Contacts of the helix formed by residues 167 - 193 (chain B) in PDB entry 2BAP
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 PRO 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ASN* 1.4 105.8 - - + +
168B VAL* 1.3 65.2 + - - +
169B SER* 3.4 21.5 + - - +
170B TRP* 3.6 10.6 + - + +
171B VAL* 3.4 16.0 - - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO* 1.3 74.0 - - - +
169B SER* 1.3 64.7 + - - +
171B VAL* 3.2 11.6 + - + +
172B GLN* 3.2 34.1 + - + +
218B ASN* 4.1 34.1 - - + +
220B PHE* 5.0 2.5 - - + +
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO* 3.4 18.9 - - - +
168B VAL* 1.3 76.0 - - - +
170B TRP* 1.3 64.1 + - - +
172B GLN* 3.1 29.8 + - - +
173B THR* 3.1 17.4 + - - -
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Residues in contact with TRP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 3.5 35.8 - - - +
136B ALA* 3.5 27.4 - - + +
139B TYR* 3.8 24.9 - + - -
159B LEU* 5.1 2.9 - - + -
162B SER* 3.8 18.4 - - - -
163B LEU* 3.9 37.9 - - + -
166B ASN* 3.2 51.5 + - + +
167B PRO* 3.6 7.5 + - + +
168B VAL 3.3 0.6 - - - -
169B SER* 1.3 77.2 + - - +
171B VAL* 1.3 66.5 + - - +
173B THR* 3.4 15.2 + - - -
174B PHE* 3.4 11.7 + + + +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.2 33.0 - - + +
167B PRO 3.4 18.6 - - - +
168B VAL* 3.3 12.3 - - - +
169B SER 3.2 0.2 - - - -
170B TRP* 1.3 78.8 - - + +
172B GLN* 1.3 57.6 + - + +
174B PHE* 3.1 7.1 + - - +
175B GLY* 2.9 23.0 + - - -
214B ALA 5.9 1.3 - - - +
215B PHE* 3.5 36.0 - - + +
218B ASN* 4.0 26.2 - - - +
220B PHE* 4.3 3.3 - - + -
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.3 18.7 - - + +
169B SER* 3.1 26.8 + - - +
171B VAL* 1.3 77.6 - - - +
173B THR* 1.3 57.3 + - - +
175B GLY* 3.1 17.0 + - - -
177B GLU* 5.1 0.5 - - - +
220B PHE* 3.5 55.0 - - + +
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 5.2 9.3 + - - +
136B ALA* 4.5 12.1 - - + +
137B MET* 4.5 30.2 - - + +
140B ILE* 3.5 15.6 - - - +
169B SER 3.1 14.9 + - - -
170B TRP* 3.4 9.7 + - - -
171B VAL 3.3 0.6 - - - -
172B GLN* 1.3 74.1 - - - +
174B PHE* 1.3 62.0 + - - +
177B GLU* 3.6 5.7 - - - +
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 4.3 12.5 - - + +
139B TYR* 3.8 28.3 - + + -
140B ILE* 3.7 22.3 - - + +
143B LEU* 3.9 15.3 - - + -
159B LEU* 3.9 16.6 - - + -
163B LEU* 4.6 15.9 - - + -
170B TRP* 3.4 10.9 + + + +
171B VAL* 3.1 12.0 + - - +
173B THR* 1.3 78.4 - - - +
175B GLY* 1.3 71.9 + - - +
177B GLU* 3.1 5.1 - - - +
178B GLY* 2.9 53.5 + - - -
179B LEU* 3.7 4.9 - - - -
182B LEU* 3.8 17.5 - - + -
215B PHE* 4.5 15.0 - + - -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL 2.9 12.8 + - - -
172B GLN 3.1 15.9 + - - -
174B PHE* 1.3 83.7 - - - +
176B ALA* 1.3 59.6 + - - -
177B GLU* 3.7 7.9 - - - -
179B LEU 3.6 7.1 + - - -
215B PHE* 3.4 23.4 - - - -
220B PHE* 4.0 16.4 - - - -
224B THR* 4.6 0.2 - - - -
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLY* 1.3 72.1 - - - -
177B GLU* 1.3 63.2 + - + +
179B LEU* 3.3 7.6 - - + +
180B ALA* 2.7 36.1 + - - +
220B PHE* 4.9 1.6 - - - -
224B THR* 3.7 24.9 - - + +
228B THR* 5.6 4.5 - - + +
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET* 6.0 0.2 - - - +
140B ILE* 3.8 11.5 - - + +
144B ARG* 2.8 39.5 + - - +
172B GLN 5.1 0.2 - - - +
173B THR 3.6 10.4 - - - +
174B PHE 3.1 19.8 - - - +
175B GLY* 3.7 3.9 - - - -
176B ALA* 1.3 92.9 + - + +
178B GLY* 1.3 60.2 + - - +
180B ALA* 3.3 6.5 - - - +
181B SER* 3.1 15.1 + - - -
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 4.2 8.6 - - - +
174B PHE* 2.9 49.1 + - - -
177B GLU* 1.3 75.2 + - - +
179B LEU* 1.3 67.6 + - - +
181B SER* 2.9 18.8 + - - -
182B LEU* 3.1 10.9 + - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 3.7 4.7 - - - -
175B GLY 3.6 14.7 + - - +
176B ALA* 3.3 8.3 - - - +
178B GLY* 1.3 73.3 - - - +
180B ALA* 1.3 66.9 + - - +
182B LEU* 3.0 20.7 + - + +
183B LEU* 3.1 30.4 + - + +
212B LEU* 3.7 30.7 - - + -
215B PHE* 3.7 23.1 - - + -
224B THR* 3.1 43.7 - - + +
225B MET* 4.0 8.3 - - - +
228B THR* 3.8 12.6 - - + -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 4.9 2.5 - - - +
176B ALA 2.7 16.8 + - - +
177B GLU* 3.3 14.4 - - - +
179B LEU* 1.3 71.9 - - - +
181B SER* 1.3 51.7 + - - +
183B LEU* 2.9 16.0 + - - +
184B ASP* 2.7 48.6 + - - +
228B THR* 5.5 4.5 - - + -
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE 4.6 2.3 + - - -
143B LEU* 4.1 24.4 - - - -
144B ARG* 2.9 37.8 + - - +
177B GLU 3.1 8.0 + - - -
178B GLY* 2.9 10.0 + - - -
180B ALA* 1.3 76.2 - - - +
182B LEU* 1.3 58.4 + - - +
184B ASP* 3.7 13.8 + - - +
185B ILE* 3.2 32.2 + - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 4.5 6.3 - - + -
156B LEU* 3.9 20.9 - - + -
159B LEU* 4.2 13.7 - - + -
163B LEU* 5.5 1.1 - - + -
174B PHE* 3.8 30.5 - - + -
178B GLY 3.1 6.2 + - - +
179B LEU* 3.0 13.3 + - + +
181B SER* 1.3 74.8 - - - +
183B LEU* 1.3 61.9 + - + +
185B ILE* 3.3 10.3 + - + +
186B LEU* 3.0 24.8 + - - +
208B ILE* 3.5 45.2 - - + +
211B CYS* 4.3 18.2 - - + -
212B LEU* 5.2 10.5 - - + -
215B PHE* 6.1 3.1 - - + -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.5 28.3 - - + +
180B ALA* 2.9 8.1 + - - +
182B LEU* 1.3 76.5 - - - +
184B ASP* 1.3 59.4 + - - +
186B LEU* 2.9 10.3 + - + +
187B LYS* 2.6 44.3 + - - +
212B LEU* 4.3 19.5 - - + -
225B MET* 3.9 24.5 - - + -
228B THR* 3.9 31.2 - - + +
230B GLU* 5.1 2.0 - - + -
231B GLY* 4.6 6.7 - - - +
234B LEU* 3.9 26.3 - - + +
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ALA* 2.7 40.8 + - - +
181B SER* 3.7 12.2 + - - +
183B LEU* 1.3 73.3 - - - +
185B ILE* 1.3 59.2 + - + +
187B LYS* 3.4 23.4 + - - +
188B ARG* 3.2 21.8 + - - +
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.8 42.8 - - + +
152B LEU* 4.1 27.6 - - + -
156B LEU* 5.3 2.9 - - + -
181B SER 3.2 17.7 + - - +
182B LEU* 3.3 10.0 + - - +
183B LEU 3.1 0.6 - - - -
184B ASP* 1.3 74.8 - - + +
186B LEU* 1.3 54.3 + - - +
188B ARG* 3.0 22.5 + - - +
189B LEU* 2.7 59.1 + - + +
208B ILE* 3.9 8.7 - - + -
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU 3.0 11.3 + - - +
183B LEU* 2.9 12.0 + - + +
185B ILE* 1.3 75.5 - - - +
187B LYS* 1.3 61.6 + - - +
189B LEU* 3.4 7.6 + - + +
190B HIS* 2.9 53.8 + - + +
205B GLN* 3.8 27.8 - - + +
208B ILE* 3.8 30.3 - - + -
209B ILE* 4.1 20.4 - - + -
212B LEU* 4.6 6.3 - - + -
234B LEU* 4.2 25.8 - - + +
238B ALA* 6.1 0.2 - - + -
246B MET* 4.9 4.5 - - + -
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LEU* 2.6 23.7 + - - +
184B ASP* 3.4 24.5 + - - +
186B LEU* 1.3 71.1 - - - +
188B ARG* 1.3 59.3 + - - +
190B HIS* 2.9 23.4 + - - +
191B ASP* 3.1 23.2 + - - +
230B GLU* 3.7 40.5 - - + +
234B LEU* 4.2 19.8 - - + +
237B ARG* 5.5 4.2 + - - +
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Residues in contact with ARG 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLY* 5.7 1.0 - - - -
148B ARG* 2.9 56.5 - - - +
149B ASP 5.6 1.4 - - - +
152B LEU* 5.3 5.9 - - - +
184B ASP 3.2 11.8 + - - +
185B ILE* 3.0 24.3 + - - +
187B LYS* 1.3 79.3 - - - +
189B LEU* 1.3 82.0 + - - +
191B ASP* 3.3 19.7 + - + +
192B GLU* 3.6 12.0 + - - +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 5.3 2.9 - - + -
185B ILE* 2.7 28.4 + - + +
186B LEU* 3.4 8.3 - - - +
188B ARG* 1.3 92.7 - - - +
190B HIS* 1.3 62.1 + - - +
192B GLU* 3.7 4.7 + - - +
193B LYS* 3.4 20.6 + - - +
201B ASP 5.4 4.0 - - - +
204B ASN* 4.6 15.3 - - + -
205B GLN* 3.7 42.4 - - + +
208B ILE* 3.8 24.0 - - + -
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Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 2.9 44.5 + - + +
187B LYS 2.9 8.8 + - - +
189B LEU* 1.3 77.9 - - - +
191B ASP* 1.3 61.8 + - - +
193B LYS* 3.0 35.7 + - - +
205B GLN* 4.0 15.3 + - - -
234B LEU* 3.6 22.2 + - + +
237B ARG* 3.5 65.8 + - + +
238B ALA* 4.8 3.2 + - - -
246B MET* 5.8 0.6 - - + +
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 3.1 21.2 + - - +
188B ARG* 3.3 13.5 + - + +
190B HIS* 1.3 79.3 - - - +
192B GLU* 1.3 57.5 + - - +
193B LYS 5.0 0.9 - - - -
237B ARG* 5.4 4.5 + - - -
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG 3.6 8.3 + - - +
189B LEU* 4.2 6.5 - - - +
190B HIS 3.2 0.4 - - - -
191B ASP* 1.3 77.9 - - - +
193B LYS* 1.3 63.8 + - + +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU 3.4 14.8 + - - +
190B HIS* 3.0 27.5 + - + +
191B ASP 5.0 1.1 - - - -
192B GLU* 1.3 83.1 - - + +
202B SER* 5.9 2.9 - - - -
205B GLN* 4.5 22.4 - - - +
240B ASP* 5.5 7.0 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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