Contacts of the helix formed by residues 226 - 253 (chain L) in PDB entry 5PRC
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 ALA 226 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H GLU* 3.5 28.9 + - - +
212L GLU* 4.6 11.0 - - - +
225L GLY* 1.3 69.3 - - - -
227L LEU* 1.3 67.3 + - - +
228L SER 3.3 0.3 + - - -
229L ILE* 3.4 10.5 - - - +
230L HIS* 2.9 23.4 + - + -
502L ATZ 3.6 13.4 - - + +
230M ASP* 3.6 23.6 - - + +
231M ARG* 5.5 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
----------------------------------------------------------
177H GLU* 4.6 1.8 + - - -
179H TYR* 3.4 32.1 - - + +
226L ALA* 1.3 75.9 - - - +
228L SER* 1.3 65.7 + - - +
230L HIS* 3.1 17.4 + - - +
231L ARG* 3.4 32.7 + - - +
4M GLN* 3.7 10.1 - - + +
5M THR* 4.7 2.7 - - - -
221M ILE* 4.6 8.5 - - + -
222M LEU* 4.0 16.8 - - + -
225M ALA* 3.8 28.3 - - + -
230M ASP* 3.7 32.4 + - + +
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Residues in contact with SER 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224L ILE* 3.2 33.2 + - - +
225L GLY 3.1 3.4 + - - -
227L LEU* 1.3 78.4 - - - +
229L ILE* 1.3 56.2 + - - +
231L ARG* 2.9 27.1 + - - +
232L LEU* 2.8 29.5 + - - +
8M THR* 5.5 1.7 + - - -
41M ILE 3.0 19.7 + - - +
42M GLY* 3.5 8.7 - - - -
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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* 5.2 5.2 - - + -
190L HIS* 3.6 31.4 - - + +
224L ILE* 3.8 22.5 - - + +
225L GLY 3.0 13.5 + - - +
226L ALA* 3.4 16.8 - - - +
228L SER* 1.3 75.4 - - - +
230L HIS* 1.3 70.0 + - + +
232L LEU* 3.8 21.3 - - + -
233L GLY* 2.9 24.3 + - - -
502L ATZ 3.8 34.3 - - + +
214M PHE* 3.8 12.0 - - + -
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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* 2.8 22.1 + + - -
226L ALA* 2.9 28.1 + - - -
227L LEU 3.1 7.2 + - - +
229L ILE* 1.3 75.7 - - + +
231L ARG* 1.3 64.4 + - - +
233L GLY 3.3 0.9 + - - -
234L LEU* 3.1 21.1 + - - +
214M PHE* 4.8 2.7 - + - -
217M HIS* 3.4 14.8 - + - -
218M GLY* 3.4 25.7 - - - +
221M ILE* 3.1 38.8 - - + +
222M LEU* 4.3 5.6 - - + -
230M ASP* 5.0 3.3 - - - -
232M GLU* 2.8 13.8 + - + -
500M FE2 2.3 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
----------------------------------------------------------
179H TYR* 5.3 0.4 + - - -
227L LEU* 3.4 20.9 + - - +
228L SER* 2.9 40.7 + - - +
230L HIS* 1.3 75.7 - - - +
232L LEU* 1.3 63.3 + - - +
234L LEU* 3.4 4.4 + - + +
235L PHE* 3.1 22.6 + - + +
4M GLN 2.7 28.3 + - - -
5M THR 2.6 22.1 + - - +
6M ILE* 3.4 20.5 + - - +
7M TYR* 4.0 10.6 - - - +
8M THR* 4.6 5.7 + - - +
41M ILE* 3.0 28.9 + - - +
222M LEU* 3.7 24.0 - - + +
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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* 5.5 1.3 - - + -
224L ILE* 5.0 19.3 - - + -
228L SER 2.8 19.8 + - - +
229L ILE* 3.6 25.6 - - + +
230L HIS 3.2 0.2 - - - -
231L ARG* 1.3 74.3 - - - +
233L GLY* 1.3 58.8 + - - +
235L PHE* 2.8 24.6 + - + +
236L LEU* 2.7 52.0 + - + +
502L ATZ 5.6 4.7 - - + -
805M BCB 5.4 11.0 - - + -
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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* 3.4 3.8 + - - -
229L ILE* 2.9 12.5 + - - +
230L HIS 3.3 0.6 + - - -
232L LEU* 1.3 75.0 - - - +
234L LEU* 1.3 55.9 + - - +
236L LEU* 4.6 3.1 - - - -
237L ALA* 3.0 33.6 + - - +
214M PHE* 3.7 45.3 - - - -
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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* 5.0 7.4 - - + +
120L ALA* 3.5 32.5 - - + +
230L HIS 3.1 16.1 + - - +
231L ARG* 3.8 4.9 - - + +
233L GLY* 1.3 74.4 - - - +
235L PHE* 1.3 58.2 + - - +
237L ALA* 4.0 0.5 - - - +
238L SER* 2.8 45.7 + - - +
214M PHE 4.1 5.9 + - - -
215M ALA* 3.7 16.8 - - - +
218M GLY 4.5 0.4 - - - -
219M ALA* 4.2 21.3 - - + +
222M LEU* 3.9 23.8 - - + -
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Residues in contact with PHE 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L PHE* 4.1 14.6 - + - -
231L ARG* 3.1 13.7 + - + +
232L LEU* 2.8 26.5 + - + +
234L LEU* 1.3 75.2 - - - +
236L LEU* 1.3 75.8 + - + +
238L SER* 3.3 4.4 + - - -
239L ASN* 3.1 53.9 + - - +
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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* 3.5 40.1 - - + +
182L VAL* 3.6 35.4 - - + -
183L ASN* 3.9 20.6 - - + +
186L ALA* 4.0 22.9 - - + -
232L LEU* 2.7 45.9 + - + +
233L GLY* 4.8 1.6 - - - -
235L PHE* 1.3 82.5 - - + +
237L ALA* 1.3 64.9 + - - +
239L ASN 3.3 5.4 + - - -
240L ILE* 3.5 8.8 + - - +
805M BCB 5.8 1.1 - - + -
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Residues in contact with ALA 237 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ASN* 3.5 16.1 - - - +
233L GLY 3.0 18.7 + - - +
234L LEU 4.0 0.9 - - - +
236L LEU* 1.3 77.6 - - - +
238L SER* 1.3 63.5 + - - +
239L ASN 3.0 1.9 + - - -
240L ILE* 3.0 32.3 + - - +
402L BPB 3.5 7.3 - - + +
211M GLY* 3.8 23.6 - - - +
215M ALA* 3.8 17.3 - - + +
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Residues in contact with SER 238 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L ALA* 4.9 4.2 + - - -
123L VAL* 3.6 26.2 - - - +
234L LEU* 2.8 36.5 + - - +
235L PHE* 3.3 4.5 + - - -
237L ALA* 1.3 76.9 - - - +
239L ASN* 1.3 59.3 + - - +
241L PHE 3.4 3.9 + - - -
242L LEU* 3.1 35.1 + - - +
402L BPB 4.0 10.6 - - - +
215M ALA* 5.0 2.6 - - - +
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Residues in contact with ASN 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L PHE* 3.4 37.8 - - + -
235L PHE* 3.1 42.8 + - - +
237L ALA 3.0 0.8 + - - -
238L SER* 1.3 74.1 - - - +
240L ILE* 1.3 61.9 + - - +
241L PHE 3.1 1.3 - - - -
242L LEU* 3.6 27.9 - - - +
243L THR* 2.8 42.1 + - - +
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Residues in contact with ILE 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L SER* 2.6 27.7 + - - +
179L PHE* 3.7 9.6 - - + +
180L LEU* 3.6 42.0 - - + +
183L ASN* 4.5 3.6 - - + -
236L LEU 3.5 8.4 + - - +
237L ALA* 3.1 27.6 - - - +
239L ASN* 1.3 80.5 - - - +
241L PHE* 1.3 80.4 + - + +
244L GLY* 3.5 6.6 + - - -
302L BCB 3.8 25.2 - - + +
402L BPB 5.0 6.5 - - + -
208M TYR* 6.3 0.2 - - + -
211M GLY* 4.4 16.4 - - - -
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Residues in contact with PHE 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L VAL* 3.5 21.3 - - + +
124L PRO* 3.7 22.4 - - + -
126L PHE* 4.8 2.0 - - + -
127L MET* 3.5 31.2 - - + +
237L ALA 4.3 0.2 + - - -
238L SER 3.4 2.4 + - - -
239L ASN 3.1 0.2 - - - -
240L ILE* 1.3 101.2 - - + +
242L LEU* 1.3 60.6 + - + +
243L THR 3.3 1.6 - - - -
244L GLY* 4.4 0.4 - - - +
245L ALA* 2.8 33.1 + - - +
302L BCB 3.5 55.0 - - + -
402L BPB 3.7 39.9 - + + -
208M TYR* 5.7 3.8 - + - -
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Residues in contact with LEU 242 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L VAL* 4.3 21.5 - - + -
126L PHE* 4.0 26.9 - - + -
238L SER* 3.1 22.6 + - - +
239L ASN* 3.5 23.7 + - - +
241L PHE* 1.3 78.1 - - - +
243L THR* 1.3 58.9 + - + +
245L ALA* 3.9 4.2 - - - +
246L PHE* 2.8 31.9 - - + -
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Residues in contact with THR 243 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L GLY* 4.1 8.4 - - - +
175L SER* 3.0 32.5 + - - +
176L SER* 3.7 6.8 + - - -
179L PHE* 3.9 12.9 - - + -
239L ASN* 2.8 34.6 + - - +
242L LEU* 1.3 76.2 - - - +
244L GLY* 1.3 65.8 + - - +
245L ALA 3.2 0.2 - - - -
246L PHE* 3.2 24.5 + - - +
247L GLY 3.8 2.6 + - - -
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Residues in contact with GLY 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L MET* 4.3 0.9 - - - -
172L GLY 4.0 4.5 - - - -
176L SER* 3.9 4.9 - - - -
240L ILE 3.5 12.3 + - - -
241L PHE* 3.3 5.5 + - - -
243L THR* 1.3 79.6 + - - +
245L ALA* 1.3 64.9 + - - +
246L PHE 3.0 1.4 + - - -
247L GLY 3.0 2.9 + - - -
248L THR* 3.0 19.8 + - - -
302L BCB 3.1 33.3 - - - +
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Residues in contact with ALA 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L PHE* 3.7 28.3 - - + -
127L MET* 4.1 13.6 - - - -
130L VAL* 4.1 14.8 - - + -
241L PHE 2.8 21.0 + - - +
242L LEU 3.9 6.7 - - - +
243L THR 3.2 0.6 - - - -
244L GLY* 1.3 71.1 - - - +
246L PHE* 1.3 61.2 + - + +
248L THR* 3.5 1.7 + - - -
249L ILE* 2.9 35.1 + - + +
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Residues in contact with PHE 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L PHE* 6.0 2.7 - + - -
172L GLY* 5.0 2.9 - - - -
242L LEU* 2.8 28.0 - - + -
243L THR* 3.5 13.2 - - - +
244L GLY 3.0 0.8 - - - -
245L ALA* 1.3 79.2 - - + +
247L GLY* 1.3 62.3 + - - +
249L ILE* 4.0 5.0 - - - +
250L ALA* 2.9 35.0 + - - +
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Residues in contact with GLY 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170L ASN* 3.1 31.9 + - - -
172L GLY* 3.8 11.4 - - - -
243L THR 3.8 4.0 + - - -
244L GLY 3.0 6.7 + - - -
246L PHE* 1.3 80.6 - - - +
248L THR* 1.3 59.7 + - - +
250L ALA* 3.7 5.0 + - - +
251L SER* 2.8 26.3 + - - -
259L TRP* 5.6 0.2 - - - -
302L BCB 4.0 2.9 - - - -
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Residues in contact with THR 248 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127L MET* 3.5 4.6 - - - +
130L VAL* 4.1 14.4 - - + -
131L LEU* 3.9 19.5 - - + -
135L ARG* 3.5 29.4 + - - -
160L PHE* 4.3 5.8 - - + -
167L TRP* 4.5 6.3 - - - -
244L GLY 3.0 6.7 + - - -
245L ALA 3.7 6.7 - - - -
247L GLY* 1.3 76.0 - - - +
249L ILE* 1.3 63.3 + - - +
251L SER* 3.2 12.6 + - - -
302L BCB 2.8 45.2 + - - +
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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 VAL* 3.6 18.4 - - + -
134L PHE* 4.1 13.2 - - + -
135L ARG* 4.0 26.0 - - - +
138L LEU* 3.7 30.3 - - + -
245L ALA* 2.9 21.0 + - + +
246L PHE* 4.0 4.7 - - - +
248L THR* 1.3 76.0 - - - +
250L ALA* 1.3 64.4 + - - +
253L PRO* 3.2 24.6 - - - +
254L PHE* 3.9 10.5 - - + -
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Residues in contact with ALA 250 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PHE* 4.1 27.6 - - + -
246L PHE 2.9 18.0 + - - +
247L GLY* 4.0 5.4 - - - +
248L THR 3.2 0.4 - - - -
249L ILE* 1.3 78.4 - - - +
251L SER* 1.3 57.9 + - - +
254L PHE* 3.0 18.9 + - + -
255L TRP* 2.9 29.8 + - - +
259L TRP* 4.4 8.1 - - + -
----------------------------------------------------------
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Residues in contact with SER 251 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L ARG* 2.8 25.8 + - - -
160L PHE* 4.0 3.4 - - - -
164L TYR* 3.4 16.2 - - - -
167L TRP* 3.2 30.8 - - - -
247L GLY 2.8 19.9 + - - -
248L THR 3.2 8.2 + - - -
249L ILE 3.2 2.0 - - - -
250L ALA* 1.3 74.8 - - - +
252L GLY* 1.3 58.5 + - - +
253L PRO* 2.9 10.1 - - - +
255L TRP 3.9 3.4 - - - -
259L TRP* 3.3 16.2 + - - -
----------------------------------------------------------
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Residues in contact with GLY 252 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 3.2 19.1 - - - +
22C VAL* 4.1 10.3 - - - -
135L ARG* 4.5 0.9 - - - -
139L LEU* 3.7 13.7 - - - -
164L TYR* 3.2 14.3 + - - -
250L ALA 3.2 0.4 + - - -
251L SER* 1.3 71.5 - - - +
253L PRO* 1.3 65.5 - - - +
254L PHE 3.2 1.2 + - - -
255L TRP 2.7 17.9 + - - -
256L THR* 3.6 9.5 - - - +
----------------------------------------------------------
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Residues in contact with PRO 253 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLU 3.5 1.4 - - - +
4C PRO 3.8 0.6 - - - -
5C PRO* 3.0 43.5 - - + +
7C ALA* 5.0 1.8 - - + +
135L ARG* 4.4 7.0 - - + +
138L LEU* 3.7 31.0 - - + +
139L LEU* 3.6 25.1 - - + -
249L ILE 3.2 17.3 - - - +
251L SER 2.9 24.5 - - - +
252L GLY* 1.3 76.3 - - - +
254L PHE* 1.3 74.0 + - + +
256L THR* 5.8 0.2 - - - -
----------------------------------------------------------
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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