Contacts of the helix formed by residues 225 - 250 (chain L) in PDB entry 1JH0
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 GLY 225 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H GLU* 5.3 3.6 - - - -
213L ASP* 3.9 10.1 - - - -
223L SER* 3.2 7.3 + - - -
224L ILE* 1.3 81.7 - - - +
226L THR* 1.3 56.7 + - - -
227L LEU 3.1 3.4 - - - -
228L GLY 2.7 22.7 + - - -
229L ILE* 2.8 16.6 + - - +
44M ASN* 3.4 15.9 - - - -
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Residues in contact with THR 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H GLU* 3.3 30.7 + - + +
177H ARG* 5.0 0.2 + - - -
190L HIS* 6.2 1.1 - - - -
209L PRO* 4.5 9.6 - - + +
212L GLU* 4.3 21.1 - - + +
213L ASP* 4.8 6.0 + - - +
225L GLY* 1.3 70.8 - - - -
227L LEU* 1.3 59.6 + - - +
229L ILE* 3.8 8.7 - - - +
230L HIS* 2.9 31.6 + - - -
232M GLU* 3.1 34.5 + - - +
233M ARG* 4.9 1.0 - - - -
234M GLU* 6.1 0.4 - - - -
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Residues in contact with LEU 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H GLU* 4.7 2.7 + - - +
175H MET* 4.1 28.7 - - + -
194H GLN* 6.0 0.2 - - - +
225L GLY 3.1 0.6 - - - -
226L THR* 1.3 80.7 + - - +
228L GLY* 1.3 60.8 + - - +
230L HIS* 3.9 3.0 + - - +
231L ARG* 3.1 59.0 + - - +
5M ASN* 3.4 24.5 - - - +
8M SER* 5.3 1.1 - - - +
42M PHE 5.1 0.2 - - - -
223M ILE* 5.3 0.9 - - + -
224M LEU* 4.1 12.8 - - + -
227M SER* 4.6 2.0 - - - -
232M GLU* 3.3 39.5 - - + +
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Residues in contact with GLY 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224L ILE* 3.6 25.1 + - - +
225L GLY* 2.7 9.1 + - - -
227L LEU* 1.3 78.4 - - - +
229L ILE* 1.3 57.7 + - - -
230L HIS 3.1 1.8 - - - -
231L ARG* 3.0 5.5 + - - +
232L LEU* 2.8 28.9 + - - +
42M PHE* 3.9 19.0 + - - -
43M GLY* 5.1 0.4 - - - -
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Residues in contact with ILE 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L ALA* 5.0 10.1 - - + +
189L LEU* 6.1 2.5 - - + -
190L HIS* 3.5 42.0 - - + +
224L ILE* 3.6 23.1 - - + +
225L GLY 2.8 12.9 + - - +
226L THR* 3.8 10.3 - - - +
228L GLY* 1.3 71.9 - - - +
230L HIS* 1.3 83.2 + - + +
232L LEU* 3.6 18.2 - - + +
233L GLY* 2.8 24.4 + - - -
216M PHE* 3.8 8.7 - - + -
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Residues in contact with HIS 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L HIS* 3.1 19.5 - + - -
226L THR* 2.9 26.2 + - - +
227L LEU* 3.9 4.9 + - - +
228L GLY 3.1 0.8 - - - -
229L ILE* 1.3 87.2 - - + +
231L ARG* 1.3 66.2 + - - +
233L GLY 3.9 0.7 - - - +
234L LEU* 3.3 21.1 + - - +
216M PHE* 4.8 3.1 - + - -
219M HIS* 2.9 17.9 + + - -
220M GLY* 3.7 13.6 - - - -
223M ILE* 3.2 43.2 - - + +
224M LEU* 4.3 7.7 - - + +
232M GLU 5.2 2.2 - - - -
234M GLU* 2.8 18.2 + - + -
856M FE 2.4 31.4 - - - -
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Residues in contact with ARG 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227L LEU* 3.1 51.4 + - - +
228L GLY 3.0 6.8 + - - +
230L HIS* 1.3 75.5 - - - +
232L LEU* 1.3 60.9 + - - +
234L LEU* 3.3 4.6 + - - +
235L LEU* 2.9 31.4 + - - +
3M TYR* 4.0 1.4 + - - -
5M ASN* 2.9 35.6 + - - +
6M ILE* 3.1 25.2 + - + +
8M SER* 3.7 22.0 + - - +
41M TRP 3.3 19.8 + - - -
42M PHE* 2.9 44.1 + - + -
224M LEU* 4.0 20.9 - - + -
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Residues in contact with LEU 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L ALA* 5.2 4.5 - - + -
224L ILE* 5.1 11.7 - - + -
228L GLY 2.8 16.2 + - - +
229L ILE* 3.6 24.2 - - + +
231L ARG* 1.3 74.8 - - - +
233L GLY* 1.3 58.6 + - - +
235L LEU* 2.9 6.7 + - + +
236L LEU* 2.7 63.3 + - + +
42M PHE* 4.0 23.3 - - + -
216M PHE* 6.4 0.2 - - + -
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Residues in contact with GLY 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ASN* 3.5 3.4 - - - +
229L ILE 2.8 11.7 + - - -
230L HIS 4.3 0.2 - - - -
231L ARG 3.3 0.2 - - - -
232L LEU* 1.3 77.9 - - - +
234L LEU* 1.3 62.8 + - - +
235L LEU 3.2 0.2 + - - -
236L LEU* 4.6 2.5 - - - -
237L SER* 3.2 25.1 + - - -
216M PHE* 3.5 45.2 - - - +
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Residues in contact with LEU 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L HIS* 4.9 7.0 - - + +
119L PHE* 6.1 4.0 - - + -
120L ALA* 4.0 18.2 - - + -
230L HIS 3.3 18.2 + - - +
231L ARG 3.3 5.7 + - - +
232L LEU 3.2 0.2 - - - -
233L GLY* 1.3 75.7 - - - +
235L LEU* 1.3 62.4 + - + +
237L SER* 3.7 1.2 - - - -
238L LEU* 3.1 60.3 + - + +
6M ILE* 4.4 13.0 - - + -
216M PHE 4.7 4.9 - - - -
217M ALA* 4.0 15.7 - - - +
220M GLY* 4.6 1.8 - - - -
221M ALA* 4.1 18.4 - - + +
224M LEU* 3.6 25.6 - - + -
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Residues in contact with LEU 235 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L PHE* 5.8 0.4 - - - -
231L ARG 2.9 17.8 + - - +
232L LEU* 2.9 10.8 + - + +
234L LEU* 1.3 83.7 - - + +
236L LEU* 1.3 64.7 + - - +
237L SER 3.1 1.6 - - - -
238L LEU* 4.6 6.7 - - + +
239L SER* 3.1 34.8 + - - +
6M ILE* 4.6 20.4 - - + -
7M PHE* 5.9 4.7 - - + -
42M PHE* 3.8 23.8 - - + -
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Residues in contact with LEU 236 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L PHE* 3.8 31.1 - - + +
182L THR* 3.3 36.1 - - + -
183L ASN* 3.4 22.2 - - + +
186L ALA* 3.8 25.6 - - + -
232L LEU* 2.7 48.7 + - + +
233L GLY* 4.9 0.9 - - - -
235L LEU* 1.3 73.2 - - - +
237L SER* 1.3 66.8 + - - +
239L SER* 3.7 1.2 - - - -
240L ALA* 3.0 21.0 + - - +
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Residues in contact with SER 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ASN* 2.8 22.7 + - - -
233L GLY 3.2 12.2 + - - -
234L LEU 3.7 4.5 - - - -
235L LEU 3.1 0.6 - - - -
236L LEU* 1.3 73.2 - - - +
238L LEU* 1.3 59.5 + - - -
239L SER 2.6 14.9 + - - -
240L ALA* 2.7 19.7 + - - +
241L VAL* 3.2 8.0 + - - +
855L BPH 4.1 6.1 - - - -
213M ALA* 3.2 28.7 + - - +
216M PHE* 3.8 1.0 - - - +
217M ALA* 3.4 21.2 + - - -
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Residues in contact with LEU 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L PHE* 4.7 13.9 - - + -
120L ALA* 3.6 37.0 - - + +
123L PHE* 3.6 36.6 - - + -
234L LEU* 3.1 37.1 + - + +
235L LEU* 4.6 7.2 - - + +
237L SER* 1.3 78.3 - - - +
239L SER* 1.3 55.1 + - - +
241L VAL* 3.3 1.6 + - - +
242L PHE* 2.8 28.5 + - - +
855L BPH 3.4 28.5 - - + -
217M ALA* 4.7 2.0 - - + -
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Residues in contact with SER 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L PHE* 4.0 31.1 - - - -
235L LEU* 3.1 26.7 + - - +
236L LEU 3.7 3.1 - - - -
237L SER 2.6 5.7 + - - -
238L LEU* 1.3 70.1 - - - +
240L ALA* 1.3 67.0 + - - -
241L VAL 3.0 1.6 - - - -
242L PHE* 2.8 20.2 + - - +
243L PHE* 2.8 20.5 + - - -
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Residues in contact with ALA 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ALA* 3.7 7.1 - - - +
179L PHE* 3.4 29.3 - - + +
180L PHE* 3.5 38.7 - - + +
183L ASN* 5.6 0.7 - - + -
236L LEU 3.0 8.6 + - - +
237L SER* 2.7 16.0 + - - +
239L SER* 1.3 71.3 - - - +
241L VAL* 1.3 52.1 + - + +
244L SER* 2.6 33.8 + - - -
213M ALA* 5.7 0.9 - - + -
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Residues in contact with VAL 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L PHE* 3.2 33.0 - - + +
124L ALA* 4.5 0.7 - - - +
126L LEU* 6.5 0.2 - - + -
127L ALA* 3.9 18.4 - - + -
180L PHE* 4.6 7.0 - - + -
237L SER 3.2 3.9 + - - +
238L LEU* 3.7 6.3 - - - +
239L SER 3.0 0.6 - - - -
240L ALA* 1.3 78.4 - - - +
242L PHE* 1.3 66.8 + - - +
244L SER* 3.0 5.8 + - - -
245L ALA* 2.9 23.5 + - + +
851L BCL 4.5 11.7 - - - -
855L BPH 3.5 48.2 - - + -
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Residues in contact with PHE 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L PHE* 4.6 19.7 - + + -
126L LEU* 5.3 13.7 - - + -
238L LEU 2.8 14.8 + - - +
239L SER* 2.8 13.1 + - - +
241L VAL* 1.3 78.3 - - - +
243L PHE* 1.3 87.0 + + - +
245L ALA* 3.3 5.9 + - + +
246L LEU* 3.0 42.1 + - + +
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Residues in contact with PHE 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L ALA* 3.6 9.3 - - + +
175L ILE* 3.3 28.3 - - + -
176L ALA* 3.7 23.3 - - + +
179L PHE* 3.5 33.4 - + - -
239L SER* 2.8 19.4 + - - +
242L PHE* 1.3 95.2 - + - +
244L SER* 1.3 57.3 + - - +
246L LEU* 3.5 23.3 - - + +
247L CYS* 2.8 30.7 + - - +
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Residues in contact with SER 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ALA* 3.4 5.3 - - - +
180L PHE* 3.5 3.6 - - - -
240L ALA 2.6 24.1 + - - -
241L VAL* 3.0 9.0 + - - -
243L PHE* 1.3 73.5 - - - +
245L ALA* 1.3 66.5 + - - +
247L CYS* 3.3 14.9 + - - -
248L MET 3.4 1.6 + - - -
851L BCL 2.8 73.3 - - - +
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Residues in contact with ALA 245 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L LEU* 5.1 10.3 - - + -
127L ALA* 4.3 16.4 - - - +
130L THR* 3.7 27.1 - - - +
241L VAL* 2.9 16.1 + - + +
242L PHE* 3.7 6.1 - - + +
244L SER* 1.3 74.6 - - - +
246L LEU* 1.3 63.2 + - - +
248L MET* 3.3 1.9 + - - -
249L ILE* 3.1 24.0 + - - +
851L BCL 3.6 12.0 - - - -
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Residues in contact with LEU 246 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L ALA* 4.4 15.3 - - + -
242L PHE* 3.0 35.7 + - + +
243L PHE* 3.5 22.0 - - + +
244L SER 3.2 0.2 - - - -
245L ALA* 1.3 73.9 - - - +
247L CYS* 1.3 57.9 + - - +
248L MET 2.9 10.6 + - - -
249L ILE* 3.2 25.3 + - + +
250L ILE* 3.3 23.7 + - + +
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Residues in contact with CYS 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L PHE* 4.4 0.9 - - - -
170L ASN* 2.8 32.3 + - - +
172L ALA* 3.4 28.4 - - + +
173L HIS* 3.4 32.5 - - - +
176L ALA* 5.8 0.2 - - - -
243L PHE 2.8 16.5 + - - +
244L SER* 3.3 12.5 + - - -
246L LEU* 1.3 71.0 - - - +
248L MET* 1.3 70.1 + - - +
250L ILE* 3.8 5.6 - - - +
251L THR* 3.1 9.5 + - - -
851L BCL 3.4 14.8 - - - -
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Residues in contact with MET 248 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L THR* 4.6 2.2 - - + -
131L LEU* 4.1 16.4 - - + -
135L ARG* 3.3 35.4 - - - +
156L TRP* 4.0 15.7 - - + -
160L THR* 4.2 10.8 - - + -
167L PHE* 3.6 33.2 - - - -
244L SER 4.0 0.2 - - - +
245L ALA 3.3 7.3 + - - +
246L LEU 3.0 0.6 - - - -
247L CYS* 1.3 79.1 - - - +
249L ILE* 1.3 64.8 + - - +
250L ILE 3.2 2.0 - - - -
251L THR* 3.2 14.5 + - + +
851L BCL 3.1 66.2 - - + +
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Residues in contact with ILE 249 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L THR* 4.4 16.1 - - + +
134L PHE* 4.4 23.8 - - + -
135L ARG* 5.0 7.7 - - - +
138L MET* 4.2 23.6 - - + +
245L ALA 3.1 13.2 + - - +
246L LEU* 3.2 27.3 + - + +
248L MET* 1.3 78.2 - - - +
250L ILE* 1.3 62.8 + - + +
251L THR 3.6 0.2 + - - -
253L THR* 2.5 34.5 + - - +
----------------------------------------------------------
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Residues in contact with ILE 250 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170L ASN* 4.2 9.2 - - - +
171L PRO* 5.3 4.5 - - + -
172L ALA* 4.6 10.8 - - + -
246L LEU* 3.5 29.4 - - + +
247L CYS 3.8 7.2 - - - +
249L ILE* 1.3 88.1 - - + +
251L THR* 1.3 61.2 + - - +
252L GLY 3.4 0.3 + - - -
253L THR* 3.5 5.6 - - - -
254L ILE* 3.5 32.2 + - + +
255L TRP* 3.4 27.2 + - - +
259L TRP* 3.5 29.2 - - + -
----------------------------------------------------------
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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