Contacts of the helix formed by residues 166 - 192 (chain A) in PDB entry 1YV5
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 TYR 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 6.0 0.2 - - - -
98A ARG* 3.3 31.4 + - - -
161A CYS* 4.0 13.9 - - + -
164A GLN* 3.5 26.2 - - + -
165A PRO* 1.3 83.7 - - + +
167A TYR* 1.3 67.3 + - - +
168A LEU 3.4 2.2 - - - -
169A ASN* 3.2 13.2 + - + +
170A LEU* 3.0 46.3 + - + +
229A TYR* 3.4 27.8 - - + +
230A MET* 3.4 50.0 - - + +
234A ASP* 5.8 0.2 - - - +
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR 4.8 1.6 + - - -
157A LEU* 3.6 28.9 - - + -
158A LYS* 3.5 30.2 + - - +
161A CYS* 3.4 33.4 - - + +
162A ARG* 3.7 30.5 - - + +
164A GLN 3.3 11.0 + - - +
165A PRO 3.4 1.0 - - - -
166A TYR* 1.3 84.9 - - - +
168A LEU* 1.3 67.0 + - + +
170A LEU* 3.1 4.9 + - + +
171A ILE* 3.1 52.7 + - + +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PRO 5.0 2.3 + - - +
166A TYR 3.4 0.4 - - - -
167A TYR* 1.3 81.9 - - + +
169A ASN* 1.3 58.3 + - - +
171A ILE* 4.5 17.7 - - + -
172A GLU* 3.0 60.4 + - + +
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO 5.1 3.4 + - - -
166A TYR* 3.2 19.0 + - - +
168A LEU* 1.3 78.6 - - - +
170A LEU* 1.3 58.9 + - - +
172A GLU* 3.9 12.2 - - - +
173A LEU* 2.9 28.4 + - - +
229A TYR* 3.6 46.9 - - + +
234A ASP* 4.1 15.6 + - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.9 26.2 - - + -
157A LEU* 4.2 17.3 - - + -
161A CYS* 4.6 3.1 - - + -
166A TYR* 3.0 44.1 + - + +
167A TYR* 3.6 8.1 - - + +
169A ASN* 1.3 75.2 - - - +
171A ILE* 1.3 64.4 + - - +
173A LEU* 3.1 8.7 + - + +
174A PHE* 2.9 35.3 + - + -
226A ALA* 3.7 41.5 - - + +
229A TYR* 4.2 9.0 - - + -
230A MET* 4.1 4.0 - - + -
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 4.1 17.0 - - + -
157A LEU* 4.4 17.0 - - + +
167A TYR* 3.1 56.8 + - + +
168A LEU* 3.9 19.3 - - + +
170A LEU* 1.3 74.9 - - - +
172A GLU* 1.3 59.1 + - + +
174A PHE* 3.4 1.9 + - - +
175A LEU* 3.0 51.0 + - + +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 3.0 45.5 + - + +
169A ASN* 3.9 14.9 - - - +
171A ILE* 1.3 80.2 - - + +
173A LEU* 1.3 56.6 + - - +
175A LEU* 3.9 10.3 - - + +
176A GLN* 3.0 31.2 + - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN 2.9 19.0 + - - +
170A LEU* 3.1 9.4 + - + +
172A GLU* 1.3 76.6 - - - +
174A PHE* 1.3 57.6 + - + +
176A GLN* 3.4 9.7 + - - +
177A SER* 2.9 32.4 + - - -
221A TYR* 3.8 31.4 - - + +
222A LEU* 3.5 24.7 - - + +
225A ALA* 3.9 9.6 - - + -
226A ALA* 3.5 38.4 - - + +
229A TYR* 4.1 14.4 - - + -
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 4.1 17.0 - - + -
105A CYS* 3.6 44.6 - - + -
106A VAL* 3.8 24.2 - - + -
109A LEU* 4.3 16.4 - - + +
153A ILE* 3.8 17.3 - - + -
154A TYR* 3.5 20.0 - - + +
157A LEU* 4.2 13.0 - - + -
170A LEU* 2.9 37.3 + - + +
171A ILE 3.8 2.9 - - - +
173A LEU* 1.3 74.1 - - + +
175A LEU* 1.3 63.8 + - - +
177A SER* 3.1 6.4 + - - -
178A SER* 2.9 28.4 + - - -
222A LEU* 4.3 17.3 - - + -
226A ALA* 4.9 2.5 - - + -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 5.8 3.4 - - - +
154A TYR* 3.4 26.7 - - + +
171A ILE* 3.0 40.0 + - + +
172A GLU* 3.9 9.2 - - + +
174A PHE* 1.3 75.5 - - - +
176A GLN* 1.3 63.6 + - - +
178A SER* 3.3 6.8 + - - +
179A TYR* 3.0 22.7 + - - +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU 3.0 20.1 + - - +
173A LEU* 3.9 11.8 - - - +
175A LEU* 1.3 78.5 - - - +
177A SER* 1.3 57.3 + - - +
179A TYR* 3.2 10.4 + - + +
180A GLN* 2.9 55.9 + - + +
221A TYR* 5.6 4.0 - - - -
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.7 4.8 - - - +
173A LEU* 2.9 19.1 + - - -
174A PHE* 3.1 13.9 + - - -
176A GLN* 1.3 77.6 - - - +
178A SER* 1.3 55.6 + - - +
180A GLN* 3.7 13.2 + - - +
181A THR* 2.8 34.0 + - - -
217A PHE* 4.7 4.3 - - - +
218A TYR* 4.5 9.4 - - - -
221A TYR* 6.3 1.6 - - - -
222A LEU* 3.5 37.5 - - - +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.4 21.3 - - - +
112A PHE* 5.2 0.2 - - - -
113A PHE* 3.8 13.0 - - - -
150A GLU* 4.4 10.6 + - - +
154A TYR* 4.2 5.3 + - - -
174A PHE 2.9 17.2 + - - -
175A LEU* 3.4 11.0 - - - -
177A SER* 1.3 72.8 + - - +
179A TYR* 1.3 67.6 + - - +
181A THR* 3.1 2.1 + - - -
182A GLU* 2.9 41.9 + - - +
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU 3.0 10.4 + - - +
176A GLN* 3.5 13.5 - - + +
178A SER* 1.3 79.0 - - - +
180A GLN* 1.3 74.1 + - + +
182A GLU* 3.1 14.3 + - + +
183A ILE* 3.0 56.8 + - + +
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLN* 2.9 49.0 + - + +
177A SER* 3.7 10.4 + - - +
179A TYR* 1.3 86.5 - - + +
181A THR* 1.3 63.4 + - - +
183A ILE* 3.3 7.2 + - - +
184A GLY 3.2 14.9 + - - -
213A TYR* 3.1 24.8 - - + +
217A PHE* 3.2 62.0 - - + +
221A TYR* 5.7 0.5 - - - -
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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
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113A PHE* 3.5 39.2 - - + -
177A SER 2.8 22.4 + - - -
178A SER 3.1 0.2 + - - -
180A GLN* 1.3 78.5 - - - +
182A GLU* 1.3 55.9 + - - +
184A GLY* 3.4 2.3 + - - -
185A GLN* 3.0 27.5 + - + +
213A TYR 3.4 9.2 + - - -
214A LYS* 3.5 20.1 - - - +
217A PHE* 5.2 0.2 - - - +
218A TYR* 3.5 29.1 + - + +
901A RIS 4.1 7.2 - - + -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.0 22.3 - - - -
113A PHE* 3.6 17.5 - - + -
150A GLU* 4.4 3.6 - - - +
178A SER* 2.9 28.4 + - - +
179A TYR* 3.6 15.9 - - + +
181A THR* 1.3 72.8 - - - +
183A ILE* 1.3 62.6 + - + +
185A GLN* 3.8 8.0 - - + +
186A THR* 2.9 30.8 + - - -
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TYR* 3.0 57.8 + - + +
180A GLN* 3.3 10.5 + - - +
182A GLU* 1.3 77.9 - - + +
184A GLY* 1.3 57.9 - - - +
186A THR* 3.1 13.4 - - + +
187A LEU* 3.0 35.8 + - + +
213A TYR* 4.3 21.3 - - + -
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Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLN 3.2 7.7 + - - -
181A THR 3.6 0.7 - - - -
183A ILE* 1.3 76.5 - - - +
185A GLN* 1.3 58.1 + - - +
187A LEU* 3.2 7.7 + - - +
188A ASP* 2.9 28.9 + - - +
210A ILE* 4.1 5.7 - - - +
213A TYR* 3.6 21.2 - - - +
214A LYS* 3.6 20.0 - - - +
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Residues in contact with GLN 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.7 9.4 + - + -
117A ASP* 2.7 35.8 + - - +
120A MET* 4.1 17.6 - - + +
181A THR* 3.0 26.1 + - + +
182A GLU* 3.8 9.4 - - + +
184A GLY* 1.3 71.3 - - - +
186A THR* 1.3 65.4 + - - +
188A ASP* 3.4 7.7 - - - +
189A LEU* 3.1 40.1 + - + +
214A LYS* 3.9 13.7 - - - +
901A RIS 3.5 30.9 - - + -
909A MG 4.3 2.9 - - - -
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU 2.9 16.4 + - - -
183A ILE* 3.1 19.0 - - + +
185A GLN* 1.3 77.2 - - - +
187A LEU* 1.3 66.7 + - + +
189A LEU* 3.3 7.6 + - - +
190A LEU* 3.1 43.5 + - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ILE* 3.0 25.2 + - + +
184A GLY* 3.2 9.2 + - - +
186A THR* 1.3 78.7 - - + +
188A ASP* 1.3 64.5 + - - +
189A LEU 3.0 0.3 + - - -
190A LEU* 3.2 12.1 + - + -
191A THR* 2.6 33.5 + - - +
206A ARG* 4.0 26.7 - - - +
209A SER* 4.2 34.3 - - - +
210A ILE* 4.0 12.1 - - + -
213A TYR* 4.9 5.4 - - + -
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP* 6.0 0.2 - - - -
184A GLY 2.9 16.5 + - - +
185A GLN* 3.4 21.4 - - - +
187A LEU* 1.3 73.2 - - - +
189A LEU* 1.3 66.1 + - - +
191A THR* 3.6 2.6 + - - -
192A ALA* 3.3 24.1 + - - +
210A ILE* 4.1 21.8 - - + +
214A LYS* 3.1 30.0 + - + +
280A LYS* 3.0 39.2 + - - +
281A CYS* 5.5 2.4 + - - +
901A RIS 5.3 0.7 - - - -
909A MG 4.2 5.7 - - - -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A MET* 4.0 48.0 - - + +
121A ASP* 4.4 1.6 - - - +
185A GLN* 3.1 33.7 + - + +
186A THR* 3.9 6.3 - - - +
187A LEU 3.1 0.2 - - - -
188A ASP* 1.3 78.4 - - - +
190A LEU* 1.3 63.3 + - + +
192A ALA* 3.4 23.1 + - - +
193A PRO* 3.8 2.9 - - - +
280A LYS* 3.8 21.5 - - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A THR* 3.1 40.0 + - + +
187A LEU* 3.8 15.7 - - + +
189A LEU* 1.3 73.4 - - - +
191A THR* 1.3 63.9 + - - +
192A ALA 3.2 0.9 - - - -
193A PRO* 3.6 12.1 - - - +
201A ARG* 4.6 4.9 - - - -
206A ARG* 4.6 8.6 + - - +
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU 2.6 22.7 + - - -
188A ASP 4.0 4.0 - - - -
190A LEU* 1.3 75.4 - - - +
192A ALA* 1.3 56.4 + - - +
193A PRO* 3.3 10.1 - - - +
198A ASP* 3.5 6.8 - - - +
201A ARG* 3.6 25.5 - - + +
202A PHE* 3.4 19.8 - - + -
206A ARG* 3.0 43.2 + - + +
210A ILE* 4.0 6.6 - - - +
281A CYS* 4.0 22.7 - - + -
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASP 3.3 18.1 + - - +
189A LEU* 3.4 10.0 - - - +
190A LEU 3.2 0.2 - - - -
191A THR* 1.3 79.0 - - - +
193A PRO* 1.3 64.5 - - - +
194A GLN* 3.4 4.7 + - - +
278A ASP 3.9 8.2 - - - +
279A ASN* 3.0 32.5 - - - +
280A LYS* 3.9 21.9 + - + +
281A CYS 4.8 0.7 - - - +
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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