Contacts of the helix formed by residues 185 - 218 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 4.1 9.0 - - + +
183A SER* 2.5 39.9 + - - +
184A ASN* 1.3 75.4 - - - +
186A GLY* 1.3 69.5 + - - +
187A TRP* 3.4 30.1 - - + +
188A CYS* 3.1 26.1 + - + +
189A ARG* 3.2 15.6 + - - +
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASN 3.9 2.0 + - - -
185A VAL* 1.3 78.3 - - - +
187A TRP* 1.3 60.9 + - - +
188A CYS 3.3 0.2 + - - -
189A ARG* 3.5 18.0 + - - +
190A LEU* 3.4 17.3 + - - +
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Residues in contact with TRP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 5.6 0.7 - - + -
175A THR* 3.2 49.6 - - + -
180A VAL* 5.0 16.4 - - + -
185A VAL* 3.4 33.7 - - + +
186A GLY* 1.3 74.0 - - - +
188A CYS* 1.3 67.4 + - + +
189A ARG 3.4 0.2 - - - -
190A LEU* 3.4 21.2 + - + +
191A VAL* 3.4 30.0 + - + +
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Residues in contact with CYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A MET* 3.6 23.2 - - + +
180A VAL* 3.8 19.5 - - + -
181A HIS* 4.7 0.2 - - - -
185A VAL* 3.1 20.4 + - + +
187A TRP* 1.3 92.3 - - + +
189A ARG* 1.3 61.5 + - - +
190A LEU 3.4 0.3 + - - -
191A VAL* 3.6 5.1 + - - +
192A THR* 3.3 19.6 + - - -
258A CYS* 2.0 52.0 - - - -
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASN* 3.4 34.5 + - - +
185A VAL 3.2 14.4 + - - +
186A GLY* 4.0 16.0 - - - +
187A TRP 3.4 0.2 - - - -
188A CYS* 1.3 74.1 - - - +
190A LEU* 1.3 60.0 + - - +
192A THR* 3.9 2.4 - - - -
193A ALA* 3.0 28.6 + - - +
251A LEU* 5.8 1.8 - - - +
255A ASN* 3.9 23.4 + - - +
258A CYS* 3.5 29.8 - - + -
259A TRP* 3.5 44.0 - - + +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLY 3.4 10.9 + - - +
187A TRP* 3.4 19.0 + - + +
188A CYS 3.2 0.6 - - - -
189A ARG* 1.3 78.5 - - - +
191A VAL* 1.3 62.2 + - + +
193A ALA* 3.3 7.7 + - + +
194A ALA* 2.8 33.1 + - + +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 4.3 7.1 - - + +
171A VAL* 3.9 26.9 - - + -
172A VAL* 3.6 28.7 - - + +
175A THR* 4.9 0.7 - - - +
176A MET* 4.8 7.4 - - + -
187A TRP* 3.4 36.7 + - + +
188A CYS 3.9 6.7 - - - +
189A ARG 3.4 0.2 - - - -
190A LEU* 1.3 77.3 - - + +
192A THR* 1.3 60.5 + - - +
194A ALA* 3.6 6.2 - - - +
195A TYR* 2.8 29.3 + - - +
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 5.6 2.4 - - - +
176A MET* 4.3 8.3 - - - +
188A CYS 3.3 9.8 + - - -
189A ARG 3.9 4.7 - - - -
190A LEU 3.3 0.2 - - - -
191A VAL* 1.3 77.3 - - - +
193A ALA* 1.3 59.0 + - - +
195A TYR* 3.7 6.3 - - + +
196A ASN* 2.8 50.9 + - - +
246A TRP* 4.2 4.5 - - + -
258A CYS* 2.9 31.1 + - - +
259A TRP* 3.9 17.3 - - - +
260A ALA* 4.0 14.8 - - + +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ARG 3.0 19.4 + - - +
190A LEU* 3.5 10.1 - - + +
192A THR* 1.3 75.8 - - - +
194A ALA* 1.3 58.0 + - - +
196A ASN* 3.8 2.0 - - - +
197A TYR* 2.9 29.3 + - - +
243A ILE* 4.1 15.9 - - + +
246A TRP* 3.9 22.2 - - + -
259A TRP* 4.4 9.2 - - + -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 4.8 8.1 - - + -
190A LEU* 2.8 20.0 + - + +
191A VAL* 3.6 8.1 - - - +
193A ALA* 1.3 75.4 - - - +
195A TYR* 1.3 65.1 + - - +
197A TYR* 3.2 11.0 + - + +
198A PHE* 3.0 38.0 + - + -
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Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG* 2.9 76.3 + - + +
168A THR* 3.8 27.1 - - + +
169A TRP* 3.3 36.5 - + + -
172A VAL* 4.1 18.4 - - + -
191A VAL 2.8 22.1 + - - +
192A THR* 3.7 7.2 - - + +
194A ALA* 1.3 74.8 - - - +
196A ASN* 1.3 68.4 + - - +
198A PHE* 3.5 4.3 + - - +
199A HIS 3.4 5.7 + - - -
352A GLU* 5.4 2.4 + - - -
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Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG* 4.9 0.2 - - - +
192A THR* 2.8 34.6 + - - +
193A ALA 4.0 4.0 - - - +
195A TYR* 1.3 82.9 - - - +
197A TYR* 1.3 65.6 + - - +
199A HIS* 3.3 11.6 + - - +
200A VAL* 3.3 25.1 + - - +
243A ILE* 3.9 11.9 - - + -
246A TRP* 3.3 28.0 - - + -
259A TRP 5.0 0.4 + - - -
272A TYR* 2.9 36.0 + - + -
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA 2.9 19.8 + - - +
194A ALA* 3.2 9.4 + - + +
196A ASN* 1.3 77.0 - - - +
198A PHE* 1.3 92.1 + + - +
200A VAL* 3.2 6.3 + - - +
201A THR* 3.0 33.6 + - - -
236A TRP* 3.1 38.5 + + - +
239A PRO* 3.5 32.1 - - + -
240A PHE* 3.9 24.6 - + + +
243A ILE* 3.7 17.7 - - + +
1202A OLA 4.8 11.7 - - + +
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA 4.6 3.4 - - - +
164A LEU* 3.5 46.2 - - + -
165A ARG* 3.7 21.8 - - + -
168A THR* 3.2 30.5 - - + -
194A ALA* 3.0 27.4 + - + -
195A TYR* 3.7 6.5 - - - +
196A ASN 3.3 0.2 - - - -
197A TYR* 1.3 105.8 - + - +
199A HIS* 1.3 53.9 + - - +
201A THR* 3.2 8.6 + - - -
202A ASN* 2.7 38.1 + - - +
236A TRP* 4.5 5.8 - + - -
1202A OLA 4.1 19.5 - - + -
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Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG* 3.4 46.7 + - - +
195A TYR 3.4 3.5 + - - +
196A ASN* 3.3 15.4 + - - +
197A TYR 3.1 0.4 - - - -
198A PHE* 1.3 76.6 - - - +
200A VAL* 1.3 64.2 + - - +
201A THR 3.3 0.2 + - - -
202A ASN* 3.3 21.8 + - - +
203A PHE* 3.5 17.8 + + - -
272A TYR* 4.7 10.4 + - + -
273A GLN* 6.0 3.9 + - - +
276A MET* 4.2 18.5 - - + +
327A TYR* 2.3 46.0 + + - -
355A GLN* 5.7 0.2 + - - -
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASN 3.3 15.3 - - - +
197A TYR 3.2 7.4 + - - +
199A HIS* 1.3 76.7 - - - +
201A THR* 1.3 62.5 + - - +
203A PHE* 3.5 1.4 + - - +
204A PHE* 3.0 48.6 + - + -
239A PRO* 3.6 29.6 - - + -
242A ILE* 3.8 11.0 - - + -
243A ILE* 4.2 10.8 - - + -
272A TYR* 4.0 32.1 - - + +
276A MET* 4.0 13.2 - - + -
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 3.5 18.8 - - + -
197A TYR* 3.0 32.7 + - - -
198A PHE* 3.2 13.8 - - - -
200A VAL* 1.3 76.5 - - - +
202A ASN* 1.3 56.7 + - - +
204A PHE* 2.8 3.3 + - - +
205A TRP* 2.7 59.5 + - + +
235A GLY 3.4 14.8 + - - +
236A TRP* 3.7 13.6 - - + -
239A PRO* 4.0 4.9 - - - +
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Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 4.2 1.7 - - - +
161A ALA* 3.6 23.6 - - - +
162A PHE* 3.2 44.4 - - + -
165A ARG* 3.2 27.2 - - - +
198A PHE 2.7 22.2 + - - +
199A HIS* 3.4 13.3 - - + +
201A THR* 1.3 74.4 - - - +
203A PHE* 1.3 62.5 + - + +
205A TRP* 3.6 1.4 + - - -
206A MET* 3.0 35.7 + - - +
355A GLN* 4.9 3.6 + - - -
1204A 1Q5 4.7 4.0 - - + +
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A HIS* 3.5 14.3 + + - +
200A VAL 3.8 7.4 - - - +
201A THR 3.2 0.6 - - - -
202A ASN* 1.3 80.2 - - + +
204A PHE* 1.3 60.8 + - + +
206A MET* 3.2 7.0 + - - +
207A PHE* 2.7 34.3 + - - +
276A MET* 3.1 62.4 - - + -
277A ALA* 5.2 0.7 - - - -
279A VAL* 3.7 8.6 - - + +
280A LEU* 4.2 21.1 - - + -
327A TYR* 3.7 25.8 - + - -
1204A 1Q5 3.3 51.9 - + + +
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 3.0 38.7 + - + +
201A THR* 2.8 5.1 + - - +
203A PHE* 1.3 82.8 - - + +
205A TRP* 1.3 58.5 + - - +
207A PHE* 3.3 9.3 - + - +
208A GLY* 3.2 16.5 + - - -
234A ILE* 3.3 47.6 - - + +
235A GLY* 4.3 9.0 - - - +
238A VAL* 3.5 25.1 - - + -
239A PRO* 4.2 2.5 - - + -
242A ILE* 3.7 18.4 - - + -
275A PRO* 4.1 18.2 - - + -
276A MET* 4.4 3.4 - - - -
279A VAL* 3.5 31.2 - - + -
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Residues in contact with TRP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 5.4 2.7 - - + -
154A ILE* 3.9 32.8 - - + -
157A ASN* 3.5 37.2 - - + -
158A LEU* 3.5 25.4 - - + +
161A ALA* 4.3 2.5 - - + -
201A THR* 2.7 42.3 + - + +
202A ASN 4.3 0.2 - - - +
204A PHE* 1.3 70.3 - - - +
206A MET* 1.3 60.5 + - - +
207A PHE 3.2 1.3 - - - -
208A GLY* 3.2 6.3 + - - -
209A GLU* 3.1 22.7 + - - +
231A PHE* 3.7 42.4 - + + -
232A ILE* 4.0 9.2 - - + -
235A GLY* 3.3 16.5 - - - -
236A TRP* 2.9 43.7 - + - +
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Residues in contact with MET 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 3.8 26.2 - - + -
162A PHE* 4.3 12.6 - - + -
202A ASN 3.0 24.5 + - - +
203A PHE 3.4 4.9 - - - +
205A TRP* 1.3 74.4 - - - +
207A PHE* 1.3 62.1 + - - +
208A GLY 3.1 0.4 - - - -
209A GLU* 3.3 7.5 + - - +
210A GLY 2.9 22.5 + - - -
283A ASN* 3.5 9.9 + - - -
319A LEU* 3.7 26.2 - - + -
323A LEU* 3.8 19.7 - - + -
359A VAL* 4.4 9.4 - - + -
362A PHE* 4.8 3.4 - - + -
1204A 1Q5 3.9 51.8 - - + +
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PHE 2.7 14.8 + - - +
204A PHE* 3.3 10.8 - + - +
206A MET* 1.3 78.8 - - - +
208A GLY* 1.3 57.7 + - - +
210A GLY 3.3 0.2 + - - -
211A CYS* 2.8 61.2 + - - -
234A ILE* 3.9 33.9 - - + -
279A VAL* 3.5 34.3 - - + -
282A ILE* 3.7 41.3 - - + -
283A ASN* 4.3 12.6 - - - +
286A PHE* 4.2 5.8 - + - -
1204A 1Q5 4.5 0.2 - - - +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.1 7.0 - - - -
204A PHE 3.2 7.7 + - - -
205A TRP* 3.2 10.6 + - - -
206A MET 3.1 0.6 - - - -
207A PHE* 1.3 81.0 - - - +
209A GLU* 1.3 56.9 + - - +
211A CYS* 3.3 0.6 + - - -
212A TYR* 2.9 29.8 + - - +
231A PHE* 3.3 34.7 - - - -
234A ILE* 6.0 0.7 - - - -
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG 4.4 0.2 - - - +
154A ILE* 3.2 21.5 - - + +
155A HIS* 2.9 42.8 + - - -
158A LEU* 3.6 27.0 - - + +
205A TRP 3.1 10.2 + - - +
206A MET* 3.3 12.1 + - - +
208A GLY* 1.3 75.0 - - - +
210A GLY* 1.3 58.3 + - - +
212A TYR* 4.0 6.8 - - - +
213A LEU* 3.1 28.9 + - - +
362A PHE* 3.8 13.1 - - + -
363A ALA* 5.4 1.6 - - - +
366A LEU* 3.8 12.8 - - - +
1204A 1Q5 4.4 12.6 - - + -
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Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A MET 2.9 10.7 + - - -
207A PHE 3.7 1.1 - - - -
208A GLY 3.2 0.2 - - - -
209A GLU* 1.3 76.3 - - - +
211A CYS* 1.3 65.5 + - - +
213A LEU* 3.6 1.0 - - - +
214A HIS* 2.9 28.1 + - - +
283A ASN* 3.3 25.1 - - - -
286A PHE* 4.3 2.0 - - - -
1204A 1Q5 3.4 18.9 - - - +
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Residues in contact with CYS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE* 2.8 60.7 + - - +
208A GLY* 3.7 4.3 - - - +
210A GLY* 1.3 75.7 - - - +
212A TYR* 1.3 65.3 + - - +
214A HIS* 3.7 0.9 - - - +
215A THR* 3.2 31.8 + - + +
226A LEU* 5.1 2.0 - - + -
231A PHE* 4.0 15.3 - - + -
234A ILE* 5.5 4.0 - - - -
286A PHE* 3.9 17.9 - - - -
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Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.4 18.2 - - + -
151A ARG* 3.0 49.3 + - + +
154A ILE* 3.7 23.3 - - + -
155A HIS* 6.0 1.8 - + - -
208A GLY 2.9 17.1 + - - +
209A GLU* 4.0 9.4 - - - +
211A CYS* 1.3 78.6 - - - +
213A LEU* 1.3 66.0 + - - +
215A THR* 3.0 17.8 + - - -
216A ALA* 3.1 16.8 + - + +
222A LEU* 3.3 38.2 - - + +
223A THR* 5.7 0.4 - - + -
226A LEU* 3.8 19.1 - - + -
231A PHE* 4.4 2.2 - + + -
1159A ASP* 5.3 0.3 + - - -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLU 3.1 16.7 + - - +
210A GLY 3.6 2.7 - - - +
212A TYR* 1.3 83.9 - - - +
214A HIS* 1.3 64.2 + - - +
216A ALA* 3.2 7.6 + - + +
217A ILE* 3.0 44.0 + - + +
287A LEU* 5.6 0.7 - - + -
290A ILE* 3.8 12.3 - - + -
312A ALA* 3.8 24.2 - - + +
313A VAL* 4.9 5.2 - - + -
316A THR* 3.8 24.2 - - - +
1204A 1Q5 3.9 22.9 - - + -
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Residues in contact with HIS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLY 2.9 17.7 + - - +
211A CYS 3.7 2.4 + - - +
212A TYR 3.3 0.2 - - - -
213A LEU* 1.3 76.2 - - - +
215A THR* 1.3 62.5 + - - +
217A ILE* 3.1 2.4 + - - -
218A VAL* 2.7 68.5 + - + +
219A LEU* 4.4 17.0 - - + -
286A PHE* 3.8 49.7 - + + -
289A ASN* 3.8 23.0 + - + -
290A ILE* 3.7 21.8 - - + -
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A CYS* 3.2 16.1 + - + +
212A TYR 3.0 10.4 + - - -
214A HIS* 1.3 82.0 - - - +
216A ALA* 1.3 57.7 + - - +
219A LEU* 2.9 52.5 + - + +
220A THR* 2.6 22.7 + - - -
222A LEU* 3.9 5.6 - - - +
226A LEU* 3.2 32.2 - - + +
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR* 3.1 25.6 + - + +
213A LEU* 3.3 9.0 - - + +
214A HIS 3.1 0.2 - - - -
215A THR* 1.3 83.3 + - - +
217A ILE* 1.3 55.0 + - + +
220A THR* 3.1 17.4 - - - +
222A LEU* 4.2 21.5 - - + -
305A GLU* 2.7 28.9 - - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.0 30.9 + - + +
214A HIS 3.8 3.8 - - - +
216A ALA* 1.3 83.4 - - + +
218A VAL* 1.3 66.9 + - + +
220A THR 4.0 9.0 - - - +
290A ILE* 3.6 35.2 - - + -
293A ILE* 5.0 4.2 - - + +
294A LEU* 3.9 15.7 - - + -
298A LEU* 4.9 16.3 - - + +
305A GLU* 4.3 6.2 - - + +
309A ALA* 3.6 43.5 - - + +
313A VAL* 4.0 2.9 - - + -
1002A ASN* 5.4 1.0 + - - +
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A HIS* 2.7 52.6 + - + +
217A ILE* 1.3 77.4 - - + +
219A LEU* 1.3 65.7 + - + +
220A THR 3.0 9.5 + - - -
289A ASN* 4.3 7.0 - - - +
290A ILE* 3.9 26.0 - - + +
292A ARG* 5.9 0.2 - - - +
293A ILE* 3.9 33.6 - - + +
1002A ASN* 3.3 21.3 + - - -
1005A GLU* 4.7 0.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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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