Contacts of the helix formed by residues 170 - 194 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J PHE* 4.1 15.0 - - - -
165J THR 4.6 1.4 + - - -
168J GLN 3.3 18.2 + - - -
169J GLU* 1.3 75.7 + - - +
171J ASP* 1.3 63.3 + - - +
172J ILE* 2.9 12.8 + - + +
173J ASN* 2.6 42.5 + - - +
174J ALA* 3.1 21.3 + - - +
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Residues in contact with ASP 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170J ASN* 1.3 75.2 - - - +
172J ILE* 1.3 63.4 + - + +
174J ALA* 3.6 7.1 + - - +
175J GLY 3.0 17.7 + - - -
233J ARG 5.9 0.9 - - - +
235J GLU 4.1 3.8 - - - +
236J ALA* 4.1 8.0 - - - +
237J PHE* 3.7 26.6 + - - +
240J MET* 3.1 30.8 - - + +
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Residues in contact with ILE 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160J PHE* 3.7 47.1 - - + -
164J PHE* 3.8 20.4 - - + -
170J ASN* 2.9 11.4 + - - +
171J ASP* 1.3 78.4 - - + +
173J ASN* 1.3 58.6 + - - +
175J GLY* 3.4 1.7 + - - -
176J LEU* 3.0 34.2 + - + +
229J ILE* 3.9 8.8 - - + +
233J ARG* 4.0 33.4 - - + +
240J MET* 4.4 6.1 - - - -
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Residues in contact with ASN 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164J PHE* 3.2 20.7 - - - -
165J THR 3.1 19.4 + - - -
166J ARG* 2.7 41.7 + - - +
167J GLU 6.0 0.2 - - - -
168J GLN 2.9 28.5 + - - +
169J GLU* 5.4 0.9 - - - -
170J ASN* 2.6 24.9 + - - +
172J ILE* 1.3 70.4 - - - +
174J ALA* 1.3 56.5 + - - +
176J LEU* 3.1 3.1 + - - +
177J ASN* 2.8 46.2 + - - +
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Residues in contact with ALA 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J LEU* 5.5 3.0 - - + +
170J ASN 3.1 17.3 + - - +
171J ASP* 3.7 9.6 - - - +
173J ASN* 1.3 76.7 - - - +
175J GLY* 1.3 56.2 + - - +
177J ASN* 3.5 9.4 + - - +
178J TYR* 2.9 30.5 + - - +
237J PHE* 3.6 24.3 - - + -
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Residues in contact with GLY 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J ASP 3.0 15.6 + - - -
172J ILE 3.7 2.0 - - - -
174J ALA* 1.3 74.5 - - - +
176J LEU* 1.3 64.4 + - - +
178J TYR* 3.7 1.1 - - - +
179J GLY* 3.0 19.1 + - - -
229J ILE* 3.6 22.2 - - - +
237J PHE* 3.7 13.2 - - - -
240J MET* 4.1 4.5 - - - -
244J LEU* 3.4 12.2 - - - +
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Residues in contact with LEU 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J PHE* 3.8 23.8 - - + -
160J PHE* 4.7 3.4 - - + -
164J PHE* 4.5 2.2 - - + -
166J ARG* 4.0 16.4 - - - +
172J ILE* 3.0 28.4 + - + +
173J ASN* 3.1 23.5 + - - +
175J GLY* 1.3 74.8 - - - +
177J ASN* 1.3 59.4 + - - +
179J GLY* 3.3 1.6 + - - -
180J TYR* 2.8 44.2 + - + +
225J VAL* 3.9 4.6 - - + +
226J ASP* 3.2 39.0 - - - +
229J ILE* 3.9 18.3 - - + +
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Residues in contact with ASN 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I TYR* 6.0 1.8 - - - +
166J ARG* 2.7 35.3 + - - +
173J ASN* 2.8 33.5 + - - +
174J ALA* 3.7 7.8 - - - +
176J LEU* 1.3 72.3 - - - +
178J TYR* 1.3 61.2 + - - +
180J TYR* 3.3 7.1 + - - +
181J THR* 2.9 29.5 + - - +
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Residues in contact with TYR 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU* 3.8 13.9 - - - +
43J GLU* 4.7 1.4 + - - +
67J CYS* 5.7 1.1 - - - -
71J ARG 4.0 8.4 + - - -
72J LEU* 4.2 11.0 - - + -
73J PRO* 3.4 35.3 - - + +
174J ALA 2.9 18.7 + - - +
175J GLY 3.7 4.7 - - - +
176J LEU 3.3 0.2 - - - -
177J ASN* 1.3 76.9 - - - +
179J GLY* 1.3 64.7 + - - +
181J THR* 3.2 9.0 + - - -
182J LEU* 3.1 44.5 + - + +
237J PHE* 4.3 7.0 - + + -
241J LYS* 3.4 49.6 + - + +
244J LEU* 3.7 13.9 - - + -
245J PHE* 3.5 22.4 - + - -
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Residues in contact with GLY 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175J GLY 3.0 10.5 + - - -
176J LEU 3.7 2.9 - - - -
178J TYR* 1.3 79.4 - - - +
180J TYR* 1.3 62.2 + - - +
182J LEU* 3.1 18.4 + - - +
183J LEU* 3.1 10.2 + - - +
225J VAL* 3.7 26.3 - - - +
244J LEU* 3.7 20.9 - - - -
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Residues in contact with TYR 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J PHE* 3.7 14.7 - + - -
166J ARG* 3.4 34.5 - - - -
176J LEU* 2.8 25.8 + - + +
177J ASN* 3.6 5.8 - - - +
179J GLY* 1.3 75.9 - - - +
181J THR* 1.3 57.6 + - - +
183J LEU* 3.3 4.3 + - + +
184J LEU* 2.9 27.2 + - - +
218J MET* 3.5 13.8 - - + +
222J ARG* 3.5 64.3 + - + +
225J VAL* 4.0 12.1 - - + -
226J ASP* 2.5 33.3 + - - -
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Residues in contact with THR 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 3.7 43.7 - - + -
81I TYR* 4.4 13.5 + - - +
65J LEU* 5.8 0.7 - - + -
73J PRO* 4.0 19.4 - - + +
177J ASN* 2.9 16.6 + - - +
178J TYR* 3.2 8.5 + - - -
180J TYR* 1.3 75.0 - - - +
182J LEU* 1.3 64.0 + - + +
184J LEU* 3.2 8.6 + - + +
185J SER* 2.8 29.6 + - - +
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Residues in contact with LEU 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU* 5.1 3.1 - - + -
63J LEU* 5.0 0.7 - - - +
65J LEU* 4.4 20.6 - - + -
73J PRO* 5.5 6.1 - - + -
178J TYR* 3.1 47.2 + - + +
179J GLY* 3.1 12.5 + - - +
181J THR* 1.3 79.9 - - + +
183J LEU* 1.3 63.3 + - - +
185J SER* 3.2 7.5 + - - -
186J ILE* 3.2 26.0 + - + +
244J LEU* 4.4 11.2 - - + +
245J PHE* 4.7 9.2 - - + -
247J LEU* 4.3 16.6 - - + -
248J PHE* 4.2 32.6 - - + -
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Residues in contact with LEU 183 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J GLY 3.1 10.4 + - - +
180J TYR* 3.5 8.7 - - + +
182J LEU* 1.3 79.4 - - - +
184J LEU* 1.3 63.9 + - - +
186J ILE* 3.0 18.0 + - + +
187J PHE* 3.2 26.6 + - + -
218J MET* 3.8 20.0 - - + -
221J PHE* 3.7 42.4 - - + +
222J ARG* 4.1 6.3 - - - +
224J LEU* 5.5 0.7 - - + -
225J VAL* 3.7 23.3 - - + -
247J LEU* 4.8 10.8 - - + -
261J LEU* 3.9 28.0 - - + -
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Residues in contact with LEU 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 4.0 25.1 - - + -
180J TYR 2.9 14.3 + - - +
181J THR* 3.2 15.0 + - + +
183J LEU* 1.3 78.1 - - - +
185J SER* 1.3 57.1 + - - +
187J PHE* 3.2 1.3 + - - -
188J ALA* 2.8 31.2 + - + +
211J PHE* 3.6 35.0 - - + -
214J ALA* 3.6 27.6 - - + +
215J SER* 3.6 28.0 - - - +
218J MET* 3.8 12.5 - - - -
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Residues in contact with SER 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 3.4 20.4 - - - -
63J LEU* 3.7 28.7 - - - +
65J LEU* 3.5 11.9 - - - +
76J LYS* 3.2 17.8 - - - +
181J THR* 2.8 15.6 + - - +
182J LEU* 3.5 8.5 - - - -
184J LEU* 1.3 78.3 - - - +
186J ILE* 1.3 62.4 + - - +
188J ALA* 4.2 2.2 - - - -
189J ARG* 3.1 21.1 + - - +
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Residues in contact with ILE 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J VAL* 6.1 0.2 - - + -
63J LEU* 4.4 11.7 - - + -
182J LEU* 3.2 14.3 + - + +
183J LEU* 3.0 16.5 + - + +
185J SER* 1.3 78.3 - - - +
187J PHE* 1.3 61.1 + - + +
189J ARG* 3.5 8.0 + - - +
190J GLU* 3.2 29.9 + - + +
247J LEU* 6.1 0.9 - - + -
248J PHE* 3.7 31.2 - - + -
261J LEU* 4.0 25.6 - - + -
262J THR* 4.5 20.0 - - + -
265J ALA* 3.5 30.3 - - + -
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Residues in contact with PHE 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J LEU* 3.2 29.5 + - + +
184J LEU 4.0 4.3 - - - +
186J ILE* 1.3 82.9 - - + +
188J ALA* 1.3 66.6 + - - +
190J GLU* 3.8 3.2 - - - +
191J LEU* 3.0 29.3 + - + +
214J ALA* 4.2 19.7 - - + +
217J LEU* 4.0 20.0 - - + -
218J MET* 3.8 18.4 - - + -
221J PHE* 3.5 49.4 - + + -
261J LEU* 5.8 1.6 - - + -
265J ALA* 3.6 30.1 - - + -
268J TYR* 4.1 7.0 - + - -
269J THR* 3.5 21.5 - - - -
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Residues in contact with ALA 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 5.3 9.6 - - + -
80I PHE* 6.4 0.7 - - + -
76J LYS* 3.9 18.4 - - + -
78J LEU* 6.0 2.0 - - + -
184J LEU* 2.8 19.3 + - + +
185J SER* 3.7 5.4 - - - +
187J PHE* 1.3 78.1 - - - +
189J ARG* 1.3 61.7 + - - +
191J LEU* 3.8 2.1 - - - +
192J VAL* 3.2 29.3 + - + +
198J THR* 3.9 11.8 - - + +
211J PHE* 5.4 2.9 - - + -
214J ALA* 3.8 16.7 - - + +
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Residues in contact with ARG 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ASP* 3.0 46.6 + - - +
39J VAL* 4.6 2.8 - - - +
61J LYS* 3.2 29.8 + - + +
62J ILE 4.8 0.2 - - - -
63J LEU* 3.4 26.9 - - + +
76J LYS* 3.6 21.2 - - - +
79J PRO* 6.2 1.3 - - + -
185J SER 3.1 11.5 + - - +
186J ILE* 3.6 8.1 + - - +
188J ALA* 1.3 83.4 - - - +
190J GLU* 1.3 82.3 + - - +
192J VAL* 3.4 5.6 + - - +
193J GLN* 3.1 31.6 + - + +
262J THR* 3.6 23.2 - - - +
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Residues in contact with GLU 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186J ILE* 3.2 18.7 + - + +
187J PHE* 3.3 3.5 + - - +
189J ARG* 1.3 105.2 + - - +
191J LEU* 1.3 63.2 + - - +
193J GLN* 3.3 14.3 - - - +
194J THR* 3.1 26.0 + - - +
262J THR* 4.0 5.7 - - - +
265J ALA* 4.0 18.6 - - + +
266J THR* 3.1 40.2 + - - +
269J THR* 3.7 23.1 - - - +
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Residues in contact with LEU 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J TRP* 5.9 0.2 - - + -
187J PHE 3.0 19.7 + - - +
188J ALA 3.8 3.8 - - - +
190J GLU* 1.3 74.9 - - - +
192J VAL* 1.3 64.0 + - - +
194J THR* 2.7 23.8 + - - -
196J CYS* 3.2 18.6 + - + -
198J THR* 4.0 11.7 - - + -
213J LEU* 3.7 33.0 - - + +
214J ALA* 3.6 34.8 - - + +
217J LEU* 3.8 14.8 - - + -
269J THR* 3.8 21.5 - - + -
273J VAL* 4.2 14.8 - - + -
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Residues in contact with VAL 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J LYS* 6.2 0.4 - - - +
78J LEU* 3.8 27.4 - - + -
79J PRO* 3.6 33.4 - - + +
80J PHE 5.3 1.1 - - - +
81J TYR 5.2 0.2 - - - +
82J GLY* 3.5 27.4 + - - +
188J ALA 3.2 13.4 + - - +
189J ARG* 3.7 9.6 - - - +
191J LEU* 1.3 77.4 - - - +
193J GLN* 1.3 64.3 + - - +
195J GLY* 3.0 14.4 + - - -
196J CYS 3.7 12.8 - - - +
198J THR* 4.1 12.3 - - + +
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Residues in contact with GLN 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J LYS* 3.0 43.9 + - + +
79J PRO* 5.4 6.3 - - - +
82J GLY* 2.9 33.6 + - - +
83J ARG* 3.1 31.0 + - - +
189J ARG* 3.1 27.5 + - + +
190J GLU* 3.3 21.8 - - - +
192J VAL* 1.3 81.6 - - - +
194J THR* 1.3 57.2 + - + +
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Residues in contact with THR 194 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ARG* 3.5 15.0 + - - +
89J GLN* 3.4 19.4 - - - +
190J GLU 3.1 17.3 - - - +
191J LEU 2.7 14.4 + - - +
193J GLN* 1.3 76.5 - - + +
195J GLY* 1.3 56.8 + - - +
196J CYS* 3.3 19.3 - - - -
269J THR* 4.3 15.5 - - + -
270J LYS* 4.5 20.4 - - + +
273J VAL* 4.1 13.3 - - + +
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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