Contacts of the helix formed by residues 196 - 223 (chain B) in PDB entry 4MCA
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 THR 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 3.8 27.6 - - + +
4B ILE* 4.1 9.2 + - - +
5B ILE* 3.8 28.6 - - + +
183B PHE* 4.2 2.2 - - - -
194B LYS 3.6 0.8 + - - -
195B SER* 1.3 95.4 + - - +
197B LEU* 1.3 64.0 + - - +
198B ALA* 3.3 12.0 + - - +
199B ALA* 3.0 25.3 + - - +
200B LEU* 3.4 9.0 + - - +
247B SER 4.5 2.0 + - - -
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG* 5.4 12.8 - - - +
183B PHE* 4.7 17.3 - - + -
196B THR* 1.3 74.7 - - - +
198B ALA* 1.3 65.1 + - - +
200B LEU* 3.6 7.5 + - + +
201B SER* 2.9 25.7 + - - -
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.9 16.4 - - + -
196B THR* 3.1 11.3 + - + +
197B LEU* 1.3 79.3 - - - +
199B ALA* 1.3 61.4 + - - +
201B SER* 3.1 7.6 + - - -
202B LEU* 2.9 32.5 + - + +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.1 6.7 - - + +
195B SER* 3.7 2.2 - - - +
196B THR* 3.0 16.1 + - - +
198B ALA* 1.3 76.4 - - - +
200B LEU* 1.3 63.8 + - - +
202B LEU* 3.3 3.3 + - - +
203B ALA* 3.0 22.3 + - - +
243B ILE* 4.3 11.0 - - - +
244B GLY* 3.9 5.0 - - - -
247B SER* 3.7 28.9 - - - +
248B SER* 3.6 20.2 - - - -
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR* 4.8 6.5 - - + -
179B ALA* 4.0 12.1 - - + +
180B GLN* 3.8 48.9 - - + +
183B PHE* 3.6 35.0 - - + -
195B SER* 4.0 1.8 - - - +
196B THR 3.4 13.9 + - - +
197B LEU* 3.9 7.0 - - + +
199B ALA* 1.3 78.2 - - - +
201B SER* 1.3 63.6 + - - +
203B ALA* 3.3 4.8 + - - +
204B ARG* 3.1 21.0 + - + +
248B SER* 3.4 11.5 + - - +
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Residues in contact with SER 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 2.9 20.2 + - - -
198B ALA* 3.1 7.6 + - - -
200B LEU* 1.3 81.0 - - - +
202B LEU* 1.3 59.2 + - - +
204B ARG* 3.3 7.8 + - - +
205B LEU* 2.9 27.6 + - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 5.3 3.1 - - + -
198B ALA* 2.9 23.5 + - + +
199B ALA* 3.8 4.5 - - - +
201B SER* 1.3 74.4 - - - +
203B ALA* 1.3 60.5 + - - +
205B LEU* 3.3 14.0 + - + +
206B CYS* 2.8 29.8 + - - +
239B TYR* 4.5 13.2 - - + -
240B LEU* 3.7 38.2 - - + +
243B ILE* 3.9 33.0 - - + -
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 3.7 25.1 - - + +
176B TYR* 3.4 15.2 + - + +
179B ALA* 3.7 28.0 - - + -
199B ALA 3.0 14.4 + - - +
200B LEU 3.5 9.0 - - - +
201B SER 3.2 0.2 - - - -
202B LEU* 1.3 77.0 - - - +
204B ARG* 1.4 59.9 + - - +
206B CYS* 3.1 18.0 - - - +
207B TYR 3.3 4.5 + - - -
240B LEU 4.7 0.2 - - - -
244B GLY* 4.1 5.3 - - - -
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR* 3.5 55.2 + - + -
200B LEU* 3.1 12.9 + - + +
201B SER* 3.7 9.4 - - - +
202B LEU 3.3 0.2 - - - -
203B ALA* 1.4 73.5 - - - +
205B LEU* 1.3 60.5 + - - +
207B TYR* 3.2 22.1 + - - +
208B ASP* 2.7 64.7 + - - +
292B GLN* 5.3 3.4 + - - -
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Residues in contact with LEU 205 (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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201B SER 2.9 16.3 + - - +
202B LEU* 3.6 14.8 - - + +
204B ARG* 1.3 75.3 - - - +
206B CYS* 1.3 55.3 + - - +
208B ASP* 4.5 11.0 - - + +
209B THR* 2.6 50.6 + - - +
235B GLU* 5.5 1.3 - - - +
240B LEU* 3.9 28.3 - - + -
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Residues in contact with CYS 206 (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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172B ALA* 3.5 36.1 - - - -
175B THR* 4.4 3.4 - - - -
202B LEU 2.8 13.8 + - - +
203B ALA* 3.1 16.4 - - - +
205B LEU* 1.3 75.8 - - - +
207B TYR* 1.3 61.9 + - - +
209B THR* 3.2 3.0 + - - -
210B LEU* 3.1 26.7 + - - +
236B ALA* 3.6 25.9 - - - +
240B LEU* 3.7 18.2 - - + +
241B SER* 4.0 9.2 - - - +
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Residues in contact with TYR 207 (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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172B ALA 5.2 1.5 + - - +
173B LEU* 4.2 23.8 - - + +
176B TYR* 3.6 23.6 - + + +
177B PHE* 3.6 29.8 - + - -
203B ALA 3.3 1.2 + - - -
204B ARG* 3.2 35.2 + - - +
206B CYS* 1.3 78.1 - - - +
208B ASP* 1.3 73.5 + - - +
210B LEU* 3.2 12.2 + - + +
211B LEU* 3.1 56.2 + - + +
292B GLN* 2.8 29.4 + - - -
295B THR* 3.7 10.6 - - - +
296B VAL* 4.1 4.0 - - + +
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Residues in contact with ASP 208 (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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204B ARG* 2.7 64.5 + - - +
205B LEU* 4.0 12.0 - - + +
207B TYR* 1.3 81.0 - - - +
209B THR* 1.3 63.0 + - - +
211B LEU* 3.5 7.2 + - - +
212B ALA* 3.0 24.1 + - - +
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Residues in contact with THR 209 (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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205B LEU* 2.6 41.9 + - - +
206B CYS 3.6 4.0 - - - -
208B ASP* 1.3 70.0 - - - +
210B LEU* 1.3 57.8 + - - +
212B ALA* 4.4 4.0 - - - +
213B GLU* 2.7 50.9 + - + +
232B ARG* 3.7 32.5 - - + +
233B ILE* 4.3 2.5 - - + -
236B ALA* 4.1 11.7 - - + -
240B LEU* 4.3 3.8 - - + +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B MET* 3.6 37.9 - - + +
172B ALA* 3.7 12.1 - - + +
173B LEU* 3.5 43.1 - - + +
206B CYS* 3.1 19.7 + - - +
207B TYR* 3.2 11.6 + - + +
209B THR* 1.3 76.3 - - - +
211B LEU* 1.3 59.3 + - + +
214B GLY* 2.8 30.1 + - - -
215B VAL 4.8 0.2 + - - -
233B ILE* 3.8 15.5 - - + -
236B ALA* 4.6 3.8 - - + -
237B ASN* 3.8 10.5 - - - +
299B PHE* 3.5 18.9 - - + -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 5.9 0.7 - - + -
207B TYR* 3.1 54.5 + - + +
208B ASP* 3.9 8.3 - - - +
210B LEU* 1.3 77.9 - - + +
212B ALA* 1.3 61.4 + - - +
214B GLY 4.8 0.5 + - - -
215B VAL* 5.8 0.3 + - - +
295B THR* 4.0 24.9 - - + -
296B VAL* 6.0 0.7 - - + -
299B PHE* 4.1 31.5 - - + -
302B ARG* 5.0 12.1 + - - +
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Residues in contact with ALA 212 (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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208B ASP 3.0 18.3 + - - +
209B THR* 3.9 3.6 - - - +
211B LEU* 1.3 78.1 - - - +
213B GLU* 1.3 73.6 + - + +
214B GLY 3.8 0.4 - - - -
216B LYS* 3.5 20.1 + - - +
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Residues in contact with GLU 213 (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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209B THR* 2.7 33.9 + - + +
212B ALA* 1.3 85.2 - - + +
214B GLY* 1.3 54.1 - - - +
215B VAL 3.4 1.6 - - - -
216B LYS* 2.9 41.8 + - - +
217B ALA* 2.8 35.5 + - - +
229B ALA* 3.3 16.1 - - - +
232B ARG* 3.6 34.8 + - + -
233B ILE* 3.8 15.9 - - + -
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Residues in contact with GLY 214 (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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169B MET* 3.6 27.5 - - - +
210B LEU 2.8 19.2 + - - -
211B LEU 4.8 0.6 + - - -
212B ALA 3.8 0.8 - - - -
213B GLU* 1.3 77.8 - - - +
215B VAL* 1.3 57.1 - - - +
217B ALA* 3.5 1.2 + - - +
218B LYS* 2.9 29.3 + - - +
233B ILE* 3.8 3.7 - - - +
299B PHE* 4.4 5.6 - - - -
303B ILE* 4.2 5.8 - - - -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLU 3.4 0.2 - - - -
214B GLY* 1.3 74.1 - - - +
216B LYS* 1.3 67.1 + - + +
218B LYS* 3.2 8.0 + - + +
219B LEU* 3.0 41.1 + - + +
299B PHE* 5.6 2.7 - - + -
302B ARG* 3.6 48.0 - - + +
303B ILE* 4.2 9.6 - - + -
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Residues in contact with LYS 216 (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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212B ALA 3.5 17.5 - - - +
213B GLU* 2.9 37.2 + - - +
215B VAL* 1.3 78.6 - - + +
217B ALA* 1.3 61.7 + - - +
219B LEU* 3.6 7.2 + - - +
220B ALA* 3.2 21.7 + - - +
227B THR* 4.7 0.7 + - - -
229B ALA* 3.7 18.2 - - + +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 4.3 9.4 - - + -
213B GLU 2.8 21.7 + - - +
214B GLY 3.6 3.1 - - - +
216B LYS* 1.3 71.7 - - - +
218B LYS* 1.3 61.7 + - - +
220B ALA* 3.2 1.9 + - - +
221B VAL* 2.9 34.3 + - - +
229B ALA* 3.7 14.1 - - - +
230B VAL* 4.0 16.6 - - + -
233B ILE* 3.6 24.9 - - + -
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Residues in contact with LYS 218 (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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162B VAL* 3.7 21.0 - - + +
165B LEU* 4.2 9.6 - - - +
166B VAL* 4.1 11.0 - - + +
169B MET* 4.5 6.7 - - + -
214B GLY 2.9 17.9 + - - +
215B VAL* 3.2 9.4 + - + +
217B ALA* 1.3 76.6 - - - +
219B LEU* 1.3 61.6 + - + +
221B VAL 3.3 1.2 + - - -
222B GLU* 2.8 56.3 + - - +
302B ARG 4.4 5.1 + - - +
303B ILE* 2.7 48.6 + - + +
304B GLY* 4.5 2.6 - - - -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 3.0 33.6 + - + +
216B LYS* 4.0 6.1 - - - +
218B LYS* 1.3 80.1 - - + +
220B ALA* 1.4 62.2 + - - +
222B GLU* 3.1 29.1 + - - +
223B ALA* 3.4 17.2 + - - +
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Residues in contact with ALA 220 (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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216B LYS 3.2 12.8 + - - +
217B ALA 3.2 2.2 + - - +
219B LEU* 1.4 74.2 - - - +
221B VAL* 1.3 58.8 + - - +
223B ALA* 3.0 16.8 + - - -
224B GLY 3.1 8.1 + - - -
225B VAL* 3.1 25.7 + - + +
227B THR* 3.7 25.1 - - + +
230B VAL* 3.4 26.5 - - + -
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE 4.7 2.2 - - - +
158B ALA* 3.5 36.7 - - + +
160B ALA 4.0 16.0 - - - +
162B VAL* 4.0 20.2 + - + +
165B LEU* 3.9 26.9 - - + -
217B ALA 2.9 20.8 + - - +
218B LYS 3.9 3.1 - - - +
220B ALA* 1.3 73.6 - - - +
222B GLU* 1.3 67.5 + - - +
224B GLY* 2.9 13.6 + - - +
225B VAL 4.3 0.7 - - - -
230B VAL* 4.0 20.2 - - + -
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Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 4.0 22.9 - - + +
218B LYS* 2.8 45.9 + - - +
219B LEU* 3.1 33.0 - - - +
220B ALA 3.2 0.2 - - - -
221B VAL* 1.3 79.0 - - - +
223B ALA* 1.3 56.9 + - - +
224B GLY 3.3 0.4 + - - -
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU 3.4 7.4 + - - +
220B ALA* 3.0 10.2 + - - +
222B GLU* 1.3 76.3 - - - +
224B GLY* 1.3 62.2 + - - +
225B VAL* 3.4 19.9 + - + +
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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