Contacts of the helix formed by residues 150 - 176 (chain F) in PDB entry 1NU9
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 THR 150 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F PRO 4.0 0.8 + - - +
149F PHE* 1.3 79.3 - - - +
151F ASP* 1.3 65.0 + - - +
152F GLU* 3.7 6.9 + - - +
153F MET* 3.2 29.7 + - + +
154F GLU* 2.9 17.2 + - - +
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Residues in contact with ASP 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F PHE 3.9 0.9 + - - +
150F THR* 1.3 72.7 - - - +
152F GLU* 1.3 58.5 + - - +
154F GLU* 3.3 15.5 + - - +
155F GLU* 2.9 30.1 + - - +
204F ARG* 4.9 5.9 + - - -
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Residues in contact with GLU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F THR* 3.2 7.0 + - - +
151F ASP* 1.3 79.1 - - - +
153F MET* 1.3 80.4 + - + +
155F GLU* 3.1 11.3 + - + +
156F LYS* 3.1 47.1 + - + +
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Residues in contact with MET 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F PHE* 3.6 30.9 - - + -
150F THR* 3.2 22.3 + - + +
152F GLU* 1.3 97.3 - - + +
154F GLU* 1.3 56.4 + - - +
156F LYS* 3.4 24.1 + - + +
157F ALA* 3.0 29.3 + - - +
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Residues in contact with GLU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F PHE* 3.5 22.2 - - + +
150F THR 2.9 15.8 + - - +
151F ASP* 3.7 12.8 - - - +
153F MET* 1.3 73.6 - - - +
155F GLU* 1.3 60.1 + - - +
157F ALA* 3.9 0.5 - - - +
158F THR* 2.7 44.9 + - - +
204F ARG* 2.9 56.1 + - - +
205F ILE 3.3 17.7 + - - +
206F SER* 4.4 8.9 - - - -
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Residues in contact with GLU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ASP 2.9 17.7 + - - +
152F GLU* 3.1 10.5 + - - +
154F GLU* 1.3 77.2 - - - +
156F LYS* 1.3 60.2 - - + +
158F THR* 3.8 5.3 - - - -
159F ALA* 3.0 28.4 + - + +
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Residues in contact with LYS 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F GLU* 3.1 38.5 + - + +
153F MET* 3.7 27.1 - - + +
155F GLU* 1.3 75.9 - - + +
157F ALA* 1.3 66.6 + - - +
159F ALA* 3.0 16.7 + - - +
160F ARG* 3.2 18.2 + - - +
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Residues in contact with ALA 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F PHE* 3.6 20.0 - - + -
153F MET 3.0 18.4 + - - +
154F GLU 3.9 2.5 - - - +
156F LYS* 1.3 75.5 - - - +
158F THR* 1.3 64.1 + - - +
160F ARG* 3.2 6.5 + - - +
161F VAL* 3.1 24.3 + - - +
205F ILE* 3.9 8.5 - - + -
211F GLU* 3.5 36.5 - - + +
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Residues in contact with THR 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F GLU* 2.7 37.6 + - - +
155F GLU* 3.8 6.1 - - - -
157F ALA* 1.3 71.8 - - - +
159F ALA* 1.3 56.7 + - - +
161F VAL* 3.3 1.6 + - - +
162F ASP* 2.9 45.0 + - - +
204F ARG* 5.4 1.4 - - - -
205F ILE* 3.4 33.0 + - + +
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Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F GLU* 3.0 14.3 + - + +
156F LYS* 3.0 12.1 + - - +
158F THR* 1.3 74.3 - - - +
160F ARG* 1.3 61.5 + - + +
162F ASP* 4.0 6.3 - - - +
163F ASP* 2.9 30.3 + - - +
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Residues in contact with ARG 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F LYS* 3.2 15.0 + - + +
157F ALA* 3.6 4.9 - - - +
159F ALA* 1.3 77.4 - - + +
161F VAL* 1.3 63.0 + - - +
163F ASP* 3.3 6.7 + - - +
164F LEU* 3.1 24.1 + - - +
211F GLU* 2.7 38.0 + - - +
215F ILE* 3.8 38.2 - - + +
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Residues in contact with VAL 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA 3.1 12.4 + - - +
158F THR 3.6 7.6 - - - +
160F ARG* 1.3 81.9 - - - +
162F ASP* 1.3 71.2 + - - +
164F LEU 3.4 0.2 + - - -
165F ALA* 3.0 18.7 + - - +
196F LEU* 4.0 16.2 - - + -
205F ILE* 4.0 26.7 - - + -
211F GLU* 4.5 2.2 - - + +
214F MET* 3.7 35.4 - - + -
215F ILE* 3.7 24.7 - - + -
218F LEU* 3.5 8.3 - - + +
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Residues in contact with ASP 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F THR* 2.9 36.0 + - - +
159F ALA* 4.0 6.0 - - - +
161F VAL* 1.3 82.7 - - - +
163F ASP* 1.3 60.5 + - - +
165F ALA* 3.3 6.2 + - - +
166F ASN* 2.9 42.3 + - - +
196F LEU* 4.8 10.7 - - - +
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Residues in contact with ASP 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F ALA 2.9 19.1 + - - +
160F ARG* 3.6 7.4 - - - +
161F VAL 3.2 0.2 - - - -
162F ASP* 1.3 76.1 - - - +
164F LEU* 1.3 63.2 + - - +
166F ASN* 3.0 18.9 + - - +
167F LYS* 3.0 27.0 + - - +
239F SER* 2.6 32.5 + - - -
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Residues in contact with LEU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F ARG 3.1 10.3 + - - +
161F VAL 3.7 7.6 - - - +
163F ASP* 1.3 79.1 + - - +
165F ALA* 1.3 65.1 + - - +
167F LYS* 2.9 22.4 + - + +
168F ALA* 3.0 10.8 + - - +
215F ILE* 3.6 31.2 - - + +
218F LEU* 3.5 28.7 - - + -
219F GLU* 3.7 16.4 - - + +
222F ILE* 3.5 24.9 - - + -
2004F IMD 4.3 16.6 - - + -
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Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F VAL 3.0 17.2 + - - +
162F ASP* 3.6 6.7 - - - +
164F LEU* 1.3 77.6 - - - +
166F ASN* 1.3 57.7 + - - +
168F ALA* 3.0 10.4 + - - +
169F TYR* 2.8 35.7 + - + -
192F VAL* 4.0 7.1 - - + +
196F LEU* 3.7 31.2 - - + -
218F LEU* 3.8 14.5 - - + +
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Residues in contact with ASN 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ASP* 2.9 29.6 + - - +
163F ASP* 3.0 12.9 + - - +
165F ALA* 1.3 75.1 - - - +
167F LYS* 1.3 61.5 + - - +
169F TYR* 3.3 17.1 + - - -
170F SER 3.1 14.2 + - - -
239F SER* 4.0 5.6 - - - -
240F TYR* 2.9 55.7 + - - +
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Residues in contact with LYS 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F ASP* 3.0 25.7 + - - +
164F LEU* 2.9 19.5 + - + +
166F ASN* 1.3 74.2 - - - +
168F ALA* 1.3 66.8 + - - +
170F SER* 3.1 13.2 + - - -
171F VAL* 3.1 13.1 + - - +
222F ILE* 5.0 1.6 - - + -
237F ILE* 2.9 47.6 + - + +
238F THR* 4.7 0.2 - - - +
239F SER* 2.6 37.9 + - - +
2004F IMD 4.0 24.9 - - + -
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Residues in contact with ALA 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LEU 3.0 8.6 + - - +
165F ALA* 3.0 13.2 + - - +
167F LYS* 1.3 78.3 - - - +
169F TYR* 1.3 57.1 + - - +
171F VAL* 3.2 8.4 + - - +
172F TYR* 2.9 27.3 + - - +
188F LEU* 3.6 8.4 - - + +
192F VAL* 3.6 28.0 - - + -
218F LEU* 5.5 1.8 - - + -
222F ILE* 3.8 27.5 - - + +
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Residues in contact with TYR 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F ALA* 2.8 22.9 + - + -
166F ASN* 3.7 23.6 - - - +
167F LYS 3.2 0.6 - - - -
168F ALA* 1.3 78.0 - - - +
170F SER* 1.3 56.0 + - - +
172F TYR* 3.2 8.8 + + + +
173F PHE* 2.8 46.2 + + + -
189F LYS* 3.8 31.4 - - + -
192F VAL* 3.5 30.0 - - + +
193F ASP* 2.3 33.1 + - - -
196F LEU* 3.7 18.3 - - + +
199F GLU* 5.3 6.8 + - - +
240F TYR* 4.2 13.9 - + + -
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Residues in contact with SER 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ASN 3.1 4.0 + - - -
167F LYS 3.1 11.1 + - - -
169F TYR* 1.3 73.4 - - - +
171F VAL* 1.3 67.5 + - - +
173F PHE* 3.0 5.3 + - - +
174F ALA* 2.8 24.1 + - - +
237F ILE* 3.8 9.6 - - - -
238F THR 2.6 27.0 + - - -
240F TYR* 3.2 15.1 + - - +
257F LEU* 3.5 30.8 - - - +
258F VAL* 5.7 0.3 - - - +
261F THR* 4.3 4.3 + - - +
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Residues in contact with VAL 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F LYS 3.1 12.4 + - - +
168F ALA* 3.2 9.2 + - - +
170F SER* 1.3 75.9 - - - +
172F TYR* 1.3 64.6 + - - +
174F ALA* 3.1 8.7 + - - -
175F PHE* 3.3 19.9 + - + +
188F LEU* 3.8 9.2 - - + -
222F ILE* 5.1 4.3 - - + -
225F PHE* 3.6 37.9 - - + -
226F PHE* 4.0 17.3 - - + -
234F PRO* 5.9 0.4 - - + -
237F ILE* 3.8 28.3 - - + -
261F THR* 4.2 13.0 - - + -
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Residues in contact with TYR 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ALA 2.9 14.0 + - - +
169F TYR* 3.3 17.0 - + + +
170F SER 3.1 0.2 - - - -
171F VAL* 1.3 79.5 - - - +
173F PHE* 1.3 104.7 + + - +
175F PHE 3.2 0.3 + - - -
176F VAL* 3.0 54.0 + - + +
185F ALA* 3.2 27.6 - - - +
186F LEU* 4.2 12.9 - - + +
188F LEU* 3.6 15.9 - - + +
189F LYS* 3.6 44.2 + - + +
2002F IMD 4.5 10.2 - - - -
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Residues in contact with PHE 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F TYR* 2.8 34.2 + + + +
170F SER* 3.6 5.8 - - - +
172F TYR* 1.3 103.1 - + - +
174F ALA* 1.3 61.9 + - - +
175F PHE 3.3 0.9 + - - -
176F VAL* 3.6 14.5 + - + +
177F ARG* 4.5 4.9 - - - -
189F LYS* 6.4 0.2 - - - -
240F TYR* 3.4 52.3 - + - -
247F TYR* 5.7 6.3 - + + -
254F PHE* 3.7 33.5 - + + -
257F LEU* 5.1 4.0 - - + -
258F VAL* 3.8 14.8 - - + +
2002F IMD 4.4 18.6 - + - -
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Residues in contact with ALA 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F SER 2.8 15.8 + - - +
171F VAL 3.1 5.8 + - - +
173F PHE* 1.3 76.9 - - - +
175F PHE* 1.3 70.6 + - + +
177F ARG* 5.3 1.1 + - - -
178F ASP 5.5 0.2 + - - -
258F VAL* 3.8 22.1 - - + +
261F THR* 3.6 30.3 - - + -
262F ARG* 3.1 28.7 + - + -
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Residues in contact with PHE 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F VAL* 3.3 20.4 - - + +
172F TYR 3.2 2.6 + - - -
174F ALA* 1.3 90.5 - - + +
176F VAL* 1.3 61.9 + - - +
177F ARG 3.1 3.6 - - - +
178F ASP* 3.0 46.7 + - - +
181F HIS* 4.2 13.7 - + + -
182F LYS* 3.7 8.1 + - - -
185F ALA* 3.8 8.1 - - + -
225F PHE* 3.7 30.3 - + + -
231F LEU* 3.7 22.9 - - + -
261F THR* 4.8 1.8 - - + -
262F ARG* 3.8 28.5 - - + -
265F VAL* 3.9 35.4 - - + -
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Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F TYR* 3.0 45.5 + - + +
173F PHE* 3.6 20.9 - - - +
175F PHE* 1.3 77.4 - - - +
177F ARG* 1.3 73.7 + - + +
178F ASP 3.4 0.2 - - - -
182F LYS* 3.8 27.5 + - + +
185F ALA* 3.8 7.2 - - - +
186F LEU* 3.9 20.4 - - + -
254F PHE* 5.7 0.2 - - + -
2002F IMD 4.4 19.5 - - + -
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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