Contacts of the helix formed by residues 166 - 191 (chain N) in PDB entry 5A31
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 166 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92N TRP* 5.6 10.5 - - + +
164N ALA* 3.3 18.2 - - + +
165N ALA* 1.3 92.9 - - - +
167N ARG* 1.3 65.6 + - - +
168N THR* 3.3 26.0 - - + +
169N PHE* 4.0 4.7 - - + -
170N GLN* 3.2 22.3 + - - +
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Residues in contact with ARG 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1765A GLN* 3.9 27.9 - - - +
1769A ASP* 5.4 1.8 + - - -
166N PRO* 1.3 73.8 - - - +
168N THR* 1.3 62.1 + - + +
170N GLN* 3.8 5.2 - - - +
171N GLU* 2.9 37.0 + - + +
174N GLN* 5.2 0.2 + - - -
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Residues in contact with THR 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166N PRO* 3.6 17.1 - - + +
167N ARG* 1.3 78.8 - - + +
169N PHE* 1.3 64.5 + - - +
171N GLU* 3.3 7.2 + - - +
172N MET* 2.9 34.3 + - - +
175N ARG* 5.3 0.5 + - - -
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Residues in contact with PHE 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162N PHE* 4.1 18.8 - + - -
165N ALA* 2.9 39.0 - - + +
166N PRO* 3.7 4.6 + - + -
167N ARG 3.4 0.4 - - - -
168N THR* 1.3 78.2 + - - +
170N GLN* 1.3 70.1 + - + +
172N MET* 3.3 11.9 + - + +
173N ILE* 3.0 44.2 + - + +
256N VAL* 3.8 31.6 - - + -
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Residues in contact with GLN 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165N ALA* 4.6 12.6 - - + -
166N PRO 3.2 18.1 + - - +
167N ARG* 3.9 6.1 - - - +
169N PHE* 1.3 82.6 - - + +
171N GLU* 1.3 56.3 + - - +
173N ILE* 3.1 20.2 - - + +
174N GLN* 3.0 49.2 + - - +
256N VAL 4.5 2.8 - - - +
259N GLU* 3.9 25.7 + - - +
260N ALA* 4.0 18.0 + - - -
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Residues in contact with GLU 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167N ARG* 2.9 26.8 + - + +
168N THR* 3.5 6.3 - - - +
170N GLN* 1.3 69.5 - - - +
172N MET* 1.3 67.2 + - - +
174N GLN* 3.2 25.7 + - - +
175N ARG* 3.0 48.8 + - - +
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Residues in contact with MET 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168N THR* 2.9 21.8 + - - +
169N PHE* 3.3 16.1 + - + +
171N GLU* 1.3 74.2 - - - +
173N ILE* 1.3 63.8 + - - +
175N ARG* 3.2 30.9 + - - +
176N LEU* 3.0 46.1 + - + +
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Residues in contact with ILE 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N PHE* 3.0 34.7 + - + +
170N GLN* 3.1 33.7 - - + +
172N MET* 1.3 75.6 - - - +
174N GLN* 1.3 61.7 + - - +
176N LEU* 3.5 7.5 + - + +
177N TYR* 3.1 48.2 + - + +
243N LEU* 6.2 1.1 - - + -
247N LEU* 5.3 4.5 - - + -
256N VAL* 3.9 39.5 - - + +
257N SER* 4.2 2.7 - - - -
260N ALA* 3.9 14.8 - - + +
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Residues in contact with GLN 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170N GLN* 3.0 48.3 + - - +
171N GLU* 3.2 33.5 - - - +
172N MET 3.3 0.2 - - - -
173N ILE* 1.3 75.3 - - - +
175N ARG* 1.3 63.9 + - + +
177N TYR 3.2 1.6 + - - -
178N GLY* 3.1 9.9 + - - -
260N ALA* 4.2 11.7 - - - -
263N THR* 4.0 21.1 + - + +
264N THR* 3.1 31.8 - - + +
267N GLN* 5.1 7.3 + - - +
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Residues in contact with ARG 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N THR 5.3 0.2 + - - -
171N GLU* 3.0 39.9 + - - +
172N MET* 3.6 34.1 - - - +
174N GLN* 1.3 80.7 - - + +
176N LEU* 1.3 68.1 + - + +
178N GLY* 3.5 1.1 + - - -
179N CYS* 3.2 32.8 + - - -
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Residues in contact with LEU 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172N MET* 3.0 41.6 + - + +
173N ILE* 3.9 8.7 - - + +
174N GLN 3.2 0.2 - - - -
175N ARG* 1.3 82.2 - - + +
177N TYR* 1.3 64.4 + - + +
179N CYS* 3.5 5.4 + - - +
180N PHE* 3.0 27.3 + - - +
240N PHE* 3.5 23.8 - - + -
243N LEU* 5.8 6.5 - - + -
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Residues in contact with TYR 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173N ILE* 3.1 45.5 + - + +
174N GLN 3.2 2.9 + - - +
176N LEU* 1.3 80.7 - - + +
178N GLY* 1.3 59.0 + - - +
180N PHE* 3.3 20.3 + + - +
181N LEU* 2.8 29.2 + - - +
240N PHE* 6.0 0.4 - + - -
243N LEU* 4.0 29.3 - - + +
244N SER* 4.1 12.5 + - - -
247N LEU* 4.3 7.5 - - + +
253N LEU* 5.3 1.0 - - - +
257N SER* 3.5 18.7 - - - -
260N ALA* 4.8 3.4 - - + -
261N VAL* 3.3 32.3 - - + -
264N THR* 4.2 16.4 - - + +
299N TRP* 3.8 17.9 - + + -
303N VAL* 4.3 16.2 - - + +
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Residues in contact with GLY 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174N GLN 3.1 13.4 + - - -
175N ARG* 4.0 2.9 - - - -
177N TYR* 1.3 75.2 - - - +
179N CYS* 1.3 57.2 + - - +
181N LEU* 3.2 4.3 + - - +
182N ARG* 2.9 42.3 + - - +
264N THR* 3.9 9.0 - - - +
268N VAL* 4.3 18.5 - - - +
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Residues in contact with CYS 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175N ARG* 3.2 26.6 + - - +
176N LEU* 3.8 7.4 - - + +
178N GLY* 1.3 73.6 - - - +
180N PHE* 1.3 59.0 + - - +
182N ARG* 3.5 32.8 + - - +
183N VAL* 2.9 38.6 + - + +
232N TRP* 5.1 15.3 - - + +
240N PHE* 4.6 5.6 - - + -
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Residues in contact with PHE 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176N LEU 3.0 14.4 + - - +
177N TYR* 3.3 26.2 - + - +
179N CYS* 1.3 75.9 - - - +
181N LEU* 1.3 54.2 - - - +
183N VAL* 3.3 5.3 + - - +
184N TYR* 3.0 24.6 + - + -
237N LEU* 5.1 2.1 - - + +
240N PHE* 3.2 56.5 - + + -
243N LEU* 5.7 0.7 - - + -
244N SER* 4.3 16.6 - - - -
299N TRP* 2.1 53.3 - + - -
302N LYS* 4.1 33.0 - - + -
303N VAL* 3.8 17.7 - - + -
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Residues in contact with LEU 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N TYR 2.8 16.7 + - - +
178N GLY* 3.2 11.0 + - - +
180N PHE* 1.3 69.8 - - - +
182N ARG* 1.3 65.9 + - - +
184N TYR* 3.0 3.5 + - + +
185N MET* 3.0 43.5 + - + +
264N THR* 5.4 4.0 - - - +
265N LEU* 4.7 25.1 - - + +
268N VAL* 4.2 23.3 - - + -
292N TRP* 5.6 0.2 - - + -
296N VAL* 4.8 11.7 - - + -
299N TRP* 3.1 55.6 - - + +
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Residues in contact with ARG 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N GLY* 2.9 25.5 + - - +
179N CYS* 3.8 31.5 - - - +
181N LEU* 1.3 73.2 - - - +
183N VAL* 1.3 56.3 + - + +
185N MET* 3.6 6.0 + - - +
186N GLN* 2.8 29.6 + - - +
189N ARG* 4.4 14.9 + - - +
232N TRP* 4.2 24.0 - - - -
268N VAL* 5.0 9.4 - - + +
271N GLU* 4.4 25.1 + - - +
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Residues in contact with VAL 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179N CYS* 2.9 28.2 + - + +
180N PHE* 3.5 7.4 - - - +
181N LEU 3.1 0.2 - - - -
182N ARG* 1.3 75.9 - - + +
184N TYR* 1.3 63.5 + - - +
186N GLN* 3.1 8.9 + - + +
187N SER* 2.9 22.5 + - - -
190N LYS* 5.2 2.5 + - - +
232N TRP* 5.0 15.9 - - + +
233N CYS* 5.2 10.5 - - - -
234N ARG 5.2 1.1 - - - +
236N ALA* 4.1 24.7 - - + -
237N LEU* 3.4 33.0 - - + -
240N PHE* 5.3 0.9 - - + -
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Residues in contact with TYR 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N PHE* 3.0 14.4 + - + +
181N LEU 3.0 7.4 + - - +
183N VAL* 1.3 77.2 - - - +
185N MET* 1.3 77.6 + - - +
187N SER* 3.0 26.5 + - - -
188N LYS* 2.9 49.9 + - + +
237N LEU* 4.6 7.2 - - + -
295N ARG 3.8 14.8 - - - -
298N GLY* 4.2 9.6 + - - -
299N TRP* 3.8 27.1 - + + -
302N LYS* 4.0 41.2 - - + +
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Residues in contact with MET 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N LEU* 3.0 33.2 + - + +
182N ARG* 4.0 5.4 - - - +
184N TYR* 1.3 93.8 - - - +
186N GLN* 1.3 50.9 + - - +
188N LYS* 3.3 5.9 + - + +
189N ARG* 2.8 50.4 + - - +
268N VAL* 6.3 0.2 - - + -
292N TRP* 3.9 32.8 - - + +
295N ARG* 3.6 48.9 - - + +
296N VAL* 4.4 7.9 - - - -
299N TRP* 5.5 0.2 - - - -
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Residues in contact with GLN 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N ARG 2.8 19.0 + - - +
183N VAL* 3.1 11.0 + - + +
185N MET* 1.3 76.4 - - - +
187N SER* 1.3 56.8 + - - +
189N ARG* 3.2 41.5 + - - +
190N LYS* 3.0 44.9 + - - +
233N CYS* 4.8 15.7 - - - -
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Residues in contact with SER 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N VAL 2.9 12.1 + - - -
184N TYR* 3.0 18.6 + - - -
186N GLN* 1.3 73.7 - - - +
188N LYS* 1.3 71.7 + - - +
190N LYS* 3.3 32.9 - - - +
191N GLY* 3.2 16.3 + - - -
237N LEU* 4.6 15.6 - - - +
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Residues in contact with LYS 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N TYR* 2.9 55.0 + - + +
185N MET* 3.3 9.1 + - + +
187N SER* 1.3 84.4 + - - +
189N ARG* 1.3 57.5 + - - +
191N GLY* 3.1 27.7 + - - +
295N ARG* 4.1 48.5 + - + +
298N GLY* 5.5 2.0 - - - -
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Residues in contact with ARG 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182N ARG* 4.4 20.9 + - - +
185N MET* 2.8 31.0 + - - +
186N GLN* 3.2 47.2 - - - +
188N LYS* 1.3 69.6 - - - +
190N LYS* 1.3 67.3 + - - +
191N GLY 3.8 5.2 - - - +
212N TYR* 6.4 0.2 - - - -
272N ARG* 5.4 17.8 - - - +
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Residues in contact with LYS 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N VAL* 5.2 2.8 + - - +
186N GLN* 3.0 29.7 + - - +
187N SER* 3.3 37.4 - - - +
189N ARG* 1.3 76.5 - - - +
191N GLY* 1.3 63.4 + - - +
233N CYS* 5.3 9.7 - - - +
234N ARG* 4.8 26.7 - - - +
237N LEU* 5.2 5.5 - - - +
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Residues in contact with GLY 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N SER 3.2 6.6 + - - -
188N LYS* 3.1 22.8 + - - -
189N ARG 3.8 5.4 - - - +
190N LYS* 1.3 83.3 - - - +
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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
------------------------------------------------------------
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