Contacts of the helix formed by residues 205 - 229 (chain B) in PDB entry 3W7F
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 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B GLU 5.7 1.2 + - - -
194B VAL* 5.8 1.8 - - - +
198B GLU* 4.0 19.2 + - - -
199B VAL* 4.0 14.5 - - - +
203B GLY 4.5 2.3 + - - +
204B VAL* 1.3 80.8 - - - +
206B ASN* 1.3 61.5 + - - +
207B HIS* 2.7 24.8 + - - +
208B TYR* 3.0 18.8 + - - +
209B ILE* 3.2 10.9 + - - +
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN* 1.3 71.0 + - - +
207B HIS* 1.3 63.4 + - + +
209B ILE* 3.9 20.3 - - - +
210B ASP* 2.9 38.3 + - - +
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 3.0 19.6 + - - +
193B GLU* 3.0 50.3 + - + +
194B VAL* 3.7 9.9 - - + +
205B ASN* 2.7 18.1 + - - +
206B ASN* 1.3 74.2 - - + +
208B TYR* 1.3 67.0 + - - +
210B ASP* 3.0 12.8 + - - +
211B LEU* 2.9 21.1 + - - +
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B VAL* 3.4 26.8 - - + +
184B PHE* 4.2 11.7 - + - -
194B VAL* 3.6 14.5 - - + +
196B ILE* 3.7 30.5 - - + -
199B VAL* 4.1 27.4 - - + -
204B VAL* 4.2 15.7 - - + -
205B ASN* 3.0 16.0 + - - +
207B HIS* 1.3 78.3 - - - +
209B ILE* 1.3 69.1 + - - +
211B LEU* 2.8 17.5 + - + +
212B TRP* 2.8 34.2 + + + +
255B VAL* 6.1 0.2 - - - +
260B TYR* 3.9 22.4 + - + +
262B LEU* 3.4 23.2 - - + +
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 3.1 36.1 - - + -
205B ASN 3.2 5.9 + - - +
206B ASN* 4.0 25.6 - - - +
208B TYR* 1.3 80.3 - - - +
210B ASP* 1.3 56.2 + - - +
212B TRP* 3.2 5.0 + - - +
213B GLU* 2.8 39.5 + - + +
259B ASN* 4.9 4.5 - - - +
260B TYR* 3.7 40.4 - - + +
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 3.8 23.0 - - + -
206B ASN* 2.9 25.2 + - - +
207B HIS* 3.0 14.8 + - - +
209B ILE* 1.3 80.0 - - - +
211B LEU* 1.3 62.6 + - - +
213B GLU* 3.5 5.9 + - - +
214B TYR* 3.1 21.3 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B PHE* 4.2 17.0 - - + -
188B ARG* 4.0 12.8 - - + +
189B LEU* 3.5 17.5 - - + -
192B TYR* 3.8 34.3 - - + -
194B VAL* 3.2 33.7 - - + -
207B HIS 2.9 10.0 + - - +
208B TYR* 2.8 17.3 + - + +
210B ASP* 1.3 71.5 - - - +
212B TRP* 1.3 66.9 + - - +
214B TYR* 3.1 14.6 + - + +
215B TYR* 3.3 35.1 + - + -
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Residues in contact with TRP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 3.0 57.7 + - + +
173B VAL* 4.5 0.4 - - + -
184B PHE* 4.4 9.0 - + - -
208B TYR* 2.8 44.3 + + + +
209B ILE* 3.5 8.7 - - - +
211B LEU* 1.3 79.5 - - - +
213B GLU* 1.3 80.9 + - - +
215B TYR 3.4 0.9 + - - -
216B ALA* 3.0 34.6 + - + +
252B LEU* 3.7 38.1 - - + -
255B VAL* 3.7 24.6 - - + +
256B ARG* 3.9 5.8 - - + -
260B TYR* 3.3 28.3 - + + -
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ILE* 2.8 25.0 + - + +
210B ASP* 4.0 6.3 - - - +
211B LEU 3.2 0.2 - - - -
212B TRP* 1.3 84.4 - - + +
214B TYR* 1.3 58.8 + - - +
216B ALA* 3.7 3.3 - - - +
217B ALA* 3.1 27.2 + - - +
256B ARG* 2.9 40.9 + - - -
260B TYR* 2.8 27.4 + - - +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASP* 3.8 8.0 + - - -
188B ARG* 3.3 51.8 + - - -
192B TYR* 3.4 27.8 - + + +
210B ASP 3.1 12.8 + - - +
211B LEU* 3.1 10.8 + - + +
213B GLU* 1.3 78.9 - - - +
215B TYR* 1.3 73.6 + + - +
217B ALA* 3.5 6.0 + - - +
218B ILE* 3.4 46.4 + - + +
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Residues in contact with TYR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASP* 2.6 40.4 + - - -
126B LEU* 3.9 15.3 - - + +
127B PHE* 4.6 4.7 - + - -
166B LEU* 3.8 22.2 - - + +
170B LEU* 3.8 20.2 - - + -
184B PHE* 3.1 36.6 - + - -
185B SER 3.5 15.9 + - - -
188B ARG* 3.5 10.0 - - + +
211B LEU* 3.3 36.3 + - + -
212B TRP 3.9 0.2 - - - +
214B TYR* 1.3 79.9 - + - +
216B ALA* 1.3 67.0 + - - +
217B ALA 3.2 0.4 - - - -
218B ILE* 3.2 17.5 + - + +
219B ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 3.6 15.7 - - + +
212B TRP* 3.0 43.5 + - + +
213B GLU* 3.8 12.3 - - - +
214B TYR 3.4 0.2 - - - -
215B TYR* 1.3 78.1 - - - +
217B ALA* 1.3 56.5 + - - +
219B ALA* 3.5 2.5 + - - +
220B GLU* 2.8 37.3 + - - +
252B LEU* 4.2 5.9 - - + +
256B ARG* 4.0 7.6 - - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLU* 3.1 19.3 + - - +
214B TYR* 3.8 7.2 - - - +
215B TYR 3.2 0.2 - - - -
216B ALA* 1.3 73.8 - - - +
218B ILE* 1.3 56.3 + - + +
220B GLU* 3.6 12.6 + - - +
221B LYS* 2.8 36.0 + - - +
224B ARG* 5.0 1.0 + - - -
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASP* 5.0 0.2 - - - +
127B PHE* 3.8 29.8 - - + -
166B LEU* 3.7 15.5 - - + -
214B TYR* 3.4 45.8 - - + +
215B TYR* 3.2 15.7 + - + +
217B ALA* 1.3 76.9 - - + +
219B ALA* 1.3 63.2 + - - +
221B LYS* 3.3 6.4 + - - +
222B ASP* 3.1 37.1 + - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B SER* 4.1 15.5 - - - +
166B LEU* 3.8 20.2 - - + -
167B ILE* 3.8 29.8 - - + +
170B LEU* 4.8 1.3 - - + -
215B TYR 3.0 15.1 + - - +
216B ALA* 3.8 6.3 - - - +
218B ILE* 1.3 76.6 - - - +
220B GLU* 1.3 64.0 + - - +
222B ASP* 3.3 4.9 + - - +
223B PHE* 3.0 23.1 + - - +
249B ILE* 4.9 2.1 - - - +
252B LEU* 5.2 0.9 - - + -
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA 2.8 24.5 + - - +
217B ALA* 3.6 12.6 - - - +
219B ALA* 1.3 72.7 - - - +
221B LYS* 1.3 68.2 + - - +
223B PHE* 3.2 9.7 + - + +
224B ARG* 3.1 42.3 + - - +
249B ILE* 4.3 11.8 - - + +
252B LEU* 3.7 17.2 - - + +
256B ARG* 2.9 37.2 + - - -
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ALA 2.8 20.8 + - - +
218B ILE* 3.8 6.7 - - - +
220B GLU* 1.3 72.4 - - - +
222B ASP* 1.3 66.8 + - - +
224B ARG* 3.1 25.3 + - + +
225B ASP* 2.8 60.1 + - - +
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ARG* 4.2 26.1 + - + -
163B SER* 3.0 26.6 + - - +
166B LEU* 5.4 1.2 - - - +
218B ILE* 3.1 26.8 + - - +
219B ALA* 3.7 5.0 - - - +
221B LYS* 1.3 80.2 - - - +
223B PHE* 1.3 62.0 + - - +
225B ASP* 3.3 13.7 + - - +
226B VAL* 3.0 28.1 + - - +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 5.0 5.4 - - + -
163B SER* 4.3 6.7 + - - -
164B LEU* 6.4 0.4 - - + -
167B ILE* 6.0 0.2 - - + -
219B ALA 3.0 13.0 + - - +
220B GLU* 3.4 10.1 - - - +
222B ASP* 1.3 76.7 - - - +
224B ARG* 1.3 68.1 + - + +
226B VAL* 3.2 8.0 + - - +
227B MET* 2.8 61.7 + - + +
245B ALA* 3.3 38.4 - - + -
246B ARG* 3.7 41.1 - - + -
249B ILE* 3.5 37.5 - - + -
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ALA 5.0 0.8 + - - -
220B GLU* 3.1 27.5 + - - +
221B LYS* 3.1 37.0 + - + +
223B PHE* 1.3 88.8 - - + +
225B ASP* 1.3 67.2 + - - +
227B MET* 3.3 6.9 + - + +
228B ASP* 3.2 26.7 + - - +
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Residues in contact with ASP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ARG* 3.8 18.3 - - - +
221B LYS* 2.8 50.7 + - - +
222B ASP* 3.3 10.2 + - - +
224B ARG* 1.3 78.5 - - - +
226B VAL* 1.3 61.2 + - - +
228B ASP* 3.3 24.9 + - - +
229B GLN* 3.6 15.9 + - - +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B VAL* 4.0 24.1 - - + +
159B ARG* 3.7 19.5 - - - +
160B LEU* 3.8 49.1 - - + +
163B SER* 5.1 0.2 - - - +
222B ASP 3.0 22.7 + - - +
223B PHE* 3.5 6.1 - - - +
225B ASP* 1.3 73.7 - - - +
227B MET* 1.3 83.8 + - + +
229B GLN* 3.1 14.0 + - - +
230B ILE* 3.2 15.1 + - + +
233B PHE* 5.4 1.1 - - + -
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Residues in contact with MET 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 2.8 58.8 + - + +
224B ARG* 3.3 7.8 + - + +
226B VAL* 1.3 93.3 - - + +
228B ASP* 1.3 64.9 + - - +
229B GLN 3.2 1.2 + - - -
230B ILE* 3.2 43.6 + - + +
241B ILE* 4.8 2.2 - - + +
242B GLU* 3.5 35.9 - - - +
245B ALA* 4.0 13.5 - - + -
246B ARG* 4.5 6.3 - - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ARG 3.2 14.9 + - - +
225B ASP* 3.4 16.7 - - - +
226B VAL 3.2 0.4 - - - -
227B MET* 1.3 77.6 - - - +
229B GLN* 1.3 61.7 + - + +
230B ILE* 3.4 1.6 + - - +
231B LYS* 5.1 3.6 + - - +
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLN* 2.4 43.0 + - - +
156B VAL* 3.8 19.5 - - + +
159B ARG* 3.3 29.1 - - - +
225B ASP* 3.6 16.2 + - - +
226B VAL 3.1 8.1 + - - +
228B ASP* 1.3 82.0 - - + +
230B ILE* 1.3 63.4 + - - +
231B LYS* 2.8 9.8 + - - +
232B VAL* 3.0 22.3 + - + +
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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
------------------------------------------------------------
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