Contacts of the helix formed by residues 170 - 194 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I PHE* 3.8 13.7 - - - -
168I GLN* 3.2 24.6 + - - +
169I GLU* 1.3 75.9 - - - +
171I ASP* 1.3 63.8 + - - +
172I ILE* 2.9 13.3 + - + +
173I ASN* 2.6 50.0 + - - +
174I ALA* 3.1 21.3 + - - +
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Residues in contact with ASP 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I ASN* 1.3 75.1 - - - +
172I ILE* 1.3 62.9 + - + +
174I ALA* 3.7 6.9 - - - +
175I GLY 3.1 11.6 + - - -
233I ARG 5.9 0.2 - - - +
235I GLU 4.1 2.7 - - - +
236I ALA* 4.0 8.0 - - - +
237I PHE* 3.6 29.3 + - - +
240I MET* 3.0 35.6 - - + +
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Residues in contact with ILE 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I PHE* 3.7 47.1 - - + -
164I PHE* 4.0 18.4 - - + -
170I ASN* 2.9 10.6 + - + +
171I ASP* 1.3 78.6 - - + +
173I ASN* 1.3 59.0 + - - +
175I GLY* 3.4 1.9 + - - -
176I LEU* 3.0 34.3 + - + +
229I ILE* 3.9 9.4 - - + +
233I ARG* 4.0 31.0 - - + +
240I MET* 4.0 9.4 - - + -
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Residues in contact with ASN 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I PHE* 3.2 22.1 - - - -
166I ARG* 2.7 47.7 + - - +
167I GLU 5.2 0.2 - - - -
168I GLN 2.7 40.0 + - - +
170I ASN* 2.6 26.8 + - - +
172I ILE* 1.3 71.9 - - - +
174I ALA* 1.3 55.9 + - - +
176I LEU* 3.1 3.3 + - - +
177I ASN* 2.8 47.1 + - - +
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Residues in contact with ALA 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I ASN 3.1 17.1 + - - +
171I ASP* 3.7 9.4 - - - +
173I ASN* 1.3 76.6 - - - +
175I GLY* 1.3 55.3 + - - +
177I ASN* 3.7 9.1 - - - +
178I TYR* 2.9 30.1 + - - +
237I PHE* 3.6 23.9 - - + -
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Residues in contact with GLY 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I ASP 3.1 15.0 + - - -
172I ILE 3.7 3.8 - - - -
174I ALA* 1.3 73.1 - - - +
176I LEU* 1.3 65.8 + - - +
178I TYR* 3.5 1.5 + - - +
179I GLY 3.0 18.0 + - - -
229I ILE* 3.4 27.1 - - - +
237I PHE* 3.7 13.0 - - - -
240I MET* 4.1 7.2 - - - -
244I LEU* 3.4 4.6 - - - +
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Residues in contact with LEU 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I PHE* 3.8 23.3 - - + -
160I PHE* 4.7 3.6 - - + -
164I PHE* 4.5 2.0 - - + -
166I ARG* 4.0 17.3 - - - +
172I ILE* 3.0 28.5 + - + +
173I ASN* 3.1 23.5 + - - +
175I GLY* 1.3 76.8 - - - +
177I ASN* 1.3 57.0 + - - +
179I GLY* 3.2 2.1 + - - -
180I TYR* 2.8 44.4 + - + +
225I VAL* 3.9 8.4 - - + +
226I ASP* 3.2 39.7 - - + +
229I ILE* 3.9 13.2 - - + +
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Residues in contact with ASN 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I ARG* 2.7 33.4 + - - +
173I ASN* 2.8 34.1 + - - +
174I ALA* 3.7 7.2 - - - +
176I LEU* 1.3 75.6 - - - +
178I TYR* 1.3 61.9 + - - +
180I TYR* 3.3 8.2 + - - +
181I THR* 2.9 29.8 + - + +
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Residues in contact with TYR 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I ALA 2.9 18.3 + - - +
175I GLY* 3.7 5.2 - - - +
176I LEU 3.3 0.2 - - - -
177I ASN* 1.3 77.1 - - - +
179I GLY* 1.3 63.4 + - - +
181I THR* 2.7 22.7 + - - -
182I LEU* 3.1 33.1 + - + +
237I PHE* 4.3 11.0 - + + -
241I LYS* 3.5 47.0 + - + +
244I LEU* 3.7 14.4 - - + -
245I PHE* 3.2 26.2 - + - -
25P T 3.5 46.5 + + + -
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Residues in contact with GLY 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175I GLY 3.0 10.5 + - - -
176I LEU 3.7 2.2 - - - -
178I TYR* 1.3 78.1 - - - +
180I TYR* 1.3 63.1 + - - +
182I LEU* 3.1 18.6 + - - +
183I LEU* 3.2 10.0 + - - +
225I VAL* 3.7 27.3 - - - +
244I LEU* 3.6 20.2 - - - -
247I LEU* 4.8 0.5 - - - +
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Residues in contact with TYR 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I PHE* 3.7 13.9 - + - -
166I ARG* 3.3 34.1 - - - -
176I LEU* 2.8 26.4 + - + +
177I ASN* 3.6 6.3 - - - +
179I GLY* 1.3 77.7 - - - +
181I THR* 1.3 56.7 + - + +
183I LEU* 3.4 4.7 + - - +
184I LEU* 2.9 27.8 + - - +
218I MET* 3.5 14.7 - - + +
222I ARG* 3.4 64.4 + - + +
225I VAL* 4.0 12.8 - - + -
226I ASP* 2.5 33.6 + - - -
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Residues in contact with THR 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 5.4 0.5 - - - +
177I ASN* 2.9 18.3 + - + +
178I TYR* 2.7 25.6 + - - -
180I TYR* 1.3 75.0 - - + +
182I LEU* 1.3 66.6 + - - +
184I LEU* 3.2 25.2 + - + +
185I SER* 3.2 12.8 + - - -
25P T 4.1 22.8 + - - +
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Residues in contact with LEU 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178I TYR* 3.1 40.3 + - + +
179I GLY* 3.1 12.3 + - - +
181I THR* 1.3 76.8 - - - +
183I LEU* 1.3 63.3 + - - +
185I SER* 2.9 25.3 + - - -
186I ILE* 3.4 11.8 + - + +
244I LEU* 4.4 11.4 - - + +
245I PHE* 4.4 8.7 - - + -
247I LEU* 4.4 16.2 - - + -
248I PHE* 4.1 29.1 - - + -
25P T 3.4 41.5 - - + +
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Residues in contact with LEU 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I GLY 3.2 8.8 + - - +
180I TYR* 3.5 8.5 - - + +
181I THR 3.3 0.2 - - - -
182I LEU* 1.3 76.8 - - - +
184I LEU* 1.3 69.7 + - - +
185I SER 3.1 0.5 + - - -
186I ILE* 3.1 17.6 + - + +
187I PHE* 3.2 25.3 - - + -
218I MET* 3.8 20.2 - - + -
221I PHE* 3.7 40.2 - - + +
222I ARG* 4.1 6.3 - - - -
224I LEU* 5.4 0.9 - - + -
225I VAL* 3.7 24.0 - - + -
247I LEU* 4.8 10.5 - - + -
261I LEU* 3.9 28.5 - - + -
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Residues in contact with LEU 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 4.8 7.9 - - + -
180I TYR 2.9 14.0 + - - +
181I THR* 3.3 23.1 - - + +
183I LEU* 1.3 78.2 - - - +
185I SER* 1.3 57.7 + - - +
187I PHE* 3.2 1.5 + - - -
188I ALA* 2.9 27.5 + - - +
209I ASN* 5.2 4.7 - - - +
211I PHE* 4.0 31.4 - - + +
214I ALA* 3.6 27.1 - - + +
215I SER* 3.6 26.0 - - - +
218I MET* 3.8 14.1 - - - -
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Residues in contact with SER 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I LYS 3.6 19.8 + - - -
71I ARG* 4.1 7.6 - - - +
72I LEU* 3.3 28.0 - - - -
181I THR 3.2 6.2 + - - -
182I LEU* 2.9 20.8 + - - -
183I LEU 3.1 0.8 - - - -
184I LEU* 1.3 77.8 - - - +
186I ILE* 1.3 68.9 + - - +
188I ALA* 3.7 0.9 - - - +
189I ARG* 3.1 35.7 + - - +
248I PHE* 5.7 1.9 - - - -
25P T 4.4 6.4 + - - -
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Residues in contact with ILE 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I LEU* 3.5 15.3 - - + +
183I LEU* 3.1 16.1 + - + +
185I SER* 1.3 84.1 - - - +
187I PHE* 1.3 62.3 + - + +
189I ARG* 3.6 28.1 - - - +
190I GLU* 3.5 19.2 + - - +
248I PHE* 3.7 29.8 - - + -
261I LEU* 4.1 26.0 - - + +
262I THR* 4.4 14.6 - - + +
265I ALA* 3.4 30.0 - - + +
266I THR* 6.2 1.1 - - + -
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Residues in contact with PHE 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I LEU* 3.2 29.3 + - + -
184I LEU 3.2 5.7 + - - +
185I SER 3.2 0.4 - - - -
186I ILE* 1.3 78.5 - - + +
188I ALA* 1.3 67.1 + - - +
189I ARG 3.2 1.6 - - - -
190I GLU* 3.8 4.2 - - - +
191I LEU* 3.1 28.6 + - + +
214I ALA* 4.2 19.5 - - + +
217I LEU* 4.1 15.5 - - + -
218I MET* 3.7 22.7 - - + -
221I PHE* 3.5 44.6 - + + -
261I LEU* 5.9 1.6 - - + -
265I ALA* 3.6 33.7 - - + -
268I TYR* 4.1 10.1 - + - -
269I THR* 3.4 20.4 - - - -
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Residues in contact with ALA 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 4.0 6.3 - - + -
73I PRO* 3.9 14.1 - - + -
184I LEU 2.9 17.6 + - - +
185I SER 3.7 5.2 - - - +
187I PHE* 1.3 79.1 - - - +
189I ARG* 1.3 61.5 - - - +
191I LEU* 3.7 1.4 - - - +
192I VAL* 3.2 28.6 + - - +
198I THR* 3.9 5.3 - - + +
211I PHE* 3.8 29.2 - - + -
214I ALA* 3.8 11.3 - - + +
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Residues in contact with ARG 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I LEU* 3.9 21.2 - - + +
43I GLU* 2.7 43.3 + - - -
65I LEU* 5.0 1.7 - - - +
67I CYS* 4.0 14.8 - - - -
71I ARG* 3.1 45.4 + - - +
73I PRO* 4.0 9.6 - - + +
185I SER* 3.1 26.9 + - - +
186I ILE* 3.6 29.2 + - - +
188I ALA* 1.3 81.3 - - - +
190I GLU* 1.3 62.2 + - - +
191I LEU 3.3 0.3 + - - -
192I VAL* 3.4 3.5 + - - +
193I GLN* 3.1 24.8 + - - +
262I THR* 4.2 17.2 - - - +
26P T 4.6 5.7 + - - -
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Residues in contact with GLU 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I ILE 3.5 9.9 + - - +
187I PHE* 3.4 5.4 + - - +
188I ALA 3.4 0.2 - - - -
189I ARG* 1.3 80.7 - - - +
191I LEU* 1.3 64.1 + - - +
193I GLN* 3.3 34.8 + - - +
194I THR* 3.1 23.2 - - - +
265I ALA 4.0 2.2 - - - +
266I THR* 3.3 59.2 - - + +
269I THR* 3.8 20.4 - - - +
270I LYS* 4.8 3.7 - - - +
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Residues in contact with LEU 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I TRP* 5.8 0.2 - - + -
187I PHE 3.1 21.1 + - - +
188I ALA 3.7 3.8 - - - +
189I ARG 3.2 0.2 - - - -
190I GLU* 1.3 79.0 - - - +
192I VAL* 1.3 62.7 + - - +
194I THR* 2.7 23.9 + - - -
196I CYS* 3.2 19.4 + - + +
198I THR* 4.0 11.4 - - + -
213I LEU* 3.7 33.4 - - + +
214I ALA* 3.6 34.5 - - + +
217I LEU* 3.9 15.0 - - + -
269I THR* 3.8 20.0 - - + -
273I VAL* 4.1 16.2 - - + -
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Residues in contact with VAL 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I LEU* 4.6 5.5 - - - +
65I LEU* 3.4 33.7 - - + +
73I PRO* 3.6 23.1 - - + -
188I ALA 3.2 13.4 + - - +
189I ARG 3.7 7.2 - - - +
191I LEU* 1.3 76.3 - - - +
193I GLN* 1.3 62.7 + - - +
195I GLY* 3.0 14.2 + - - -
196I CYS 3.8 12.7 - - - +
198I THR* 4.0 15.0 - - + +
80J PHE* 3.4 24.7 - - + -
81J TYR* 4.3 6.1 - - - +
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Residues in contact with GLN 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I THR* 3.2 32.4 + - - +
7I VAL* 5.4 1.8 - - - +
39I VAL* 4.2 17.4 - - + +
41I LEU* 3.4 26.0 - - + +
63I LEU* 3.9 16.2 - - - +
65I LEU* 3.9 22.4 - - + +
84I HIS* 5.4 1.2 - - - -
86I SER* 4.5 2.4 - - - -
189I ARG* 3.1 13.4 + - - +
190I GLU* 3.3 40.6 + - - +
192I VAL* 1.3 78.4 - - - +
194I THR* 1.3 61.2 + - + +
195I GLY 3.5 0.3 + - - -
266I THR* 5.3 2.2 - - - +
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Residues in contact with THR 194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I SER* 4.4 6.9 - - - +
89I GLN* 3.4 19.6 - - - +
190I GLU* 3.1 26.2 - - - +
191I LEU* 2.7 18.6 + - - +
193I GLN* 1.3 77.6 - - + +
195I GLY* 1.3 56.4 + - - +
196I CYS* 3.3 19.4 - - - -
269I THR* 4.5 10.5 - - + -
270I LYS* 4.6 14.4 - - + -
273I VAL* 4.1 16.8 - - + +
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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