Contacts of the helix formed by residues 166 - 190 (chain A) in PDB entry 3NA0
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 ASN 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A GLU 3.6 11.7 + - - -
163A ALA* 3.0 21.4 + - - +
165A LYS* 1.3 86.7 - - - +
167A PHE* 1.3 63.0 + - - +
168A LEU 3.2 0.7 + - - -
169A PRO* 3.4 17.1 - - - +
170A LEU* 4.1 11.3 - - - +
298A TYR* 3.4 54.5 - - + +
304A ARG* 3.4 16.5 - - - +
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Residues in contact with PHE 167 (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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157A GLU 3.5 22.7 - - - -
158A VAL* 4.0 4.5 - - - -
163A ALA 4.2 6.5 - - - -
164A THR* 3.0 41.2 + - + +
166A ASN* 1.3 78.0 - - - +
168A LEU* 1.3 65.5 + - - +
170A LEU* 3.0 6.7 + - - +
171A LEU* 2.9 39.8 + - + +
213A VAL* 4.0 18.4 - - + -
298A TYR* 3.3 29.4 - + - -
301A ILE* 3.8 21.8 - - + -
467A ILE* 3.5 31.2 - - + -
470A LEU* 4.2 10.3 - - + -
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A THR 4.1 3.1 - - - +
165A LYS* 3.4 20.6 - - + +
166A ASN 3.2 0.2 - - - -
167A PHE* 1.3 75.8 - - - +
169A PRO* 1.4 65.5 - - + +
171A LEU* 3.3 0.7 + - - -
172A ASP* 2.9 30.9 + - - +
367A MET* 4.5 11.7 - - + -
368A ALA* 3.6 39.0 - - + +
371A LEU* 3.6 17.3 - - + -
470A LEU* 3.7 38.4 - - + -
474A ILE* 3.9 14.1 - - + +
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Residues in contact with PRO 169 (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 LYS 4.2 3.4 - - - +
166A ASN* 3.4 17.7 - - - +
168A LEU* 1.4 95.6 - - + +
170A LEU* 1.3 59.5 + - + +
172A ASP* 3.9 6.4 - - + +
173A ALA* 3.0 30.1 + - - +
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Residues in contact with LEU 170 (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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166A ASN 4.1 9.4 - - - +
167A PHE* 3.0 7.5 + - - +
169A PRO* 1.3 81.0 - - + +
171A LEU* 1.3 62.5 + - - +
173A ALA* 3.8 1.8 + - - +
174A VAL* 3.5 12.8 + - - +
212A ASN* 2.8 60.9 + - - +
213A VAL* 3.9 20.6 - - + +
216A GLY* 4.7 12.3 - - - +
298A TYR* 3.8 37.0 - - + +
299A ARG 5.5 0.4 - - - -
300A GLY* 4.9 0.4 - - - -
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Residues in contact with LEU 171 (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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167A PHE* 2.9 37.5 + - + +
168A LEU 4.0 2.2 - - - +
170A LEU* 1.3 74.2 - - - +
172A ASP* 1.3 66.2 + - - +
174A VAL* 3.1 7.9 + - - +
175A SER* 3.0 24.3 + - - +
205A PHE* 5.2 0.7 - - - -
209A SER* 3.8 31.6 - - - +
213A VAL* 3.9 17.9 - - + -
467A ILE* 4.4 9.2 - - + +
470A LEU* 3.9 13.5 - - + -
471A GLU* 3.8 39.5 - - + +
474A ILE* 4.1 13.7 - - + -
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Residues in contact with ASP 172 (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 LEU 2.9 18.0 + - - +
169A PRO* 3.9 7.6 - - + +
171A LEU* 1.3 77.4 - - - +
173A ALA* 1.3 57.0 + - - +
175A SER 3.3 0.2 + - - -
176A ARG* 2.8 55.2 + - - +
360A ARG* 5.1 4.0 + - - -
367A MET* 3.6 27.9 - - + +
474A ILE* 3.4 13.5 - - + +
478A ASN* 2.8 29.5 + - - +
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Residues in contact with ALA 173 (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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169A PRO 3.0 19.5 + - - +
170A LEU* 3.9 6.7 - - - +
171A LEU 3.3 0.2 - - - -
172A ASP* 1.3 75.7 - - - +
174A VAL* 1.3 61.4 + - - +
176A ARG* 3.6 7.7 + - - +
177A ASP* 3.2 29.5 + - - +
212A ASN* 4.7 4.0 - - - +
218A ARG* 3.8 14.6 - - - +
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Residues in contact with VAL 174 (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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170A LEU 3.5 15.7 - - - +
171A LEU 3.1 7.2 + - - +
173A ALA* 1.3 74.6 - - - +
175A SER* 1.3 59.4 + - - +
177A ASP* 3.1 6.2 + - - +
178A PHE* 2.9 24.1 + - - +
205A PHE* 3.6 15.3 - - + -
208A GLU* 3.5 33.9 - - + +
209A SER* 3.5 25.8 - - - +
212A ASN* 3.9 12.8 - - - +
218A ARG* 4.0 20.2 - - - +
222A LEU* 3.5 9.1 - - + +
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Residues in contact with SER 175 (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* 3.0 15.8 + - - +
172A ASP 3.7 1.3 - - - -
174A VAL* 1.3 76.1 - - - +
176A ARG* 1.3 61.4 + - - +
178A PHE* 3.1 5.1 + - - +
179A VAL* 3.1 26.7 + - - +
205A PHE* 3.6 18.7 - - - -
471A GLU 4.4 1.0 + - - -
474A ILE* 3.8 7.7 - - - +
475A PHE* 3.3 28.1 + - - -
478A ASN* 3.5 26.6 - - - +
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Residues in contact with ARG 176 (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 ASP* 2.8 44.6 + - - +
173A ALA* 3.9 7.4 - - - +
175A SER* 1.3 72.0 - - - +
177A ASP* 1.3 60.7 + - - +
179A VAL* 3.5 9.9 - - - +
180A SER* 3.2 26.2 + - - -
360A ARG* 5.2 10.1 - - - +
478A ASN* 3.7 21.9 + - - +
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Residues in contact with ASP 177 (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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173A ALA 3.2 9.3 + - - +
174A VAL 3.1 9.5 + - - +
176A ARG* 1.3 77.6 - - - +
178A PHE* 1.3 63.1 + - - +
180A SER* 3.2 12.8 + - - -
181A VAL* 3.0 25.6 + - - +
184A ARG* 4.7 4.6 + - - +
218A ARG* 2.7 39.7 + - - +
222A LEU* 3.9 11.7 - - + -
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Residues in contact with PHE 178 (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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174A VAL 2.9 13.0 + - - +
175A SER* 3.1 9.6 + - - +
177A ASP* 1.3 74.8 - - - +
179A VAL* 1.3 64.3 + - - +
181A VAL* 3.2 20.9 + - + +
182A LEU* 3.2 36.3 + - + +
198A ILE* 4.2 13.0 - - + -
201A ASP* 3.7 36.3 - - + -
202A LEU* 3.8 17.7 - - + -
205A PHE* 3.8 27.4 - + + -
222A LEU* 3.6 18.1 - - + +
475A PHE* 3.5 26.9 - + + -
479A MET* 3.9 12.1 - - + -
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Residues in contact with VAL 179 (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 SER 3.1 14.8 + - - +
176A ARG* 3.5 11.7 - - - +
178A PHE* 1.3 75.5 - - + +
180A SER* 1.3 63.7 + - - +
182A LEU 3.2 2.1 + - - -
183A HIS* 3.0 35.4 + - + -
478A ASN* 3.7 35.9 - - + +
479A MET* 4.2 8.1 - - + +
482A ASN* 3.5 29.2 - - - +
483A PHE* 3.5 21.3 - - + -
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Residues in contact with SER 180 (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 ARG 3.2 15.2 + - - -
177A ASP* 3.2 17.1 + - - -
179A VAL* 1.3 78.8 - - - +
181A VAL* 1.3 61.3 + - - +
183A HIS* 3.2 10.3 + - - +
184A ARG* 2.9 42.4 + - - +
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Residues in contact with VAL 181 (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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177A ASP 3.0 18.7 + - - +
178A PHE* 3.2 17.0 + - + +
180A SER* 1.3 73.0 - - - +
182A LEU* 1.3 62.6 + - + +
184A ARG* 3.1 24.9 + - - +
185A ARG* 3.0 61.0 + - - +
201A ASP* 5.3 2.9 - - + +
222A LEU* 3.2 39.7 - - + +
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Residues in contact with LEU 182 (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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178A PHE* 3.2 26.7 + - + +
179A VAL 3.2 1.5 + - - +
181A VAL* 1.3 79.3 - - + +
183A HIS* 1.3 59.7 + - - +
185A ARG* 3.1 14.4 + - - +
186A ILE* 2.9 36.2 + - + +
194A TYR* 3.9 31.1 - - + +
198A ILE* 4.4 10.1 - - + -
479A MET* 3.6 32.5 - - + -
483A PHE* 3.6 26.5 - - + -
511A PHE* 4.3 21.1 - - + -
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Residues in contact with HIS 183 (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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179A VAL* 3.0 36.2 + - + +
180A SER* 3.6 10.3 - - - +
182A LEU* 1.3 74.7 - - - +
184A ARG* 1.3 63.3 + - + +
186A ILE* 3.3 12.0 + - - +
187A LYS* 3.1 23.6 + - - +
482A ASN* 3.1 31.9 + - - -
483A PHE* 3.6 19.3 - + - -
513A PRO* 4.9 12.3 - - + +
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Residues in contact with ARG 184 (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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177A ASP* 4.7 4.2 + - - +
180A SER* 2.9 26.6 + - - +
181A VAL* 3.3 33.6 - - - +
183A HIS* 1.3 75.1 - - + +
185A ARG* 1.3 58.9 + - + +
187A LYS* 3.3 9.6 + - + +
188A LYS* 2.9 30.8 + - - +
222A LEU* 3.9 23.2 + - - +
223A GLU* 4.6 10.9 + - - -
224A GLU* 4.0 36.6 - - - +
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Residues in contact with ARG 185 (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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181A VAL* 3.0 36.7 + - + +
182A LEU* 3.1 13.0 + - - +
184A ARG* 1.3 78.1 - - + +
186A ILE* 1.3 55.7 + - - +
188A LYS* 3.9 12.4 - - + +
189A ALA* 3.0 28.9 + - - +
194A TYR* 3.4 55.6 + - + -
198A ILE* 4.3 3.2 - - - +
201A ASP* 2.9 44.8 + - - +
204A ARG* 4.7 2.6 - - - +
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Residues in contact with ILE 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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182A LEU* 2.9 19.7 + - + +
183A HIS* 3.6 12.1 - - - +
184A ARG 3.2 0.2 - - - -
185A ARG* 1.3 73.1 - - - +
187A LYS* 1.3 66.8 + - - +
189A ALA* 3.2 12.0 + - - +
190A GLY* 3.3 9.7 + - - -
191A SER 4.3 2.4 + - - -
192A GLY* 3.8 9.8 + - - -
193A ASN 3.3 32.0 - - - +
194A TYR* 3.6 18.2 - - + -
483A PHE* 3.8 29.6 - - + -
511A PHE* 4.3 7.9 - - + +
513A PRO* 3.9 31.0 - - + -
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Residues in contact with LYS 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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183A HIS 3.1 13.0 + - - +
184A ARG* 3.5 10.8 - - + +
186A ILE* 1.3 77.6 - - - +
188A LYS* 1.3 61.1 + - - +
190A GLY* 3.3 14.9 + - - -
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Residues in contact with LYS 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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184A ARG 2.9 17.5 + - - +
185A ARG* 3.9 12.6 - - + +
187A LYS* 1.3 76.6 - - - +
189A ALA* 1.3 62.2 + - - +
190A GLY* 3.4 0.9 + - - -
200B ASP* 5.8 1.8 + - - -
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Residues in contact with ALA 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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185A ARG 3.0 19.3 + - - +
186A ILE 3.2 1.3 + - - +
188A LYS* 1.3 76.2 - - - +
190A GLY* 1.3 63.1 + - - +
191A SER* 3.3 7.2 + - - +
193A ASN 3.4 23.3 - - - +
194A TYR* 4.9 7.6 - - + -
197B ASP* 4.6 3.8 - - - +
506B PRO* 3.4 17.7 - - - +
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Residues in contact with GLY 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 ILE 3.3 6.6 + - - -
187A LYS 3.3 10.0 + - - -
188A LYS 3.3 3.9 - - - -
189A ALA* 1.3 78.2 - - - +
191A SER* 1.3 58.2 + - - +
192A GLY 3.8 1.6 - - - -
505B LYS* 4.7 3.3 - - - +
506B PRO* 3.1 21.7 - - - +
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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