Contacts of the helix formed by residues 171 - 198 (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 PRO 171 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PHE* 5.7 2.5 - - + -
169L TYR 3.1 10.5 - - - +
170L ASN* 1.3 82.5 - - - +
172L GLY* 1.3 62.7 + - - +
174L MET* 3.2 15.1 + - + +
175L SER* 3.1 23.2 + - - -
259L TRP* 3.6 22.4 - - + -
262L TRP* 3.6 33.9 - - + -
263L TRP* 3.8 15.7 - - + +
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Residues in contact with GLY 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170L ASN* 2.9 12.6 + - - -
171L PRO* 1.3 76.3 - - - +
173L HIS* 1.3 62.0 + - - +
175L SER* 3.5 6.1 + - - -
176L SER* 3.0 22.3 + - - -
243L THR 4.1 7.1 - - - +
244L GLY* 4.0 5.5 - - - -
246L PHE* 5.3 1.8 - - - -
247L GLY* 3.8 18.7 - - - -
302L BCB 4.0 6.1 - - - -
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Residues in contact with HIS 173 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L TRP* 3.0 34.2 + + - +
168L HIS* 4.3 14.8 + + - -
170L ASN* 2.8 34.6 + - + +
172L GLY* 1.3 68.9 - - - +
174L MET* 1.3 65.7 + - - +
176L SER* 2.9 3.4 + - - -
177L VAL* 2.8 36.2 + - + +
302L BCB 2.0 89.6 + + + -
805M BCB 4.9 1.4 + - - -
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Residues in contact with MET 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168L HIS 3.4 17.9 - - - +
169L TYR 4.0 4.7 - - - +
170L ASN 2.8 11.1 + - - +
171L PRO* 3.2 16.6 + - + +
173L HIS* 1.3 71.9 - - - +
175L SER* 1.3 56.7 + - - +
177L VAL 3.6 0.3 + - - -
178L SER* 2.6 35.3 + - - -
263L TRP* 3.7 30.1 - - + -
89M PHE* 4.7 8.1 - - + -
177M ILE* 5.9 0.2 - - + -
178M TRP* 3.7 33.2 - - + -
805M BCB 3.3 42.6 - - - +
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Residues in contact with SER 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171L PRO 3.1 12.5 + - - -
172L GLY* 3.7 9.9 - - - -
174L MET* 1.3 75.6 - - - +
176L SER* 1.3 63.5 + - - +
178L SER* 3.3 6.5 + - - -
179L PHE* 3.1 39.2 + - - -
243L THR* 3.0 26.2 + - - +
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Residues in contact with SER 176 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L GLY 3.0 13.3 + - - -
173L HIS* 2.9 13.3 + - - -
175L SER* 1.3 76.9 - - - +
177L VAL* 1.3 58.0 + - - -
179L PHE* 3.2 5.4 + - - +
180L LEU* 2.9 27.2 + - - +
240L ILE* 2.6 28.9 + - - +
243L THR* 3.7 7.8 + - - -
244L GLY* 3.9 9.6 - - - -
302L BCB 3.3 29.4 - - - +
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Residues in contact with VAL 177 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173L HIS* 2.8 45.9 + - + +
176L SER* 1.3 71.7 - - - +
178L SER* 1.3 59.5 + - - +
180L LEU* 3.1 8.9 + - - +
181L PHE* 2.9 60.3 + - + -
302L BCB 3.6 24.0 - - + -
805M BCB 3.5 36.1 - - + +
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Residues in contact with SER 178 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174L MET 2.6 23.3 + - - -
175L SER* 3.5 6.2 - - - -
177L VAL* 1.3 77.8 - - - +
179L PHE* 1.3 60.3 + - - +
181L PHE* 3.2 3.9 + - - +
182L VAL* 2.8 37.4 + - - +
805M BCB 3.6 41.7 + - - +
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Residues in contact with PHE 179 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175L SER* 3.1 37.6 + - - -
176L SER 3.6 6.1 - - - +
178L SER* 1.3 79.6 - - - +
180L LEU* 1.3 62.4 + - - +
182L VAL* 4.0 4.2 - - + +
183L ASN* 2.9 28.8 + - - +
235L PHE* 4.1 12.3 - + - -
236L LEU* 3.5 47.2 - - + +
239L ASN* 3.4 43.3 - - + -
240L ILE* 3.7 12.3 - - + +
243L THR* 3.9 8.1 - - + -
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Residues in contact with LEU 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L SER 2.9 14.3 + - - +
177L VAL 3.1 8.3 + - - +
179L PHE* 1.3 74.1 - - - +
181L PHE* 1.3 67.9 + - + +
183L ASN* 4.0 2.1 - - - +
184L ALA* 3.2 26.6 + - + +
240L ILE* 3.6 26.4 - - + +
302L BCB 3.7 43.5 - - + -
402L BPB 6.5 0.2 - - + -
207M ALA* 3.9 41.5 - - + +
208M TYR* 4.2 15.3 - - + -
211M GLY 5.7 0.2 - - - +
806M BCB 4.5 9.4 - - + -
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Residues in contact with PHE 181 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177L VAL* 2.9 37.5 + - + +
178L SER* 3.8 4.0 - - - +
180L LEU* 1.3 84.5 - - + +
182L VAL* 1.3 65.9 + - - +
183L ASN 3.2 0.4 - - - -
184L ALA* 3.4 4.3 + - + -
185L MET* 3.0 23.0 + - - +
302L BCB 3.8 28.7 - - + -
207M ALA* 6.4 0.2 - - + -
401M BPB 3.0 43.7 - - + +
805M BCB 3.8 37.9 - + + -
806M BCB 3.3 44.2 - + + -
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Residues in contact with VAL 182 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178L SER* 2.8 31.4 + - - +
179L PHE* 4.0 5.6 - - + +
181L PHE* 1.3 72.7 - - - +
183L ASN* 1.3 53.2 + - - +
185L MET* 3.2 3.3 + - - +
186L ALA* 2.7 32.6 + - + +
236L LEU* 3.6 32.5 - - + -
805M BCB 3.5 60.5 - - + +
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Residues in contact with ASN 183 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L PHE 2.9 19.5 + - - +
180L LEU 4.0 2.8 - - - +
182L VAL* 1.3 76.6 - - - +
184L ALA* 1.3 57.7 + - - +
186L ALA* 4.4 0.2 - - - -
187L LEU* 2.8 30.1 + - - +
233L GLY 3.4 15.8 + - - -
236L LEU* 3.9 18.0 - - + +
237L ALA* 3.5 18.7 - - - +
240L ILE* 4.5 3.3 - - + +
210M CYS* 3.3 29.5 - - - +
211M GLY* 3.4 5.4 + - - -
214M PHE* 3.2 31.1 - - - +
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Residues in contact with ALA 184 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180L LEU* 3.2 16.7 + - + +
181L PHE* 3.7 6.3 - - + +
183L ASN* 1.3 79.1 + - - +
185L MET* 1.3 61.9 + - - +
187L LEU* 3.7 2.4 - - - +
188L GLY 3.1 17.0 + - - -
207M ALA* 5.4 4.7 - - + -
210M CYS* 4.0 25.5 - - + +
271M SER* 3.2 13.3 + - - -
274M VAL* 5.0 7.6 - - + -
401M BPB 4.0 22.4 - - + -
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Residues in contact with MET 185 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181L PHE 3.0 14.2 + - - +
182L VAL 3.5 6.3 - - - +
184L ALA* 1.3 76.4 - - - +
186L ALA* 1.3 58.1 + - - +
188L GLY* 3.1 4.2 + - - -
189L LEU* 2.8 50.6 + - + +
401M BPB 3.6 82.7 - - + +
805M BCB 2.9 54.1 - - + -
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Residues in contact with ALA 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182L VAL* 2.7 21.7 + - + +
183L ASN 3.8 2.0 - - - +
185L MET* 1.3 73.5 - - + +
187L LEU* 1.3 62.5 + - - +
189L LEU* 3.8 11.3 - - + +
190L HIS* 2.8 32.2 + - - +
229L ILE* 5.2 9.2 - - + -
232L LEU* 5.5 1.6 - - + -
236L LEU* 4.0 18.2 - - + -
502L ATZ 4.5 2.5 - - + +
214M PHE* 3.5 15.5 - - + -
805M BCB 5.6 6.1 - - + -
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Residues in contact with LEU 187 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ASN 2.8 18.1 + - - +
184L ALA* 3.7 5.6 - - - +
186L ALA* 1.3 72.5 - - - +
188L GLY* 1.3 66.9 + - - +
190L HIS* 5.4 2.2 - - + -
191L GLY* 2.9 25.2 + - - +
210M CYS* 3.5 45.8 - - + +
213M LEU* 3.9 17.3 - - + -
214M PHE* 3.4 35.3 - - + +
217M HIS* 5.3 8.1 - - + -
264M HIS* 6.3 1.6 - - + -
267M GLY* 3.8 30.3 - - - +
271M SER* 4.6 0.4 - - - -
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Residues in contact with GLY 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L ALA 3.1 8.3 + - - -
185L MET 3.1 7.4 + - - -
187L LEU* 1.3 76.6 - - - +
189L LEU* 1.3 55.4 + - - +
192L GLY* 2.8 28.4 + - - -
144M ILE* 5.2 0.7 - - - +
147M ASN* 3.9 15.5 - - - +
268M TRP* 3.9 9.7 - - - -
271M SER* 3.3 25.9 + - - -
401M BPB 4.9 1.3 - - - -
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Residues in contact with LEU 189 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L MET* 2.8 47.9 + - + +
186L ALA* 3.3 9.2 + - + +
188L GLY* 1.3 73.0 - - - +
190L HIS* 1.3 58.2 + - - +
192L GLY 3.4 0.2 + - - -
193L LEU* 2.9 31.4 + - - +
216L PHE* 4.1 13.2 - - + -
502L ATZ 3.8 28.2 - - + +
144M ILE* 3.7 22.5 - - + +
401M BPB 3.7 48.4 - - + +
805M BCB 5.6 2.9 - - + -
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Residues in contact with HIS 190 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L ALA 2.8 21.8 + - - +
187L LEU* 4.1 4.0 - - + +
189L LEU* 1.3 73.3 - - - +
191L GLY* 1.3 61.4 + - - +
193L LEU* 4.0 7.5 - - - +
194L ILE* 3.2 37.2 + - + +
212L GLU* 5.8 0.4 - - - -
226L ALA* 6.4 0.2 - - - -
229L ILE* 3.6 24.0 - - + +
230L HIS* 2.8 18.1 + + - -
502L ATZ 3.8 8.8 + - - +
214M PHE* 4.0 18.8 - + + -
217M HIS* 3.6 13.5 - + - -
232M GLU* 3.1 14.4 - - - -
264M HIS* 2.8 15.9 + + - -
500M FE2 1.9 33.4 - - - -
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Residues in contact with GLY 191 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LEU* 2.9 19.3 + - - +
188L GLY 3.9 0.2 - - - -
190L HIS* 1.3 76.0 - - - +
192L GLY* 1.3 63.4 + - - +
194L ILE* 3.4 0.9 + - - -
195L LEU* 3.0 32.6 + - - +
264M HIS* 3.8 31.3 - - - +
267M GLY 5.4 0.2 - - - -
268M TRP* 4.4 4.7 - - - -
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Residues in contact with GLY 192 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L GLY 2.8 18.7 + - - -
189L LEU 3.9 0.7 - - - -
191L GLY* 1.3 71.5 - - - +
193L LEU* 1.3 57.4 + - - +
195L LEU* 4.6 0.4 - - - -
196L SER* 2.8 31.0 + - - -
143M HIS* 3.5 14.9 - - - +
144M ILE* 3.6 13.9 - - - -
268M TRP* 3.6 22.2 - - - -
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Residues in contact with LEU 193 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L LEU 2.9 19.0 + - - +
190L HIS* 4.0 8.3 - - - +
191L GLY 3.2 0.2 - - - -
192L GLY* 1.3 72.6 - - - +
194L ILE* 1.3 69.1 + - + +
196L SER* 2.6 27.7 + - - +
197L VAL* 3.0 12.0 + - + +
212L GLU* 3.6 52.3 - - + +
215L TYR* 4.0 30.3 - - + -
216L PHE* 4.1 12.1 - - + -
502L ATZ 4.0 18.8 - - + +
140M LEU* 5.0 1.3 - - + -
144M ILE* 3.8 9.1 - - + +
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Residues in contact with ILE 194 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L HIS* 3.2 28.5 + - + +
193L LEU* 1.3 77.4 - - + +
195L LEU* 1.3 64.6 + - + +
197L VAL* 3.5 2.3 + - - +
198L ALA* 3.1 22.3 + - - +
212L GLU* 3.9 21.1 - - - +
232M GLU* 3.2 37.0 - - + +
233M ILE* 3.9 17.6 - - + +
236M ILE* 3.8 23.6 - - + -
264M HIS* 3.7 29.2 - - + +
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Residues in contact with LEU 195 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191L GLY 3.0 22.1 + - - +
192L GLY 3.8 3.4 - - - +
194L ILE* 1.3 78.6 - - + +
196L SER* 1.3 56.6 + - - +
199L ASN* 2.9 38.0 + - - +
143M HIS* 3.5 24.0 - - + +
261M GLU* 3.7 41.5 - - + +
264M HIS* 3.9 20.0 - - + +
265M ARG* 3.7 37.5 - - + +
268M TRP* 4.2 15.3 - - + -
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Residues in contact with SER 196 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L GLY 2.8 20.0 + - - -
193L LEU* 2.6 28.3 + - - +
195L LEU* 1.3 73.5 - - - +
197L VAL* 1.3 66.7 + - - +
199L ASN 4.0 0.4 - - - -
200L PRO* 3.7 8.1 - - - +
140M LEU* 3.7 14.1 - - - +
141M GLY 2.8 49.0 + - - +
143M HIS* 3.3 14.1 + - - -
144M ILE* 5.2 3.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 197 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L LEU* 3.0 23.1 + - + +
196L SER* 1.3 82.5 + - - +
198L ALA* 1.3 62.4 + - - +
199L ASN 3.3 0.7 + - - -
200L PRO* 3.6 6.9 - - - +
206L VAL* 3.8 0.2 - - - -
207L LYS* 3.3 55.1 + - + +
208L THR 3.7 4.5 - - - +
212L GLU* 3.7 27.6 - - + +
140M LEU* 3.8 22.0 - - + -
233M ILE* 3.5 31.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 198 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H PHE* 3.4 25.3 - - + -
194L ILE 3.1 17.7 + - - +
195L LEU* 4.9 0.2 - - - -
197L VAL* 1.3 77.6 - - - +
199L ASN* 1.3 68.7 + - - +
200L PRO* 3.5 7.3 - - - +
206L VAL* 3.5 15.2 - - + +
233M ILE* 4.8 5.4 - - + -
236M ILE* 3.7 36.3 - - + -
261M GLU* 4.6 1.6 - - - +
----------------------------------------------------------
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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