Contacts of the helix formed by residues 219 - 244 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.0 1.4 - - - +
221A GLU* 6.2 0.9 - - - -
276A HIS* 3.8 15.8 + - - -
217D SER* 2.9 16.7 + - - -
218D THR* 1.3 76.9 - - - +
220D TYR* 1.3 65.7 + - - +
221D GLU* 4.7 3.1 - - - -
222D ALA* 3.5 18.7 - - - +
223D ASN* 3.0 23.6 + - - +
275D GLN* 5.6 0.2 - - - -
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Residues in contact with TYR 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D THR 3.6 4.4 + - - -
219D SER* 1.3 72.2 - - - +
221D GLU* 1.3 64.3 + - - +
223D ASN* 3.1 6.2 + - + +
224D VAL* 2.9 44.5 + - + +
272D VAL* 3.5 33.2 - - + -
273D THR* 3.4 25.2 + - - +
275D GLN* 6.1 2.7 - - - +
276D HIS* 3.4 42.2 - + + +
279D LYS* 5.8 1.5 - - - +
213E THR* 5.1 6.9 + - - +
214E ALA* 5.8 0.9 - - - -
216E TRP 5.7 0.9 - - - -
217E SER* 3.2 36.8 - - - -
219E SER* 4.0 5.4 - - - +
222E ALA* 4.0 20.4 - - + -
223E ASN* 5.2 0.2 - - - -
226E LEU* 5.7 3.1 - - + +
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Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 2.8 38.4 - - + +
221C GLU* 4.9 1.2 - - - +
219D SER* 3.4 3.1 - - - -
220D TYR* 1.3 79.5 - - - +
222D ALA* 1.3 62.3 + - - +
224D VAL* 3.0 13.2 - - - +
225D THR* 3.0 29.4 + - - -
219E SER* 6.2 1.3 - - - -
221E GLU* 3.4 32.7 - - + +
222E ALA* 3.5 30.2 - - + +
225E THR* 3.7 9.5 + - - -
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 3.6 28.0 - - + -
221A GLU* 3.1 29.3 + - + +
224A VAL* 4.4 3.6 - - + -
219D SER* 3.5 22.3 + - - +
220D TYR 3.4 0.4 - - - -
221D GLU* 1.3 79.4 - - - +
223D ASN* 1.3 58.9 + - - +
225D THR* 3.5 1.0 + - - -
226D LEU* 3.0 36.6 + - - +
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Residues in contact with ASN 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.6 0.9 - - - -
214D ALA* 3.3 24.2 + - + +
217D SER* 2.8 50.7 + - - -
219D SER 3.0 18.2 + - - +
220D TYR* 3.1 7.3 + - - +
222D ALA* 1.3 78.5 - - - +
224D VAL* 1.3 61.6 + - - +
226D LEU* 3.9 1.2 - - - +
227D VAL* 3.2 30.5 + - - +
272D VAL* 3.7 30.0 - - + +
275D GLN* 4.2 8.1 - - - +
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D TYR* 2.9 49.3 + - + +
221D GLU* 3.0 35.7 - - - +
223D ASN* 1.3 78.7 - - - +
225D THR* 1.3 65.8 + - - +
227D VAL* 3.5 2.4 + - - -
228D VAL* 3.0 31.9 + - + +
269D VAL* 6.5 0.9 - - - -
272D VAL* 5.2 5.8 - - + -
222E ALA* 4.3 7.4 - - + +
225E THR* 4.5 5.8 - - + -
226E LEU* 3.7 32.3 - - + -
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Residues in contact with THR 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 3.3 22.7 + - - +
224A VAL* 3.8 22.0 - - + +
225A THR* 4.6 14.1 + - - +
228A VAL* 5.4 3.1 - - + -
221D GLU* 3.0 21.4 + - - -
222D ALA 3.7 1.8 - - - -
224D VAL* 1.3 77.0 - - - +
226D LEU* 1.3 64.3 + - - +
228D VAL* 4.8 2.9 - - - -
229D SER* 2.9 35.9 + - - +
225E THR* 4.4 13.8 + - + +
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.9 2.7 - - + +
224A VAL* 3.4 35.9 - - + -
228A VAL* 4.4 12.5 - - + +
269A VAL* 5.3 1.8 - - + -
210D ILE* 3.1 43.5 - - + +
211D SER* 4.1 8.1 - - - +
213D THR* 3.9 18.4 - - + -
214D ALA* 4.3 7.9 - - + -
222D ALA 3.0 26.9 + - - +
223D ASN 3.9 6.7 - - - +
224D VAL 3.2 0.2 - - - -
225D THR* 1.3 77.8 - - - +
227D VAL* 1.3 57.6 + - - +
229D SER* 3.8 1.2 - - - -
230D THR* 2.8 36.7 + - + +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D SER* 4.0 17.5 - - - +
214D ALA* 4.9 4.3 - - + -
223D ASN 3.2 19.3 + - - +
224D VAL* 3.5 4.0 + - - +
226D LEU* 1.3 74.7 - - + +
228D VAL* 1.3 58.9 + - + +
230D THR* 2.9 16.5 + - - -
231D LEU* 3.0 19.4 + - + +
265D TYR* 3.9 25.9 - - + +
268D ALA* 4.4 12.6 - - + -
269D VAL* 3.4 34.3 - - + +
272D VAL* 4.7 11.7 - - + -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D VAL* 3.0 22.7 + - - +
225D THR* 4.1 2.5 - - - +
227D VAL* 1.3 79.9 - - + +
229D SER* 1.3 66.5 + - - +
231D LEU* 3.1 7.7 + - + +
232D ALA* 3.0 30.3 + - + +
269D VAL* 5.6 4.0 - - + -
210E ILE* 5.2 8.7 - - + -
225E THR* 5.1 6.3 - - + +
226E LEU* 4.7 28.5 - - + +
229E SER* 3.4 38.4 - - - +
230E THR* 5.5 4.3 - - + -
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.3 32.4 - - - +
229A SER* 5.2 2.6 + - - -
232A ALA* 5.9 3.1 - - - +
225D THR* 2.9 26.2 + - - +
226D LEU 4.2 0.7 - - - -
228D VAL* 1.3 81.9 - - - +
230D THR* 1.3 61.5 + - - +
232D ALA* 4.2 6.8 - - - +
233D ALA* 4.0 14.7 + - - +
229E SER* 5.7 0.2 + - - -
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Residues in contact with THR 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 5.2 5.2 - - + -
231A LEU* 6.1 2.0 - - + -
207D ILE* 3.4 42.2 - - + +
210D ILE* 4.1 15.5 - - + -
211D SER* 3.2 26.8 - - - +
226D LEU* 2.8 22.7 + - + +
227D VAL 2.9 12.6 + - - -
229D SER* 1.3 79.4 - - - +
231D LEU* 1.3 62.6 + - - +
232D ALA 3.3 0.2 - - - -
233D ALA* 3.4 2.8 + - - +
234D HIS* 3.0 22.0 + - - +
265D TYR* 3.3 6.3 - - - -
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D VAL* 3.0 22.3 + - + +
228D VAL* 3.1 7.6 + - + +
230D THR* 1.3 76.2 + - - +
232D ALA* 1.3 57.3 + - - +
234D HIS* 3.1 7.6 + - - +
235D ILE* 2.9 35.3 + - + +
262D TYR* 4.2 25.8 - - + -
265D TYR* 3.3 38.6 - - + -
269D VAL* 6.0 0.4 - - + -
206E PHE* 6.4 0.2 - - + -
207E ILE* 4.6 16.8 - - + -
210E ILE* 3.9 29.6 - - + -
230E THR* 6.5 0.2 - - + -
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D VAL* 3.0 17.3 + - + +
229D SER* 4.3 8.7 - - - +
231D LEU* 1.3 76.5 - - - +
233D ALA* 1.3 62.6 + - - +
235D ILE* 3.2 15.0 + - - +
236D ALA* 3.0 20.7 + - - +
229E SER 5.6 5.8 - - - +
233E ALA* 5.6 6.3 - - + -
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 5.7 5.8 - - + -
235A ILE* 3.8 30.1 - - + -
207D ILE* 4.1 7.6 - - + -
229D SER 4.0 10.6 + - - +
230D THR* 3.4 8.8 + - - +
232D ALA* 1.3 79.0 - - - +
234D HIS* 1.3 58.0 + - - +
236D ALA* 3.1 10.9 + - + +
237D PHE* 2.9 35.9 + - + -
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Residues in contact with HIS 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D MET* 3.7 25.5 - - + -
207D ILE* 3.7 12.3 - - + +
208D LEU* 6.1 0.2 - - + -
230D THR 3.0 14.5 + - - +
231D LEU* 3.1 24.0 + - - +
233D ALA* 1.3 74.1 - - - +
235D ILE* 1.3 60.8 + - - +
237D PHE* 3.4 7.2 + - - +
238D ASN* 2.9 24.3 + - - +
258D ILE* 3.7 34.2 - - + +
261D ILE* 3.1 37.1 - - + +
262D TYR* 4.1 20.1 - + - -
265D TYR* 4.1 9.8 - + - +
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D LEU* 2.9 29.3 + - + +
232D ALA* 3.5 7.6 - - - +
234D HIS* 1.3 72.5 - - - +
236D ALA* 1.3 60.9 + - - +
238D ASN* 3.1 2.1 + - + +
239D ILE* 2.9 42.4 + - + +
262D TYR* 3.1 36.1 - - + +
207E ILE* 3.9 27.6 - - + -
233E ALA* 4.1 21.1 - - + +
236E ALA* 6.0 2.0 - - + -
237E PHE* 3.5 25.4 - - + -
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Residues in contact with ALA 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE* 5.9 2.7 - - + -
239A ILE* 5.2 13.1 - - + +
232D ALA 3.0 13.1 + - - +
233D ALA* 3.2 14.8 - - - +
235D ILE* 1.3 78.1 - - - +
237D PHE* 1.3 57.3 + - + +
239D ILE* 3.3 9.7 + - - +
240D LEU* 2.9 28.6 + - - +
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Residues in contact with PHE 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE* 3.6 41.5 - - + -
238A ASN* 4.9 1.6 - - - -
239A ILE* 4.8 10.5 - - + -
262A TYR* 3.8 14.4 - - - -
199D ASN 3.7 18.8 - - - -
200D ILE* 4.0 33.2 - - + -
203D PRO* 3.9 14.6 - - + -
204D MET* 4.5 24.9 - - + -
207D ILE* 4.6 9.4 - - + -
233D ALA 2.9 27.2 + - - -
234D HIS* 3.6 9.6 - - - +
236D ALA* 1.3 72.7 - - - +
238D ASN* 1.3 65.4 + - - +
240D LEU* 3.1 11.3 + - + +
241D VAL* 2.9 28.0 + - - +
258D ILE* 4.9 0.9 - - - -
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Residues in contact with ASN 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D HIS 2.9 14.6 + - - +
235D ILE 3.1 8.9 + - - +
237D PHE* 1.3 75.0 - - - +
239D ILE* 1.3 61.9 + - - +
241D VAL* 3.8 1.7 - - - +
242D GLU* 2.9 57.8 + - - +
258D ILE* 3.4 44.2 - - + +
262D TYR* 3.8 25.5 + - + +
198E PRO 4.9 1.0 - - - +
199E ASN* 4.0 24.8 + - - +
237E PHE* 5.0 2.4 - - - -
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ILE* 2.9 32.5 + - + +
236D ALA* 3.5 11.7 - - - +
238D ASN* 1.3 76.9 - - - +
240D LEU* 1.3 67.8 + - - +
242D GLU* 3.9 9.5 - - - +
243D THR* 2.9 38.8 + - - +
236E ALA* 4.8 17.3 - - + +
237E PHE* 4.9 8.5 - - + +
240E LEU* 3.6 39.7 - - + -
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.7 44.2 - - + -
242A GLU* 4.1 8.7 - - - +
243A THR* 4.9 7.4 - - - +
200D ILE* 3.8 29.2 - - + -
236D ALA 2.9 15.0 + - - +
237D PHE* 3.1 12.3 + - + +
239D ILE* 1.3 78.3 - - - +
241D VAL* 1.3 62.2 + - + +
243D THR* 3.7 7.3 - - + -
244D ASN* 3.7 26.4 + - - +
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Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TYR* 4.5 22.7 - - + +
200D ILE* 4.1 34.5 - - + -
204D MET* 6.5 0.2 - - - -
237D PHE* 2.9 20.8 + - + +
238D ASN* 3.8 4.9 - - - +
240D LEU* 1.3 74.4 - - + +
242D GLU* 1.3 62.8 + - - +
243D THR 3.0 5.4 + - - -
244D ASN* 3.3 13.9 + - - +
245D LEU* 3.4 22.0 + - + +
254D THR* 4.8 16.8 - - + -
258D ILE* 5.1 9.0 - - + -
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Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ASN* 2.9 39.7 + - - +
239D ILE* 3.9 7.4 - - - +
241D VAL* 1.3 73.1 - - - +
243D THR* 1.3 57.8 + - - +
245D LEU* 3.0 25.0 - - - +
247D LYS* 3.0 34.4 + - - +
199E ASN* 3.6 25.2 - - - +
200E ILE* 3.3 27.9 - - - +
240E LEU* 4.2 12.5 - - - +
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Residues in contact with THR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LYS* 3.1 32.5 + - - +
239D ILE* 2.9 30.2 + - - +
240D LEU* 3.7 8.3 - - + +
241D VAL 3.0 0.2 - - - -
242D GLU* 1.3 75.4 - - - +
244D ASN* 1.3 72.5 + - - +
245D LEU 3.1 7.6 + - - -
240E LEU* 4.3 13.2 - - - +
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Residues in contact with ASN 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ASP* 4.1 11.4 - - - +
32D LYS* 3.6 15.1 - - - +
118D TYR* 5.5 6.1 - - - +
240D LEU* 3.7 17.4 + - - +
241D VAL* 3.3 6.7 + - - +
243D THR* 1.3 92.4 - - - +
245D LEU* 1.3 68.5 + - + +
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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