Contacts of the helix formed by residues 230 - 257 (chain D) in PDB entry 5AQM
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 PHE 230 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D SER* 3.3 27.4 - - - -
154D GLN* 3.9 17.3 - - + -
155D GLU* 3.2 49.3 - - + +
158D GLU* 3.9 22.9 - - + -
226D LEU* 4.3 7.2 - - + -
227D PRO* 2.9 41.0 + - + +
228D GLU 4.1 1.1 - - - -
229D ASN* 1.3 97.3 - - - +
231D LYS* 1.3 57.0 + - - +
233D SER* 4.0 6.1 - - - -
234D ARG* 3.0 28.6 + - - +
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D GLU 4.3 9.0 - - - +
229D ASN 2.9 12.7 + - - +
230D PHE* 1.3 71.8 - - - +
232D ASP* 1.3 61.8 + - - +
234D ARG* 3.4 6.3 + - - +
235D LEU* 3.0 30.2 + - - +
1261D GOL 3.0 14.9 + - - +
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Residues in contact with ASP 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ASN* 4.4 7.4 + - - -
155D GLU* 3.9 4.5 - - - +
159D LEU* 4.1 16.1 - - + +
231D LYS* 1.3 75.1 - - - +
233D SER* 1.4 56.6 + - - +
235D LEU* 3.4 9.1 + - - +
236D LYS* 3.0 30.3 + - - +
1261D GOL 2.9 32.6 + - - +
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Residues in contact with SER 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D GLU* 2.8 40.6 + - - +
158D GLU* 3.8 8.7 - - - +
159D LEU* 3.5 19.3 - - - +
162D LEU* 3.4 11.1 - - - +
226D LEU* 3.7 23.3 - - - -
230D PHE* 3.8 9.9 - - - -
231D LYS 3.3 0.2 - - - -
232D ASP* 1.4 68.7 - - - +
234D ARG* 1.3 60.5 + - - +
236D LYS 3.3 0.3 + - - -
237D ARG* 2.8 31.2 + - - +
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Residues in contact with ARG 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLU* 3.7 16.8 + - - -
285C ASP* 4.4 1.9 - - - +
294C TYR* 4.2 28.1 - - - +
226D LEU* 2.8 43.3 + - + -
227D PRO* 3.6 8.7 + - - +
228D GLU* 4.0 27.9 - - - +
230D PHE 3.0 20.3 + - - +
231D LYS* 3.7 6.3 - - - +
233D SER* 1.3 74.9 - - - +
235D LEU* 1.4 57.7 + - - +
237D ARG* 3.4 14.4 + - - +
238D LYS* 3.0 30.0 + - - +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D LYS 3.0 17.6 + - - +
232D ASP* 3.7 9.2 - - - +
234D ARG* 1.4 78.1 - - - +
236D LYS* 1.3 56.6 + - - +
238D LYS* 3.4 9.4 + - + +
239D GLY* 2.9 26.2 + - - -
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Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D LEU* 3.9 19.1 - - + +
162D LEU* 3.7 26.5 - - + -
163D LYS* 3.8 29.1 - - - +
166D GLU* 3.0 46.7 + - + +
232D ASP 3.0 17.5 + - - +
233D SER* 3.7 4.0 - - - +
235D LEU* 1.3 71.9 - - - +
237D ARG* 1.3 60.4 + - - +
239D GLY* 3.4 1.5 + - - +
240D LEU* 2.9 31.8 + - + +
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Residues in contact with ARG 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLU* 2.9 40.8 + - - +
285C ASP* 3.7 22.6 + - - +
294C TYR* 3.5 23.4 + - - -
162D LEU* 3.9 16.3 - - + +
221D ILE* 3.6 32.5 + - + -
224D LEU* 3.2 26.5 + - - -
226D LEU* 3.7 22.7 - - + +
233D SER 2.8 17.8 + - - +
234D ARG* 3.7 22.0 + - - +
235D LEU 3.3 0.2 - - - -
236D LYS* 1.3 75.9 - - - +
238D LYS* 1.3 57.1 + - - +
240D LEU* 3.2 3.6 + - - +
241D VAL* 2.9 30.1 + - + +
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Residues in contact with LYS 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ASP* 3.2 24.8 + - + +
286C SER* 4.0 13.5 - - - -
290C GLY* 3.7 15.4 + - - -
292C ASP* 2.7 36.2 + - - +
294C TYR* 5.6 0.2 - - - +
234D ARG 3.0 18.3 + - - +
235D LEU* 3.7 11.4 - - + +
237D ARG* 1.3 76.8 - - - +
239D GLY* 1.3 56.4 + - - +
241D VAL* 3.4 2.8 + - - +
242D LYS* 3.0 46.6 + - + +
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Residues in contact with GLY 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D LEU 2.9 16.5 + - - -
236D LYS* 3.9 1.8 - - - -
238D LYS* 1.3 75.3 - - - +
240D LEU* 1.3 57.3 + - - +
242D LYS* 3.4 7.8 + - - +
243D LYS* 2.9 29.6 + - - +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D LEU* 4.1 11.7 - - + +
165D LEU* 3.8 25.8 - - + -
166D GLU* 3.9 31.4 + - + +
169D VAL* 3.8 32.3 - - + -
221D ILE* 3.7 24.7 - - + -
236D LYS 2.9 18.5 + - - +
237D ARG* 3.7 4.5 - - - +
239D GLY* 1.3 72.9 - - - +
241D VAL* 1.3 65.9 + - - +
243D LYS* 3.2 13.9 + - + +
244D VAL* 2.9 27.3 + - - +
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Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG* 4.0 11.0 - - - +
285C ASP* 3.6 37.9 - - + +
286C SER* 3.9 6.7 - - - -
218D LEU* 4.1 14.6 - - + -
221D ILE* 3.7 31.4 - - + -
237D ARG 2.9 20.2 + - - +
238D LYS 3.9 4.0 - - - +
240D LEU* 1.3 74.2 - - - +
242D LYS* 1.3 57.4 + - - +
244D VAL* 3.2 2.4 + - - +
245D GLN* 2.8 48.8 + - - +
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Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C SER* 5.2 4.7 - - - +
238D LYS* 3.0 39.7 + - + +
239D GLY* 3.6 7.2 - - - +
240D LEU 3.3 0.2 - - - -
241D VAL* 1.3 76.5 - - - +
243D LYS* 1.3 55.9 + - - +
245D GLN* 3.3 13.8 + - - +
246D ALA* 2.9 30.2 + - - +
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 4.7 9.9 - - + -
170D GLU* 6.4 1.3 - - + -
239D GLY 2.9 18.3 + - - +
240D LEU* 3.5 15.7 - - + +
242D LYS* 1.3 73.7 - - - +
244D VAL* 1.3 63.7 + - - +
246D ALA* 3.3 7.1 + - - +
247D PHE* 3.0 55.7 + - + -
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 3.5 37.7 - - + -
214D PHE* 3.8 30.5 - - + +
217D ILE* 4.0 10.5 - - + -
218D LEU* 3.6 32.1 - - + -
221D ILE* 4.9 0.2 - - + -
240D LEU* 2.9 21.8 + - + +
241D VAL 3.7 3.6 - - - +
243D LYS* 1.3 76.4 - - - +
245D GLN* 1.4 56.8 + - - +
247D PHE* 3.1 9.4 + - - +
248D LEU* 2.8 30.6 + - + +
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Residues in contact with GLN 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG* 3.3 10.1 - - - +
286C SER* 2.6 49.4 + - - -
1383C TRS 3.1 40.2 + - - +
218D LEU* 4.5 6.1 - - + -
241D VAL* 2.8 31.4 + - + +
242D LYS* 3.7 9.6 - - - +
244D VAL* 1.4 72.0 - - - +
246D ALA* 1.4 57.7 + - - +
248D LEU* 3.3 8.4 + - - +
249D ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LYS 2.9 17.1 + - - +
243D LYS* 3.3 7.4 + - - +
245D GLN* 1.4 74.2 - - - +
247D PHE* 1.3 65.2 + - + +
249D ALA* 3.2 9.9 + - - +
250D GLU* 3.1 26.0 + - - +
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Residues in contact with PHE 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 3.8 16.4 - - + -
173D ALA* 3.6 23.3 - - + -
176D LEU* 3.6 14.0 - - + +
214D PHE* 3.4 36.8 - + + -
243D LYS* 3.0 50.8 + - + -
244D VAL* 3.5 5.2 - - - +
246D ALA* 1.3 76.8 - - + +
248D LEU* 1.3 58.3 + - - +
250D GLU* 3.1 24.4 + - - +
251D CYS* 2.9 31.2 + - - -
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ARG* 3.8 20.9 - - - +
1383C TRS 4.0 12.6 - - - +
211D ILE* 3.8 35.0 - - + +
214D PHE* 3.7 25.4 - - + -
215D MET* 4.0 12.1 - - + -
218D LEU* 3.8 28.3 - - + -
244D VAL* 2.8 20.5 + - + +
245D GLN* 3.3 11.2 + - - +
247D PHE* 1.3 75.0 - - - +
249D ALA* 1.3 57.9 + - - +
251D CYS* 3.2 6.6 + - - +
252D ASP* 2.9 34.5 + - - +
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D GLN 3.0 12.9 + - - +
246D ALA* 3.2 13.2 + - - +
248D LEU* 1.3 76.6 - - - +
250D GLU* 1.4 57.0 + - + +
252D ASP* 3.2 13.5 + - - +
253D THR* 3.0 30.0 + - - -
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Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 3.8 15.2 - - + +
180D ASN* 3.4 23.6 + - - +
246D ALA* 3.1 17.7 + - - +
247D PHE* 3.1 32.6 + - - +
249D ALA* 1.4 72.1 - - + +
251D CYS* 1.4 65.7 + - - +
253D THR* 3.1 11.6 + - - -
254D VAL* 3.0 25.6 + - - +
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Residues in contact with CYS 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 4.0 11.9 - - - -
207D VAL* 3.7 10.1 - - + +
210D THR* 3.8 29.8 - - - -
211D ILE* 3.4 29.6 - - + -
214D PHE* 3.9 14.4 - - - -
247D PHE 2.9 17.2 + - - -
248D LEU* 3.3 9.2 - - - +
250D GLU* 1.4 76.7 - - - +
252D ASP* 1.4 57.0 + - - +
254D VAL* 3.1 7.1 + - - +
255D GLU* 3.0 31.8 + - - +
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Residues in contact with ASP 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ARG* 2.7 43.2 + - - -
211D ILE* 4.3 3.3 - - - +
248D LEU 2.9 16.0 + - - +
249D ALA* 3.2 12.6 + - - +
251D CYS* 1.4 73.7 - - - +
253D THR* 1.3 59.3 + - - +
255D GLU* 3.3 12.0 + - - +
256D GLN* 3.0 36.3 + - - +
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Residues in contact with THR 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D LEU* 6.5 0.7 - - + -
249D ALA 3.0 14.1 + - - -
250D GLU* 3.1 13.4 + - - -
252D ASP* 1.3 73.9 - - - +
254D VAL* 1.3 64.9 + - + +
256D GLN* 3.1 25.4 + - - +
257D ASN* 2.9 36.0 + - - +
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D LEU* 4.4 12.3 - - + -
179D LEU* 5.3 8.5 - - + -
180D ASN* 3.5 29.4 - - - +
183D LEU* 4.5 17.5 - - + -
203D LEU* 5.3 6.3 - - + -
207D VAL* 3.8 23.3 - - + -
250D GLU 3.0 17.1 + - - +
251D CYS 3.1 8.3 + - - +
253D THR* 1.3 76.7 - - + +
255D GLU* 1.3 56.7 + - - +
257D ASN* 2.9 23.4 + - - +
258D ILE* 3.2 27.7 + - + +
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Residues in contact with GLU 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ARG* 5.0 1.6 + - - -
204D ASP* 4.1 0.9 - - - +
207D VAL* 3.8 16.8 - - + +
208D LYS* 2.9 40.5 + - - +
211D ILE* 3.5 24.1 - - + +
251D CYS 3.0 16.8 + - - +
252D ASP* 3.3 15.0 + - - +
254D VAL* 1.3 75.8 - - - +
256D GLN* 1.4 55.8 + - + +
258D ILE* 3.2 18.1 - - + +
260D GLN* 3.1 17.7 + - - -
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Residues in contact with GLN 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D ASP* 3.0 19.6 + - - +
253D THR* 3.1 28.1 + - - +
255D GLU* 1.4 75.3 - - - +
257D ASN* 1.3 64.4 + - - +
260D GLN* 3.1 26.7 - - - +
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Residues in contact with ASN 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LEU* 4.2 23.5 - - + +
187D GLN* 4.5 13.6 + - - +
200D LEU* 4.0 15.2 - - - +
253D THR* 2.9 35.3 + - - +
254D VAL* 2.9 9.3 + - - +
256D GLN* 1.3 84.7 + - - +
258D ILE* 1.3 63.4 + - - +
260D GLN* 4.2 6.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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