Contacts of the helix formed by residues 185 - 218 (chain C) in PDB entry 4Z9G
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 VAL 185 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C VAL* 6.3 0.7 - - + -
183C SER* 2.8 37.8 + - - +
184C ASN* 1.3 75.6 - - - +
186C GLY* 1.3 69.1 + - - +
187C TRP* 3.3 33.7 - - + +
188C CYS* 3.1 9.6 + - + +
189C ARG* 3.1 20.0 + - - +
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Residues in contact with GLY 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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117B HIS* 5.5 9.2 - - - -
121B ILE* 3.4 25.1 - - - +
184C ASN 3.7 1.0 + - - -
185C VAL* 1.3 78.0 - - - +
187C TRP* 1.3 56.7 + - - +
189C ARG* 3.4 13.5 + - - +
190C LEU* 3.0 23.3 + - - +
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Residues in contact with TRP 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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171C VAL* 6.4 1.3 - - + -
174C LEU 5.5 13.2 - - - -
180C VAL* 4.5 25.4 - - + -
185C VAL* 3.5 27.3 - - + +
186C GLY* 1.3 73.4 - - - +
188C CYS* 1.3 73.4 + - + +
190C LEU* 3.3 14.7 + - + +
191C VAL* 3.3 41.0 + - + +
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Residues in contact with CYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 3.7 29.6 - - + -
181C HIS* 5.2 0.9 - - - -
183C SER 4.4 3.8 - - - +
185C VAL* 3.1 14.2 + - + +
187C TRP* 1.3 93.1 - - + +
189C ARG* 1.3 61.8 + - - +
190C LEU 3.6 0.2 + - - -
191C VAL* 3.8 4.6 + - - +
192C THR* 3.3 21.1 + - - -
258C CYS* 2.0 49.8 - - - +
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Residues in contact with ARG 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B HIS* 4.5 26.8 + - - +
118B VAL* 4.7 13.7 - - - +
121B ILE* 3.6 14.8 - - + +
184C ASN* 2.7 48.3 + - - +
185C VAL* 3.1 8.2 + - - +
186C GLY* 3.5 22.1 - - - +
188C CYS* 1.3 77.5 - - - +
190C LEU* 1.3 61.2 + - - +
192C THR* 3.2 7.6 + - - -
193C ALA* 3.1 18.9 + - - +
255C ASN* 4.3 13.3 + - - +
258C CYS* 4.2 8.3 - - - -
259C TRP* 3.3 55.5 - - + +
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Residues in contact with LEU 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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121B ILE* 3.9 26.2 - - + +
124B TYR* 3.5 37.7 - - + -
125B LEU* 4.1 27.6 - - + -
128B CYS* 6.2 0.2 - - - -
186C GLY 3.0 15.2 + - - +
187C TRP* 3.3 18.4 + - + +
189C ARG* 1.3 77.1 - - - +
191C VAL* 1.3 59.7 + - + +
193C ALA* 3.0 9.7 + - + +
194C ALA* 2.9 27.1 + - + +
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Residues in contact with VAL 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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168C THR* 4.1 9.8 - - + +
171C VAL* 4.5 18.2 - - + -
172C VAL* 3.6 36.8 - - + +
187C TRP* 3.3 30.0 + - + +
188C CYS* 4.1 6.3 - - - +
189C ARG 3.4 0.4 - - - -
190C LEU* 1.3 79.1 - - + +
192C THR* 1.3 58.9 + - - +
194C ALA* 3.4 6.5 + - - +
195C TYR* 2.9 28.2 + - - +
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Residues in contact with THR 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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172C VAL* 5.7 5.0 - - - +
188C CYS 3.3 9.9 + - - -
189C ARG 3.2 8.0 + - - -
190C LEU 3.2 0.4 - - - -
191C VAL* 1.3 77.0 - - - +
193C ALA* 1.3 62.2 + - - +
195C TYR* 3.9 5.1 - - + +
196C ASN* 2.3 51.9 + - - +
246C TRP* 4.2 0.2 - - + -
258C CYS* 2.9 30.7 + - - +
259C TRP* 3.9 21.8 - - + +
260C ALA* 4.2 10.9 - - + +
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Residues in contact with ALA 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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121B ILE* 4.7 7.2 - - + -
125B LEU* 4.3 18.2 - - + -
189C ARG 3.1 11.5 + - - +
190C LEU* 3.0 15.8 + - + +
192C THR* 1.3 77.0 - - - +
194C ALA* 1.3 57.6 + - - +
196C ASN* 3.7 2.4 - - - +
197C TYR* 2.8 29.7 + - - +
243C ILE* 4.2 9.3 - - + +
246C TRP* 4.0 19.7 - - + -
247C ALA* 6.4 0.4 - - + -
259C TRP* 4.5 9.4 - - + -
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Residues in contact with ALA 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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125B LEU* 4.1 17.2 - - + +
168C THR* 5.0 3.8 - - + -
190C LEU* 2.9 13.4 + - + +
191C VAL* 3.7 10.1 - - - +
193C ALA* 1.3 74.5 - - - +
195C TYR* 1.3 55.4 + - - +
197C TYR* 3.0 9.8 + - + +
198C PHE* 2.7 54.5 + - + -
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Residues in contact with TYR 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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127C HIS* 5.5 0.9 + - - -
165C ARG* 2.5 51.5 + - + -
168C THR* 3.7 21.9 - - + +
169C TRP* 3.7 42.6 - + + +
172C VAL* 3.5 26.5 - - + -
191C VAL 2.9 17.9 + - - +
192C THR* 3.9 5.4 - - - +
194C ALA* 1.3 76.4 - - - +
196C ASN* 1.3 66.9 + - - +
198C PHE* 3.3 8.2 + - - +
199C HIS* 3.0 27.3 + + + +
352C GLU* 5.6 1.7 + - - -
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Residues in contact with ASN 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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192C THR* 2.3 53.7 + - - +
193C ALA* 3.7 3.8 - - - +
195C TYR* 1.3 80.0 - - - +
197C TYR* 1.3 65.9 + - - +
199C HIS* 3.0 18.6 + - - +
200C VAL* 3.0 17.8 + - - +
243C ILE* 3.9 13.9 - - + -
246C TRP* 3.5 14.5 - - + -
259C TRP 5.1 0.4 + - - -
272C TYR* 2.6 39.8 + - + -
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Residues in contact with TYR 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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125B LEU* 4.9 9.2 - - + -
129B ILE* 3.5 36.6 - - + +
193C ALA 2.8 15.8 + - - +
194C ALA* 3.2 10.3 - - - +
196C ASN* 1.3 77.0 - - - +
198C PHE* 1.3 75.8 + + - +
200C VAL* 3.1 7.5 + - - +
201C THR* 2.7 43.8 + - - -
236C TRP* 2.3 43.8 + + - -
239C PRO* 3.6 26.0 - - + -
240C PHE* 3.8 16.4 - + - -
243C ILE* 3.6 28.9 - - + +
1201C OLA 5.3 2.2 - - + -
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Residues in contact with PHE 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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161C ALA 4.8 3.4 - - - +
164C LEU* 3.4 47.8 - - + -
165C ARG* 3.9 20.9 - - + -
168C THR* 3.0 30.1 - - + -
194C ALA* 2.7 33.3 + - + -
195C TYR* 3.4 8.1 - - - +
197C TYR* 1.3 93.5 - + - +
199C HIS* 1.3 59.0 + - - +
201C THR* 3.1 10.1 + - - -
202C ASN* 2.7 33.7 + - - +
236C TRP* 4.8 3.6 - + - -
1201C OLA 4.2 21.3 - - + -
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Residues in contact with HIS 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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165C ARG* 3.2 39.4 + - - +
195C TYR* 3.0 14.2 + + + +
196C ASN* 3.0 15.0 + - - +
198C PHE* 1.3 77.2 - - - +
200C VAL* 1.3 61.2 + - - +
202C ASN* 3.4 18.5 + - + +
203C PHE* 3.6 12.2 + + - -
272C TYR* 4.9 6.9 + - + -
276C MET* 3.5 15.7 - - + +
327C TYR* 2.4 33.8 + + - -
355C GLN* 5.6 0.7 - - - -
1203C OLA 3.5 39.1 + - + +
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Residues in contact with VAL 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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196C ASN 3.0 17.4 + - - +
197C TYR* 3.5 6.1 - - - +
199C HIS* 1.3 75.7 - - - +
201C THR* 1.3 62.0 + - - +
203C PHE* 3.2 2.8 + - - +
204C PHE* 3.1 54.4 + - + -
239C PRO* 3.7 20.0 - - + -
242C ILE* 4.3 13.0 - - + -
243C ILE* 4.2 13.0 - - + -
272C TYR* 3.9 27.1 - - + +
276C MET* 4.1 17.3 - - + -
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Residues in contact with THR 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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161C ALA* 3.7 13.9 - - + -
197C TYR* 2.7 38.7 + - - -
198C PHE* 3.2 15.7 - - - -
200C VAL* 1.3 77.9 - - - +
202C ASN* 1.3 57.3 + - - +
204C PHE* 3.3 1.3 + - - +
205C TRP* 2.9 53.4 + - + +
235C GLY 3.6 15.7 + - - +
236C TRP* 3.7 18.2 - - + -
239C PRO* 4.6 2.4 - - - +
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Residues in contact with ASN 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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161C ALA* 3.4 23.1 - - - +
162C PHE* 3.1 49.2 - - + -
165C ARG* 3.2 28.6 - - - +
198C PHE 2.7 23.2 + - - +
199C HIS* 3.6 11.5 - - + +
200C VAL 3.2 0.4 - - - -
201C THR* 1.3 76.5 - - - +
203C PHE* 1.3 63.6 + - + +
205C TRP* 3.6 1.3 + - - +
206C MET* 3.1 30.5 + - - +
355C GLN* 4.3 4.2 + - - -
1205C 1Q5 4.6 7.4 - - + -
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Residues in contact with PHE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C HIS* 3.7 6.5 - + - +
200C VAL 3.2 8.5 + - - +
202C ASN* 1.3 80.0 - - + +
204C PHE* 1.3 59.2 + - + +
206C MET* 3.2 7.0 + - - +
207C PHE* 2.7 32.7 + - - +
276C MET* 3.2 65.7 - - + -
279C VAL* 3.8 5.3 - - + +
280C LEU* 4.3 15.7 - - + -
327C TYR* 3.6 31.9 - + - -
1203C OLA 4.4 8.5 - - + -
1205C 1Q5 3.4 57.6 - + + +
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Residues in contact with PHE 204 (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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200C VAL* 3.1 39.1 + - + +
201C THR 3.9 2.7 - - - +
203C PHE* 1.3 81.0 - - + +
205C TRP* 1.3 59.6 + - - +
207C PHE* 3.1 9.1 - + - +
208C GLY* 2.8 24.3 + - - -
234C ILE* 3.2 44.2 - - + +
235C GLY* 4.1 6.5 - - - -
238C VAL* 3.6 24.5 - - + -
239C PRO* 3.9 10.1 - - + -
242C ILE* 3.8 22.2 - - + -
275C PRO* 4.6 9.4 - - + -
276C MET* 4.9 2.0 - - - -
279C VAL* 3.5 32.1 - - + -
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Residues in contact with TRP 205 (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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153C ILE* 5.6 1.6 - - + -
154C ILE* 4.0 30.9 - - + +
157C ASN* 3.4 39.0 - - + -
158C LEU* 3.9 26.9 - - + +
161C ALA* 4.0 10.5 - - + -
201C THR* 2.9 38.0 + - + +
202C ASN 4.3 0.2 - - - +
204C PHE* 1.3 75.6 - - - +
206C MET* 1.3 60.7 + - - +
208C GLY* 3.8 3.6 - - - -
209C GLU* 3.1 26.9 + - - +
231C PHE* 3.4 47.3 - + + -
232C ILE* 4.1 4.5 - - + -
235C GLY* 3.5 19.4 - - - -
236C TRP* 3.4 29.8 - + - +
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Residues in contact with MET 206 (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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158C LEU* 3.9 20.4 - - + -
162C PHE* 3.9 22.0 - - + -
202C ASN 3.1 19.9 + - - +
203C PHE 3.5 4.9 - - - +
205C TRP* 1.3 73.9 - - - +
207C PHE* 1.3 60.1 + - - +
209C GLU* 3.2 9.0 - - - +
210C GLY 3.0 19.1 + - - -
283C ASN* 3.2 11.5 + - - -
319C LEU* 3.9 15.9 - - + -
323C LEU* 3.5 28.9 - - + -
359C VAL* 4.0 9.2 - - + -
362C PHE* 5.0 3.1 - - + -
1205C 1Q5 3.6 49.3 - - + +
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Residues in contact with PHE 207 (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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203C PHE 2.7 14.6 + - - +
204C PHE* 3.1 11.7 - + - +
206C MET* 1.3 73.3 - - - +
208C GLY* 1.3 56.5 + - - +
209C GLU 3.0 1.3 - - - -
210C GLY* 2.7 21.7 + - - -
211C CYS* 2.9 29.6 + - - -
234C ILE* 4.0 29.6 - - + -
279C VAL* 3.4 38.6 - - + -
282C ILE* 4.1 28.0 - - + -
283C ASN* 4.0 9.6 - - - +
286C PHE* 3.5 29.8 - + - -
1205C 1Q5 4.2 0.6 - - - +
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Residues in contact with GLY 208 (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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154C ILE* 3.9 4.1 - - - +
204C PHE 2.8 15.1 + - - -
205C TRP* 3.7 5.1 + - - -
206C MET 3.4 0.2 - - - -
207C PHE* 1.3 77.1 - - - +
209C GLU* 1.3 60.8 + - - +
211C CYS* 4.1 6.5 - - - -
212C TYR* 3.2 13.9 + - - +
231C PHE* 3.1 42.1 - - - -
234C ILE* 5.3 5.2 - - - -
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Residues in contact with GLU 209 (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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151C ARG 4.5 0.5 - - - +
154C ILE* 3.2 22.5 - - + +
155C HIS* 2.9 35.4 + - - -
158C LEU* 3.8 20.0 - - + -
205C TRP 3.1 17.7 + - - +
206C MET* 3.2 14.6 - - - +
207C PHE 3.0 0.4 - - - -
208C GLY* 1.3 78.8 - - - +
210C GLY* 1.3 60.3 + - - +
212C TYR* 3.7 8.9 + - - +
213C LEU* 3.4 20.6 + - - +
362C PHE* 5.3 6.0 - - + -
366C LEU* 4.9 6.4 - - - +
1205C 1Q5 4.3 12.2 - - + +
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Residues in contact with GLY 210 (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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206C MET 3.0 6.3 + - - -
207C PHE 2.7 14.9 + - - -
209C GLU* 1.3 71.4 - - - +
211C CYS* 1.3 56.5 + - - -
213C LEU* 3.3 2.8 + - - +
214C HIS* 2.9 30.5 + - - +
283C ASN* 3.3 22.0 - - - -
286C PHE* 4.2 3.1 - - - -
1205C 1Q5 3.4 20.4 - - - +
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Residues in contact with CYS 211 (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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207C PHE* 2.9 56.3 + - - +
208C GLY* 3.9 7.9 - - - +
210C GLY* 1.3 73.6 - - - +
212C TYR* 1.3 66.4 + - - +
214C HIS* 4.4 2.2 - - - -
215C THR* 3.2 34.1 + - + +
226C LEU* 5.2 3.4 - - + -
231C PHE* 4.4 11.2 - - + -
234C ILE* 5.4 5.8 - - + -
286C PHE* 3.8 14.6 - - + -
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Residues in contact with TYR 212 (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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150C LEU* 3.8 32.9 - - + +
151C ARG* 3.4 43.7 + - + +
154C ILE* 3.7 24.0 - - + -
208C GLY 3.2 14.9 + - - +
209C GLU* 3.7 11.9 - - - +
210C GLY 3.2 0.2 - - - -
211C CYS* 1.3 80.5 - - - +
213C LEU* 1.3 70.0 + - + +
215C THR* 3.3 3.3 + - - -
216C ALA* 3.0 32.9 + - + +
222C LEU* 4.1 19.1 - - + +
226C LEU* 4.1 15.3 - - + +
231C PHE* 4.4 2.6 - + + -
1159C ASP* 5.0 4.0 + - - -
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Residues in contact with LEU 213 (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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209C GLU* 3.4 11.9 + - - +
210C GLY* 3.3 9.2 + - - +
212C TYR* 1.3 86.1 - - + +
214C HIS* 1.3 66.8 + - - +
216C ALA* 3.1 12.1 + - + +
217C ILE* 3.2 33.1 + - + +
287C LEU* 5.6 1.8 - - + -
290C ILE* 4.1 20.4 - - + -
309C ALA* 4.6 5.2 - - + +
312C ALA* 4.1 34.8 - - + +
313C VAL* 4.3 13.9 - - + -
316C THR* 4.8 6.5 - - - +
1205C 1Q5 4.6 9.9 - - + -
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Residues in contact with HIS 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C GLY 2.9 16.8 + - - +
211C CYS* 3.8 4.9 - - - +
213C LEU* 1.3 79.0 - - - +
215C THR* 1.3 70.4 + - + +
217C ILE* 3.9 0.3 - - - +
218C VAL* 2.9 55.2 + - + +
219C LEU* 4.5 14.1 - - + -
286C PHE* 3.7 57.0 - + + -
289C ASN* 3.8 22.3 + - + -
290C ILE* 4.1 10.7 - - + +
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Residues in contact with THR 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C CYS* 3.2 17.6 + - + +
212C TYR 3.3 0.5 + - - -
214C HIS* 1.3 88.3 - - - +
216C ALA* 1.3 64.1 + - - +
217C ILE 3.3 0.2 - - - -
219C LEU* 3.2 54.5 + - + +
220C THR* 3.6 1.6 + - - -
222C LEU* 5.1 5.5 - - - +
225C ARG* 5.3 7.2 - - - +
226C LEU* 3.2 38.9 - - + +
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR* 3.0 32.4 + - + +
213C LEU* 3.4 11.7 - - + +
214C HIS 3.1 0.4 - - - -
215C THR* 1.3 78.0 + - - +
217C ILE* 1.3 64.6 + - + +
220C THR* 3.2 19.2 + - - +
222C LEU* 4.4 23.0 - - + +
305C GLU* 3.5 17.4 - - - +
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Residues in contact with ILE 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LEU* 3.2 28.7 + - + +
214C HIS 4.0 0.9 - - - +
216C ALA* 1.3 81.4 - - + +
218C VAL* 1.3 70.4 + - + +
220C THR* 3.7 13.7 - - - +
290C ILE* 3.6 30.1 - - + -
293C ILE* 3.9 18.2 - - + +
294C LEU* 4.3 13.9 - - + -
298C LEU* 3.9 29.3 - - + +
305C GLU* 5.1 2.9 - - - +
306C THR* 6.5 0.4 - - - -
309C ALA* 3.5 33.9 - - + +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C HIS* 2.9 42.1 + - + +
217C ILE* 1.3 82.6 - - + +
219C LEU* 1.3 70.8 + - + +
220C THR* 2.4 24.1 + - - +
289C ASN* 3.9 10.1 - - - +
290C ILE* 4.7 5.8 - - + -
292C ARG* 5.2 2.9 - - - +
293C ILE* 3.7 41.2 - - + +
1002C ASN* 4.3 7.3 + - - -
1005C GLU* 4.8 0.5 - - - +
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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