Contacts of the helix formed by residues 205 - 230 (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 GLY 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A THR* 3.9 3.4 - - - -
203A VAL 4.3 1.0 + - - -
204A VAL* 1.3 80.0 - - - +
206A LEU* 1.3 66.2 + - - -
207A GLY 3.1 3.8 + - - -
208A ILE* 3.3 6.9 + - - +
209A GLU* 3.0 20.8 + - - +
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Residues in contact with LEU 206 (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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13A GLU* 3.9 30.5 - - + +
82A ASP* 6.1 5.2 - - + -
84A TYR* 5.5 11.2 - - + -
87A ARG* 6.2 2.5 - - - +
198A THR* 3.5 28.9 - - + +
205A GLY* 1.3 70.8 - - - -
207A GLY* 1.3 59.9 + - - +
209A GLU* 3.9 10.3 - - + +
210A THR* 2.8 44.3 + - - +
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO* 6.1 3.8 - - - -
13A GLU* 4.5 13.9 + - - -
16A TRP* 3.3 22.4 + - - -
205A GLY 3.1 1.6 + - - -
206A LEU* 1.3 77.6 - - - +
208A ILE* 1.3 64.2 + - - +
210A THR* 3.5 0.3 + - - -
211A LEU* 3.1 15.9 + - - +
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 6.2 0.7 - - + +
204A VAL* 3.5 23.3 - - + -
205A GLY* 3.3 6.0 + - - +
207A GLY* 1.3 73.5 - - - +
209A GLU* 1.3 56.0 + - - +
211A LEU* 2.9 18.5 + - + +
212A ALA* 2.6 35.0 + - + +
306A BNG 3.6 57.7 - - - +
308A BNG 6.1 1.6 - - - -
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.2 3.3 + - - -
193A LEU* 3.7 26.5 - - + +
197A GLY* 3.3 3.7 - - - -
198A THR* 2.6 42.4 + - - +
199A GLU* 2.7 34.6 - - - +
204A VAL* 3.6 9.0 - - + +
205A GLY 3.0 15.9 + - - +
206A LEU* 3.8 10.8 - - + +
208A ILE* 1.3 76.0 - - - +
210A THR* 1.3 56.9 + - - +
212A ALA* 3.1 3.5 + - - +
213A PHE* 2.8 50.9 + - + -
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.8 19.2 - - + +
16A TRP* 3.8 17.5 - - + -
17A LEU* 3.8 29.6 - - + -
61A TYR* 5.2 0.3 + - - -
84A TYR* 5.9 1.4 - - - -
87A ARG* 4.7 12.6 + - - +
206A LEU* 2.8 34.1 + - - +
207A GLY 3.8 4.3 - - - -
209A GLU* 1.3 74.0 - - - +
211A LEU* 1.3 66.0 + - - +
213A PHE* 3.9 6.0 - - - +
214A MET* 3.0 24.0 + - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.8 53.3 - - + -
207A GLY 3.1 14.1 + - - +
208A ILE* 2.9 29.3 + - + +
210A THR* 1.3 76.0 - - - +
212A ALA* 1.3 63.7 + - - +
214A MET* 3.4 11.9 + - + +
215A VAL* 3.1 36.8 + - + +
306A BNG 4.3 23.1 - - - +
308A BNG 4.6 20.9 - - - +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.7 23.3 - - + -
208A ILE* 2.6 19.9 + - + +
209A GLU* 3.4 5.2 - - - +
211A LEU* 1.3 74.8 - - - +
213A PHE* 1.3 56.1 + - - +
215A VAL* 3.3 2.9 + - - +
216A LEU* 2.9 33.1 + - + +
306A BNG 4.0 37.5 - - + +
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Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.9 3.6 - - - +
87A ARG* 3.7 35.7 - - - +
91A TRP* 3.9 15.9 - + - -
190A TYR* 3.5 48.9 - + - -
193A LEU* 3.5 32.1 - - + -
194A TRP* 4.5 13.7 - + + -
199A GLU* 4.8 2.2 - - - -
209A GLU* 2.8 49.2 + - + +
210A THR* 4.0 4.0 - - + +
212A ALA* 1.3 71.3 - - - +
214A MET* 1.3 56.5 + - - +
216A LEU* 3.7 3.0 - - + +
217A ASP* 2.7 45.9 + - - +
260A RET 5.0 0.4 - - + -
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Residues in contact with MET 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.4 33.7 - - + +
19A ILE* 3.9 21.8 - - + -
20A GLY* 3.7 17.0 - - - -
23A LEU* 4.1 22.9 - - + -
24A MET* 5.4 0.5 - - - +
61A TYR* 3.3 17.9 + - + +
210A THR* 3.0 18.4 + - + +
211A LEU* 3.5 25.4 - - + +
213A PHE* 1.3 74.8 - - - +
215A VAL* 1.3 72.8 + - + +
217A ASP* 3.9 0.5 - - - +
218A VAL* 3.0 30.9 + - - +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.1 28.6 + - + +
212A ALA 3.6 7.2 - - - +
214A MET* 1.3 86.7 - - + +
216A LEU* 1.3 63.3 + - + +
218A VAL* 3.0 16.0 - - + +
219A THR* 2.8 29.0 + - - +
306A BNG 4.2 28.3 - - + -
308A BNG 4.1 33.9 - - + -
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 4.2 22.4 - - + +
189A ALA* 3.7 38.8 - - + -
190A TYR* 3.4 18.6 - - + +
193A LEU* 3.7 29.8 - - + -
212A ALA* 2.9 16.5 + - + +
213A PHE* 3.7 10.5 - - + +
215A VAL* 1.3 78.1 - - + +
217A ASP* 1.3 62.9 + - - +
219A THR* 3.9 4.2 - - - -
220A ALA* 2.9 27.7 + - - +
306A BNG 4.4 24.5 - - + -
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 3.8 15.0 - - + -
61A TYR* 2.8 31.8 + - - +
87A ARG* 5.5 2.3 + - - +
90A ASP* 4.9 0.6 - - - +
91A TRP* 3.2 31.7 + - - -
190A TYR* 2.7 28.7 + - - -
213A PHE* 2.7 25.8 + - - +
214A MET 3.9 1.1 - - - +
216A LEU* 1.3 73.4 - - - +
218A VAL* 1.3 61.9 + - - +
220A ALA* 3.8 0.8 - - - -
221A LYS* 3.1 36.6 + - - +
260A RET 3.4 3.8 - - - +
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Residues in contact with VAL 218 (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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20A GLY* 6.3 0.9 - - - -
23A LEU* 4.1 31.4 - - + -
24A MET* 3.9 14.1 - - + +
214A MET* 3.0 23.9 + - - +
215A VAL* 3.0 22.9 - - + +
217A ASP* 1.3 76.7 - - - +
219A THR* 1.3 61.2 + - - +
222A VAL* 2.8 46.6 + - + -
223A GLY 3.1 4.7 + - - -
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Residues in contact with THR 219 (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 LEU* 5.0 6.2 - - + +
186A LEU* 3.7 28.6 - - + +
215A VAL* 2.8 23.3 + - - +
216A LEU* 3.9 3.1 - - - -
218A VAL* 1.3 82.0 - - - +
220A ALA* 1.3 57.7 + - - +
221A LYS 3.2 0.2 - - - -
223A GLY* 3.0 13.7 - - - +
224A PHE* 2.8 26.9 + - - -
308A BNG 3.8 29.4 - - + +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.7 17.8 - - - +
186A LEU* 3.6 21.7 - - + +
187A TRP* 4.5 8.0 + - + +
190A TYR* 4.0 11.7 - - + +
216A LEU 2.9 17.9 + - - +
217A ASP 4.0 3.6 - - - +
219A THR* 1.3 77.2 - - - +
221A LYS* 1.3 59.0 + - - +
224A PHE* 3.2 19.4 - - - +
260A RET 4.1 17.3 - - + -
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Residues in contact with LYS 221 (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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24A MET* 3.5 24.5 - - + -
31A PHE* 4.0 5.5 - - - -
50A THR* 4.9 1.9 - - - +
53A VAL* 3.4 23.8 - - + +
54A PRO* 4.6 8.9 - - - +
57A ALA* 3.7 14.8 - - + -
90A ASP* 3.7 17.8 + - - -
91A TRP* 4.0 1.6 - - - -
94A THR* 3.2 18.5 - - - +
98A LEU* 4.8 1.4 - - - +
217A ASP* 3.1 24.4 + - - +
218A VAL 4.3 0.7 - - - +
219A THR 3.2 0.2 - - - -
220A ALA* 1.3 80.7 - - - +
222A VAL* 1.3 62.8 + - + +
223A GLY 3.5 0.4 - - - -
224A PHE* 4.3 0.7 - - - +
225A GLY* 3.0 24.4 + - - -
260A RET 1.4 73.4 - - + +
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 4.0 19.3 - - - +
24A MET* 4.2 6.3 - - - -
27A GLY* 4.1 20.4 - - - -
30A TYR* 6.1 1.1 - - + -
31A PHE* 3.5 14.3 - - + -
54A PRO* 4.1 21.1 - - + -
218A VAL* 2.8 27.2 + - + +
221A LYS* 1.3 71.9 - - - +
223A GLY* 1.3 60.9 - - - +
226A PHE* 2.8 34.0 + - + +
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Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 4.7 2.2 - - - -
218A VAL 3.1 5.7 + - - -
219A THR* 3.0 21.6 + - - -
222A VAL* 1.3 77.4 - - - +
224A PHE* 1.3 62.7 + - - +
226A PHE* 3.1 8.7 + - - +
227A VAL* 3.1 28.0 + - - +
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Residues in contact with PHE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 5.8 0.4 - - + -
98A LEU* 3.6 33.4 - - + -
101A ASP* 4.4 19.5 - - + -
102A LEU* 4.1 26.5 - - + -
179A LEU* 3.7 38.5 - - + +
182A LEU* 3.7 30.2 - - + +
183A VAL* 3.8 17.5 - - + -
186A LEU* 6.2 0.2 - - + -
187A TRP* 5.7 2.5 - - - -
219A THR 2.8 6.8 + - - +
220A ALA* 3.2 26.7 - - - +
221A LYS 4.1 0.4 + - - +
223A GLY* 1.3 74.8 - - - +
225A GLY* 1.3 69.2 + - - +
227A VAL* 3.2 3.7 + - - +
228A LEU* 3.1 23.4 + - + +
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Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.7 8.5 - - - -
50A THR* 3.7 21.8 - - - -
221A LYS 3.0 21.5 + - - -
222A VAL 3.8 0.2 - - - -
224A PHE* 1.3 82.8 - - - +
226A PHE* 1.3 55.8 + - - +
228A LEU* 3.5 2.8 + - - +
229A LEU* 2.9 36.1 + - - +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.8 32.5 - + - -
31A PHE* 3.6 9.6 - - + -
34A ARG* 5.6 1.1 - - - -
222A VAL* 2.8 23.6 + - + +
223A GLY* 3.1 7.4 + - - +
225A GLY* 1.3 70.7 - - - +
227A VAL* 1.3 73.0 + - + +
229A LEU* 4.0 2.1 - - - +
230A ARG* 3.1 75.7 + - + +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A THR* 4.7 4.4 - - + +
178A THR* 4.3 20.2 - - + -
179A LEU* 3.3 24.2 - - + -
182A LEU* 4.6 9.6 - - + -
223A GLY 3.1 14.9 + - - +
224A PHE 3.5 7.2 - - - +
226A PHE* 1.3 85.1 - - + +
228A LEU* 1.3 63.4 + - - +
230A ARG* 3.7 12.2 - - - +
231A SER* 3.6 14.6 - - - -
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 4.3 8.3 - - + -
50A THR* 3.7 15.5 - - + +
101A ASP* 3.5 37.7 - - + +
105A LEU* 3.9 19.5 - - + -
175A THR* 4.7 3.8 - - + -
179A LEU* 3.8 27.6 - - + +
224A PHE* 3.1 18.9 + - + +
225A GLY* 3.8 2.5 - - - +
227A VAL* 1.3 79.9 - - - +
229A LEU* 1.3 65.3 + - + +
231A SER* 3.0 32.2 + - - +
234A ILE* 3.7 28.7 - - + +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 3.8 27.8 - - + -
34A ARG* 3.6 9.9 + - - -
46A TYR* 4.2 1.8 - - + +
47A TYR* 3.2 67.1 + - + +
50A THR* 3.6 38.4 - - + +
225A GLY 2.9 23.2 + - - +
226A PHE* 4.3 2.9 - - - +
228A LEU* 1.3 84.1 - - + +
230A ARG* 1.3 57.7 + - - +
231A SER 3.3 1.8 + - - +
234A ILE* 3.7 18.0 - - + +
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 4.5 1.4 + - - -
34A ARG* 3.6 22.7 - - - +
226A PHE* 3.1 70.5 + - + +
227A VAL* 3.7 9.4 - - - +
229A LEU* 1.3 75.7 - - - +
231A SER* 1.3 61.5 + - - +
232A ARG* 4.1 0.9 + - - +
239B GLU* 2.9 44.1 + - - +
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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