Contacts of the helix formed by residues 170 - 192 (chain V) in PDB entry 3A68
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 170 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56V GLU* 4.3 7.0 - - - -
94V HIS* 2.7 51.0 + + + -
97V LYS* 3.3 21.4 - - + +
98V LEU* 3.1 27.0 + - + +
147V LEU* 3.7 34.8 - - + +
150V LEU* 6.5 0.2 - - + -
165V PHE* 3.6 34.8 - + - -
166V VAL* 3.0 15.1 + - + +
169V GLU* 1.3 92.7 - - + +
171V LEU* 1.3 61.9 + - - +
172V GLY 3.5 1.6 - - - -
173V GLU* 3.5 7.3 + - - +
174V GLN* 3.0 30.0 + - - +
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Residues in contact with LEU 171 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 3.4 38.6 - - + -
161B GLN* 3.6 19.4 - - + +
164B ASP* 5.8 0.4 - - - +
144V ASN* 4.5 7.9 - - - +
147V LEU* 3.9 31.2 - - + -
148V LEU* 4.1 14.8 - - + -
151V HIS* 4.6 2.7 - - + -
166V VAL* 3.1 23.3 + - + +
167V GLU* 3.5 25.0 + - + +
170V TYR* 1.3 76.6 - - - +
172V GLY* 1.3 64.5 + - - +
174V GLN* 3.3 5.1 + - - +
175V VAL* 3.1 25.8 + - - +
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Residues in contact with GLY 172 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLN* 3.6 23.2 - - - +
164B ASP* 5.4 2.0 + - - -
167V GLU 3.9 6.1 + - - -
170V TYR 3.5 0.2 - - - -
171V LEU* 1.3 77.4 - - - +
173V GLU* 1.3 67.4 + - - +
175V VAL* 3.2 4.7 + - - +
176V GLU* 3.0 29.6 + - - +
223V CA 4.5 5.8 - - - -
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Residues in contact with GLU 173 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94V HIS* 5.4 13.9 - - + +
168V THR 3.7 2.9 - - - +
169V GLU* 3.2 31.2 - - - +
170V TYR* 3.5 9.7 + - + +
172V GLY* 1.3 74.7 + - - +
174V GLN* 1.3 57.1 + - - +
176V GLU* 3.3 10.6 + - - +
177V ALA* 3.0 28.1 + - - +
223V CA 2.6 28.7 - - - -
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Residues in contact with GLN 174 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94V HIS* 5.9 0.5 - - - -
140V GLU* 2.7 56.7 + - - +
143V THR* 3.7 16.0 - - - +
144V ASN* 3.4 39.5 - - + +
147V LEU* 3.8 11.0 - - + +
170V TYR 3.0 18.1 + - - +
171V LEU 3.6 6.1 - - - +
172V GLY 3.2 0.2 - - - -
173V GLU* 1.3 73.8 - - - +
175V VAL* 1.3 67.2 + - - +
177V ALA* 3.3 4.3 + - - +
178V ILE* 3.0 31.1 + - + +
222V CA 4.0 8.1 - - - -
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Residues in contact with VAL 175 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 5.3 1.8 - - + -
104B LYS* 3.9 30.8 - - + +
105B ARG* 3.8 29.6 - - - +
161B GLN* 3.6 29.2 - - + +
144V ASN* 5.2 10.8 - - - +
171V LEU 3.1 16.7 + - - +
172V GLY 3.5 8.5 - - - +
174V GLN* 1.3 76.8 - - - +
176V GLU* 1.3 64.8 + - + +
178V ILE* 3.3 8.8 + - + +
179V LYS* 3.0 21.5 + - - +
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Residues in contact with GLU 176 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 2.8 45.0 + - - +
172V GLY 3.0 19.6 + - - +
173V GLU* 3.5 9.6 - - - +
174V GLN 3.3 0.2 - - - -
175V VAL* 1.3 77.2 - - + +
177V ALA* 1.3 58.6 + - - +
179V LYS* 3.3 6.7 + - - +
180V ARG* 3.0 29.7 + - - +
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Residues in contact with ALA 177 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94V HIS* 6.6 0.2 - - + -
140V GLU* 4.1 22.9 - - + +
173V GLU 3.0 16.8 + - - +
174V GLN* 3.6 7.0 - - - +
175V VAL 3.2 0.2 - - - -
176V GLU* 1.3 76.9 - - - +
178V ILE* 1.3 63.6 + - - +
180V ARG* 3.4 9.4 + - - +
181V ILE* 3.1 32.9 + - + +
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Residues in contact with ILE 178 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 3.6 34.8 - - + +
39B GLN* 3.6 24.2 - - + +
104B LYS 5.8 0.4 - - - +
137V LEU* 3.8 15.7 - - + +
140V GLU* 3.9 35.2 - - + +
141V LYS* 4.2 7.9 - - + +
144V ASN* 3.9 15.7 - - + +
174V GLN* 3.0 23.2 + - - +
175V VAL* 3.7 7.2 - - + +
176V GLU 3.3 0.2 - - - -
177V ALA* 1.3 74.7 - - - +
179V LYS* 1.3 64.1 + - - +
182V SER* 2.8 29.3 + - - -
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Residues in contact with LYS 179 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 4.3 4.4 - - + +
100B GLU 5.3 0.4 + - - -
103B ASN* 3.8 23.5 - - - +
104B LYS* 3.8 31.8 - - + +
71F ASP* 3.0 46.2 + - - -
73F ASP* 4.0 16.2 - - + +
175V VAL 3.0 17.4 + - - +
176V GLU* 3.8 5.8 - - - +
178V ILE* 1.3 75.2 - - - +
180V ARG* 1.3 64.2 + - - +
182V SER* 3.2 5.6 + - - -
183V GLU* 2.9 54.1 + - - +
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Residues in contact with ARG 180 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83V PHE* 3.6 29.2 - - - -
86V GLU* 5.3 5.5 + - - -
87V SER* 5.4 1.0 + - - -
90V GLU* 4.8 15.4 + - - -
176V GLU 3.0 17.1 + - - +
177V ALA* 3.7 9.0 - - - +
178V ILE 3.3 0.2 - - - -
179V LYS* 1.3 78.1 - - - +
181V ILE* 1.3 64.0 + - + +
183V GLU* 3.4 15.6 + - - +
184V TYR* 2.8 57.8 + - + +
204V LEU* 5.1 1.4 - - - +
207V GLU* 4.3 6.1 + - - +
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Residues in contact with ILE 181 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63V TYR* 3.7 13.2 - - - +
83V PHE* 4.1 24.9 - - + -
133V MET* 3.5 32.8 - - - +
136V ALA* 4.2 9.9 - - + +
137V LEU* 3.6 18.2 - - + +
140V GLU* 3.5 33.0 - - + -
177V ALA* 3.1 15.9 + - + +
178V ILE 4.1 1.8 - - - +
180V ARG* 1.3 77.4 - - + +
182V SER* 1.3 66.7 + - - +
184V TYR* 3.0 8.7 + - + +
185V VAL* 2.9 20.8 + - - +
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Residues in contact with SER 182 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.5 19.2 - - - +
37B ALA* 3.3 23.2 + - - -
73F ASP* 3.5 27.8 - - - -
137V LEU* 3.4 14.1 - - - +
178V ILE 2.8 24.1 + - - -
179V LYS 3.5 4.5 - - - -
181V ILE* 1.3 77.8 - - - +
183V GLU* 1.3 57.7 + - - +
185V VAL* 3.2 4.8 + - - -
186V ALA* 2.9 25.1 + - - +
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Residues in contact with GLU 183 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ASP* 4.6 3.1 - - - +
72F ARG 5.3 0.3 - - - +
73F ASP* 3.7 26.2 - - + +
76F ALA* 4.1 10.6 - - + -
78F ARG* 4.9 20.2 - - - +
179V LYS* 2.9 49.4 + - - +
180V ARG* 3.5 16.3 - - - +
182V SER* 1.3 77.1 - - - +
184V TYR* 1.3 58.0 + - + +
186V ALA* 3.4 1.6 + - - +
187V GLN* 3.0 46.6 + - - +
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Residues in contact with TYR 184 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83V PHE* 3.7 25.6 - + - -
133V MET* 3.5 31.4 - - + -
180V ARG* 2.8 48.3 + - + +
181V ILE* 3.0 12.8 + - - +
183V GLU* 1.3 75.5 - - + +
185V VAL* 1.3 66.2 + - - +
187V GLN* 3.3 10.8 + - - +
188V LEU* 2.9 29.9 + - - +
200V PHE* 3.6 27.3 - + + -
203V MET* 4.8 0.4 - - + -
204V LEU* 3.3 16.5 - - + +
207V GLU* 2.6 37.0 + - - -
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Residues in contact with VAL 185 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 5.4 0.4 - - + -
36B LEU* 3.8 16.2 - - + -
130V LEU* 4.0 13.5 - - + -
133V MET* 3.7 35.4 - - + +
134V GLU* 3.9 14.1 - - + +
137V LEU* 4.5 9.9 - - + -
181V ILE 2.9 18.9 + - - +
182V SER* 3.2 8.3 + - - +
184V TYR* 1.3 77.4 - - - +
186V ALA* 1.3 63.2 + - - +
188V LEU* 3.3 4.0 + - - +
189V ARG* 3.0 50.9 + - - +
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Residues in contact with ALA 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 4.0 8.0 - - + +
73F ASP 3.3 25.6 - - - +
74F ASN* 3.7 22.0 - - - +
75F VAL 4.8 1.8 - - - +
76F ALA* 3.8 8.5 - - + -
182V SER 2.9 10.0 + - - +
183V GLU 3.6 4.3 - - - +
185V VAL* 1.3 75.7 - - - +
187V GLN* 1.3 63.0 + - - +
189V ARG* 3.3 9.3 + - - +
190V ARG* 3.0 23.3 + - - +
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Residues in contact with GLN 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ALA* 3.8 23.4 - - + +
78F ARG* 3.0 33.7 + - - +
198F TRP* 2.9 33.5 + - + +
183V GLU* 3.0 39.3 + - - +
184V TYR* 4.0 13.7 - - - +
186V ALA* 1.3 73.2 - - - +
188V LEU* 1.3 66.1 + - - +
190V ARG* 3.1 8.4 + - - +
191V VAL* 3.0 30.3 + - - +
200V PHE* 3.8 16.2 - - + -
203V MET* 3.7 7.4 - - - +
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Residues in contact with LEU 188 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80V LEU* 5.5 0.7 - - + -
129V ALA* 3.7 35.2 - - + +
130V LEU* 4.0 17.8 - - + +
133V MET* 3.6 34.1 - - + -
184V TYR 2.9 17.6 + - - +
185V VAL 3.7 3.8 - - - +
187V GLN* 1.3 77.0 - - - +
189V ARG* 1.3 61.5 + - - +
191V VAL* 3.6 4.8 - - - +
192V GLY* 3.3 21.8 + - - -
197V VAL* 4.1 22.8 - - + +
200V PHE* 3.5 38.1 - - + -
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Residues in contact with ARG 189 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.9 13.9 + - - +
29B PRO 3.1 28.9 + - - -
30B THR* 4.2 14.1 + - - +
31B VAL 5.4 2.2 + - - -
32B PRO* 6.1 1.4 - - - +
36B LEU* 3.5 15.3 - - - +
126V LYS* 5.4 1.4 - - - +
130V LEU* 3.9 19.2 - - + +
134V GLU* 2.8 31.5 + - - -
185V VAL* 3.0 31.4 + - - +
186V ALA* 3.6 8.1 - - - +
187V GLN 3.2 0.2 - - - -
188V LEU* 1.3 76.8 - - - +
190V ARG* 1.3 64.0 + - - +
192V GLY* 3.9 7.0 + - - -
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Residues in contact with ARG 190 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ASN 5.0 1.8 + - - -
75F VAL* 3.1 27.9 + - - +
76F ALA 5.2 0.6 + - - -
77F LEU* 3.7 32.3 - - - +
128F ASP* 3.2 37.2 + - - -
194F GLY* 3.3 46.2 - - - +
197F VAL* 4.0 10.9 - - - +
198F TRP* 4.1 14.1 - - + +
186V ALA 3.0 14.4 + - - +
187V GLN* 3.1 10.8 + - - +
189V ARG* 1.3 79.6 - - - +
191V VAL* 1.3 62.4 + - + +
192V GLY* 4.6 0.3 - - - -
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Residues in contact with VAL 191 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F HIS* 3.7 22.6 + - + +
198F TRP* 3.5 49.4 - - + -
187V GLN 3.0 23.6 + - - +
188V LEU* 3.6 12.8 - - - +
190V ARG* 1.3 76.0 - - - +
192V GLY* 1.3 67.2 + - - +
193V LYS 4.9 0.3 - - - +
196V GLY* 3.5 41.9 + - - +
197V VAL* 3.9 4.5 - - - +
200V PHE* 4.4 5.4 - - + -
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Residues in contact with GLY 192 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188V LEU 3.3 13.8 + - - -
189V ARG 3.9 5.6 + - - -
190V ARG 3.4 3.2 - - - -
191V VAL* 1.3 79.3 - - - +
193V LYS* 1.3 66.1 + - - -
196V GLY* 3.5 0.7 - - - -
197V VAL* 3.1 28.0 + - - +
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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) + - + + + + + -
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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