Contacts of the helix formed by residues 198 - 220 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASP 3.8 1.0 + - - -
197A HIS* 1.3 79.6 - - - +
199A LEU* 1.3 65.7 + - - +
200A LYS* 3.1 37.2 + - - +
201A ARG* 3.2 27.2 + - - +
202A CYS 3.3 8.0 + - - -
236A PRO* 4.1 2.7 - - - -
240A CYS* 4.0 15.7 - - - -
242A ILE* 4.3 8.5 - - + -
244A TYR* 3.4 14.4 + - - +
99I GLN 6.1 1.1 - - - +
100I ASP* 4.9 7.4 - - - +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASP* 1.3 72.8 - - - +
200A LYS* 1.3 66.0 + - - +
202A CYS* 3.1 4.0 + - - +
203A GLN* 3.0 20.1 + - - +
234A VAL* 3.3 20.0 - - + +
235A THR* 3.2 32.8 - - - -
236A PRO* 3.8 13.7 - - + +
244A TYR* 3.3 43.7 + - + -
248A GLU* 3.7 28.3 - - + +
249A ILE* 4.4 5.8 - - + -
252A ALA* 3.9 14.1 - - + -
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASP* 3.1 20.1 + - - +
199A LEU* 1.3 78.7 - - - +
201A ARG* 1.3 63.7 + - - +
203A GLN* 3.1 10.3 + - - +
204A TYR* 3.0 21.4 + - - +
244A TYR* 4.8 0.4 + - - -
6D PRO* 4.8 15.8 - - - +
71I LYS* 5.4 8.6 - - - +
100I ASP* 4.0 27.4 - - + +
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.4 19.5 - - + +
155A SER 3.3 24.7 + - - -
156A GLU* 4.6 1.2 + - - +
157A ARG* 5.6 0.4 - - - +
158A THR 5.5 0.2 - - - +
159A PRO* 4.8 4.8 - - - +
197A HIS* 3.7 23.1 - - + -
198A ASP* 3.2 18.9 + - - +
200A LYS* 1.3 80.6 - - - +
202A CYS* 1.3 64.0 + - - +
204A TYR* 3.1 8.0 + - - +
205A VAL* 2.9 38.7 + - + +
157C ARG* 3.8 16.2 - - - +
3D HIS* 3.1 43.8 + - - +
4D SER* 4.5 12.1 + - - +
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Residues in contact with CYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.1 17.9 - - - -
191A ILE* 5.2 4.5 - - - -
192A LEU 6.1 0.2 - - - -
197A HIS* 4.0 11.4 - - + -
198A ASP 3.3 2.6 + - - +
199A LEU 3.1 8.5 + - - +
201A ARG* 1.3 78.4 - - - +
203A GLN* 1.3 58.0 + - - +
205A VAL* 3.9 0.5 - - - +
206A THR* 2.8 41.3 + - - -
232A ASN* 4.2 6.7 - - - -
233A MET 4.4 1.1 - - - -
234A VAL* 3.5 11.0 - - - -
235A THR* 3.2 44.9 - - - +
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Residues in contact with GLN 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 3.0 12.2 + - - +
200A LYS* 3.4 13.0 - - - +
202A CYS* 1.3 77.2 - - - +
204A TYR* 1.3 56.7 + - - +
206A THR* 3.2 3.0 + - - -
207A GLU* 2.6 59.8 + - - +
234A VAL* 3.8 16.3 - - + +
252A ALA* 3.4 36.3 - - + +
255A THR* 3.7 15.6 - - - +
256A ALA* 3.9 6.0 - - + +
259A ARG* 3.2 16.0 - - - +
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Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LYS 3.0 11.5 + - - +
201A ARG* 3.3 13.2 - - + +
203A GLN* 1.3 75.4 - - - +
205A VAL* 1.3 67.7 + - + +
207A GLU* 3.1 13.0 + - - +
208A LYS* 3.0 62.9 + - + +
3D HIS* 3.0 58.4 + + - +
4D SER* 3.5 27.6 - - - +
221D HIS* 3.6 16.7 - - - -
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.9 25.8 - - + -
159A PRO* 3.6 32.8 - - + -
164A ILE* 6.0 0.7 - - + -
191A ILE* 3.7 16.6 - - + -
201A ARG* 2.9 41.7 + - + +
202A CYS 4.0 0.7 - - - +
204A TYR* 1.3 75.8 - - + +
206A THR* 1.3 64.6 + - - +
208A LYS* 3.2 6.3 + - + +
209A VAL* 2.9 25.2 + - + +
3D HIS* 4.4 9.9 - - + +
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 3.4 16.5 - - + +
202A CYS* 2.8 28.0 + - - -
203A GLN* 3.5 6.1 - - - -
205A VAL* 1.3 76.6 - - - +
207A GLU* 1.3 64.5 + - - +
209A VAL* 3.8 0.7 - - - +
210A LEU* 2.9 45.7 + - + +
231A PRO* 5.8 1.8 - - + -
232A ASN* 3.3 28.4 + - - +
234A VAL* 4.4 8.2 - - + +
256A ALA* 4.1 15.5 - - + -
257A LEU* 5.9 0.9 - - + -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLN* 2.6 52.8 + - - +
204A TYR* 3.1 12.0 + - - +
206A THR* 1.3 77.5 - - - +
208A LYS* 1.3 60.7 + - + +
210A LEU* 4.8 0.4 - - - -
211A ALA* 2.9 31.2 + - - +
256A ALA* 3.7 23.8 - - - +
259A ARG* 3.0 32.2 + - - +
260A THR* 3.4 16.1 - - + +
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ILE* 4.7 13.7 - - + +
204A TYR* 3.0 60.8 + - + +
205A VAL* 3.7 7.0 - - + +
207A GLU* 1.3 76.1 - - + +
209A VAL* 1.3 67.1 + - - +
211A ALA* 3.4 6.3 + - - +
212A ALA* 3.1 22.0 + - - +
3D HIS* 6.3 0.4 - - + -
215D LYS* 6.0 0.2 - - - -
218D SER* 3.0 40.4 + - - +
219D ASP* 5.0 1.8 - - - +
221D HIS* 3.5 18.2 + - - +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU* 3.3 36.6 - - + -
159A PRO* 4.8 0.9 - - + -
164A ILE* 4.4 22.0 - - + -
189A PRO* 4.2 14.8 - - + +
191A ILE* 3.6 19.5 - - + -
205A VAL* 2.9 28.4 + - + +
206A THR 3.8 2.7 - - - +
208A LYS* 1.3 75.5 - - - +
210A LEU* 1.3 65.0 + - + +
212A ALA* 3.0 5.9 + - - +
213A VAL* 2.9 37.2 + - + +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PRO* 4.0 17.0 - - + -
191A ILE* 6.5 0.2 - - + -
206A THR* 2.9 39.1 + - + +
207A GLU* 4.0 0.7 - - - +
209A VAL* 1.3 76.9 - - + +
211A ALA* 1.3 65.3 + - - +
213A VAL* 2.9 17.2 + - + +
214A TYR* 2.9 23.3 + - + -
229A LEU* 3.9 33.7 - - + -
231A PRO* 4.7 7.6 - - + -
256A ALA 5.0 0.9 - - - +
257A LEU* 3.8 25.4 - - + -
260A THR* 3.5 28.7 - - - +
261A VAL* 4.5 0.7 - - + -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU 2.9 19.8 + - - +
208A LYS* 3.6 6.1 - - - +
209A VAL 3.3 0.2 - - - -
210A LEU* 1.3 76.6 - - - +
212A ALA* 1.3 60.9 + - - +
214A TYR* 3.8 4.2 + - - +
215A LYS* 3.3 21.1 + - - +
260A THR* 4.1 14.9 - - + +
215D LYS* 4.1 12.8 - - + +
218D SER* 3.8 28.0 - - - +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ILE* 3.5 28.9 - - + +
165A LEU* 6.1 0.7 - - - -
168A ALA* 4.1 8.6 - - + +
208A LYS 3.1 8.5 + - - +
209A VAL 3.0 8.4 + - - +
211A ALA* 1.3 75.7 - - - +
213A VAL* 1.3 68.2 + - - +
215A LYS* 3.2 3.5 + - - +
216A ALA* 3.0 23.7 + - - +
215D LYS* 4.3 16.8 - - - +
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ALA* 4.0 16.6 - - + +
171A LEU* 4.2 12.6 - - + -
187A VAL* 3.9 27.8 - - + -
189A PRO* 4.1 17.7 - - + -
209A VAL* 2.9 34.7 + - + +
210A LEU* 2.9 12.3 + - + +
212A ALA* 1.3 76.7 - - - +
214A TYR* 1.3 66.0 + - + +
216A ALA* 3.3 4.0 + - - +
217A LEU* 3.0 35.3 + - + +
229A LEU* 5.3 0.7 - - + -
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 5.7 1.4 - - + +
210A LEU* 2.9 25.3 + - + +
211A ALA* 4.5 2.9 - - - +
213A VAL* 1.3 77.4 - - + +
215A LYS* 1.3 65.4 + - - +
217A LEU* 3.2 17.6 + - + +
218A SER* 2.9 22.3 + - - -
224A LEU* 3.6 35.5 - - + +
227A THR* 5.1 2.9 + - - -
228A LEU 5.2 0.7 - - - -
229A LEU* 3.4 40.0 - - + +
260A THR 3.9 17.3 - - - +
261A VAL* 3.7 21.6 - - + +
262A PRO* 3.7 18.8 - - + -
265A VAL* 3.5 25.5 - - + +
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ALA 3.3 16.9 + - - +
212A ALA* 3.2 5.7 + - - +
214A TYR* 1.3 77.7 - - - +
216A ALA* 1.3 58.4 + - - +
218A SER* 3.2 9.1 + - - -
219A ASP* 2.9 68.0 + - - +
208D LYS 6.0 0.2 - - - -
211D ALA* 4.0 19.5 - - + +
212D ALA* 4.2 23.6 - - - +
215D LYS* 4.1 29.6 - - + -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ALA* 3.4 34.8 - - + +
169A ASN* 4.3 4.7 - - - +
172A ALA* 3.8 7.2 - - + -
212A ALA 3.0 12.0 + - - +
213A VAL 3.4 7.9 - - - +
215A LYS* 1.3 74.8 - - - +
217A LEU* 1.3 66.4 + - - +
219A ASP* 2.9 10.6 + - - +
220A HIS* 2.9 29.4 + - + -
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA* 3.7 23.1 - - - +
175A ALA* 3.9 9.0 - - + -
187A VAL* 4.4 18.4 - - + -
213A VAL* 3.0 28.1 + - + +
214A TYR* 3.2 39.7 + - + +
216A ALA* 1.3 75.3 - - - +
218A SER* 1.3 63.2 + - - +
220A HIS 3.2 1.4 + - - -
221A HIS 3.1 3.8 + - - -
222A VAL* 3.0 60.1 + - + +
224A LEU* 4.0 15.7 - - + -
227A THR* 5.5 2.0 - - + +
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TYR 2.9 13.3 + - - -
215A LYS* 3.3 11.1 - - - +
216A ALA 3.1 0.2 - - - -
217A LEU* 1.3 76.5 - - - +
219A ASP* 1.3 60.2 + - - +
221A HIS* 2.9 12.5 + - - +
222A VAL 5.0 3.1 - - - +
207D GLU 5.1 0.3 + - - -
208D LYS* 2.6 42.0 + - - +
211D ALA* 3.6 28.3 - - - +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 2.9 51.2 + - - +
216A ALA* 2.9 11.1 + - - +
218A SER* 1.3 78.5 + - - +
220A HIS* 1.3 63.1 + - + +
221A HIS* 3.2 18.3 + - - -
162B LEU* 3.6 15.9 - - + +
165B LEU* 3.8 28.7 - - + +
208D LYS* 4.8 2.4 - - - +
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Residues in contact with HIS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 2.8 27.8 + - - -
172A ALA* 3.4 29.7 - - + +
173A ARG* 3.8 34.3 + - + +
176A SER* 3.7 18.8 + - - -
216A ALA* 2.9 22.8 + - - +
217A LEU 3.2 2.7 + - - +
218A SER 3.1 0.2 - - - -
219A ASP* 1.3 79.9 - - + +
221A HIS* 1.3 75.9 + - - +
222A VAL* 3.3 3.2 + - + -
116B LEU* 5.7 1.8 - - + +
117B ALA 4.2 3.6 - - - +
162B LEU* 3.4 32.3 - - + +
165B LEU* 3.9 5.4 - - + +
166B GLU* 4.0 10.3 - - + -
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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
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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