Contacts of the helix formed by residues 198 - 220 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ASP 3.8 1.2 + - - -
197E HIS* 1.3 79.0 - - - +
199E LEU* 1.3 66.1 + - - +
200E LYS* 3.1 36.9 + - - +
201E ARG* 3.2 27.2 + - - +
202E CYS* 3.3 8.1 + - - +
236E PRO* 4.1 2.0 - - - -
240E CYS* 4.0 15.5 - - - -
242E ILE* 4.3 9.5 - - + +
244E TYR* 3.4 14.9 + - - +
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Residues in contact with LEU 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E ASP* 1.3 74.1 - - - +
200E LYS* 1.3 65.0 + - - +
202E CYS* 3.1 4.2 + - - +
203E GLN* 3.0 21.2 + - - +
234E VAL* 3.3 19.5 - - + +
235E THR* 3.2 33.0 - - - -
236E PRO* 3.8 14.0 - - + +
244E TYR* 3.3 42.7 + - + -
248E GLU* 3.6 28.7 - - + +
249E ILE* 4.4 5.6 - - + -
252E ALA* 3.9 13.7 - - + -
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Residues in contact with LYS 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E ASP* 3.1 20.0 + - - +
199E LEU* 1.3 78.8 - - - +
201E ARG* 1.3 63.2 + - - +
203E GLN* 3.1 10.7 + - - +
204E TYR* 3.0 21.3 + - - +
244E TYR* 4.8 0.2 + - - -
6H PRO* 4.2 22.6 - - - +
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Residues in contact with ARG 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ILE* 3.4 19.8 - - + +
155E SER 3.3 24.2 + - - -
156E GLU* 4.6 0.4 + - - -
159E PRO* 4.8 1.6 - - - +
197E HIS* 3.7 21.7 - - + +
198E ASP* 3.2 19.8 + - - +
200E LYS* 1.3 78.4 - - - +
202E CYS* 1.3 65.0 + - - +
204E TYR* 3.1 7.7 + - - +
205E VAL* 2.9 35.2 + - + +
157G ARG* 3.4 15.2 - - - +
3H HIS* 2.8 48.1 + - - +
4H SER* 3.3 21.1 + - - +
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Residues in contact with CYS 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E ILE* 4.1 18.2 - - - -
191E ILE* 5.2 4.0 - - - -
192E LEU 6.1 0.2 - - - -
197E HIS* 4.0 12.5 - - + +
198E ASP 3.3 3.2 + - - +
199E LEU 3.1 7.9 + - - +
201E ARG* 1.3 79.0 - - - +
203E GLN* 1.3 58.6 + - - +
205E VAL* 4.0 0.7 - - - +
206E THR* 2.8 41.5 + - - -
232E ASN* 4.2 7.0 - - - -
233E MET 4.4 0.9 - - - -
234E VAL* 3.5 10.5 - - - -
235E THR* 3.2 44.0 - - - +
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Residues in contact with GLN 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E LEU 3.0 11.6 + - - +
200E LYS* 3.4 12.8 - - - +
202E CYS* 1.3 78.4 - - - +
204E TYR* 1.3 56.6 + - - +
206E THR* 3.2 3.1 + - - -
207E GLU* 2.6 59.3 + - - +
234E VAL* 3.8 15.4 - - + +
252E ALA* 3.4 36.9 + - - +
255E THR* 3.7 14.6 - - - +
256E ALA* 3.9 6.5 - - + +
259E ARG* 3.2 16.4 - - - +
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Residues in contact with TYR 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E LYS 3.0 11.7 + - - +
201E ARG* 3.3 9.9 - - - +
203E GLN* 1.3 75.1 - - - +
205E VAL* 1.3 68.1 - - + +
207E GLU* 3.1 13.8 + - - +
208E LYS* 3.0 54.0 + - + +
118G GLY 4.9 1.4 + - - -
3H HIS* 2.9 48.2 + + + +
4H SER* 3.2 32.7 - - - -
5H TYR 5.0 0.9 - - - -
221H HIS* 3.1 31.0 - + + -
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Residues in contact with VAL 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E ILE* 3.9 26.2 - - + -
159E PRO* 3.6 31.2 - - + -
164E ILE* 6.0 0.2 - - + -
191E ILE* 3.7 16.2 - - + -
201E ARG* 2.9 29.0 + - + +
202E CYS 4.0 0.2 - - - +
204E TYR* 1.3 78.6 - - + +
206E THR* 1.3 64.0 + - - +
208E LYS* 3.2 6.1 + - + +
209E VAL* 2.9 25.7 + - + +
3H HIS* 3.9 23.6 - - + +
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Residues in contact with THR 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E ILE* 3.4 16.8 - - + +
202E CYS* 2.8 27.5 + - - -
203E GLN* 3.5 6.3 - - - -
205E VAL* 1.3 76.8 - - - +
207E GLU* 1.3 63.3 + - - +
209E VAL* 3.8 0.3 - - - +
210E LEU* 2.9 46.1 + - + +
231E PRO* 5.8 2.0 - - + -
232E ASN* 3.3 28.7 + - - +
234E VAL* 4.4 8.6 - - + +
256E ALA* 4.1 16.2 - - + -
257E LEU* 5.9 0.9 - - + -
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Residues in contact with GLU 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E GLN* 2.6 52.3 + - - +
204E TYR* 3.1 12.2 + - - +
206E THR* 1.3 78.0 - - - +
208E LYS* 1.3 61.6 + - + +
210E LEU* 4.8 0.2 - - - -
211E ALA* 2.9 30.2 + - - +
256E ALA* 3.7 23.8 - - - +
259E ARG* 3.0 31.7 + - - +
260E THR* 3.4 16.9 - - + +
218H SER* 5.6 0.2 - - - -
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Residues in contact with LYS 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E ILE* 4.7 13.5 - - + +
204E TYR* 3.0 60.7 + - + +
205E VAL* 3.7 7.4 - - + +
207E GLU* 1.3 76.3 - - + +
209E VAL* 1.3 66.6 + - - +
211E ALA* 3.4 5.8 + - - +
212E ALA* 3.1 22.7 + - - +
3H HIS* 6.5 0.4 - - + -
218H SER* 2.7 39.7 + - - +
219H ASP* 5.9 1.1 - - - -
221H HIS* 3.0 24.2 + - + +
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Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E LEU* 3.3 37.9 - - + -
159E PRO* 4.8 0.4 - - + -
164E ILE* 4.4 20.3 - - + +
189E PRO* 4.2 14.1 - - + -
191E ILE* 3.6 20.0 - - + -
205E VAL* 2.9 28.5 + - + +
206E THR 3.8 3.1 - - - +
208E LYS* 1.3 76.1 - - - +
210E LEU* 1.3 67.7 + - + +
212E ALA* 3.0 5.4 + - - +
213E VAL* 2.9 36.8 + - + +
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Residues in contact with LEU 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E PRO* 4.0 17.7 - - + -
206E THR* 2.9 39.6 + - + +
207E GLU 4.0 0.4 - - - +
209E VAL* 1.3 76.8 - - + +
211E ALA* 1.3 65.5 + - - +
213E VAL* 2.9 16.0 + - + +
214E TYR* 2.9 23.5 + - + -
229E LEU* 3.9 33.2 - - + -
231E PRO* 4.7 7.0 - - + -
256E ALA 5.0 1.1 - - - +
257E LEU* 3.8 26.2 - - + -
260E THR* 3.5 28.5 - - - +
261E VAL* 4.5 0.2 - - + -
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Residues in contact with ALA 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E GLU 2.9 19.5 + - - +
208E LYS 3.6 5.2 - - - +
209E VAL 3.3 0.2 - - - -
210E LEU* 1.3 77.6 - - - +
212E ALA* 1.3 61.5 + - - +
214E TYR* 3.8 4.2 + - - +
215E LYS* 3.3 20.8 + - - +
260E THR* 4.1 14.9 - - + +
215H LYS* 3.9 9.4 - - + +
218H SER* 3.4 33.0 - - - +
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Residues in contact with ALA 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E ILE* 3.5 29.8 - - + +
165E LEU* 6.1 0.4 - - - -
168E ALA* 4.1 9.4 - - + +
208E LYS 3.1 8.0 + - - +
209E VAL 3.0 8.6 + - - +
211E ALA* 1.3 74.3 - - - +
213E VAL* 1.3 67.1 + - - +
215E LYS* 3.2 3.3 + - - +
216E ALA* 3.0 23.9 + - - +
215H LYS* 4.0 19.9 - - - +
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Residues in contact with VAL 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ALA* 4.0 16.3 - - + +
171E LEU* 4.2 12.8 - - + -
187E VAL* 3.9 27.8 - - + -
189E PRO* 4.1 18.4 - - + -
209E VAL* 2.9 34.7 + - + +
210E LEU* 2.9 11.6 + - + +
212E ALA* 1.3 77.5 - - - +
214E TYR* 1.3 65.3 + - + +
216E ALA* 3.3 3.8 + - - +
217E LEU* 3.0 35.7 + - + +
229E LEU* 5.3 0.9 - - + -
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Residues in contact with TYR 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E VAL* 5.7 1.4 - - + +
210E LEU* 2.9 25.6 + - + +
211E ALA* 4.5 2.9 - - - +
213E VAL* 1.3 78.5 - - + +
215E LYS* 1.3 65.3 + - - +
217E LEU* 3.2 16.5 + - + +
218E SER* 2.9 23.2 + - - -
224E LEU* 3.6 35.7 - - + +
227E THR* 5.1 2.6 + - - -
228E LEU 5.2 0.5 - - - -
229E LEU* 3.4 41.1 + - + +
260E THR 3.9 17.0 - - - +
261E VAL* 3.7 21.3 - - + +
262E PRO* 3.7 20.2 - - + -
265E VAL* 3.5 26.2 - - + +
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Residues in contact with LYS 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E ALA 3.3 16.8 + - - +
212E ALA 3.2 5.5 + - - +
214E TYR* 1.3 78.7 - - - +
216E ALA* 1.3 58.6 + - - +
218E SER* 3.2 5.4 + - - -
219E ASP* 2.9 69.1 + - - +
211H ALA* 3.7 23.8 - - + +
212H ALA* 3.9 27.1 - - - +
215H LYS* 3.7 33.7 - - + -
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Residues in contact with ALA 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ALA* 3.4 35.2 - - + +
169E ASN* 4.3 4.5 - - - +
172E ALA* 3.8 6.5 - - + -
212E ALA 3.0 12.7 + - - +
213E VAL 3.4 7.9 - - - +
215E LYS* 1.3 74.7 - - - +
217E LEU* 1.3 68.3 + - - +
219E ASP* 2.9 10.6 + - - +
220E HIS* 2.9 28.2 + - + -
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Residues in contact with LEU 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E LEU 4.7 0.2 - - - -
172E ALA* 3.7 22.0 - - + +
175E ALA* 3.9 8.7 - - + -
187E VAL* 4.4 18.6 - - + -
213E VAL* 3.0 27.9 + - + +
214E TYR* 3.2 38.6 + - + +
216E ALA* 1.3 75.5 - - - +
218E SER* 1.3 63.5 + - - +
220E HIS 3.2 1.4 + - - -
221E HIS 3.1 3.6 + - - -
222E VAL* 2.9 60.9 + - + +
224E LEU* 4.0 15.0 - - + -
227E THR* 5.5 2.2 - - + +
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Residues in contact with SER 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E TYR 2.9 12.6 + - - -
215E LYS* 3.3 11.9 - - - -
217E LEU* 1.3 76.0 - - - +
219E ASP* 1.3 63.1 + - - +
221E HIS* 2.9 18.1 + - - +
222E VAL 5.0 2.9 - - - +
207H GLU 5.1 0.2 + - - -
208H LYS* 3.0 31.3 + - - +
211H ALA* 3.4 30.1 - - - +
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Residues in contact with ASP 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LYS* 2.9 51.8 + - - +
216E ALA* 2.9 11.2 + - - +
218E SER* 1.3 78.1 + - - +
220E HIS* 1.3 67.2 + - + +
221E HIS* 3.4 12.1 + - - -
162F LEU* 3.4 23.8 - - + +
165F LEU* 3.9 25.1 - - + +
208H LYS* 4.9 2.5 - - - +
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Residues in contact with HIS 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E ASN* 2.8 29.6 + - - -
172E ALA* 3.4 29.7 - - + +
173E ARG* 3.8 34.3 + - + +
176E SER* 3.7 19.2 + - - -
216E ALA* 2.9 21.8 + - - +
217E LEU 3.9 2.7 - - - +
218E SER 3.1 0.4 - - - -
219E ASP* 1.3 79.1 - - + +
221E HIS* 1.3 75.5 + - - +
222E VAL* 3.3 3.0 + - + -
116F LEU* 5.5 3.9 - - + +
117F ALA* 3.9 4.3 - - - +
162F LEU* 3.7 29.4 - - + +
165F LEU* 4.3 2.8 - - + +
166F GLU* 4.0 11.9 - - + -
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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