Contacts of the helix formed by residues 220 - 252 (chain B) in PDB entry 3N9Z
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 ARG 220 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 3.7 34.3 - - - -
207B PRO* 3.1 43.2 + - - +
208B MET* 4.0 13.0 - - + -
211B LEU* 4.1 18.8 - - + +
216B PHE* 2.9 19.0 + - + +
219B PHE* 1.3 103.3 + - + +
221B THR* 1.3 59.1 + - - +
222B LYS 3.3 2.9 - - - -
223B THR* 3.3 10.5 + - - -
224B TRP* 2.9 28.6 + - - +
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Residues in contact with THR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE 3.6 0.9 + - - -
217B ARG 2.9 24.7 + - - +
218B LEU* 3.7 13.0 + - - -
219B PHE 3.6 1.7 - - - -
220B ARG* 1.3 76.0 - - - +
222B LYS* 1.3 57.1 + - - +
224B TRP* 3.7 9.0 - - + +
225B LYS* 3.0 29.9 + - + +
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Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG 3.3 0.6 - - - -
221B THR* 1.3 78.5 - - - +
223B THR* 1.3 64.0 + - - +
225B LYS* 3.3 11.2 + - + +
226B ASP* 3.1 48.7 + - - +
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B THR* 3.0 37.8 - - + +
207B PRO* 3.9 32.7 - - + +
208B MET* 4.1 7.6 - - + -
220B ARG* 3.3 15.7 + - - -
222B LYS* 1.3 79.6 - - - +
224B TRP* 1.3 58.0 + - - +
226B ASP* 3.2 8.7 + - - +
227B HIS* 2.8 28.1 + - - +
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Residues in contact with TRP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 3.6 20.0 - - + -
89B ALA* 4.0 8.7 - - + -
90B TYR* 3.7 27.8 - - + -
93B TYR* 5.3 2.9 - + + -
94B TYR* 4.5 14.5 + + - -
208B MET* 3.7 31.6 - - + -
216B PHE* 3.7 21.5 - + - +
217B ARG* 4.1 38.5 - - + +
220B ARG 2.9 17.6 + - - +
221B THR* 3.7 10.8 - - + +
223B THR* 1.3 76.9 - - - +
225B LYS* 1.3 59.2 + - + +
227B HIS* 3.3 11.9 + + - +
228B VAL* 2.9 51.8 + - + +
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Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B THR* 3.0 19.0 + - + +
222B LYS* 3.5 10.5 - - + +
224B TRP* 1.3 81.7 - - + +
226B ASP* 1.3 63.9 - - - +
228B VAL* 3.5 6.7 + - - +
229B ALA* 3.1 26.7 + - + +
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Residues in contact with ASP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLN* 5.6 2.4 - - - +
204B THR* 4.0 19.0 - - + +
222B LYS* 3.1 44.9 + - - +
223B THR* 3.6 9.0 - - - +
225B LYS* 1.3 81.1 - - - +
227B HIS* 1.3 65.8 + - - +
229B ALA* 3.2 8.7 + - - +
230B ALA* 3.0 23.2 + - - +
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Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 3.7 17.6 + - + +
87B TRP* 3.6 14.1 - + - -
90B TYR* 4.9 1.3 - - + -
201B MET* 3.3 10.8 + - + -
204B THR* 2.9 26.5 + - - +
205B SER* 3.3 30.5 + - - -
208B MET* 3.6 21.3 - - + -
223B THR 2.8 17.1 + - - +
224B TRP* 3.4 12.3 - + - +
226B ASP* 1.3 76.3 - - - +
228B VAL* 1.3 62.4 + - - +
230B ALA* 3.1 6.6 + - - +
231B TRP* 3.1 56.3 + + - -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.8 20.0 - - + -
94B TYR* 3.8 34.8 - - + +
224B TRP* 2.9 56.4 + - + +
225B LYS* 3.7 7.4 - - - +
227B HIS* 1.3 74.5 - - - +
229B ALA* 1.3 64.1 + - - +
230B ALA 3.3 0.2 + - - -
231B TRP 3.5 0.5 + - - -
232B ASP* 3.0 36.8 + - - +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LYS* 3.1 15.3 + - + +
226B ASP* 3.2 11.8 + - - +
228B VAL* 1.3 77.4 - - - +
230B ALA* 1.3 62.6 + - - +
232B ASP* 3.4 10.1 + - - +
233B VAL* 3.2 27.2 + - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA* 3.5 28.3 - - - +
200B GLN* 4.0 11.7 - - + -
201B MET* 3.6 17.9 - - - +
226B ASP 3.0 12.4 + - - +
227B HIS* 3.1 9.4 + - - +
229B ALA* 1.3 74.1 - - - +
231B TRP* 1.3 66.7 + - - +
233B VAL* 3.3 6.8 + - - +
234B ILE* 3.1 26.2 + - - +
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Residues in contact with TRP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 3.8 29.0 - + - +
90B TYR* 3.3 39.3 - + + -
91B HIS* 3.9 22.2 - + - -
101B LEU* 5.8 2.5 - - + -
201B MET* 3.4 37.8 - - + +
227B HIS* 3.1 51.9 + + - -
228B VAL 3.9 0.9 - - - +
230B ALA* 1.3 76.1 - - - +
232B ASP* 1.3 53.0 + - - +
234B ILE* 3.1 27.0 + - + +
235B PHE* 2.8 61.5 + + - -
282B THR* 5.4 2.5 - - + -
283B GLU* 6.0 6.1 - - + -
286B ALA* 5.3 4.3 - - + -
602B HC9 5.0 10.5 - - + -
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 2.7 28.3 + - - -
94B TYR* 5.3 5.1 - - - -
96B ARG* 3.3 20.5 + - - +
228B VAL* 3.0 33.7 + - - +
229B ALA* 3.5 10.2 - - - +
230B ALA 3.2 0.2 - - - -
231B TRP* 1.3 74.9 - - - +
233B VAL* 1.3 54.6 + - + +
235B PHE* 4.1 2.7 - - - +
236B SER* 2.6 39.1 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 3.5 44.6 - - - +
194B PHE* 4.1 6.3 - - - -
197B ALA* 3.6 24.2 - - + -
229B ALA* 3.2 15.1 + - + +
230B ALA* 3.6 7.2 - - - +
231B TRP 3.3 0.2 - - - -
232B ASP* 1.3 74.3 - - + +
234B ILE* 1.3 67.3 + - - +
236B SER* 3.4 3.9 + - - -
237B LYS* 3.0 42.6 + - + +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 3.6 22.0 - - + -
197B ALA* 4.1 9.6 - - + +
198B ILE* 4.1 27.1 - - + -
201B MET* 3.8 31.9 - - + -
230B ALA 3.1 15.6 + - - +
231B TRP* 3.1 32.5 + - + +
233B VAL* 1.3 75.1 - - - +
235B PHE* 1.3 61.9 + - - +
238B ALA* 3.1 24.9 + - - +
282B THR* 3.7 21.5 - - + -
286B ALA* 4.4 10.1 - - + -
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Residues in contact with PHE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.8 19.3 - + - +
91B HIS* 3.4 36.3 - + - -
96B ARG* 3.6 36.8 - - + +
97B PRO* 3.9 24.2 - - + -
231B TRP* 2.8 46.7 + + - +
232B ASP 4.2 1.3 - - - +
234B ILE* 1.3 71.0 - - - +
236B SER* 1.3 65.5 - - - +
239B ASP* 3.0 44.1 + - - +
279B ALA* 5.6 2.7 - - - -
282B THR* 4.0 28.9 - - + -
283B GLU* 6.3 2.0 - - + -
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 5.2 3.3 + - - +
232B ASP* 2.6 25.3 + - - +
233B VAL* 3.8 4.9 - - - -
235B PHE* 1.3 76.8 - - - +
237B LYS* 1.3 69.0 + - - +
239B ASP* 3.9 3.0 - - - +
240B ILE* 3.1 37.9 + - - +
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU* 2.8 60.5 + - + +
193B ARG* 3.7 20.7 - - - +
194B PHE* 3.4 36.1 - - + +
233B VAL* 3.0 23.4 + - + +
236B SER* 1.3 80.6 - - - +
238B ALA* 1.3 66.1 + - - +
239B ASP 3.3 0.2 + - - -
240B ILE* 3.3 14.4 + - + +
241B TYR* 3.0 41.3 + - + +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 4.4 3.0 - - + -
234B ILE 3.1 19.6 + - - +
235B PHE 4.1 0.9 - - - +
237B LYS* 1.3 77.1 - - - +
239B ASP* 1.3 59.7 + - - +
241B TYR* 3.4 4.0 + - - +
242B THR* 3.0 32.2 + - - -
281B VAL* 4.8 1.5 - - + +
282B THR* 3.3 39.0 - - + +
285B LEU* 4.0 22.0 - - + -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 5.6 1.4 + - - -
97B PRO* 5.8 2.9 - - - +
235B PHE* 3.0 33.3 + - - +
236B SER* 4.0 3.6 - - - +
238B ALA* 1.3 74.9 - - - +
240B ILE* 1.3 59.7 + - + +
242B THR* 3.3 4.1 + - - -
243B GLN* 2.9 50.1 + - - +
278B LYS* 3.2 35.1 + - - +
282B THR* 3.6 13.3 + - - -
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 3.1 28.3 + - - +
237B LYS* 3.8 14.6 - - + +
239B ASP* 1.3 75.3 - - + +
241B TYR* 1.3 60.8 + - + +
243B GLN* 4.1 5.8 - - - +
244B ASN* 3.0 55.2 + - - +
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Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.9 28.9 - + - -
172B THR* 5.5 1.1 - - + -
176B PHE* 3.5 30.1 - + + -
180B GLN* 3.9 23.7 + - - -
188B ASN* 5.8 1.0 + - - -
190B GLU* 5.2 0.7 - - - +
191B ALA* 3.9 19.2 + - - +
194B PHE* 5.3 3.1 - + - -
237B LYS* 3.0 41.1 + - + +
238B ALA* 3.6 9.6 - - - +
240B ILE* 1.3 80.5 - - + +
242B THR* 1.3 61.8 + - - +
244B ASN* 3.9 6.4 - - - +
245B PHE* 3.1 24.9 + - - +
285B LEU* 4.4 12.3 - - + -
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Residues in contact with THR 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PHE* 4.6 0.2 - - - -
238B ALA 3.0 18.6 + - - -
239B ASP 3.9 3.1 - - - -
241B TYR* 1.3 74.3 - - - +
243B GLN* 1.3 57.6 + - - +
245B PHE* 3.3 3.6 + - - +
246B TYR* 3.0 27.8 + - - +
263B LEU* 4.3 27.6 - - + +
267B LEU* 5.4 0.8 - - + +
274B PHE* 3.9 26.9 - - + -
277B ILE* 5.1 0.7 - - + -
278B LYS* 4.2 25.7 + - + +
281B VAL* 3.5 23.4 - - + +
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Residues in contact with GLN 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP* 2.9 28.7 + - - +
240B ILE* 4.1 4.9 - - - +
242B THR* 1.3 75.6 - - - +
244B ASN* 1.3 63.7 + - - +
246B TYR* 3.4 6.9 + - - +
247B TRP* 3.1 37.6 + - + -
274B PHE* 4.7 7.4 - - + -
278B LYS* 3.1 33.1 - - - +
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Residues in contact with ASN 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 3.0 40.9 + - - +
241B TYR* 3.9 6.8 - - - +
243B GLN* 1.3 74.4 - - - +
245B PHE* 1.3 60.2 + - - +
247B TRP* 3.4 4.1 + - - +
248B GLU* 2.9 48.1 + - - +
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PHE* 3.5 42.8 - + + -
178B GLU* 4.9 12.3 - - - -
241B TYR 3.1 19.2 + - - +
242B THR 3.6 4.0 - - - +
244B ASN* 1.3 76.6 - - - +
246B TYR* 1.3 64.5 + - - +
248B GLU* 3.5 10.0 + - + +
249B LEU* 3.0 45.2 + - + +
260B ARG* 5.0 3.6 - - + -
263B LEU* 3.5 26.0 - - + -
264B TYR* 3.7 40.4 - + + -
267B LEU* 3.8 11.7 - - + -
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B THR 3.0 14.4 + - - +
243B GLN* 3.4 12.1 - - - +
245B PHE* 1.3 82.2 - - - +
247B TRP* 1.3 96.1 + + - +
249B LEU* 3.3 15.3 - - + +
250B ARG* 2.9 65.4 + - - -
267B LEU* 4.2 17.9 - - + -
274B PHE* 3.7 38.8 - + + -
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Residues in contact with TRP 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLN* 3.1 33.2 + - + +
244B ASN* 4.1 4.3 - - - +
245B PHE 3.3 0.2 - - - -
246B TYR* 1.3 96.8 - + - +
248B GLU* 1.3 59.7 + - - +
249B LEU 3.2 1.6 - - - -
250B ARG* 3.1 32.6 + - + +
251B GLN* 3.0 41.4 + - + +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 4.2 19.2 - - - +
244B ASN* 2.9 35.6 + - - +
245B PHE* 3.9 8.7 - - - +
247B TRP* 1.3 73.1 - - - +
249B LEU* 1.3 60.4 + - - +
251B GLN* 3.6 21.8 - - - +
252B LYS* 2.9 51.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.0 26.9 + - + +
246B TYR* 3.3 13.2 - - + +
248B GLU* 1.3 77.2 - - - +
250B ARG* 1.3 67.3 + - - +
252B LYS* 3.8 2.2 - - - -
253B GLY* 2.9 26.9 + - - -
254B SER 4.6 0.7 + - - -
264B TYR* 3.4 40.4 - - + +
267B LEU* 4.3 32.3 - - + -
268B GLY* 5.7 1.6 - - - +
----------------------------------------------------------
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 2.9 74.0 + - - -
247B TRP* 3.1 29.7 + - + +
249B LEU* 1.3 88.4 - - - +
251B GLN* 1.3 65.4 + - + +
253B GLY* 3.5 9.7 + - - -
----------------------------------------------------------
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Residues in contact with GLN 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TRP* 3.0 35.5 + - + +
248B GLU* 3.6 22.5 - - - +
249B LEU 3.3 0.2 - - - -
250B ARG* 1.3 76.0 - - + +
252B LYS* 1.3 62.0 + - + +
253B GLY* 3.0 8.5 + - - -
----------------------------------------------------------
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 5.2 6.5 + - - -
248B GLU* 2.9 37.6 + - + +
249B LEU* 3.8 3.4 - - - +
251B GLN* 1.3 75.0 - - + +
253B GLY* 1.3 63.6 + - - +
254B SER* 2.7 24.5 + - - +
256B HIS* 5.8 2.9 - - - +
260B ARG* 5.2 14.2 - - - +
----------------------------------------------------------
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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