Contacts of the helix formed by residues 198 - 220 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ASP 3.8 1.4 + - - -
197B HIS* 1.3 78.3 - - - +
199B LEU* 1.3 64.4 + - - +
200B LYS* 3.1 37.1 + - - +
201B ARG* 3.2 26.5 + - - +
202B CYS 3.3 8.1 + - - -
236B PRO* 4.1 2.9 - - - -
240B CYS* 4.0 15.9 - - - -
242B ILE* 4.3 8.8 - - + +
244B TYR* 3.4 14.1 + - - +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 1.3 74.1 - - - +
200B LYS* 1.3 66.4 + - - +
202B CYS* 3.1 4.0 + - - +
203B GLN* 3.0 20.3 + - - +
234B VAL* 3.3 20.0 - - + +
235B THR* 3.2 32.8 - - - -
236B PRO* 3.8 13.5 - - + +
244B TYR* 3.3 42.4 + - + -
248B GLU* 3.7 28.3 - - + +
249B ILE* 4.4 5.8 - - + -
252B ALA* 3.9 13.7 - - + -
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 3.1 20.2 + - - +
199B LEU* 1.3 78.0 - - - +
201B ARG* 1.3 62.5 + - - +
203B GLN* 3.1 10.8 + - - +
204B TYR* 3.0 21.2 + - - +
6C PRO* 4.5 18.9 - - - +
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Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.4 20.0 - - + +
155B SER 3.3 24.4 + - - -
156B GLU* 4.6 0.8 + - - +
157B ARG* 5.6 0.2 - - - +
158B THR 5.5 0.2 - - - +
159B PRO* 4.8 3.8 - - - +
197B HIS* 3.7 23.8 - - + +
198B ASP* 3.2 19.6 + - - +
200B LYS* 1.3 79.8 - - - +
202B CYS* 1.3 63.4 + - - +
204B TYR* 3.1 7.5 + - - +
205B VAL* 2.9 38.3 + - + +
3C HIS* 3.1 43.3 + - - +
4C SER* 4.1 15.2 + - - +
157D ARG* 3.7 18.3 - - - +
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Residues in contact with CYS 202 (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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154B ILE* 4.1 17.9 - - - +
191B ILE* 5.2 4.5 - - - -
197B HIS* 4.0 11.6 - - + -
198B ASP 3.3 2.6 + - - +
199B LEU 3.1 8.6 + - - +
201B ARG* 1.3 78.4 - - - +
203B GLN* 1.3 58.5 + - - +
205B VAL* 4.0 0.9 - - - +
206B THR* 2.8 41.8 + - - -
232B ASN* 4.2 7.2 - - - -
233B MET 4.4 0.7 - - - -
234B VAL* 3.5 11.4 - - + -
235B THR* 3.2 44.4 - - - +
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 3.0 12.4 + - - +
200B LYS* 3.4 13.0 - - - +
202B CYS* 1.3 78.6 - - - +
204B TYR* 1.3 56.8 + - - +
206B THR* 3.2 2.8 + - - -
207B GLU* 2.6 58.9 + - - +
234B VAL* 3.8 15.4 - - + +
252B ALA* 3.4 37.7 + - - +
255B THR* 3.7 15.4 - - - +
256B ALA* 3.9 5.8 - - + +
259B ARG* 3.2 16.2 - - - +
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Residues in contact with TYR 204 (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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200B LYS 3.0 12.7 + - - +
201B ARG* 3.3 12.3 - - - +
203B GLN* 1.3 75.4 - - - +
205B VAL* 1.3 66.7 + - + +
207B GLU* 3.1 13.4 + - - +
208B LYS* 3.0 62.5 + - + +
3C HIS* 2.8 56.3 + + - +
4C SER* 3.2 31.8 - - - +
5C TYR 5.3 0.2 - - - -
221C HIS* 3.5 17.4 - - - -
118D GLY 5.4 0.2 + - - -
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.9 24.9 - - + -
159B PRO* 3.6 32.3 - - + -
164B ILE* 6.0 0.4 - - + -
191B ILE* 3.7 16.4 - - + -
201B ARG* 2.9 42.2 + - + +
202B CYS 4.0 0.4 - - - +
204B TYR* 1.3 77.6 - - + +
206B THR* 1.3 64.5 + - - +
208B LYS* 3.2 5.9 + - + +
209B VAL* 2.9 25.5 + - + +
3C HIS* 4.2 11.4 - - + +
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Residues in contact with THR 206 (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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191B ILE* 3.4 16.1 - - + +
202B CYS* 2.8 28.4 + - - -
203B GLN* 3.5 6.5 - - - -
205B VAL* 1.3 75.1 - - - +
207B GLU* 1.3 64.4 + - - +
209B VAL* 3.8 0.7 - - - +
210B LEU* 2.9 45.3 + - + +
231B PRO* 5.8 2.5 - - + -
232B ASN* 3.3 28.6 + - - +
234B VAL* 4.4 9.3 - - + +
256B ALA* 4.1 15.5 - - + -
257B LEU* 5.9 0.7 - - + -
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Residues in contact with GLU 207 (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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203B GLN* 2.6 52.4 + - - +
204B TYR* 3.4 12.0 + - - +
206B THR* 1.3 78.1 - - - +
208B LYS* 1.3 61.3 + - + +
210B LEU* 4.8 0.2 - - - -
211B ALA* 2.9 30.4 + - - +
256B ALA* 3.7 24.0 - - - +
259B ARG* 3.0 31.0 + - - +
260B THR* 3.4 16.0 - - + +
218C SER* 5.9 0.2 - - - -
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Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 4.7 13.0 - - + +
204B TYR* 3.0 61.1 + - + +
205B VAL* 3.7 7.2 - - - +
207B GLU* 1.3 74.7 - - + +
209B VAL* 1.3 67.6 + - + +
211B ALA* 3.4 6.1 + - - +
212B ALA* 3.1 21.8 + - - +
3C HIS* 6.2 1.1 - - + -
218C SER* 3.0 38.4 + - - +
219C ASP* 5.1 1.2 - - - +
221C HIS* 3.2 20.2 + - - +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.3 37.0 - - + -
159B PRO* 4.8 0.9 - - + -
164B ILE* 4.4 22.4 - - + +
189B PRO* 4.2 15.7 - - + +
191B ILE* 3.6 19.5 - - + -
205B VAL* 2.9 28.8 + - + +
206B THR 3.8 3.1 - - - +
208B LYS* 1.3 76.4 - - - +
210B LEU* 1.3 65.1 + - + +
212B ALA* 3.0 5.9 + - - +
213B VAL* 2.9 36.9 + - + +
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Residues in contact with LEU 210 (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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189B PRO* 4.0 17.3 - - + -
191B ILE* 6.5 0.2 - - + -
206B THR* 2.9 39.4 + - + +
207B GLU 4.0 0.2 - - - +
209B VAL* 1.3 77.3 - - + +
211B ALA* 1.3 64.3 + - - +
213B VAL* 2.9 16.9 + - + +
214B TYR* 2.9 24.4 + - + -
229B LEU* 3.9 33.2 - - + -
231B PRO* 4.7 7.4 - - + -
256B ALA 5.0 1.1 - - - +
257B LEU* 3.8 26.0 - - + -
260B THR* 3.5 28.7 - - - +
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Residues in contact with ALA 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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207B GLU 2.9 19.4 + - - +
208B LYS* 3.6 6.1 - - - +
209B VAL 3.3 0.2 - - - -
210B LEU* 1.3 76.4 - - - +
212B ALA* 1.3 60.7 + - - +
214B TYR* 3.8 3.6 + - - +
215B LYS* 3.3 21.1 + - - +
260B THR* 4.1 14.5 - - + +
215C LYS* 4.1 11.0 - - + +
218C SER* 3.7 29.2 - - - +
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Residues in contact with ALA 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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164B ILE* 3.5 29.4 - - + +
165B LEU* 6.1 0.4 - - - -
168B ALA* 4.1 9.4 - - + +
208B LYS 3.1 8.4 + - - +
209B VAL 3.0 9.7 + - - +
211B ALA* 1.3 74.1 - - - +
213B VAL* 1.3 68.0 + - - +
215B LYS* 3.2 3.6 + - - +
216B ALA* 3.0 23.7 + - - +
215C LYS* 4.3 18.1 - - - +
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Residues in contact with VAL 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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168B ALA* 4.0 16.3 - - + +
171B LEU* 4.2 13.0 - - + -
187B VAL* 3.9 27.1 - - + -
189B PRO* 4.1 17.5 - - + -
209B VAL* 2.9 35.2 + - + +
210B LEU* 2.9 12.5 + - + +
212B ALA* 1.3 76.3 - - - +
214B TYR* 1.3 67.2 + - + +
216B ALA* 3.3 3.6 + - - +
217B LEU* 3.0 36.5 + - + +
229B LEU* 5.3 1.1 - - + -
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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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187B VAL* 5.7 1.8 - - + +
210B LEU* 2.9 24.5 + - + +
211B ALA* 4.5 3.1 - - - +
213B VAL* 1.3 78.7 - - + +
215B LYS* 1.3 67.0 + - - +
217B LEU* 3.2 17.0 + - + +
218B SER* 2.9 22.2 + - - -
224B LEU* 3.6 35.5 - - + +
227B THR* 5.1 2.5 + - - -
228B LEU 5.2 0.9 - - - -
229B LEU* 3.4 40.3 - - + +
260B THR 3.9 16.8 - - - +
261B VAL* 3.7 21.6 - - + +
262B PRO* 3.7 20.2 - - + -
265B VAL* 3.5 25.8 - - + +
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Residues in contact with LYS 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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211B ALA 3.3 17.1 + - - +
212B ALA* 3.2 5.5 + - - +
214B TYR* 1.3 77.9 - - - +
216B ALA* 1.3 58.2 + - - +
218B SER* 3.2 8.4 + - - -
219B ASP* 2.9 66.3 + - - +
211C ALA* 4.0 18.4 - - + +
212C ALA* 4.3 22.7 - - - +
215C LYS* 4.0 32.3 - - + -
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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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168B ALA* 3.4 35.0 - - + +
169B ASN* 4.3 4.7 - - - +
172B ALA* 3.8 6.7 - - + -
212B ALA 3.0 12.8 + - - +
213B VAL 3.4 7.2 - - - +
215B LYS* 1.3 74.4 - - - +
217B LEU* 1.3 68.4 + - - +
219B ASP* 2.9 10.4 + - - +
220B HIS* 2.9 28.4 + - + -
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Residues in contact with LEU 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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168B ALA 5.8 0.2 - - - +
171B LEU 4.7 0.4 - - - -
172B ALA* 3.7 22.4 - - + +
175B ALA* 3.9 8.7 - - + -
187B VAL* 4.4 17.9 - - + -
213B VAL* 3.0 26.6 + - + +
214B TYR* 3.5 38.8 - - + +
216B ALA* 1.3 75.9 - - - +
218B SER* 1.3 63.6 + - - +
220B HIS 3.2 1.2 + - - -
221B HIS 3.1 4.0 + - - -
222B VAL* 3.0 60.9 + - + +
224B LEU* 4.0 15.0 - - + -
227B THR* 5.5 2.2 - - - +
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Residues in contact with SER 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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214B TYR 2.9 13.7 + - - -
215B LYS* 3.3 12.1 - - - -
216B ALA 3.1 0.2 - - - -
217B LEU* 1.3 76.1 - - - +
219B ASP* 1.3 61.7 + - - +
221B HIS* 2.9 18.8 + - - +
222B VAL 5.0 2.7 - - - +
224B LEU* 6.0 0.2 - - - +
207C GLU 5.3 0.2 + - - -
208C LYS* 3.0 32.4 + - - +
211C ALA* 3.6 27.2 - - - +
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Residues in contact with ASP 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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162A LEU* 3.5 21.3 - - + +
165A LEU* 3.6 30.6 - - + +
215B LYS* 2.9 51.8 + - - +
216B ALA* 2.9 10.6 + - - +
218B SER* 1.3 78.0 + - - +
220B HIS* 1.3 63.2 + - + +
221B HIS* 3.2 13.1 + - - -
208C LYS* 5.0 2.0 - - - +
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Residues in contact with HIS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 5.6 2.9 - - + +
117A ALA* 4.1 3.5 - - - +
162A LEU* 3.6 29.8 - - + +
165A LEU* 4.0 3.8 - - + +
166A GLU* 3.9 11.4 - - + -
169B ASN* 2.8 28.4 + - - -
172B ALA* 3.4 30.6 - - + +
173B ARG* 3.8 35.6 + - + +
176B SER* 3.7 19.1 + - - -
216B ALA* 2.9 23.1 + - - +
217B LEU 3.9 2.5 - - - +
218B SER 3.1 0.4 - - - -
219B ASP* 1.3 80.3 - - + +
221B HIS* 1.3 74.0 + - - +
222B VAL* 3.3 3.5 + - + -
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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) + - + + + + + -
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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