Contacts of the helix formed by residues 169 - 196 (chain A) in PDB entry 1VGO
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 SER 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 1.3 76.1 - - - +
170A GLU* 1.3 59.7 + - - +
172A VAL* 3.0 20.1 + - - +
173A ARG* 2.8 27.3 + - - +
400A SO4 2.6 36.6 + - - -
171B GLU* 3.9 6.5 + - - -
232B ARG* 3.5 23.2 + - - -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 1.3 72.7 - - - +
171A GLU* 1.3 60.6 + - - +
173A ARG* 3.1 40.3 + - - +
174A SER* 2.7 50.7 + - - -
170B GLU* 3.5 35.6 - - - +
171B GLU* 5.1 0.9 + - - +
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.2 2.8 + - - +
170A GLU* 1.3 85.2 - - - +
172A VAL* 1.3 61.3 + - - +
174A SER* 3.4 8.7 + - - -
175A THR* 3.1 30.8 + - - +
231A SER* 6.2 0.2 - - - -
232A ARG* 3.2 47.6 + - + +
233A ALA* 4.1 9.0 - - - +
169B SER* 3.9 13.7 + - - -
170B GLU* 5.6 4.2 - - - +
171B GLU* 3.2 31.7 + - - +
232B ARG* 4.4 3.6 - - - +
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.3 39.2 - - + +
165A ALA* 5.0 1.8 - - + +
168A ARG* 3.6 30.1 - - + +
169A SER* 3.0 24.1 + - - +
171A GLU* 1.3 74.5 - - - +
173A ARG* 1.3 65.0 + - - +
174A SER 3.3 0.2 + - - -
175A THR* 3.3 3.3 + - - -
176A PHE* 3.0 23.7 + - + +
233A ALA* 3.7 17.9 - - + +
400A SO4 3.1 14.6 - - - +
232B ARG* 4.2 10.5 - - - +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA* 3.7 15.2 + - + +
166A ALA* 3.4 39.2 + - - +
168A ARG 3.6 11.5 + - - -
169A SER* 2.8 13.1 + - - +
170A GLU* 3.1 44.3 + - - +
172A VAL* 1.3 78.3 - - - +
174A SER* 1.3 61.9 + - - +
176A PHE* 3.5 5.6 + - - +
177A ASN* 3.1 43.1 + - - +
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU* 2.7 37.2 + - - -
171A GLU* 3.6 11.3 + - - -
172A VAL 3.2 0.2 - - - -
173A ARG* 1.3 75.2 - - - +
175A THR* 1.3 63.6 + - - +
177A ASN* 3.3 8.3 + - - +
178A THR* 3.0 29.9 + - - -
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.6 4.9 - - + -
171A GLU* 3.1 13.8 + - - +
172A VAL 3.9 0.7 - - - -
174A SER* 1.3 77.1 + - - +
176A PHE* 1.3 65.0 + - - +
178A THR* 3.4 5.9 + - - -
179A LEU* 3.0 44.3 + - + +
227A VAL* 4.7 6.1 - - + +
228A LEU* 4.7 7.2 - - + -
231A SER* 3.5 29.0 + - - +
233A ALA* 3.5 23.4 + - + +
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 3.4 42.5 - - + +
105A LEU* 4.0 22.1 - - + +
106A ALA* 3.7 8.3 - - + -
157A LEU* 3.9 7.9 - - + -
161A LEU* 3.3 30.3 - - + -
162A ARG* 3.4 27.1 - - + -
165A ALA* 3.7 21.5 - - + -
172A VAL* 3.0 17.1 + - + +
173A ARG 3.7 4.3 - - - +
175A THR* 1.3 77.6 - - - +
177A ASN* 1.3 65.8 + - - +
179A LEU* 3.5 2.8 + - - +
180A THR* 2.7 51.9 + - - -
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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
----------------------------------------------------------
162A ARG* 3.8 22.0 + - - +
165A ALA* 6.0 0.2 - - - +
173A ARG* 3.1 32.4 + - - +
174A SER* 3.6 6.1 - - - +
176A PHE* 1.3 90.1 - - - +
178A THR* 1.3 64.8 + - - +
180A THR* 3.4 5.5 + - - -
181A ALA* 3.0 23.9 + - - +
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A SER* 3.0 22.6 + - - -
175A THR* 3.7 8.4 - - - -
176A PHE 3.3 0.2 - - - -
177A ASN* 1.3 75.8 - - - +
179A LEU* 1.3 59.3 + - - +
181A ALA* 3.1 9.4 + - - +
182A LEU* 3.0 27.3 + - + +
227A VAL* 4.3 20.6 - - + -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.0 8.1 - - + -
105A LEU* 3.9 11.0 - - + -
175A THR* 3.0 33.9 + - + +
176A PHE 3.9 3.1 - - - +
178A THR* 1.3 72.1 - - - +
180A THR* 1.3 60.8 + - - +
182A LEU* 3.4 12.0 + - + +
183A VAL* 3.1 31.1 + - - +
224A PHE* 3.7 39.6 - - + +
227A VAL* 3.3 35.0 - - + -
228A LEU* 3.8 26.5 - - + +
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.4 6.5 - - - +
154A LEU* 5.9 1.5 - - + +
157A LEU* 4.0 33.9 - - + +
158A LEU* 4.1 22.4 - - + -
162A ARG* 6.0 1.3 - - + -
176A PHE* 2.7 46.8 + - + -
177A ASN* 3.8 7.6 - - - -
178A THR 3.2 0.2 - - - -
179A LEU* 1.3 74.5 - - - +
181A ALA* 1.3 61.6 + - - +
183A VAL* 3.3 9.0 + - - +
184A ALA* 3.0 26.9 + - + +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASN 3.0 13.3 + - - +
178A THR* 3.4 11.2 - - - +
180A THR* 1.3 77.7 - - - +
182A LEU* 1.3 60.1 + - - +
184A ALA* 3.2 9.2 + - - +
185A VAL* 3.0 28.7 + - - +
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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
----------------------------------------------------------
178A THR* 3.0 14.5 + - + +
179A LEU* 3.5 18.8 - - + +
181A ALA* 1.3 77.0 - - - +
183A VAL* 1.3 56.5 + - - +
185A VAL* 3.1 10.6 - - + +
186A LEU* 3.0 60.2 + - + +
219A THR* 5.0 6.3 - - + -
223A GLY 4.7 0.7 - - - -
224A PHE* 3.7 44.6 - - + +
227A VAL* 4.6 10.5 - - + -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 6.3 0.2 - - + -
99A LEU* 5.7 0.2 - - + -
102A LEU* 4.3 14.4 - - + -
150A PHE* 4.7 0.2 - - - -
153A VAL* 5.6 0.2 - - + -
154A LEU* 4.6 7.0 - - + -
157A LEU* 4.0 20.9 - - + -
179A LEU 3.1 14.8 + - - +
180A THR* 3.5 8.7 - - - +
181A ALA 3.2 0.2 - - - -
182A LEU* 1.3 76.3 - - - +
184A ALA* 1.3 61.3 + - - +
187A TRP* 2.9 84.5 + - + +
188A THR 3.9 0.2 + - - -
224A PHE* 3.8 21.1 - - + -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.4 26.7 - - + -
158A LEU* 5.9 3.1 - - + -
180A THR* 3.0 15.6 + - + +
181A ALA* 3.2 13.7 + - - +
183A VAL* 1.3 76.3 - - - +
185A VAL* 1.3 55.8 + - - +
188A THR* 2.5 28.1 + - - +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA 3.0 18.7 + - - +
182A LEU* 3.1 20.9 - - + +
184A ALA* 1.3 78.6 - - - +
186A LEU* 1.3 71.9 + - + +
188A THR* 3.9 4.0 + - - -
189A ALA* 3.8 12.0 + - - +
306A BNG 3.6 31.5 - - + +
307A BNG 4.1 18.7 - - + +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.0 44.3 + - + +
185A VAL* 1.3 80.6 - - + +
187A TRP* 1.3 73.0 + - + +
189A ALA* 3.1 21.4 + - - +
190A TYR* 3.4 12.0 - - + -
216A LEU* 4.2 18.4 - - + +
219A THR* 3.7 22.9 - - + -
220A ALA* 3.6 37.0 - - + +
224A PHE* 6.2 0.2 - - + -
306A BNG 4.3 25.4 - - + -
308A BNG 6.0 0.4 - - + -
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Residues in contact with TRP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 3.7 21.8 - - + -
98A LEU* 3.8 19.5 - - + +
99A LEU* 3.4 31.9 - - + -
120A ASP* 3.7 17.5 - - - -
123A MET* 4.3 3.1 - - + -
150A PHE* 3.4 24.4 - + + -
153A VAL* 4.4 9.0 - - + -
183A VAL* 2.9 55.6 + - + +
186A LEU* 1.3 76.5 - - + +
188A THR* 1.3 65.0 + - - +
189A ALA 3.0 2.8 + - - -
190A TYR* 3.2 13.8 + + - +
191A PRO* 3.1 19.1 - - - +
220A ALA* 4.5 7.1 + - + +
224A PHE* 5.7 1.8 - - - -
260A RET 3.5 50.9 - - + +
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Residues in contact with THR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PHE* 3.5 21.8 - - - -
154A LEU* 5.0 1.4 - - - +
183A VAL 3.9 0.8 + - - -
184A ALA* 2.5 28.8 + - - +
185A VAL* 3.9 5.1 + - - -
186A LEU 3.2 0.8 - - - -
187A TRP* 1.3 78.2 - - - +
189A ALA* 1.3 61.6 + - - +
191A PRO* 3.1 15.7 - - - +
192A ILE* 3.4 21.0 - - + +
305A BNG 4.0 23.1 - - + -
307A BNG 5.7 4.5 - - + -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL 3.8 9.4 + - - +
186A LEU 3.1 15.0 + - - +
187A TRP 3.0 0.6 - - - -
188A THR* 1.3 77.6 - - - +
190A TYR* 1.3 57.9 + - - +
192A ILE* 3.3 8.9 + - - +
193A LEU* 2.8 32.2 + - + +
216A LEU* 3.7 26.7 - - + -
306A BNG 6.0 1.6 - - + -
307A BNG 4.7 16.1 - - + +
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Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP* 3.6 14.8 - + - -
186A LEU 3.4 21.3 - - - -
187A TRP* 3.2 14.5 + + - -
189A ALA* 1.3 75.8 - - - +
191A PRO* 1.3 73.4 - - + +
192A ILE 3.2 0.2 + - - -
193A LEU* 3.2 2.3 + - - +
194A TRP* 3.0 23.9 + - - +
213A PHE* 3.5 30.1 - + - -
216A LEU* 3.4 19.0 + - + -
217A ASP* 2.7 45.4 + - - -
220A ALA* 4.0 3.6 - - + +
260A RET 3.5 63.6 - - + +
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Residues in contact with PRO 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 3.1 29.0 + - + +
147A THR* 4.0 9.6 - - + +
150A PHE* 4.6 3.6 - - + -
187A TRP 3.1 17.5 - - - +
188A THR* 3.1 20.0 - - - +
190A TYR* 1.3 86.9 - - + +
192A ILE* 1.3 55.2 + - + +
194A TRP* 3.4 2.2 + - + -
195A ILE* 3.0 26.4 + - - +
260A RET 3.7 36.5 - - + -
305A BNG 4.6 16.4 - - + -
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 5.5 0.2 - - - -
188A THR* 3.4 31.6 - - + +
189A ALA* 3.3 9.6 + - - +
190A TYR 3.1 0.6 - - - -
191A PRO* 1.3 77.7 - - + +
193A LEU* 1.3 60.6 + - - +
195A ILE* 3.2 19.2 - - + +
196A VAL* 3.0 31.9 - - + +
305A BNG 4.2 37.5 - - + +
307A BNG 5.4 8.3 - - + -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 2.8 21.2 + - + +
190A TYR 3.8 2.9 - - - +
192A ILE* 1.3 74.3 - - - +
194A TRP* 1.3 56.5 + - - +
196A VAL* 3.7 9.5 - - + +
197A GLY* 3.0 24.5 + - - -
204A VAL* 5.1 9.0 - - + -
209A GLU* 3.7 26.2 - - + +
212A ALA* 3.7 26.5 - - + -
213A PHE* 3.5 46.2 - - + -
216A LEU* 3.7 12.8 - - + -
306A BNG 6.1 0.7 - - - +
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Residues in contact with TRP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 6.2 0.4 - - - -
88A TYR* 3.2 23.6 + - - -
91A TRP* 5.6 0.4 - + - -
127A GLY 4.1 5.6 + - - -
130A GLY* 4.1 7.6 - - - -
131A ALA* 3.8 24.9 - - - -
139A ARG* 4.0 26.0 - - + -
140A TYR* 4.7 4.0 - + - -
143A TRP* 3.2 37.2 - + + -
190A TYR 3.0 17.0 + - - +
191A PRO 3.5 4.5 - - - +
193A LEU* 1.3 79.3 - - - +
195A ILE* 1.3 70.3 + - + +
197A GLY 3.3 5.4 + - - -
199A GLU* 3.5 50.8 - - + +
200A GLY 3.3 18.2 + - - -
213A PHE* 4.5 10.1 - + + -
260A RET 3.6 35.0 - - + +
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 4.1 20.2 - - + -
143A TRP* 3.8 33.4 - - + +
191A PRO 3.0 13.5 + - - +
192A ILE* 3.2 21.1 - - + +
194A TRP* 1.3 83.0 - - + +
196A VAL* 1.3 66.9 + - + +
200A GLY* 3.3 2.1 - - - -
201A ALA* 2.8 26.3 + - - +
304A BNG 3.6 39.4 - - + +
305A BNG 3.9 23.2 + - + -
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 3.0 31.2 + - + +
193A LEU* 3.7 13.2 - - + +
195A ILE* 1.3 87.1 - - + +
197A GLY* 1.3 63.2 + - - +
201A ALA* 4.2 5.6 - - - +
202A GLY 4.0 1.8 - - - -
203A VAL* 2.9 50.3 + - + +
204A VAL* 3.3 9.5 + - + +
305A BNG 3.7 38.4 - - - +
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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