Contacts of the helix formed by residues 198 - 220 (chain F) in PDB entry 1XFB
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 ASP 198 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F ASP 3.8 1.0 + - - -
197F HIS* 1.3 77.9 - - - +
199F LEU* 1.3 65.7 + - - +
200F LYS* 3.1 36.8 + - - +
201F ARG* 3.2 27.2 + - - +
202F CYS 3.3 8.1 + - - -
236F PRO* 4.1 2.7 - - - -
240F CYS* 4.0 15.3 - - - -
242F ILE* 4.3 8.9 - - + +
244F TYR* 3.4 14.8 + - - +
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F ASP* 1.3 73.7 - - - +
200F LYS* 1.3 65.6 + - - +
202F CYS* 3.1 4.5 + - - +
203F GLN* 3.0 21.0 + - - +
234F VAL* 3.3 19.7 - - + +
235F THR* 3.2 33.9 - - - -
236F PRO* 3.8 13.3 - - + +
244F TYR* 3.3 43.2 + - + -
248F GLU* 3.7 28.5 - - + +
249F ILE* 4.4 5.8 - - + -
252F ALA* 3.9 12.6 - - + -
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Residues in contact with LYS 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F ASP* 3.1 20.7 + - - +
199F LEU* 1.3 79.1 - - - +
201F ARG* 1.3 63.7 + - - +
203F GLN* 3.1 10.0 + - - +
204F TYR* 3.0 21.4 + - - +
4G SER* 6.3 0.4 - - - -
6G PRO* 4.2 22.6 - - - +
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Residues in contact with ARG 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F ILE* 3.4 19.7 - - + +
155F SER 3.3 24.7 + - - -
156F GLU* 4.6 0.8 + - - +
158F THR 5.5 0.2 - - - +
159F PRO* 4.8 1.4 - - - +
197F HIS* 3.7 24.2 - - + +
198F ASP* 3.2 20.0 + - - +
200F LYS* 1.3 78.5 - - - +
202F CYS* 1.3 64.6 + - - +
204F TYR* 3.1 7.2 + - - +
205F VAL* 2.9 34.8 + - + +
3G HIS* 2.6 51.7 + - - +
4G SER* 3.6 20.6 + - - +
157H ARG* 3.8 12.9 - - - +
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Residues in contact with CYS 202 (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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154F ILE* 4.1 18.8 - - - +
191F ILE* 5.2 4.7 - - - -
192F LEU 6.1 0.2 - - - -
197F HIS* 4.0 12.5 - - + -
198F ASP 3.3 2.9 + - - +
199F LEU 3.1 8.5 + - - +
201F ARG* 1.3 78.6 - - - +
203F GLN* 1.3 57.9 - - - +
205F VAL* 3.9 0.5 - - - +
206F THR* 2.8 41.1 + - - -
232F ASN* 4.2 6.7 - - - -
233F MET 4.4 0.7 - - - -
234F VAL* 3.5 11.4 - - - -
235F THR 3.2 43.7 - - - +
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Residues in contact with GLN 203 (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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199F LEU* 3.0 12.2 + - - +
200F LYS* 3.4 12.9 - - - +
202F CYS* 1.3 78.1 - - - +
204F TYR* 1.3 57.3 + - - +
206F THR* 3.2 3.3 + - - -
207F GLU* 2.6 58.3 + - - +
234F VAL* 3.8 16.7 - - + +
252F ALA* 3.4 37.0 + - + +
255F THR* 3.7 15.2 - - - +
256F ALA* 3.9 6.2 - - + +
259F ARG* 3.2 16.2 - - - +
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Residues in contact with TYR 204 (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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200F LYS 3.0 12.3 + - - +
201F ARG* 3.3 8.7 - - - +
203F GLN* 1.3 76.7 - - - +
205F VAL* 1.3 68.9 + - + +
207F GLU* 3.1 12.7 + - - +
208F LYS* 3.0 53.0 + - + +
3G HIS* 2.9 51.8 + + + +
4G SER* 3.3 32.1 - - - -
5G TYR 5.1 0.8 + - - -
221G HIS* 2.9 33.2 - + + -
118H GLY 5.4 0.3 + - - -
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Residues in contact with VAL 205 (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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154F ILE* 3.9 24.9 - - + -
159F PRO* 3.6 31.0 - - + -
164F ILE* 6.0 0.4 - - + -
191F ILE* 3.7 15.7 - - + -
201F ARG* 2.9 27.2 + - + +
202F CYS 4.0 0.4 - - - +
204F TYR* 1.3 78.1 - - + +
206F THR* 1.3 63.6 + - - +
208F LYS* 3.2 5.9 + - + +
209F VAL* 2.9 26.1 + - + +
3G HIS* 3.7 26.7 - - + +
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Residues in contact with THR 206 (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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191F ILE* 3.4 16.2 - - + +
202F CYS* 2.8 28.6 + - - -
203F GLN* 3.5 5.6 - - - -
205F VAL* 1.3 75.7 - - - +
207F GLU* 1.3 64.2 + - - +
209F VAL* 3.8 0.5 - - - +
210F LEU* 2.9 45.7 + - + +
231F PRO* 5.8 2.2 - - + -
232F ASN* 3.3 28.5 + - - +
234F VAL* 4.4 9.5 - - + +
256F ALA* 4.1 15.3 - - + -
257F LEU* 5.9 1.3 - - + -
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Residues in contact with GLU 207 (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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203F GLN* 2.6 50.9 + - - +
204F TYR* 3.1 12.3 + - + +
206F THR* 1.3 78.0 - - - +
208F LYS* 1.3 62.8 + - + +
210F LEU* 4.8 0.4 - - - -
211F ALA* 2.9 30.9 + - - +
256F ALA* 3.7 23.5 - - - +
259F ARG* 3.0 31.9 + - - +
260F THR* 3.4 15.8 - - + +
218G SER* 5.4 0.4 - - - -
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Residues in contact with LYS 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F ILE* 4.7 13.9 - - + +
204F TYR* 3.0 61.1 + - + +
205F VAL* 3.7 6.7 - - - +
207F GLU* 1.3 75.3 - - - +
209F VAL* 1.3 67.0 + - + +
211F ALA* 3.4 6.0 + - - +
212F ALA* 3.1 22.2 + - - +
3G HIS* 6.5 0.2 - - + -
215G LYS* 5.7 0.3 - - - -
218G SER* 2.5 42.1 + - - +
219G ASP* 4.7 1.8 - - - +
221G HIS* 2.9 23.0 + - + +
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Residues in contact with VAL 209 (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 LEU* 3.3 36.6 - - + -
159F PRO* 4.8 0.7 - - + -
164F ILE* 4.4 21.7 - - + +
189F PRO* 4.2 15.0 - - + +
191F ILE* 3.6 18.8 - - + -
205F VAL* 2.9 28.8 + - + +
206F THR 3.8 3.1 - - - +
208F LYS* 1.3 76.6 - - - +
210F LEU* 1.3 66.4 + - + +
212F ALA* 3.0 5.7 + - - +
213F VAL* 2.9 37.3 + - + +
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Residues in contact with LEU 210 (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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189F PRO* 4.0 17.5 - - + -
191F ILE* 6.5 0.2 - - + -
206F THR* 2.9 38.5 + - + +
207F GLU 4.0 0.4 - - - +
209F VAL* 1.3 77.1 - - + +
211F ALA* 1.3 65.1 + - - +
213F VAL* 2.9 17.1 + - + +
214F TYR* 2.9 23.8 + - + -
229F LEU* 3.9 33.0 - - + -
231F PRO* 4.7 7.2 - - + -
256F ALA 5.0 0.9 - - - +
257F LEU* 3.8 26.2 - - + -
260F THR* 3.5 29.4 - - + +
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Residues in contact with ALA 211 (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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207F GLU 2.9 19.4 + - - +
208F LYS 3.6 4.7 - - - +
209F VAL 3.3 0.2 - - - -
210F LEU* 1.3 76.4 - - - +
212F ALA* 1.3 62.5 + - - +
214F TYR* 3.8 3.5 + - - +
215F LYS* 3.3 21.1 + - - +
260F THR* 4.1 16.0 - - + +
215G LYS* 3.7 11.2 - - + +
218G SER* 3.4 33.4 - - - +
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Residues in contact with ALA 212 (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 ILE* 3.5 28.7 - - + -
165F LEU* 6.1 0.4 - - - -
168F ALA* 4.1 9.9 - - + +
208F LYS 3.1 7.2 + - - +
209F VAL 3.0 9.7 + - - +
211F ALA* 1.3 74.7 - - - +
213F VAL* 1.3 67.9 + - - +
215F LYS* 3.2 3.3 + - - +
216F ALA* 3.0 23.7 + - - +
215G LYS* 3.8 20.3 - - - +
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Residues in contact with VAL 213 (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* 4.0 17.4 - - + +
171F LEU* 4.2 12.8 - - + -
187F VAL* 3.9 27.6 - - + -
189F PRO* 4.1 17.9 - - + -
209F VAL* 2.9 34.9 + - + +
210F LEU* 3.3 11.7 - - + +
212F ALA* 1.3 76.3 - - - +
214F TYR* 1.3 65.4 + - + +
216F ALA* 3.3 4.6 + - - +
217F LEU* 3.0 35.0 + - + +
229F LEU* 5.3 1.1 - - + -
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Residues in contact with TYR 214 (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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187F VAL* 5.7 2.0 - - + +
210F LEU* 2.9 25.6 + - + +
211F ALA* 4.5 2.5 - - - +
213F VAL* 1.3 78.7 - - + +
215F LYS* 1.3 67.1 + - - +
217F LEU* 3.2 16.3 + - + +
218F SER* 2.9 22.5 + - - -
224F LEU* 3.6 35.9 - - + +
227F THR* 5.1 2.7 + - - -
228F LEU 5.2 0.7 - - - -
229F LEU* 3.4 39.6 - - + +
260F THR 3.9 16.8 - - - +
261F VAL* 3.7 21.5 - - + +
262F PRO* 3.7 19.1 - - + -
265F VAL* 3.5 25.5 - - + +
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Residues in contact with LYS 215 (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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211F ALA 3.3 16.8 + - - +
212F ALA 3.2 5.6 + - - +
214F TYR* 1.3 76.8 - - - +
216F ALA* 1.3 58.6 + - - +
218F SER* 3.2 5.1 + - - -
219F ASP* 2.9 67.5 + - - +
211G ALA* 3.8 23.3 - - + +
212G ALA* 3.9 26.7 - - - +
215G LYS* 3.7 31.6 - - + -
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Residues in contact with ALA 216 (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* 3.4 35.2 - - + +
169F ASN* 4.3 4.3 - - - +
172F ALA* 3.8 6.5 - - + -
212F ALA 3.0 12.4 + - - +
213F VAL 3.4 7.9 - - - +
215F LYS* 1.3 75.0 - - - +
217F LEU* 1.3 67.9 + - - +
219F ASP* 2.9 11.1 + - - +
220F HIS* 2.9 29.3 + - + -
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Residues in contact with LEU 217 (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 5.8 0.2 - - - +
171F LEU 4.7 0.2 - - - -
172F ALA* 3.7 21.8 - - + +
175F ALA* 3.9 9.0 - - + -
187F VAL* 4.4 17.9 - - + -
213F VAL* 3.0 27.5 + - + +
214F TYR* 3.5 39.3 - - + +
216F ALA* 1.3 76.8 - - - +
218F SER* 1.3 62.0 + - - +
220F HIS 3.2 1.6 + - - -
221F HIS 3.1 4.0 + - - -
222F VAL* 3.0 60.1 + - + +
224F LEU* 4.0 15.5 - - + -
227F THR* 5.5 2.0 - - + +
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Residues in contact with SER 218 (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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214F TYR 2.9 13.9 + - - -
215F LYS* 3.3 10.5 - - - -
217F LEU* 1.3 76.1 - - - +
219F ASP* 1.3 60.9 + - - +
221F HIS* 2.9 13.0 + - - +
222F VAL 5.0 2.9 - - - +
207G GLU 5.1 0.3 + - - -
208G LYS* 2.7 41.8 + - - +
211G ALA* 3.5 30.5 - - - +
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Residues in contact with ASP 219 (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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162E LEU* 3.3 22.9 - - + +
165E LEU* 3.8 25.1 - - + +
215F LYS* 2.9 51.0 + - - +
216F ALA* 2.9 11.2 + - - +
218F SER* 1.3 77.5 + - - +
220F HIS* 1.3 66.9 + - + +
221F HIS* 3.4 12.5 + - - -
208G LYS* 4.9 2.4 - - - +
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Residues in contact with HIS 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E LEU* 5.4 3.5 - - + +
117E ALA 3.8 5.7 - - - +
162E LEU* 3.6 30.7 - - + +
165E LEU* 4.2 2.6 - - - +
166E GLU* 3.9 12.1 - - + -
169F ASN* 2.8 28.9 + - - -
172F ALA* 3.4 29.3 - - + +
173F ARG* 3.8 35.4 + - + +
176F SER* 3.7 18.3 + - - -
216F ALA* 2.9 22.4 + - - +
217F LEU 3.9 2.7 - - - +
218F SER 3.1 0.4 - - - -
219F ASP* 1.3 80.5 - - + +
221F HIS* 1.3 74.1 + - - +
222F VAL* 3.3 3.3 + - + -
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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