7 15.3 + - - -
182H PHE* 1.3 69.2 - - - +
184H ALA* 1.3 63.0 + - - -
186H SER* 3.2 8.4 + - - -
187H PHE* 2.9 21.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 184 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C PHE* 3.5 33.7 - - + -
153H ILE* 4.1 16.7 - - + +
180H PHE* 3.0 16.7 + - + +
181H TYR* 3.9 11.7 - - + +
183H GLY* 1.3 75.3 - - - +
185H LEU* 1.3 62.2 + - - +
187H PHE* 2.9 16.7 + - - +
188H ILE* 2.9 18.7 + - + +
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Residues in contact with LEU 185 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H TYR 2.9 19.0 + - - +
182H PHE* 4.0 6.5 - - - +
184H ALA* 1.3 75.5 - - - +
186H SER* 1.3 64.0 + - - +
188H ILE* 3.1 21.4 + - + +
189H ILE* 2.9 43.4 + - + +
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Residues in contact with SER 186 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ALA* 3.3 26.3 - - - +
23H LEU* 3.5 23.5 - - - +
24H MET* 4.2 6.3 - - - -
182H PHE 2.9 20.7 + - - -
183H GLY* 3.3 9.4 - - - -
185H LEU* 1.3 76.1 - - - +
187H PHE* 1.3 63.1 + - - +
189H ILE* 3.9 2.6 - - - -
190H ALA* 2.9 25.7 + - - +
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Residues in contact with PHE 187 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C PHE* 6.5 0.4 - - + -
146H GLY* 4.7 4.5 - - - +
149H ASN* 4.0 26.0 - - + -
150H ILE* 4.2 20.9 - - + -
153H ILE* 5.1 2.2 - - + -
183H GLY 2.9 10.8 + - - +
184H ALA* 2.9 14.1 + - - +
186H SER* 1.3 74.2 - - - +
188H ILE* 1.3 57.9 + - + +
190H ALA* 3.2 8.5 - - - +
191H GLU* 2.9 34.6 + - - +
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Residues in contact with ILE 188 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C VAL* 6.1 3.4 - - + -
531C PHE* 4.2 26.5 - - + -
534C ILE* 5.1 15.5 - - + -
150H ILE* 6.3 0.4 - - + -
184H ALA* 2.9 16.0 + - + +
185H LEU* 3.1 25.1 + - + +
187H PHE* 1.3 74.4 - - + +
189H ILE* 1.3 63.7 + - + +
191H GLU* 2.7 31.6 + - + +
192H MET* 3.0 20.2 + - + +
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Residues in contact with ILE 189 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H VAL* 5.7 0.7 - - + -
16H GLY* 4.4 20.9 - - - +
19H ALA* 4.6 14.6 - - + -
20H ALA* 5.1 1.8 - - + -
185H LEU* 2.9 38.3 + - + +
186H SER* 4.1 4.9 - - - +
188H ILE* 1.3 78.6 - - + +
190H ALA* 1.3 62.8 + - - +
192H MET* 3.3 11.4 + - + +
193H VAL* 2.9 21.9 + - + +
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Residues in contact with ALA 190 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLY 5.4 0.7 - - - -
20H ALA* 3.9 14.0 - - + +
115H LEU* 4.7 7.2 - - + -
142H PHE* 2.9 48.6 - - + +
143H VAL* 6.2 0.4 - - - -
146H GLY* 5.2 6.5 - - - -
186H SER 2.9 19.4 + - - +
187H PHE* 3.2 10.3 - - - +
189H ILE* 1.3 76.7 - - - +
191H GLU* 1.3 66.6 + - + +
193H VAL* 3.0 2.5 + - - -
194H GLY 2.9 4.0 + - - -
----------------------------------------------------------
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Residues in contact with GLU 191 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C ILE* 3.9 27.6 - - + -
535C GLY* 4.8 6.7 - - - -
538C VAL* 4.3 18.2 - - + +
143H VAL* 3.5 30.4 - - - +
146H GLY* 3.0 38.9 - - - -
147H LEU* 3.8 2.7 + - - +
150H ILE* 4.7 6.6 - - + +
187H PHE 2.9 19.6 + - - +
188H ILE* 2.7 15.0 + - + +
190H ALA* 1.3 70.8 - - - +
192H MET* 1.3 64.3 + - + +
194H GLY* 3.0 4.8 + - - +
195H VAL* 2.9 26.1 + - - +
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Residues in contact with MET 192 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C VAL* 6.2 1.6 - - - -
188H ILE* 3.0 24.6 + - + +
189H ILE* 3.7 14.8 - - + +
191H GLU* 1.3 76.6 - - + +
193H VAL* 1.3 63.8 + - - +
195H VAL* 2.9 30.7 + - + +
196H LEU* 2.9 14.0 + - - +
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Residues in contact with VAL 193 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 4.6 10.3 - - - +
13H THR* 5.0 11.5 + - + +
16H GLY* 4.3 20.0 - - - -
142H PHE* 3.5 18.4 - - + -
189H ILE 2.9 14.2 + - - +
190H ALA* 3.3 9.2 - - - +
192H MET* 1.3 76.1 - - - +
194H GLY* 1.3 57.9 + - - +
196H LEU* 3.4 7.6 + - - +
197H ALA* 2.9 26.9 + - - +
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Residues in contact with GLY 194 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C VAL* 5.6 0.7 - - - -
139H GLY 5.2 0.4 - - - -
142H PHE* 3.2 21.0 - - - -
143H VAL* 3.8 18.2 - - - -
190H ALA 2.9 11.3 + - - -
191H GLU 3.0 4.2 + - - -
193H VAL* 1.3 74.1 - - - +
195H VAL* 1.3 64.0 + - - +
197H ALA* 3.0 6.1 + - - +
198H VAL* 2.9 29.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C VAL* 3.9 31.0 - - + -
541C PHE* 5.1 8.1 - - + -
573C ILE* 4.6 29.8 - - + -
191H GLU 2.9 13.8 + - - +
192H MET* 2.9 26.8 + - + +
194H GLY* 1.3 75.3 - - - +
196H LEU* 1.3 64.0 + - - +
198H VAL* 3.3 8.8 - - - +
199H HIS* 2.9 31.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H GLN* 5.1 10.1 - - + +
12H LEU* 5.0 15.3 - - + -
13H THR* 5.3 7.6 - - - +
192H MET 2.9 11.9 + - - +
193H VAL* 3.7 9.6 - - - +
195H VAL* 1.3 76.7 - - - +
197H ALA* 1.3 58.3 + - - +
199H HIS* 3.7 7.5 - - - +
200H MET* 2.9 29.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H THR* 5.5 11.0 + - + +
122H ILE* 6.0 5.4 - - + -
135H ILE* 5.2 8.3 - - + +
139H GLY* 4.4 17.0 - - - -
142H PHE* 5.4 2.2 - - + -
193H VAL 2.9 14.0 + - - +
194H GLY* 3.0 15.2 + - - +
196H LEU* 1.3 76.2 - - - +
198H VAL* 1.3 65.0 + - - +
200H MET* 2.9 18.0 + - - +
201H PHE* 2.9 12.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C VAL* 6.2 2.7 - - + -
541C PHE* 4.3 21.1 - - + -
542C LEU* 3.8 34.5 - - + -
545C ARG* 5.9 2.5 - - + -
135H ILE 5.9 0.9 - - - +
136H LEU* 5.2 9.4 - - + +
139H GLY* 4.7 20.4 - - - -
140H ILE* 5.2 0.9 - - + +
143H VAL* 5.3 4.9 - - + -
194H GLY 2.9 19.8 + - - +
195H VAL* 3.3 16.2 - - - +
197H ALA* 1.3 71.2 - - - +
199H HIS* 1.3 67.1 + - - +
201H PHE* 3.0 11.4 + - - +
202H ILE* 2.9 30.1 + - + +
----------------------------------------------------------
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Residues in contact with HIS 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C PHE* 5.0 16.9 - + + -
573C ILE* 6.3 3.4 - - + -
195H VAL* 2.9 24.6 + - + +
196H LEU* 3.7 8.1 - - - +
198H VAL* 1.3 79.3 - - + +
200H MET* 1.3 56.9 + - - +
202H ILE* 3.1 32.4 - - + +
203H ASP* 2.8 42.0 + - - +
----------------------------------------------------------
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Residues in contact with MET 200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H GLN* 4.3 21.5 - - + -
10H MET* 5.5 4.9 - - + -
135H ILE* 6.5 0.4 - - + -
196H LEU 2.9 14.1 + - - +
197H ALA* 2.9 11.2 + - - +
199H HIS* 1.3 73.2 - - - +
201H PHE* 1.3 60.6 + - - +
203H ASP* 3.1 15.3 + - - +
204H ARG* 2.9 26.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H ILE* 4.6 11.8 - - + +
136H LEU* 3.4 42.8 - - + +
197H ALA 2.9 11.3 + - - +
198H VAL* 3.0 11.4 + - - +
200H MET* 1.3 75.9 - - - +
202H ILE* 1.3 58.2 + - - +
204H ARG* 2.9 23.7 + - - +
205H HIS* 2.9 19.5 + - + +
----------------------------------------------------------
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Residues in contact with ILE 202 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C PHE* 5.9 1.1 - - + -
545C ARG* 3.4 49.1 - - + +
546C PHE* 4.4 4.0 - - - +
548C PRO* 6.5 0.2 - - + -
571C PHE* 5.6 12.8 - - + -
136H LEU* 5.4 3.1 - - + -
198H VAL* 2.9 17.8 + - + +
199H HIS* 3.1 42.8 - - + +
201H PHE* 1.3 76.9 - - + +
203H ASP* 1.3 62.7 + - - +
205H HIS* 3.4 18.4 + - + +
206H LYS* 2.9 26.9 + - + +
----------------------------------------------------------
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Residues in contact with ASP 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H HIS* 2.8 38.8 + - - +
200H MET* 3.1 21.0 - - - +
202H ILE* 1.3 84.9 - - - +
204H ARG* 1.3 62.8 + - - +
206H LYS* 2.9 18.6 + - - +
207H GLN* 2.9 13.6 + - - +
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Residues in contact with ARG 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ARG* 4.5 17.3 - - + +
200H MET 2.9 10.3 + - - +
201H PHE* 2.9 12.1 + - - +
203H ASP* 1.3 73.9 - - - +
205H HIS* 1.3 64.8 + - + +
207H GLN* 3.0 9.0 + - - +
208H LEU* 2.9 32.8 + - + +
----------------------------------------------------------
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Residues in contact with HIS 205 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C PHE* 5.3 2.3 - + - -
548C PRO* 4.0 37.0 - - + +
132H HIS* 4.2 20.9 + - + +
136H LEU* 3.3 32.6 - - + +
201H PHE* 2.9 34.9 + - + +
202H ILE* 3.5 19.3 - - + +
204H ARG* 1.3 76.0 - - + +
206H LYS* 1.3 57.6 + - - +
208H LEU* 3.8 10.6 - - + +
209H ARG* 2.9 34.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 206 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H ILE* 2.9 14.0 + - + +
203H ASP* 2.9 15.0 + - - +
205H HIS* 1.3 75.6 - - - +
207H GLN* 1.3 49.1 + - - +
209H ARG* 5.2 1.6 - - - -
210H ALA* 2.5 41.3 + - - +
----------------------------------------------------------
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Residues in contact with GLN 207 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H ASP 2.9 11.9 + - - +
204H ARG* 3.0 11.9 + - - +
206H LYS* 1.3 77.3 - - - +
208H LEU* 1.3 59.5 + - + +
210H ALA* 3.5 3.8 - - - +
211H THR* 2.9 31.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 208 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ARG* 3.8 31.6 - - + -
132H HIS* 5.4 6.7 - - + +
204H ARG* 2.9 24.4 + - + +
205H HIS* 3.8 10.5 - - - +
207H GLN* 1.3 76.9 - - + +
209H ARG* 1.3 67.1 + - - +
210H ALA 3.1 0.3 + - - -
211H THR* 3.2 3.8 + - - -
212H ALA* 2.9 22.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 209 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C PRO* 6.2 3.8 - - + -
205H HIS* 2.9 18.3 + - + +
206H LYS* 4.8 1.8 - - - +
208H LEU* 1.3 74.9 - - - +
210H ALA* 1.3 63.0 + - - +
212H ALA* 3.2 19.9 - - - +
213H ARG* 4.1 2.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 210 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H LYS 2.5 25.8 + - - +
207H GLN* 3.5 5.8 - - - +
209H ARG* 1.3 79.2 - - - +
211H THR* 1.3 60.0 + - - +
212H ALA 3.1 4.9 + - - -
213H ARG* 3.6 13.0 + - - +
----------------------------------------------------------
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Residues in contact with THR 211 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H GLN 2.9 19.6 + - - -
208H LEU* 3.6 3.8 - - - -
210H ALA* 1.3 70.9 - - - +
212H ALA* 1.3 63.9 + - - +
213H ARG 3.3 5.5 + - - -
----------------------------------------------------------
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Residues in contact with ALA 212 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208H LEU 2.9 12.6 + - - +
209H ARG* 3.2 20.0 - - - +
210H ALA 3.0 1.6 - - - -
211H THR* 1.3 79.1 - - - +
213H ARG* 1.3 65.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 213 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H ARG 4.1 2.1 + - - +
210H ALA 3.6 10.3 + - - +
211H THR 3.3 7.2 - - - -
212H ALA* 1.3 85.0 - - - +
----------------------------------------------------------
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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