Contacts of the helix formed by residues 170 - 195 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 3.8 11.5 - - - -
168A GLN* 3.2 28.3 + - - +
169A GLU* 1.3 75.5 - - - +
171A ASP* 1.3 63.2 + - - +
172A ILE* 2.9 13.0 + - + +
173A ASN* 2.6 49.9 + - - +
174A ALA* 3.1 21.1 + - - +
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASN* 1.3 76.1 - - - +
172A ILE* 1.3 64.0 + - + +
174A ALA* 3.6 6.6 + - - +
175A GLY 3.0 17.7 + - - -
233A ARG 5.9 1.6 - - - +
235A GLU 4.1 7.7 - - - +
236A ALA* 4.1 7.8 - - - +
237A PHE* 3.6 30.3 + - + +
240A MET* 3.1 22.0 - - - +
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.7 49.8 - - + -
164A PHE* 4.0 18.8 - - + -
170A ASN* 2.9 11.6 + - + +
171A ASP* 1.3 80.0 - - + +
173A ASN* 1.3 59.5 + - - +
175A GLY* 3.4 2.1 + - - -
176A LEU* 3.0 34.1 + - + +
229A ILE* 4.5 4.3 - - + +
233A ARG* 4.0 30.3 - - + +
240A MET* 3.7 11.8 - - + +
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Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 3.2 20.9 - - - -
165A THR 3.1 23.2 + - - -
166A ARG* 2.7 41.8 + - - +
168A GLN 2.8 26.9 + - - +
169A GLU* 5.7 0.2 - - - -
170A ASN* 2.6 24.0 + - - +
172A ILE* 1.3 70.0 - - - +
174A ALA* 1.3 57.1 + - - +
176A LEU* 3.1 3.1 + - - +
177A ASN* 2.7 47.0 + - - +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.4 3.2 - - + +
170A ASN 3.1 16.9 + - - +
171A ASP* 3.7 8.7 - - - +
173A ASN* 1.3 76.7 - - - +
175A GLY* 1.3 57.5 + - - +
177A ASN* 3.5 8.6 + - - +
178A TYR* 2.9 30.1 + - - +
237A PHE* 3.5 24.7 - - + -
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASP 3.0 10.3 + - - -
172A ILE 3.8 0.2 - - - -
174A ALA* 1.3 75.9 - - - +
176A LEU* 1.3 63.5 + - - +
178A TYR* 3.5 1.7 + - - +
179A GLY* 3.0 19.1 + - - -
225A VAL* 4.4 0.2 - - - +
229A ILE* 4.0 8.5 - - - +
237A PHE* 3.6 13.0 - - - -
240A MET* 3.5 24.2 - - - -
244A LEU* 3.4 13.1 - - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.8 23.6 - - + -
160A PHE* 4.6 1.1 - - + -
164A PHE* 4.5 2.0 - - + -
166A ARG* 4.0 17.3 - - - +
172A ILE* 3.0 22.7 + - + +
173A ASN* 3.5 23.8 - - - +
175A GLY* 1.3 75.6 - - - +
177A ASN* 1.3 53.4 + - - +
179A GLY* 3.2 1.7 + - - -
180A TYR* 2.8 50.0 + - + +
225A VAL* 3.9 5.5 - - + +
226A ASP* 3.2 27.8 - - - +
229A ILE* 2.5 39.4 - - + +
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Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 2.7 36.0 + - - +
173A ASN* 2.7 33.7 + - - +
174A ALA* 3.7 7.9 - - - +
176A LEU* 1.3 73.7 - - - +
178A TYR* 1.3 61.5 + - - +
180A TYR* 3.3 6.0 + - - +
181A THR* 2.9 29.6 + - - -
81B TYR* 5.8 4.0 - - - +
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.0 13.3 - - - +
43A GLU* 4.8 1.4 + - - +
67A CYS* 5.8 1.1 - - - -
71A ARG 4.1 7.9 + - - -
72A LEU* 4.2 10.5 - - + -
73A PRO* 3.4 36.1 - - + +
174A ALA 2.9 19.0 + - - +
175A GLY* 3.7 4.7 - - - +
176A LEU 3.3 0.2 - - - -
177A ASN* 1.3 75.1 - - - +
179A GLY* 1.3 63.8 + - - +
181A THR* 3.2 9.6 + - - -
182A LEU* 3.1 45.2 + - + +
237A PHE* 4.3 6.3 - + + -
241A LYS* 3.5 48.5 - - + +
244A LEU* 3.8 13.9 - - + -
245A PHE* 3.6 22.3 - + - -
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLY 3.0 11.1 + - - -
176A LEU 3.7 3.1 - - - -
178A TYR* 1.3 78.1 - - - +
180A TYR* 1.3 62.6 + - - +
182A LEU* 3.1 18.6 + - - +
183A LEU* 3.1 10.4 + - - +
225A VAL* 3.7 24.9 - - - +
244A LEU* 3.7 20.4 - - - -
247A LEU* 4.8 0.6 - - - +
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.7 13.6 - + - -
166A ARG* 3.4 34.1 - - - -
176A LEU* 2.8 26.5 + - + +
177A ASN* 3.6 6.3 - - - +
179A GLY* 1.3 76.7 - - - +
181A THR* 1.3 55.7 + - - +
183A LEU* 3.3 4.8 + - + +
184A LEU* 2.9 27.6 + - - +
218A MET* 3.5 14.1 - - + +
222A ARG* 3.5 64.8 + - + +
225A VAL* 4.0 12.8 - - + -
226A ASP* 2.5 33.5 + - - -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 5.7 0.4 - - + -
73A PRO* 4.0 19.5 - - + +
177A ASN* 2.9 17.2 + - - +
178A TYR* 3.4 8.8 - - - -
180A TYR* 1.3 73.6 - - - +
182A LEU* 1.3 64.7 + - + +
184A LEU* 3.3 8.7 + - + +
185A SER* 2.7 29.5 + - - +
80B PHE* 3.5 45.1 - - + -
81B TYR* 4.5 12.0 + - + +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 5.8 1.8 - - + -
63A LEU* 4.9 1.3 - - - +
65A LEU* 4.3 22.0 - - + -
73A PRO* 5.6 4.9 - - + -
178A TYR* 3.1 47.6 + - + +
179A GLY* 3.1 13.4 + - - +
181A THR* 1.3 78.6 - - + +
183A LEU* 1.3 63.6 + - - +
185A SER* 3.2 7.8 + - - -
186A ILE* 3.2 25.0 + - + +
244A LEU* 4.4 10.3 - - + +
245A PHE* 4.7 9.6 - - + -
247A LEU* 4.4 15.9 - - + -
248A PHE* 4.1 32.9 - - + -
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 3.1 10.4 + - - +
180A TYR* 3.5 8.3 - - + +
182A LEU* 1.3 77.2 - - - +
184A LEU* 1.3 67.9 + - - +
186A ILE* 3.0 18.4 + - + +
187A PHE* 3.2 26.2 + - + -
218A MET* 3.8 19.5 - - + -
221A PHE* 3.6 44.9 - - + +
222A ARG* 4.0 6.5 - - - -
224A LEU* 5.5 1.1 - - + -
225A VAL* 3.7 20.9 - - + -
247A LEU* 4.8 10.1 - - + -
261A LEU* 3.9 28.3 - - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR 2.9 14.3 + - - +
181A THR* 3.4 13.2 - - + +
183A LEU* 1.3 77.7 - - - +
185A SER* 1.3 57.3 + - - +
187A PHE* 3.2 1.4 + - - -
188A ALA* 2.8 31.6 + - + +
211A PHE* 3.6 35.4 - - + -
214A ALA* 3.6 27.7 - - + +
215A SER* 3.6 27.8 - - - +
218A MET* 3.8 12.9 - - - -
80B PHE* 4.1 24.9 - - + -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.7 27.7 - - - +
65A LEU* 3.6 11.1 - - - +
76A LYS* 3.2 18.8 - - - +
181A THR* 2.7 15.7 + - - +
182A LEU* 3.5 9.6 - - - -
184A LEU* 1.3 78.5 - - - +
186A ILE* 1.3 62.9 + - - +
188A ALA* 4.2 1.8 - - - -
189A ARG* 3.1 20.6 + - - +
80B PHE* 3.4 20.8 - - - -
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.5 11.2 - - + -
182A LEU* 3.2 15.8 + - + +
183A LEU* 3.0 17.1 + - + +
185A SER* 1.3 77.5 - - - +
187A PHE* 1.3 61.6 + - + +
189A ARG* 3.5 8.2 + - - +
190A GLU* 3.2 29.6 + - + +
247A LEU* 6.0 0.9 - - + -
248A PHE* 3.7 32.1 - - + -
261A LEU* 4.0 26.0 - - + +
262A THR* 4.5 20.0 - - + -
265A ALA* 3.5 29.4 - - + -
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.2 33.1 + - + +
184A LEU 4.0 2.2 - - - +
186A ILE* 1.3 83.1 - - + +
188A ALA* 1.3 67.1 + - - +
190A GLU* 3.8 3.4 - - - +
191A LEU* 3.0 28.9 + - - +
214A ALA* 4.2 19.3 - - + +
217A LEU* 4.0 19.7 - - + -
218A MET* 3.9 17.3 - - + -
221A PHE* 3.5 48.2 - + + -
261A LEU* 5.8 1.6 - - + -
265A ALA* 3.7 30.5 - - + -
268A TYR* 4.1 7.4 - + - -
269A THR* 3.4 21.3 - - - -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 3.9 19.1 - - + -
78A LEU* 5.7 3.1 - - + -
184A LEU* 2.8 20.4 + - + +
185A SER* 3.7 5.6 - - - +
187A PHE* 1.3 78.1 - - - +
189A ARG* 1.3 62.3 + - - +
191A LEU* 3.4 1.9 + - - +
192A VAL* 3.2 29.1 + - - +
198A THR* 3.9 12.2 - - + +
211A PHE* 5.4 4.9 - - + -
214A ALA* 3.8 15.8 - - + +
78B LEU* 5.4 6.3 - - + -
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 3.0 47.8 + - - +
39A VAL* 4.8 2.4 - - - +
61A LYS* 3.1 34.7 + - + -
62A ILE* 4.1 0.6 - - - +
63A LEU* 3.3 27.5 - - + +
76A LYS* 3.6 18.5 - - - +
79A PRO* 6.2 1.3 - - + -
185A SER 3.1 14.2 + - - +
186A ILE* 3.6 8.8 + - - +
188A ALA* 1.3 82.1 - - - +
190A GLU* 1.3 79.8 + - - +
192A VAL* 3.3 5.6 + - - +
193A GLN* 3.1 22.9 + - + +
262A THR* 3.5 24.5 - - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.2 18.5 + - - +
187A PHE* 3.3 3.5 + - - +
189A ARG* 1.3 97.5 + - - +
191A LEU* 1.3 64.0 + - - +
193A GLN* 3.4 14.7 + - - +
194A THR* 2.9 27.7 + - - -
262A THR* 3.9 6.2 - - - +
265A ALA* 4.0 8.3 - - + +
266A THR* 3.0 50.5 + - - +
269A THR* 3.7 22.0 - - - +
270A LYS* 5.1 0.5 + - - -
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE 3.0 20.4 + - - +
188A ALA 3.8 3.8 - - - +
190A GLU* 1.3 77.5 - - - +
192A VAL* 1.3 63.9 + - - +
194A THR* 3.0 14.5 + - - -
195A GLY 3.1 8.5 + - - -
196A CYS* 3.1 23.5 + - + +
198A THR* 4.0 13.0 - - + -
213A LEU* 3.7 32.8 - - + +
214A ALA* 3.6 34.5 - - + +
217A LEU* 3.8 15.5 - - + -
269A THR* 3.8 21.1 - - + -
273A VAL* 4.2 11.4 - - + -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.8 27.1 - - + -
79A PRO* 3.7 33.9 - - + +
80A PHE 5.3 0.9 - - - +
81A TYR 5.3 0.2 - - - +
82A GLY* 3.5 27.1 + - - +
188A ALA 3.2 13.8 + - - +
189A ARG* 3.7 9.0 - - - +
191A LEU* 1.3 76.4 - - - +
193A GLN* 1.3 63.4 + - - +
195A GLY* 3.1 14.0 + - - -
196A CYS 3.8 11.7 - - - +
198A THR* 4.0 11.9 - - + +
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 4.8 22.7 - - + +
82A GLY* 3.9 19.7 + - - +
83A ARG* 3.1 25.8 + - - +
189A ARG* 3.1 14.8 + - + +
190A GLU* 3.4 20.3 - - - +
191A LEU 3.2 0.2 - - - -
192A VAL* 1.3 78.4 - - - +
194A THR* 1.3 55.1 + - - +
266A THR* 5.0 1.7 - - - +
270A LYS* 2.5 31.5 + - - -
34Q T 3.1 25.6 + - - -
35Q C 4.6 6.5 + - - -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.3 21.8 + - - +
89A GLN* 3.4 19.0 - - - +
190A GLU 2.9 15.3 + - - -
191A LEU 3.0 6.9 + - - -
193A GLN* 1.3 75.9 - - - +
195A GLY* 1.3 58.3 + - - +
196A CYS* 3.6 2.2 - - - -
269A THR* 4.0 12.5 - - - +
270A LYS* 3.7 31.8 + - + +
273A VAL* 4.1 33.4 - - + -
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.9 11.4 - - - -
86A SER* 4.5 10.5 - - - -
89A GLN* 3.5 17.3 - - - +
90A LEU* 3.0 30.4 - - - +
192A VAL 3.1 14.4 + - - -
193A GLN 3.2 0.8 + - - -
194A THR* 1.3 78.7 - - - +
196A CYS* 1.3 61.1 + - - +
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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