Contacts of the helix formed by residues 219 - 244 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D TYR* 4.0 7.1 - - - +
221D GLU* 6.2 1.6 - - - -
276D HIS* 4.9 7.6 + - - -
217E SER* 3.1 13.5 + - - -
218E THR* 1.3 79.0 - - - +
220E TYR* 1.3 64.6 + - - +
221E GLU* 4.6 3.1 - - - -
222E ALA* 3.2 20.3 - - - +
223E ASN* 3.1 24.5 + - - +
275E GLN* 5.1 0.2 - - - -
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Residues in contact with TYR 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B THR* 4.3 9.9 + - - +
214B ALA* 4.9 2.9 - - + -
217B SER* 3.4 31.4 - - - -
219B SER* 4.1 3.6 - - - +
222B ALA* 3.6 28.7 - - + -
223B ASN* 5.2 0.4 - - - -
226B LEU* 5.2 3.0 - - + +
218E THR 3.6 4.9 + - - -
219E SER* 1.3 71.6 - - - +
221E GLU* 1.3 63.1 - - - +
223E ASN* 2.9 16.6 + - - +
224E VAL* 2.9 34.5 + - + +
272E VAL* 3.3 32.3 - - + -
273E THR* 2.8 34.0 + - + +
275E GLN* 5.4 4.5 - - - +
276E HIS* 3.4 36.8 - + + +
279E LYS* 5.8 1.5 - - - +
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Residues in contact with GLU 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER* 5.9 1.1 - - - +
221B GLU* 3.1 38.1 - - + +
222B ALA* 3.5 16.8 - - + +
225B THR* 3.4 18.9 + - - -
221D GLU* 3.4 32.4 - - + +
219E SER* 3.4 3.3 - - - -
220E TYR* 1.3 79.0 - - - +
222E ALA* 1.3 63.4 + - - +
224E VAL* 3.1 24.9 - - - +
225E THR* 3.0 32.3 + - - -
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Residues in contact with ALA 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D TYR* 4.0 22.0 - - + -
221D GLU* 3.5 22.0 + - + +
224D VAL* 4.3 11.0 - - + -
219E SER* 3.2 24.4 + - - +
220E TYR 3.3 0.8 - - - -
221E GLU* 1.3 78.8 - - - +
223E ASN* 1.3 62.1 + - - +
225E THR* 3.6 1.8 + - - -
226E LEU* 3.0 37.0 + - + +
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Residues in contact with ASN 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D TYR* 5.2 0.2 - - - -
214E ALA* 3.1 30.7 + - + +
217E SER* 3.3 33.2 + - - -
219E SER 3.1 14.5 + - - +
220E TYR* 2.9 10.8 + - - +
222E ALA* 1.3 79.9 - - - +
224E VAL* 1.3 60.0 + - - +
226E LEU* 3.5 5.9 - - - +
227E VAL* 3.0 36.3 + - - +
272E VAL* 3.5 32.2 - - + +
275E GLN* 4.0 9.1 - - - +
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Residues in contact with VAL 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ALA* 4.3 4.5 - - + -
225B THR* 3.8 14.8 - - + +
226B LEU* 3.5 28.3 - - + -
220E TYR* 2.9 47.5 + - + +
221E GLU* 3.1 32.8 - - - +
223E ASN* 1.3 75.6 - - - +
225E THR* 1.3 71.4 + - - +
227E VAL* 5.1 2.0 - - - -
228E VAL* 3.0 32.8 + - + +
272E VAL* 5.3 5.8 - - + -
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Residues in contact with THR 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 4.4 13.2 + - - +
221D GLU* 3.7 7.0 + - - -
224D VAL* 4.5 11.2 - - + -
225D THR* 4.4 22.6 + - - +
228D VAL* 5.1 6.7 - - + -
221E GLU* 3.0 32.8 + - - -
222E ALA 3.8 3.8 - - - -
224E VAL* 1.3 76.7 - - - +
226E LEU* 1.3 66.5 + - + +
228E VAL* 5.1 0.7 - - - -
229E SER* 3.0 41.7 + - - +
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Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D TYR* 5.7 2.7 - - + +
224D VAL* 3.7 35.4 - - + -
228D VAL* 4.7 15.4 - - + +
269D VAL* 5.8 1.1 - - + -
210E ILE* 3.2 40.6 - - + +
211E SER* 4.3 6.5 - - - +
213E THR* 4.0 16.2 - - + -
214E ALA* 4.5 9.2 - - + -
222E ALA* 3.0 27.5 + - + +
223E ASN* 3.5 9.0 - - - +
225E THR* 1.3 79.9 - - + +
227E VAL* 1.3 64.6 - - - +
229E SER* 3.8 0.7 - - - -
230E THR* 2.9 25.5 + - + +
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E SER* 3.9 19.5 - - - +
212E TRP* 5.8 0.2 - - - -
214E ALA* 4.8 6.7 - - + -
223E ASN 3.0 21.0 + - - +
224E VAL* 4.5 2.0 - - - +
226E LEU* 1.3 72.5 - - + +
228E VAL* 1.3 58.3 + - + +
230E THR* 2.7 19.9 + - - -
231E LEU* 3.0 16.5 + - + +
265E TYR* 3.6 25.5 - - + +
268E ALA* 4.2 15.7 - - + -
269E VAL* 3.7 27.8 - - + -
272E VAL* 4.6 16.4 - - + -
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Residues in contact with VAL 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 4.6 12.1 - - + -
225B THR* 5.0 5.2 - - + +
226B LEU* 4.4 27.4 - - + -
229B SER* 3.3 40.4 - - - +
230B THR* 5.3 4.3 - - + -
224E VAL* 3.0 20.0 + - - +
225E THR 4.4 0.7 - - - +
227E VAL* 1.3 78.2 - - + +
229E SER* 1.3 62.9 + - - +
231E LEU* 2.9 15.0 + - + +
232E ALA* 2.9 28.5 + - + +
269E VAL* 5.1 6.5 - - + -
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Residues in contact with SER 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 5.4 2.1 + - - -
228D VAL* 3.4 31.5 - - - +
232D ALA* 5.6 5.5 - - - +
225E THR* 3.0 28.3 + - - +
226E LEU 4.1 0.7 - - - -
228E VAL* 1.3 80.0 - - - +
230E THR* 1.3 61.1 + - - +
232E ALA* 4.0 9.3 - - - +
233E ALA* 3.9 14.4 + - - +
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Residues in contact with THR 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D VAL* 5.5 5.6 - - + -
231D LEU* 6.5 0.4 - - + -
207E ILE* 3.4 32.4 - - + +
210E ILE* 4.3 14.1 - - + -
211E SER* 3.3 19.8 - - - +
226E LEU* 2.9 18.1 + - + +
227E VAL 2.7 21.0 + - - -
229E SER* 1.3 75.7 - - - +
231E LEU* 1.3 60.3 + - - +
232E ALA 3.2 0.4 - - - -
233E ALA* 3.3 5.3 + - - -
234E HIS 3.0 23.0 + - - -
265E TYR* 3.1 23.7 + - - -
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Residues in contact with LEU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PHE* 6.5 0.4 - - + -
207B ILE* 4.4 17.7 - - + -
210B ILE* 3.8 30.3 - - + -
230B THR* 6.2 1.8 - - + -
227E VAL* 3.0 15.3 + - + +
228E VAL* 2.9 17.6 + - + +
230E THR* 1.3 77.9 + - - +
232E ALA* 1.3 55.8 + - - +
234E HIS* 3.2 5.9 + - - +
235E ILE* 2.9 40.6 + - + +
262E TYR* 4.3 25.6 - - + -
265E TYR* 3.2 35.2 - - + -
269E VAL* 5.9 1.1 - - + -
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Residues in contact with ALA 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER 6.0 1.6 - - - +
233B ALA* 6.0 1.6 - - + -
228E VAL* 2.9 15.0 + - + +
229E SER* 4.0 11.7 - - - +
231E LEU* 1.3 76.9 - - - +
233E ALA* 1.3 57.7 + - - +
235E ILE* 3.1 17.1 + - - +
236E ALA* 2.9 25.1 + - - +
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Residues in contact with ALA 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D ALA* 5.6 8.3 - - + -
235D ILE* 4.1 25.4 - - + -
207E ILE* 3.8 14.4 - - + -
229E SER 3.9 8.1 + - - +
230E THR* 3.3 10.2 + - - +
232E ALA* 1.3 76.5 - - - +
234E HIS* 1.3 60.4 + - - +
236E ALA* 3.2 10.0 + - - +
237E PHE* 2.9 33.9 + - + -
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Residues in contact with HIS 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E MET* 3.8 24.1 - - + -
207E ILE* 3.5 11.8 - - + +
230E THR 3.0 14.0 + - - +
231E LEU* 3.5 16.5 - - + +
233E ALA* 1.3 73.6 - - - +
235E ILE* 1.3 61.2 + - - +
237E PHE* 3.4 3.8 + - - +
238E ASN* 2.9 28.8 + - - +
258E ILE* 3.2 37.3 + - + +
261E ILE* 3.3 36.7 - - + +
262E TYR* 3.6 33.5 + + - -
265E TYR* 4.3 6.1 - + + +
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Residues in contact with ILE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 4.5 5.2 - - + -
233B ALA* 3.6 29.6 - - + -
236B ALA* 5.3 7.6 - - + -
237B PHE* 4.0 26.9 - - + -
231E LEU* 2.9 32.5 + - + +
232E ALA* 3.2 15.0 - - - +
234E HIS* 1.3 76.8 - - - +
236E ALA* 1.3 56.2 + - - +
238E ASN* 3.4 1.6 + - - +
239E ILE* 2.9 47.7 + - + +
262E TYR* 3.6 28.0 - - + +
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Residues in contact with ALA 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ILE* 6.0 2.0 - - + -
239D ILE* 4.8 15.9 - - + +
232E ALA 2.9 11.5 + - - +
233E ALA* 3.3 15.0 - - - +
235E ILE* 1.3 78.3 - - - +
237E PHE* 1.3 58.0 + - + +
239E ILE* 3.2 8.7 + - - +
240E LEU* 2.9 29.4 + - - +
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Residues in contact with PHE 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ILE* 3.5 42.8 - - + -
238D ASN* 5.0 1.6 - - - -
239D ILE* 4.9 9.2 - - + -
262D TYR* 4.0 3.4 - - - -
199E ASN 3.5 20.6 - - - -
200E ILE* 4.0 30.7 - - + -
203E PRO* 3.9 23.1 - - + -
204E MET* 4.5 24.5 - - + -
207E ILE* 4.4 15.3 - - + -
233E ALA 2.9 27.2 + - - -
234E HIS* 3.8 5.8 - - - +
236E ALA* 1.3 71.2 - - + +
238E ASN* 1.3 66.4 + - - +
240E LEU* 3.2 8.7 + - + +
241E VAL* 3.0 30.7 + - - +
258E ILE* 4.8 1.1 - - - -
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Residues in contact with ASN 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO 4.6 1.2 - - - +
199B ASN* 3.6 24.6 + - - +
237B PHE* 5.2 1.6 - - - -
234E HIS* 2.9 18.1 + - + +
235E ILE 3.4 5.8 - - - +
237E PHE* 1.3 75.3 - - - +
239E ILE* 1.3 64.4 + - - +
241E VAL* 3.4 1.7 + - - +
242E GLU* 2.9 55.8 + - - +
258E ILE* 3.4 41.9 - - + +
262E TYR* 3.7 28.0 + - + +
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Residues in contact with ILE 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ALA* 5.3 11.9 - - + +
237B PHE* 5.3 2.7 - - + -
240B LEU* 3.7 43.7 - - + -
235E ILE* 2.9 39.1 + - + +
236E ALA* 3.6 7.2 - - - +
238E ASN* 1.3 80.8 - - - +
240E LEU* 1.3 63.8 + - - +
242E GLU* 3.2 10.9 + - - +
243E THR* 2.9 33.3 + - - +
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Residues in contact with LEU 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ILE* 3.6 44.9 - - + -
242D GLU* 4.2 11.7 - - - +
243D THR* 4.3 12.1 - - - +
200E ILE* 3.9 27.8 - - + -
236E ALA 2.9 17.6 + - - +
237E PHE* 3.6 7.9 - - + +
239E ILE* 1.3 79.0 - - - +
241E VAL* 1.3 62.6 + - + +
243E THR* 3.6 16.3 + - + -
244E ASN* 3.8 17.8 + - - +
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Residues in contact with VAL 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E TYR* 4.0 31.1 + - + +
196E TYR* 6.5 0.7 - - + -
200E ILE* 3.8 40.4 - - + -
237E PHE 3.0 17.4 + - - +
238E ASN 4.1 2.0 - - - +
240E LEU* 1.3 73.7 - - + +
242E GLU* 1.3 63.5 + - - +
243E THR 3.1 6.3 + - - -
244E ASN* 3.3 14.3 + - - +
245E LEU* 3.8 16.2 - - + +
254E THR* 5.2 11.0 - - + -
258E ILE* 5.0 10.8 - - + -
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Residues in contact with GLU 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASN* 3.8 25.3 - - - +
200B ILE* 3.5 23.8 - - - +
240B LEU* 4.2 18.1 - - - +
238E ASN* 2.9 36.6 + - - +
239E ILE* 3.6 9.7 - - - +
241E VAL* 1.3 76.3 - - - +
243E THR* 1.3 59.8 + - - +
245E LEU* 3.4 18.1 - - - +
247E LYS* 3.4 30.5 + - - +
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Residues in contact with THR 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 5.3 5.2 - - - +
32E LYS* 3.4 25.7 + - - +
239E ILE* 2.9 25.9 + - - +
240E LEU* 3.6 9.8 - - + +
241E VAL 3.1 0.6 - - - -
242E GLU* 1.3 76.4 - - - +
244E ASN* 1.3 71.3 + - - +
245E LEU 3.1 8.6 + - - -
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Residues in contact with ASN 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LYS* 5.8 3.6 - - - +
247D LYS* 6.3 1.2 - - - +
31E ASP* 3.7 14.0 - - - +
32E LYS* 3.8 9.9 - - - +
118E TYR* 5.2 6.5 - - - +
240E LEU* 3.8 16.5 + - - +
241E VAL* 3.3 10.2 + - - +
243E THR* 1.3 89.5 - - - +
245E LEU* 1.3 70.0 + - + +
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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