Contacts of the helix formed by residues 170 - 195 (chain L) in PDB entry 5XVO
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 ASN 170 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L PHE* 3.6 18.8 - - - -
168L GLN* 3.2 29.0 - - + +
169L GLU* 1.3 74.0 - - - +
171L ASP* 1.3 65.7 + - - +
172L ILE* 2.8 13.8 + - + +
173L ASN* 2.9 28.9 + - - +
174L ALA* 3.2 12.2 + - - +
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Residues in contact with ASP 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170L ASN* 1.3 73.4 - - - +
172L ILE* 1.3 63.6 + - + +
174L ALA* 3.7 8.1 - - - +
175L GLY 3.0 17.7 + - - -
233L ARG 5.9 0.9 - - - +
235L GLU 4.1 3.9 - - - +
236L ALA* 4.1 7.6 - - - +
237L PHE* 3.7 26.2 + - - +
240L MET* 3.1 31.2 - - + +
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Residues in contact with ILE 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160L PHE* 3.7 48.9 - - + -
164L PHE* 4.0 15.5 - - + -
170L ASN* 2.8 19.8 + - + +
171L ASP* 1.3 77.0 - - + +
173L ASN* 1.3 59.4 + - - +
175L GLY* 3.4 1.9 + - - -
176L LEU* 2.9 33.7 + - + +
229L ILE* 3.9 9.6 - - + +
233L ARG* 4.0 34.3 - - + +
240L MET* 4.4 6.1 - - - -
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Residues in contact with ASN 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L PHE* 3.2 13.2 - - - -
165L THR 3.0 6.9 + - - -
166L ARG* 2.7 34.0 - - - +
167L GLU* 4.9 1.1 - - - -
168L GLN* 2.7 50.6 - - - +
169L GLU* 4.7 2.0 - - - +
170L ASN* 2.9 15.5 + - - +
172L ILE* 1.3 74.5 - - - +
174L ALA* 1.3 56.4 + - - +
176L LEU* 3.1 5.6 + - - +
177L ASN* 2.8 50.9 + - - +
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Residues in contact with ALA 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L LEU* 5.3 4.6 - - + +
170L ASN 3.2 9.3 + - - +
171L ASP* 3.7 12.8 - - - +
173L ASN* 1.3 78.7 - - - +
175L GLY* 1.3 56.7 + - - +
177L ASN* 3.5 8.8 + - - +
178L TYR* 3.0 30.0 + - - +
237L PHE* 3.5 25.4 - - + -
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Residues in contact with GLY 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171L ASP 3.0 11.5 + - - -
172L ILE 3.7 2.5 - - - -
174L ALA* 1.3 76.8 - - - +
176L LEU* 1.3 64.9 + - - +
178L TYR* 3.4 1.6 + - - +
179L GLY* 3.0 19.1 + - - -
229L ILE* 3.6 22.9 - - - +
237L PHE* 3.6 12.7 - - - -
240L MET* 4.1 4.9 - - - -
244L LEU* 3.4 11.7 - - - +
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Residues in contact with LEU 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156L PHE* 3.8 25.8 - - + -
160L PHE* 4.6 3.8 - - + -
164L PHE* 4.5 2.5 - - + -
166L ARG* 4.4 8.7 - - - +
172L ILE* 2.9 29.2 + - + +
173L ASN* 3.5 23.1 - - - +
175L GLY* 1.3 75.5 - - - +
177L ASN* 1.3 57.7 + - - +
179L GLY* 3.3 1.6 + - - -
180L TYR* 2.8 50.4 + - + +
225L VAL* 3.9 3.5 - - + +
226L ASP* 3.2 39.9 - - - +
229L ILE* 3.9 18.3 - - + +
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Residues in contact with ASN 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K TYR* 5.5 6.1 - - - +
166L ARG* 2.4 35.7 + - - +
173L ASN* 2.8 38.8 + - - +
174L ALA* 3.7 7.6 - - - +
176L LEU* 1.3 72.9 - - - +
178L TYR* 1.3 62.1 + - - +
180L TYR* 3.3 7.5 + - - +
181L THR* 2.9 29.9 + - - +
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Residues in contact with TYR 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L LEU* 4.0 12.3 - - - +
43L GLU* 4.6 2.4 + - - +
67L CYS* 5.8 0.4 - - - -
71L ARG 4.0 8.2 + - - -
72L LEU* 4.2 10.8 - - + -
73L PRO* 3.4 36.7 - - + +
174L ALA 3.0 17.9 + - - +
175L GLY 3.7 4.7 - - - +
177L ASN* 1.3 76.9 - - - +
179L GLY* 1.3 64.2 + - - +
181L THR* 3.2 9.3 + - - -
182L LEU* 3.2 46.5 + - + +
237L PHE* 4.4 5.6 - - + -
241L LYS* 3.5 50.5 + - + +
244L LEU* 3.7 14.6 - - + -
245L PHE* 3.6 22.6 - + - -
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Residues in contact with GLY 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175L GLY 3.0 8.1 + - - -
176L LEU 3.7 2.7 - - - -
178L TYR* 1.3 80.8 - - - +
180L TYR* 1.3 61.6 + - - +
182L LEU* 3.1 19.0 + - - +
183L LEU* 3.2 10.6 + - - +
225L VAL* 3.7 25.8 - - - +
244L LEU* 3.7 20.6 - - - -
247L LEU* 4.8 0.3 - - - +
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Residues in contact with TYR 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156L PHE* 3.7 14.0 - - - -
166L ARG* 3.1 34.5 - - - -
176L LEU* 2.8 30.1 + - + +
177L ASN* 3.6 5.4 - - - +
178L TYR 3.3 0.2 - - - -
179L GLY* 1.3 77.7 - - - +
181L THR* 1.3 57.4 + - - +
183L LEU* 3.3 5.6 + - + +
184L LEU* 2.9 25.9 + - - +
218L MET* 3.5 16.7 - - + +
222L ARG* 3.2 62.7 + - + +
225L VAL* 4.0 12.1 - - + -
226L ASP* 2.5 34.0 + - - -
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Residues in contact with THR 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K PHE* 3.5 44.0 - - + -
81K TYR* 4.4 12.4 + - - +
65L LEU* 5.8 0.9 - - + -
73L PRO* 4.0 20.4 - - + +
177L ASN* 2.9 16.4 + - - +
178L TYR* 3.2 8.8 + - - -
180L TYR* 1.3 74.1 - - - +
182L LEU* 1.3 65.6 + - + +
184L LEU* 3.2 8.2 + - + +
185L SER* 2.8 29.4 + - - +
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Residues in contact with LEU 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L LEU* 5.7 2.2 - - + -
63L LEU* 5.1 0.9 - - - +
65L LEU* 4.3 21.3 - - + -
73L PRO* 5.6 6.1 - - + -
178L TYR* 3.2 45.7 + - + +
179L GLY* 3.1 13.1 + - - +
181L THR* 1.3 78.5 - - + +
183L LEU* 1.3 64.7 + - - +
185L SER* 3.2 7.9 + - - -
186L ILE* 3.2 26.0 + - + +
244L LEU* 4.4 11.0 - - + +
245L PHE* 4.7 8.5 - - + -
247L LEU* 4.4 15.9 - - + -
248L PHE* 4.2 32.6 - - + -
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Residues in contact with LEU 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L GLY 3.2 10.0 + - - +
180L TYR* 3.5 8.5 - - + +
182L LEU* 1.3 77.0 - - - +
184L LEU* 1.3 65.9 + - - +
186L ILE* 3.0 17.7 + - + +
187L PHE* 3.2 26.3 + - + -
218L MET* 3.9 20.0 - - + +
221L PHE* 3.6 43.5 - - + +
222L ARG* 4.1 6.3 - - - -
224L LEU* 5.5 1.3 - - + -
225L VAL* 3.7 20.9 - - + -
247L LEU* 4.8 10.8 - - + -
261L LEU* 3.9 28.0 - - + -
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Residues in contact with LEU 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K PHE* 3.8 29.6 - - + -
180L TYR 2.9 14.2 + - - +
181L THR* 3.4 13.0 - - + +
183L LEU* 1.3 76.6 - - - +
185L SER* 1.3 58.6 + - - +
187L PHE* 3.2 1.6 + - - -
188L ALA* 2.8 31.8 + - + +
211L PHE* 3.7 36.3 - - + -
214L ALA* 3.6 15.1 - - + +
215L SER* 3.6 36.1 - - - +
218L MET* 3.8 12.3 - - - -
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Residues in contact with SER 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K PHE* 3.4 19.3 - - - -
63L LEU* 3.7 26.4 - - - +
65L LEU* 3.5 13.4 - - - +
76L LYS* 3.3 18.9 - - - +
181L THR* 2.8 15.5 + - - +
182L LEU* 3.5 8.8 - - - -
184L LEU* 1.3 75.9 - - - +
186L ILE* 1.3 66.6 + - - +
188L ALA* 4.2 0.7 - - - -
189L ARG* 3.1 21.5 + - - +
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Residues in contact with ILE 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L LEU* 4.4 11.4 - - + -
182L LEU* 3.2 13.9 + - + +
183L LEU* 3.0 17.3 + - + +
185L SER* 1.3 77.2 - - - +
187L PHE* 1.3 62.2 + - + +
189L ARG* 3.5 12.2 + - - +
190L GLU* 3.2 28.5 + - + +
247L LEU* 6.0 0.9 - - + -
248L PHE* 3.8 31.2 - - + -
261L LEU* 4.0 25.6 - - + -
262L THR* 4.3 18.4 - - - +
265L ALA* 3.5 29.8 - - + -
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Residues in contact with PHE 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L LEU* 3.2 30.7 + - + -
184L LEU 4.0 4.3 - - - +
186L ILE* 1.3 82.4 - - + +
188L ALA* 1.3 66.6 + - - +
190L GLU* 3.8 3.7 - - - +
191L LEU* 3.0 28.9 + - + +
214L ALA* 4.2 18.8 - - + +
217L LEU* 4.1 15.3 - - + -
218L MET* 3.8 22.4 - - + -
221L PHE* 3.5 45.8 - + + -
261L LEU* 5.8 1.6 - - + -
265L ALA* 3.6 32.3 - - + -
268L TYR* 4.2 9.6 - + - -
269L THR* 3.4 21.9 + - - -
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Residues in contact with ALA 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K LEU* 5.3 8.3 - - + -
80K PHE* 6.3 0.2 - - + -
76L LYS* 3.5 25.6 - - + +
78L LEU* 5.9 2.5 - - + -
184L LEU* 2.8 21.0 + - + +
185L SER* 4.2 0.7 - - - -
186L ILE 3.4 0.2 - - - -
187L PHE* 1.3 78.7 - - - +
189L ARG* 1.3 62.9 + - - +
191L LEU* 3.8 2.1 - - - +
192L VAL* 3.2 28.8 + - + +
198L THR* 3.9 12.3 - - + +
211L PHE* 5.4 2.5 - - + -
214L ALA* 3.8 16.2 - - + +
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Residues in contact with ARG 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L MET* 4.1 13.5 - - - +
38L ASP* 3.0 48.8 + - - +
39L VAL* 4.6 3.8 - - - +
61L LYS* 3.1 28.9 + - + +
62L ILE* 4.1 0.6 - - - +
63L LEU* 3.4 27.5 - - + +
76L LYS* 3.7 15.6 - - - +
79L PRO* 6.2 2.5 - - + -
185L SER 3.1 14.4 + - - +
186L ILE* 3.6 9.1 + - - +
188L ALA* 1.3 81.4 - - - +
190L GLU* 1.3 72.6 + - - +
192L VAL* 3.4 5.2 + - - +
193L GLN* 3.1 34.3 + - + +
248L PHE* 6.4 0.2 - - - -
262L THR* 3.7 23.8 + - - +
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Residues in contact with GLU 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L MET* 4.6 10.2 - - - +
186L ILE* 3.2 19.6 + - + +
187L PHE* 3.3 3.5 + - - +
189L ARG* 1.3 100.3 + - - +
191L LEU* 1.3 62.4 + - - +
193L GLN* 3.3 13.3 - - - +
194L THR* 3.1 27.2 + - - +
262L THR* 4.1 5.4 - - - +
265L ALA* 4.0 17.7 - - + +
266L THR* 3.1 43.6 + - - +
269L THR* 3.7 22.9 - - - +
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Residues in contact with LEU 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L PHE 3.0 20.7 + - - +
188L ALA 3.8 3.8 - - - +
189L ARG 3.2 0.2 - - - -
190L GLU* 1.3 74.9 - - - +
192L VAL* 1.3 66.0 + - - +
194L THR* 2.7 24.4 + - - -
196L CYS* 3.2 19.7 + - + -
198L THR* 3.9 11.7 - - + -
213L LEU* 3.7 33.0 - - + +
214L ALA* 3.6 35.0 - - + +
217L LEU* 3.8 15.3 - - + -
269L THR* 3.8 21.3 - - + -
273L VAL* 4.2 15.5 - - + -
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Residues in contact with VAL 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L LYS* 6.0 0.2 - - - +
78L LEU* 3.8 26.7 - - + -
79L PRO* 3.7 30.1 - - + +
80L PHE 5.3 0.7 - - - -
82L GLY* 3.4 28.9 + - - +
86L SER* 5.4 0.2 + - - -
188L ALA 3.2 14.2 + - - +
189L ARG* 3.7 9.0 - - - +
191L LEU* 1.3 77.5 - - - +
193L GLN* 1.3 68.4 + - - +
195L GLY* 3.1 14.0 + - - -
196L CYS 3.7 12.3 - - - +
198L THR* 4.0 11.9 - - + +
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Residues in contact with GLN 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L MET* 5.8 3.8 - - + -
61L LYS* 2.9 56.6 - - + +
79L PRO* 5.1 5.9 - - - +
82L GLY* 3.4 21.7 + - - -
83L ARG* 3.7 18.4 - - - +
189L ARG* 3.1 26.0 + - + +
190L GLU* 3.3 20.6 - - - +
191L LEU 3.1 0.4 - - - -
192L VAL* 1.3 83.2 - - - +
194L THR* 1.3 59.6 + - + +
195L GLY 3.5 0.3 + - - -
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Residues in contact with THR 194 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L ARG* 3.4 19.9 + - - +
89L GLN* 3.4 17.8 - - - +
190L GLU* 3.1 17.9 - - + +
191L LEU* 2.7 14.6 + - - +
193L GLN* 1.3 76.6 - - + +
195L GLY* 1.3 56.8 + - - +
196L CYS* 3.4 19.1 - - - -
266L THR 5.9 0.2 - - - +
269L THR* 4.3 14.8 - - + -
270L LYS* 4.6 18.6 - - + +
273L VAL* 4.1 13.4 - - + +
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Residues in contact with GLY 195 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L ARG* 4.5 7.4 - - - -
86L SER* 3.8 23.0 + - - +
89L GLN* 3.6 20.0 - - - +
90L LEU* 3.8 18.2 + - - +
192L VAL 3.1 13.4 + - - -
193L GLN 3.3 0.8 - - - -
194L THR* 1.3 80.8 - - - +
196L CYS* 1.3 63.6 + - - +
----------------------------------------------------------
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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