Contacts of the helix formed by residues 219 - 244 (chain B) in PDB entry 4LML
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 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B SER* 3.1 14.8 + - - -
218B THR* 1.3 76.7 - - - +
220B TYR* 1.3 65.5 + - - +
221B GLU* 4.6 3.6 - - - -
222B ALA* 3.5 18.4 - - - +
223B ASN* 3.2 24.2 + - - +
275B GLN* 5.4 0.2 - - - -
220E TYR* 4.1 5.7 - - - +
221E GLU* 5.9 1.3 - - - +
276E HIS* 4.3 8.7 + - - -
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B THR 3.7 4.0 + - - -
219B SER* 1.3 71.6 - - - +
221B GLU* 1.3 64.1 + - - +
223B ASN* 2.9 21.1 + - + +
224B VAL* 2.9 33.6 + - + +
272B VAL* 3.8 22.2 - - + -
273B THR* 3.3 25.7 + - - +
275B GLN* 5.7 3.6 - - - +
276B HIS* 3.5 44.9 - + + +
279B LYS* 5.9 1.4 - - - +
213C THR* 4.4 11.8 + - - +
214C ALA* 5.2 2.0 - - - -
216C TRP* 6.1 0.2 - - - +
217C SER* 3.6 31.5 - - - -
219C SER* 4.2 4.0 - - - +
222C ALA* 3.7 25.4 - - + -
223C ASN* 4.9 1.6 - - - -
226C LEU* 5.2 2.5 - - + +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER* 3.4 4.0 - - - -
220B TYR* 1.3 77.6 - - - +
222B ALA* 1.3 62.1 + - - +
224B VAL* 3.0 19.3 - - - +
225B THR* 3.0 28.7 + - - -
219C SER* 6.6 0.2 - - - -
221C GLU* 3.4 29.5 - - + +
222C ALA* 3.3 34.6 - - + +
225C THR* 3.7 8.8 + - - -
221E GLU* 3.1 38.8 - - + +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER* 3.5 22.3 + - - +
220B TYR 3.4 0.6 - - - -
221B GLU* 1.3 77.6 - - - +
223B ASN* 1.3 59.9 + - - +
225B THR* 3.5 1.0 + - - -
226B LEU* 3.0 35.6 + - - +
220E TYR* 3.6 29.8 - - + -
221E GLU* 3.5 23.1 + - + +
224E VAL* 4.3 8.3 - - + -
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Residues in contact with ASN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 3.3 33.2 + - + +
217B SER* 3.4 31.1 + - - -
219B SER 3.2 14.8 + - - +
220B TYR* 2.9 14.5 + - + +
222B ALA* 1.3 79.5 - - - +
224B VAL* 1.3 62.0 - - - +
226B LEU 4.1 0.2 - - - -
227B VAL* 3.2 28.2 + - - +
272B VAL* 3.7 32.3 - - + +
275B GLN* 3.8 14.8 + - - +
291B THR* 6.4 0.4 - - - +
220E TYR* 5.2 0.2 - - - -
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 2.9 45.8 + - + +
221B GLU* 3.0 37.7 + - - +
223B ASN* 1.3 75.7 - - - +
225B THR* 1.3 66.7 + - - +
227B VAL* 5.3 0.9 - - - -
228B VAL* 3.0 33.1 + - + +
272B VAL* 5.9 3.1 - - + -
222C ALA* 4.5 3.6 - - + +
225C THR* 3.9 17.3 - - + -
226C LEU* 3.6 30.5 - - + -
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Residues in contact with THR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 3.0 19.4 + - - -
222B ALA 3.8 3.8 - - - -
224B VAL* 1.3 80.0 - - - +
226B LEU* 1.3 65.2 + - + +
228B VAL* 5.0 0.9 - - - -
229B SER* 2.9 40.8 + - - +
225C THR* 4.6 12.2 + - - +
221E GLU* 3.4 16.7 + - - +
224E VAL* 3.8 24.0 - - + +
225E THR* 4.4 18.7 + - - +
228E VAL* 5.1 3.4 - - + -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 3.1 41.7 - - + +
211B SER 4.3 2.5 - - - +
213B THR* 3.7 18.6 - - + -
214B ALA* 3.9 20.2 - - + -
222B ALA* 3.0 23.0 + - + +
223B ASN 4.1 0.9 - - - +
225B THR* 1.3 77.8 - - + +
227B VAL* 1.3 57.4 + - - +
229B SER* 3.8 0.9 - - - -
230B THR* 2.8 37.5 + - - +
220E TYR* 5.2 3.1 - - + +
224E VAL* 3.5 36.1 - - + -
228E VAL* 4.4 11.8 - - + +
269E VAL* 5.4 1.3 - - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER* 3.8 18.2 - - - +
212B TRP* 5.8 0.4 - - - -
214B ALA* 4.9 5.6 - - + -
215B PHE* 6.1 2.5 - - + -
223B ASN 3.2 20.2 + - - +
224B VAL* 4.5 0.9 - - - +
226B LEU* 1.3 75.4 - - + +
228B VAL* 1.3 58.2 + - + +
230B THR* 2.9 16.8 + - - -
231B LEU* 3.0 17.4 + - + +
265B TYR* 3.6 21.0 - - + +
268B ALA* 4.2 15.9 - - + -
269B VAL* 3.6 30.5 - - + -
272B VAL* 4.7 16.4 - - + -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 3.0 23.2 + - - +
225B THR* 4.4 1.1 - - - +
227B VAL* 1.3 78.0 - - + +
229B SER* 1.3 63.1 + - - +
231B LEU* 2.9 13.7 + - + +
232B ALA* 2.9 28.1 + - + +
269B VAL* 5.4 4.0 - - + -
210C ILE* 5.0 11.4 - - + -
225C THR* 5.2 5.4 - - + +
226C LEU* 4.5 27.4 - - + -
229C SER* 3.5 37.2 - - - +
230C THR* 5.4 5.6 - - + -
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 2.9 27.6 + - - +
226B LEU 4.2 0.2 - - - -
228B VAL* 1.3 80.6 - - - +
230B THR* 1.3 60.8 + - - +
232B ALA* 3.9 9.6 - - - +
233B ALA* 3.7 16.1 + - - +
229C SER* 5.5 1.6 + - - -
228E VAL* 3.3 32.2 - - - +
229E SER* 5.4 2.3 + - - -
232E ALA* 6.0 1.6 - - - +
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Residues in contact with THR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.2 35.6 - - + +
210B ILE* 3.9 17.3 - - + -
211B SER* 3.4 19.1 - - - +
226B LEU* 2.8 25.8 + - + +
227B VAL* 2.9 13.9 + - - -
229B SER* 1.3 76.5 - - - +
231B LEU* 1.3 59.2 + - - +
232B ALA 3.2 0.4 - - - -
233B ALA* 3.2 5.7 + - - +
234B HIS 2.9 23.9 + - - -
265B TYR* 3.1 19.2 + - - -
228E VAL* 5.3 4.7 - - + -
231E LEU* 6.2 1.6 - - + -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 3.0 15.9 + - + +
228B VAL* 2.9 17.5 + - + +
230B THR* 1.3 76.6 - - - +
232B ALA* 1.3 56.8 + - - +
234B HIS* 3.1 2.8 + - + +
235B ILE* 2.9 40.3 + - + +
262B TYR* 3.9 27.4 - - + -
265B TYR* 3.1 35.6 - - + -
269B VAL* 5.9 1.6 - - + -
206C PHE* 6.3 0.4 - - + -
207C ILE* 3.9 25.4 - - + -
210C ILE* 4.4 24.7 - - + -
230C THR* 5.9 3.4 - - + -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B VAL* 2.9 16.3 + - + +
229B SER* 3.9 10.8 - - - +
230B THR 3.2 0.2 - - - -
231B LEU* 1.3 76.0 - - - +
233B ALA* 1.3 57.2 + - - +
235B ILE* 3.1 15.0 + - - +
236B ALA* 2.9 27.8 + - - +
229C SER 5.9 2.7 - - - +
233C ALA* 6.0 2.0 - - + -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.8 17.7 - - + -
229B SER 3.7 10.5 + - - +
230B THR* 3.2 9.9 + - - +
232B ALA* 1.3 77.7 - - - +
234B HIS* 1.3 58.0 + - - +
236B ALA* 3.1 9.8 + - - +
237B PHE* 2.9 33.4 + - + -
232E ALA* 6.0 1.8 - - + -
235E ILE* 3.6 29.8 - - + -
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Residues in contact with HIS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B MET* 3.9 15.2 - - - +
207B ILE* 3.3 13.1 - - + +
230B THR 2.9 13.1 + - - +
231B LEU* 3.5 7.9 - - + +
232B ALA 3.1 0.2 - - - -
233B ALA* 1.3 75.6 - - - +
235B ILE* 1.3 60.3 + - - +
237B PHE* 3.5 3.5 + - - +
238B ASN* 2.9 24.1 + - - +
258B ILE* 3.0 43.7 + - + +
261B ILE* 3.3 35.7 - - + +
262B TYR* 3.4 37.7 + + - -
265B TYR* 3.9 15.4 - + + -
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 2.9 34.9 + - + +
232B ALA* 3.5 9.2 - - - +
234B HIS* 1.3 75.4 - - - +
236B ALA* 1.3 57.8 + - - +
238B ASN* 3.2 3.2 - - + +
239B ILE* 2.9 42.5 + - + +
262B TYR* 3.0 33.0 - - + +
207C ILE* 4.0 13.9 - - + -
233C ALA* 3.8 29.4 - - + +
236C ALA* 5.7 3.1 - - + -
237C PHE* 3.7 24.9 - - + -
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ALA 2.9 12.7 + - - +
233B ALA* 3.2 15.0 - - - +
235B ILE* 1.3 76.0 - - - +
237B PHE* 1.3 58.9 + - + +
239B ILE* 3.2 11.2 + - - +
240B LEU* 2.9 28.2 + - - +
235E ILE* 5.3 5.2 - - + -
239E ILE* 5.3 13.0 - - + +
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Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASN 3.5 21.5 - - - -
200B ILE* 4.3 27.8 - - + -
203B PRO* 3.6 24.5 - - + -
204B MET* 4.4 23.3 - - + -
207B ILE* 4.3 18.8 - - + -
233B ALA 2.9 32.0 + - - +
234B HIS 3.8 4.0 - - - +
236B ALA* 1.3 68.9 - - - +
238B ASN* 1.3 66.2 + - - +
240B LEU* 3.1 14.4 + - + +
241B VAL* 2.9 29.2 + - + +
258B ILE* 5.8 1.3 - - - -
235E ILE* 4.0 30.7 - - + -
238E ASN* 5.2 2.9 - - - -
239E ILE* 5.3 1.5 - - + +
262E TYR* 3.7 13.9 - - - -
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Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B HIS* 2.9 18.0 + - + +
235B ILE 3.2 11.5 + - - +
237B PHE* 1.3 75.5 - - - +
239B ILE* 1.3 62.1 + - - +
241B VAL* 4.0 2.8 - - - +
242B GLU* 2.9 50.0 + - - +
258B ILE* 3.6 29.5 - - + +
262B TYR* 3.7 23.9 + - + +
198C PRO 4.5 2.3 - - - +
199C ASN* 3.5 32.0 + - - +
237C PHE* 4.8 3.6 - - - -
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 2.9 32.7 + - + +
236B ALA* 3.6 9.4 - - - +
237B PHE 3.2 0.2 - - - -
238B ASN* 1.3 79.9 - - - +
240B LEU* 1.3 60.3 + - - +
242B GLU* 3.3 16.2 + - - +
243B THR* 2.9 44.4 + - - +
236C ALA* 4.8 17.7 - - + +
237C PHE* 5.4 5.8 - - + +
240C LEU* 4.2 31.2 - - + -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ILE* 3.6 31.2 - - + -
236B ALA 2.9 13.6 + - - +
237B PHE* 3.1 17.2 + - + +
239B ILE* 1.3 78.4 - - - +
241B VAL* 1.3 60.2 + - - +
243B THR* 3.6 15.0 + - + -
244B ASN* 4.0 13.9 + - - +
239E ILE* 3.7 46.4 - - + -
242E GLU* 4.2 13.2 - - - +
243E THR* 5.3 4.9 - - - +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 4.1 31.0 + - + +
200B ILE* 3.7 39.9 - - + -
237B PHE 2.9 19.1 + - - +
238B ASN* 4.1 2.5 - - - +
240B LEU* 1.3 74.1 - - + +
242B GLU* 1.3 63.2 + - - +
243B THR 3.1 5.6 + - - -
244B ASN* 3.4 13.2 + - - +
245B LEU* 3.9 15.9 + - + +
254B THR* 5.2 10.8 - - + -
258B ILE* 5.3 11.7 - - + -
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASN* 2.9 37.2 + - - +
239B ILE* 3.6 10.3 - - - +
241B VAL* 1.3 75.7 - - - +
243B THR* 1.3 62.3 + - - +
245B LEU* 3.5 17.2 - - - +
247B LYS* 3.6 27.3 + - - +
199C ASN* 4.0 28.9 - - - +
200C ILE* 3.6 23.3 - - - +
240C LEU* 3.7 17.9 - - - +
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 3.7 22.9 + - - +
239B ILE* 2.9 27.6 + - - +
240B LEU* 3.7 9.6 - - + +
241B VAL 3.1 0.6 - - - -
242B GLU* 1.3 81.5 - - - +
244B ASN* 1.3 72.2 + - - +
245B LEU 3.2 4.8 + - - +
240C LEU* 5.2 6.9 - - - +
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Residues in contact with ASN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 3.9 11.1 - - - +
32B LYS* 3.7 15.5 + - - +
118B TYR* 5.3 5.8 - - - +
240B LEU* 4.0 12.2 + - - +
241B VAL* 3.4 8.5 + - - +
243B THR* 1.3 91.8 - - - +
245B LEU* 1.3 70.1 + - + +
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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