Contacts of the helix formed by residues 186 - 211 (chain A) in PDB entry 5LUQ
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 PRO 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A MSE 5.9 0.4 - - + -
147A PHE 6.0 0.7 - - - +
150A GLY* 4.6 7.6 - - - +
151A GLU* 3.6 47.3 - - + +
154A SER* 4.9 6.5 - - - +
181A LEU 5.0 4.5 - - - +
184A VAL* 4.0 14.8 - - + -
185A HIS* 1.4 86.7 - - + +
187A SER* 1.3 65.0 + - - +
188A GLU 3.7 1.1 - - - -
189A MSE 2.9 17.7 + - + +
190A ILE 2.8 18.7 + - - -
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Residues in contact with SER 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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151A GLU* 5.3 0.4 + - - -
185A HIS 2.6 10.2 + - - -
186A PRO* 1.3 66.6 - - - +
188A GLU* 1.3 69.6 + - - +
190A ILE* 2.6 40.5 + - - +
191A ASN* 3.0 7.6 + - - -
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO 3.7 0.4 - - - -
187A SER* 1.3 86.9 + - - +
189A MSE 1.3 56.6 + - - +
191A ASN* 3.6 17.6 - - + +
192A ASN* 3.0 40.5 + - - +
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Residues in contact with MSE 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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151A GLU* 5.6 2.5 - - + -
154A SER* 2.9 41.1 - - - +
155A LYS* 4.1 17.5 - - + +
158A GLY* 4.4 15.3 - - - -
178A LEU* 5.6 3.1 - - + -
181A LEU* 3.4 29.4 - - + +
182A GLY* 6.2 0.7 - - - -
186A PRO* 2.9 26.3 + - + +
188A GLU* 1.3 75.3 - - - +
190A ILE* 1.3 66.9 + - - +
192A ASN* 4.5 5.4 - - - +
193A ALA* 2.9 46.0 + - + +
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Residues in contact with ILE 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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182A GLY* 3.2 34.5 - - - +
184A VAL 4.6 1.1 - - - +
185A HIS* 4.0 22.9 - - - +
186A PRO 2.8 10.1 + - - +
187A SER* 2.6 26.6 + - - +
189A MSE 1.3 73.4 - - - +
191A ASN* 1.3 64.7 + - - +
193A ALA* 3.9 3.3 - - - +
194A GLU* 3.0 58.1 + - + +
233A ASN* 3.5 21.5 - - + +
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Residues in contact with ASN 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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187A SER* 3.0 8.2 + - - -
188A GLU* 3.6 30.1 - - + +
190A ILE* 1.3 83.0 - - - +
192A ASN* 1.3 72.0 + - - +
194A GLU* 3.0 10.2 + - - +
195A ASN* 3.0 34.2 + - - +
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Residues in contact with ASN 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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188A GLU* 3.0 28.1 + - - +
189A MSE 4.1 5.7 - - - +
191A ASN* 1.3 80.0 - - - +
193A ALA* 1.3 62.3 + - - +
195A ASN* 3.5 8.5 + - - +
196A LEU* 2.9 40.3 + - + +
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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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162A LEU* 6.3 0.4 - - - -
178A LEU* 5.5 3.4 - - + +
181A LEU* 5.0 4.9 - - + -
182A GLY* 5.9 2.9 - - - -
189A MSE 2.9 41.6 + - + +
190A ILE* 3.9 4.5 - - - +
192A ASN* 1.3 75.3 - - - +
194A GLU* 1.3 55.8 + - + +
196A LEU* 2.7 30.9 + - - +
197A PHE* 2.9 34.3 + - + -
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Residues in contact with GLU 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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190A ILE* 3.0 33.5 + - + +
191A ASN* 3.0 12.6 + - - +
193A ALA* 1.3 76.2 - - + +
195A ASN* 1.3 64.0 + - - +
197A PHE* 3.3 20.7 + - + +
198A ARG* 4.3 4.0 + - - +
230A LEU* 3.2 25.2 - - + +
233A ASN* 3.1 16.3 - - - +
234A PHE* 2.9 66.6 + - + -
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Residues in contact with ASN 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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191A ASN* 3.0 22.8 + - - +
192A ASN* 3.9 8.1 + - - +
194A GLU* 1.3 77.4 - - - +
196A LEU* 1.3 67.1 + - + +
197A PHE 3.2 0.9 + - - -
198A ARG* 3.4 34.0 + - - +
234A PHE* 4.3 14.5 - - - -
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Residues in contact with LEU 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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162A LEU* 3.4 47.6 - - + -
192A ASN* 2.9 34.0 + - + +
193A ALA* 2.7 13.5 + - - +
195A ASN* 1.3 74.6 - - + +
197A PHE* 1.3 60.8 + - - +
198A ARG 3.2 0.6 + - - -
199A ALA* 3.4 20.2 + - - +
200A PHE* 4.0 8.7 - - + -
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Residues in contact with PHE 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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175A TYR* 5.2 4.7 - + - -
178A LEU* 3.2 63.5 - - + -
179A GLY 4.8 0.4 - - - -
182A GLY* 6.3 0.4 - - - -
193A ALA* 2.9 49.6 + - + -
194A GLU* 3.3 17.7 - - + +
195A ASN 3.1 1.0 - - - -
196A LEU* 1.3 75.4 - - - +
198A ARG* 1.3 66.0 + - - +
200A PHE* 2.8 24.7 + + + +
201A LEU* 3.0 29.0 + - + +
226A GLY* 5.1 3.8 - - - -
230A LEU* 3.4 44.0 - - + -
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Residues in contact with ARG 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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194A GLU 4.3 4.2 + - - +
195A ASN* 3.4 26.0 + - - +
197A PHE* 1.3 76.5 - - - +
199A ALA* 1.3 62.7 + - - +
201A LEU* 3.4 13.6 + - + +
202A GLY* 2.9 21.0 + - - -
234A PHE* 5.4 12.1 - - - -
240A GLU* 4.6 16.9 + - - +
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Residues in contact with ALA 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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196A LEU* 3.4 13.5 + - + +
197A PHE 3.0 1.2 + - - -
198A ARG* 1.3 79.6 - - - +
200A PHE* 1.3 70.7 + - + +
202A GLY* 3.1 2.1 + - - -
203A GLU* 2.9 31.6 + - + +
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Residues in contact with PHE 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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161A ALA* 3.7 28.7 - - + -
162A LEU* 4.7 15.9 - - + -
171A LEU* 5.2 4.5 - - + -
174A VAL* 4.3 14.1 - - + -
175A TYR* 3.1 45.8 - + + +
178A LEU* 4.3 16.6 - - + -
196A LEU* 4.0 17.0 - - + -
197A PHE* 2.8 19.1 + + + +
199A ALA* 1.3 75.1 - - + +
201A LEU* 1.3 65.7 + - + +
203A GLU* 3.0 20.2 + - - +
204A LEU* 3.0 29.8 + - - +
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Residues in contact with LEU 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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175A TYR* 6.1 1.6 - - + -
197A PHE* 3.0 34.7 + - + +
198A ARG* 3.5 12.1 - - + +
200A PHE* 1.3 76.7 - - + +
202A GLY* 1.3 58.8 + - - +
204A LEU* 4.0 0.7 - - - +
205A LYS* 2.9 37.3 + - + +
223A CYS* 4.3 19.6 - - - +
227A LEU* 3.9 46.0 - - + +
230A LEU* 6.0 0.7 - - + -
240A GLU* 3.4 28.3 - - + +
244A THR* 6.0 5.2 - - + -
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Residues in contact with GLY 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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198A ARG 2.9 14.8 + - - -
199A ALA 3.6 2.9 - - - -
201A LEU* 1.3 75.6 - - - +
203A GLU* 1.3 58.0 + - - +
205A LYS* 4.8 2.9 - - - -
206A THR* 2.1 46.0 + - - -
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Residues in contact with GLU 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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171A LEU* 5.5 1.9 - - - +
175A TYR* 3.9 6.2 + - - -
199A ALA* 2.9 23.9 + - + +
200A PHE* 3.0 33.5 + - - +
202A GLY* 1.3 74.1 - - - +
204A LEU* 1.3 59.5 + - + +
206A THR* 3.8 2.0 + - - -
207A GLN* 2.5 38.7 + - - +
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Residues in contact with LEU 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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171A LEU* 5.2 3.6 - - + -
175A TYR* 3.0 39.3 - - + +
200A PHE 3.0 16.9 + - - +
203A GLU* 1.3 86.6 - - + +
205A LYS* 1.3 58.4 + - - +
207A GLN* 3.2 27.4 - - - +
208A MSE 2.9 37.3 + - + +
219A VAL* 3.5 21.8 - - + +
220A LEU* 5.9 0.4 - - + -
223A CYS* 3.4 37.2 - - + -
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Residues in contact with LYS 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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201A LEU* 2.9 20.7 + - + +
202A GLY* 4.4 1.6 - - - +
204A LEU* 1.3 73.6 - - - +
206A THR* 1.3 65.7 + - + +
207A GLN 3.0 4.0 - - - -
208A MSE 2.8 39.9 + - + +
209A THR* 3.1 12.9 + - + +
240A GLU* 4.7 6.6 + - + +
243A GLN* 2.3 54.4 + - - +
244A THR* 4.1 21.8 - - + -
247A GLU* 4.4 16.2 - - - +
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Residues in contact with THR 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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202A GLY* 2.1 39.7 + - - +
203A GLU* 3.8 2.6 + - - -
205A LYS* 1.3 81.8 - - + +
207A GLN* 1.3 59.1 + - - +
209A THR* 2.7 24.6 + - + +
210A SER* 3.8 6.1 + - - -
211A ALA* 4.6 1.9 + - - +
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Residues in contact with GLN 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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168A ASP* 5.7 1.4 + - - -
171A LEU* 6.2 0.6 - - - +
203A GLU 2.5 25.6 + - - +
204A LEU* 3.2 36.5 - - - +
205A LYS 3.0 0.2 - - - -
206A THR* 1.3 76.1 + - - +
208A MSE 1.3 63.5 + - - +
209A THR 3.1 2.9 + - - -
210A SER 3.6 0.2 + - - -
211A ALA* 3.3 36.1 + - + -
212A VAL* 3.7 16.1 + - + +
216A LYS* 3.9 32.3 + - - +
219A VAL* 4.9 11.3 - - - +
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Residues in contact with MSE 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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204A LEU* 2.9 34.4 + - + +
205A LYS* 2.8 41.6 + - + +
207A GLN* 1.3 74.6 - - - +
209A THR* 1.3 62.3 + - + +
212A VAL* 4.0 18.6 - - + +
213A ARG 4.9 4.2 - - - +
214A GLU 5.8 1.7 - - - -
215A PRO* 5.5 8.5 - - + -
216A LYS 6.3 0.2 - - - +
220A LEU* 3.5 34.1 - - + -
223A CYS* 5.0 3.4 - - - -
224A LEU* 4.9 8.1 - - + -
244A THR* 5.2 9.6 - - + +
247A GLU* 3.7 26.7 - - - +
248A ILE* 5.5 1.8 - - - -
251A PHE* 4.1 27.0 - - + -
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Residues in contact with THR 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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205A LYS* 3.1 16.5 + - + +
206A THR* 2.7 32.5 + - + +
207A GLN 3.1 0.2 - - - -
208A MSE 1.3 84.5 - - + +
210A SER* 1.3 65.2 + - - +
212A VAL 4.3 4.3 - - - +
213A ARG* 5.4 2.1 - - - +
247A GLU* 4.7 14.6 - - - +
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Residues in contact with SER 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 THR 3.8 3.6 + - - -
207A GLN 3.6 0.6 + - - -
209A THR* 1.3 89.1 + - - +
211A ALA* 1.3 69.1 + - - +
212A VAL 3.3 7.4 + - - +
213A ARG* 4.6 3.5 + - - +
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Residues in contact with ALA 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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206A THR 4.6 1.8 + - - +
207A GLN* 3.3 28.3 + - + +
210A SER* 1.3 78.4 - - - +
212A VAL* 1.3 59.2 + - + +
213A ARG* 4.3 1.4 + - - +
216A LYS* 5.9 1.6 - - - +
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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