Contacts of the helix formed by residues 179 - 200 (chain B) in PDB entry 1O2D
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 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B SER 3.3 4.0 + - - -
178B MSE 1.3 73.2 - - - +
180B ASP* 1.3 60.6 + - - +
181B GLU* 3.5 11.0 + - - +
182B LEU* 3.0 27.2 + - - +
183B THR* 2.8 32.2 + - - -
1801B NAP 4.8 1.4 - - - -
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Residues in contact with ASP 180 (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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178B MSE 5.0 0.2 - - - +
179B SER* 1.3 74.4 - - - +
181B GLU* 1.3 62.9 + - - +
183B THR* 3.4 4.6 + - - -
184B LEU* 3.0 23.0 + - - +
226B ILE* 3.2 40.9 - - + +
227B GLU* 5.2 2.6 - - - -
233B ARG* 4.2 4.9 + - - -
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B SER* 3.2 9.8 + - - +
180B ASP* 1.3 79.4 - - - +
182B LEU* 1.3 58.1 + - - +
184B LEU* 3.4 10.5 + - + +
185B SER* 3.0 27.7 + - - -
269B LYS* 3.3 29.8 + - + +
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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
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137B THR* 4.3 3.4 - - + -
178B MSE 3.8 19.3 - - + -
179B SER* 3.0 21.7 + - - +
181B GLU* 1.3 74.7 - - - +
183B THR* 1.3 61.1 + - - +
185B SER* 4.4 1.8 - - - +
186B THR* 2.8 57.7 + - + +
269B LYS* 4.2 22.4 - - + +
1801B NAP 3.4 66.4 - - + +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ALA 4.9 0.7 - - - +
178B MSE 3.3 27.7 - - + +
179B SER 2.8 23.7 + - - -
180B ASP 3.6 5.2 - - - -
181B GLU 3.3 0.2 - - - -
182B LEU* 1.3 76.5 - - - +
184B LEU* 1.3 57.2 + - - +
186B THR* 3.6 0.5 + - - -
187B GLY* 3.0 26.9 + - - -
222B LEU* 3.9 5.3 - - + +
225B ALA* 3.8 37.7 - - + +
226B ILE* 3.8 9.2 - - + +
233B ARG* 3.1 23.7 + - + +
236B MSE 5.8 2.0 - - + -
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Residues in contact with LEU 184 (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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180B ASP 3.0 17.2 + - - +
181B GLU* 3.6 10.3 - - + +
183B THR* 1.3 76.4 - - - +
185B SER* 1.3 63.9 + - - +
187B GLY* 3.7 0.3 - - - -
188B VAL* 2.9 35.9 + - + +
222B LEU* 4.7 2.4 - - + +
226B ILE* 3.8 28.4 - - + +
272B LYS* 5.7 5.4 - - + -
311B LEU* 3.8 47.1 - - + +
312B GLY 4.5 8.7 - - - +
313B LEU* 4.2 19.1 - - + -
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Residues in contact with SER 185 (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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181B GLU* 3.0 17.5 + - - -
182B LEU* 3.3 2.9 + - - -
184B LEU* 1.3 77.5 - - - +
186B THR* 1.3 60.9 + - - +
188B VAL* 3.3 3.5 + - - -
189B ASP 3.0 22.3 + - - -
269B LYS* 3.2 41.3 - - - +
271B GLY* 3.3 12.6 + - - -
272B LYS* 3.2 26.1 + - - +
313B LEU* 5.7 0.2 - - - -
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Residues in contact with THR 186 (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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137B THR* 3.8 15.7 - - + +
138B ALA 3.6 7.2 + - - -
139B GLY* 2.9 30.9 + - - +
178B MSE 3.5 14.9 - - - +
182B LEU* 2.8 44.2 + - + +
183B THR 3.6 2.8 + - - -
185B SER* 1.3 76.6 - - - +
187B GLY* 1.3 64.4 + - - +
189B ASP* 3.2 8.9 + - - +
190B ALA 3.0 14.4 + - - -
1801B NAP 3.6 23.3 - - - +
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Residues in contact with GLY 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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138B ALA 3.4 12.6 - - - -
183B THR 3.0 18.9 + - - -
184B LEU 3.7 0.9 - - - -
186B THR* 1.3 79.9 + - - +
188B VAL* 1.3 57.2 + - - +
190B ALA* 3.3 4.2 + - - +
191B LEU* 2.9 26.2 + - - +
218B ILE* 4.4 1.7 - - - +
222B LEU* 4.1 9.2 - - - -
236B MSE 3.6 18.8 - - - +
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Residues in contact with VAL 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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184B LEU* 2.9 38.1 + - + +
185B SER 3.8 3.4 - - - +
186B THR 3.2 0.2 - - - -
187B GLY* 1.3 73.9 - - - +
189B ASP* 1.3 60.5 + - - +
191B LEU* 3.5 7.9 - - + +
192B SER* 2.8 34.6 + - - +
222B LEU* 4.1 4.5 - - + -
271B GLY 3.4 21.3 - - - +
275B GLY* 3.6 20.9 - - - -
308B LEU* 4.2 11.9 - - + -
311B LEU* 4.1 14.4 - - + -
313B LEU* 4.1 18.8 - - + -
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Residues in contact with ASP 189 (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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139B GLY 4.1 2.2 - - - +
140B THR* 3.4 28.9 - - - +
185B SER 3.0 14.0 + - - +
186B THR* 3.3 13.5 - - - +
188B VAL* 1.3 76.4 - - - +
190B ALA* 1.3 57.1 + - - +
192B SER* 3.1 4.9 + - - -
193B HIS* 2.9 36.5 + - - -
256B HIS* 3.5 3.8 + - - -
270B HIS* 3.0 20.8 + - - -
271B GLY* 3.7 11.6 - - - +
274B THR* 5.0 0.3 + - - -
900B FE 2.1 31.1 - - - -
1801B NAP 4.8 2.8 + - - +
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Residues in contact with ALA 190 (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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138B ALA 4.4 2.5 - - - +
139B GLY 3.5 17.9 + - - +
186B THR 3.0 9.5 + - - +
187B GLY* 3.5 8.7 - - - +
188B VAL 3.3 0.2 - - - -
189B ASP* 1.3 75.0 - - - +
191B LEU* 1.3 63.5 + - - +
193B HIS* 3.3 5.9 + - - -
194B ALA* 3.1 20.8 + - - +
218B ILE* 3.8 13.1 - - + +
236B MSE 4.6 1.8 - - + -
240B SER* 3.8 26.9 - - - +
243B ALA* 3.4 11.4 - - + +
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Residues in contact with LEU 191 (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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187B GLY 2.9 14.0 + - - +
188B VAL* 3.5 13.9 - - + +
190B ALA* 1.3 76.9 - - - +
192B SER* 1.3 61.2 + - - +
194B ALA* 3.2 3.8 + - - +
195B VAL* 2.9 48.1 + - + +
218B ILE* 3.6 20.8 - - + +
222B LEU* 4.9 2.7 - - + -
278B LEU* 4.0 13.9 - - + -
300B PHE* 3.6 33.7 - - + -
304B LEU* 3.9 19.5 - - + -
307B PHE* 3.9 18.4 - - + -
308B LEU* 4.1 14.6 - - + -
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Residues in contact with SER 192 (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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188B VAL* 2.8 21.4 + - - +
189B ASP* 3.6 5.4 - - - -
191B LEU* 1.3 76.4 - - - +
193B HIS* 1.3 58.6 + - - +
196B GLU* 2.8 41.4 + - - +
256B HIS* 4.0 3.4 - - - -
274B THR* 3.6 33.2 - - - +
275B GLY* 3.9 11.3 + - - -
278B LEU* 3.7 22.1 - - - +
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Residues in contact with HIS 193 (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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139B GLY 4.4 0.2 + - - -
140B THR 3.0 33.2 + - - -
189B ASP* 2.9 23.4 + - - -
190B ALA* 3.6 9.7 - - - +
192B SER* 1.3 78.2 - - - +
194B ALA* 1.3 58.6 + - - +
196B GLU* 4.8 1.6 - - - -
197B GLY* 2.9 25.5 + - - -
240B SER 5.5 0.4 + - - -
243B ALA* 3.8 17.6 + - + +
246B VAL* 4.1 1.7 - - - +
247B ILE* 3.5 40.4 - - + +
252B THR* 4.4 2.2 - - + -
256B HIS* 3.2 16.6 + + - -
900B FE 2.3 30.1 - - - -
1801B NAP 3.4 14.7 - + - -
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Residues in contact with ALA 194 (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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190B ALA 3.1 13.0 + - - +
191B LEU* 3.6 8.7 - - - +
193B HIS* 1.3 78.2 - - - +
195B VAL* 1.3 62.7 + - - +
197B GLY* 3.9 0.2 - - - -
198B TYR* 3.0 24.6 + - - +
211B ALA* 3.5 15.8 - - - +
214B ALA* 3.9 24.0 - - + -
215B MSE 3.9 22.0 - - + +
218B ILE* 5.0 0.4 - - + -
243B ALA* 3.9 6.2 - - + +
246B VAL* 4.8 2.7 - - - -
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Residues in contact with VAL 195 (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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191B LEU* 2.9 36.0 + - + +
192B SER 4.1 2.0 - - - +
194B ALA* 1.3 75.3 - - - +
196B GLU* 1.3 64.4 + - - +
198B TYR* 3.2 3.0 + - - +
199B LEU* 3.0 44.8 + - + +
215B MSE 3.8 25.4 - - + -
278B LEU* 4.2 15.9 - - + -
282B MSE 4.1 18.6 - - - -
296B VAL* 4.0 14.4 - - + -
300B PHE* 4.0 7.2 - - + -
304B LEU* 4.4 1.3 - - + -
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Residues in contact with GLU 196 (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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192B SER* 2.8 24.1 + - - +
193B HIS* 4.2 2.5 - - - +
195B VAL* 1.3 72.3 - - - +
197B GLY* 1.3 56.7 + - - +
199B LEU* 4.8 2.5 - - - -
200B SER* 2.9 31.9 + - - -
251B GLY 4.9 1.8 - - - -
252B THR* 4.3 7.2 - - + -
253B THR* 2.6 55.6 + - + +
255B ALA* 3.7 8.3 - - - -
256B HIS* 2.4 46.1 + - - -
274B THR* 3.2 11.8 - - - +
278B LEU* 3.9 17.0 - - + -
285B MSE 5.5 1.3 - - + -
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Residues in contact with GLY 197 (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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193B HIS 2.9 19.1 + - - -
196B GLU* 1.3 80.4 - - - +
198B TYR* 1.3 60.3 + - - +
200B SER* 3.7 6.9 + - - -
203B SER* 3.9 6.9 - - - -
207B SER* 4.9 1.0 + - - -
208B ASP* 4.4 1.3 - - - +
246B VAL* 3.7 13.5 - - - -
250B THR* 3.4 40.4 - - - +
251B GLY 4.5 2.1 + - - -
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Residues in contact with TYR 198 (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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194B ALA 3.0 18.8 + - - +
195B VAL 3.6 4.3 - - - +
197B GLY* 1.3 77.7 - - - +
199B LEU* 1.3 73.8 + - + +
200B SER 3.7 1.6 + - - +
203B SER* 5.0 0.3 - - - -
208B ASP* 3.5 28.9 - - + -
211B ALA* 4.0 5.5 - - + +
212B ILE* 3.8 27.3 - - + +
215B MSE 3.7 17.3 - - + -
292B LYS* 2.8 80.4 + - + +
295B THR* 3.7 25.5 + - + +
296B VAL* 3.8 11.9 - - + -
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Residues in contact with LEU 199 (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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195B VAL* 3.0 38.0 + - + +
196B GLU* 4.2 2.7 - - - +
198B TYR* 1.3 85.7 - - + +
200B SER* 1.3 66.3 + - - +
253B THR* 5.1 0.7 - - + -
282B MSE 3.7 23.6 - - + -
285B MSE 3.8 25.1 - - + -
289B ILE* 3.6 15.0 - - + +
292B LYS* 3.7 39.3 - - + +
293B VAL* 4.0 6.7 - - + +
296B VAL* 3.9 9.6 - - + -
341B PRO* 3.2 22.5 - - - +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU 2.9 18.3 + - - -
197B GLY 3.8 9.6 - - - -
198B TYR 3.4 2.2 - - - +
199B LEU* 1.3 82.0 - - - +
201B ARG* 1.3 65.7 + - - +
202B LYS* 2.9 20.3 + - - +
203B SER* 3.1 16.9 + - - -
250B THR* 3.9 14.5 + - - -
251B GLY 5.0 1.6 - - - -
252B THR 5.0 1.1 + - - -
253B THR* 4.2 10.5 - - - +
292B LYS* 5.2 2.1 + - - -
339B ASN* 3.6 17.3 + - - +
341B PRO* 4.5 0.2 - - - -
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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