Contacts of the helix formed by residues 252 - 281 (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 THR 252 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D PHE* 3.2 38.4 - - + +
116D ARG* 4.2 3.8 - - - +
118D TYR* 6.1 0.7 - - - -
245D LEU* 5.2 12.1 - - + +
248D ALA* 4.4 12.7 - - + +
250D TYR* 3.8 13.0 + - + -
251D MET* 1.3 78.7 - - - +
253D TYR* 1.3 60.1 + - - +
254D THR* 4.3 3.4 - - - -
255D GLY* 3.4 23.8 + - - -
256D ALA* 3.1 26.9 + - - +
313D PHE* 3.6 3.0 - - - -
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Residues in contact with TYR 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ARG 3.1 23.4 + - - +
117D ARG* 4.8 0.4 - - - -
118D TYR 4.5 11.0 - - - +
120D PHE* 4.3 16.4 - + - -
252D THR* 1.3 69.5 - - - +
254D THR* 1.3 65.7 + - - +
256D ALA* 3.1 4.0 + - - +
257D ILE* 3.0 59.8 + - + +
306D ASN* 4.9 6.6 + - - -
309D LEU* 4.2 2.0 - - + -
310D ALA* 3.7 41.9 + - - +
313D PHE* 3.2 40.7 - + + -
314D PHE* 3.9 25.8 - + + -
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Residues in contact with THR 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TYR* 2.5 43.8 + - + +
119D PRO* 3.9 7.5 - - + +
200D ILE* 6.1 4.0 - - + -
201D ILE* 5.8 6.7 - - + -
204D MET* 6.1 4.5 - - + -
241D VAL* 4.8 20.2 - - + -
245D LEU* 6.0 2.2 - - - -
252D THR* 3.5 3.4 - - - -
253D TYR* 1.3 80.5 - - - +
255D GLY* 1.3 58.2 + - - +
257D ILE* 3.5 15.9 - - + +
258D ILE* 3.0 37.6 + - + +
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Residues in contact with GLY 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D MET* 5.0 5.2 - - - +
252D THR* 3.4 21.3 + - - -
253D TYR 3.3 0.6 - - - -
254D THR* 1.3 78.9 - - - +
256D ALA* 1.3 60.2 + - - +
258D ILE* 3.3 23.3 - - - +
259D PHE* 3.4 9.9 + - - +
198E PRO* 4.7 8.4 - - - +
199E ASN* 5.7 4.2 - - - +
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Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D MET* 4.3 19.5 - - + -
252D THR 3.1 19.1 + - - +
253D TYR* 3.1 9.1 + - - +
255D GLY* 1.3 74.2 - - - +
257D ILE* 1.3 68.0 + - - +
258D ILE 3.0 1.1 - - - -
259D PHE* 2.8 17.8 + - - +
260D MET* 2.9 11.3 + - - +
309D LEU* 4.1 17.9 - - + -
313D PHE* 4.4 7.2 - - + -
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Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ILE* 5.7 8.5 - - + -
204D MET* 5.0 14.6 - - + -
253D TYR* 3.0 41.7 + - + +
254D THR* 3.5 21.5 - - + +
256D ALA* 1.3 73.3 - - - +
258D ILE* 1.3 61.8 + - + +
260D MET* 3.4 16.3 - - + +
261D ILE* 2.9 43.1 + - + +
306D ASN* 5.0 15.0 - - - +
309D LEU* 3.6 21.1 - - + +
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Residues in contact with ILE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D MET* 4.5 16.4 - - + -
234D HIS* 3.7 20.9 - - + +
237D PHE 4.9 1.3 - - - -
238D ASN* 3.4 49.8 - - - +
241D VAL* 5.1 11.7 - - + -
254D THR* 3.0 22.3 + - + +
255D GLY* 3.3 20.6 - - - +
256D ALA 3.0 0.4 + - - -
257D ILE* 1.3 81.1 - - + +
259D PHE* 1.3 61.6 + - + +
261D ILE* 3.4 7.5 + - - +
262D TYR* 3.0 34.0 + - + -
198E PRO 5.3 4.3 - - - +
199E ASN* 5.3 3.1 - - - +
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Residues in contact with PHE 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D MET* 6.0 7.0 - - + -
255D GLY 3.4 10.7 + - - +
256D ALA* 2.8 10.4 + - - +
258D ILE* 1.3 79.9 - - + +
260D MET* 1.3 66.8 + - - +
262D TYR* 3.2 14.3 + + + +
263D LEU* 3.0 44.6 + - + +
197E ILE* 5.9 0.9 - - + -
198E PRO* 4.2 31.9 - - + +
202E LEU* 3.4 41.3 - - + -
203E PRO* 5.3 0.9 - - + -
206E PHE* 3.9 16.8 - + - -
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Residues in contact with MET 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ALA 2.9 10.8 + - - +
257D ILE* 3.4 14.1 - - + +
259D PHE* 1.3 77.8 - - - +
261D ILE* 1.3 57.4 + - + +
263D LEU* 2.9 31.2 + - + +
264D PHE* 2.9 38.5 + - + -
302D PHE* 4.7 3.8 - - + -
305D ALA* 3.9 33.0 - - + +
306D ASN* 3.9 25.6 - - - +
309D LEU* 3.5 29.4 - - + -
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Residues in contact with ILE 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D MET* 4.1 24.9 - - + +
205D LEU* 5.9 4.3 - - + -
208D LEU* 3.8 20.9 - - + -
234D HIS* 3.1 31.4 - - + +
257D ILE* 2.9 32.8 + - + +
258D ILE* 3.6 2.9 - - - +
260D MET* 1.3 72.8 - - + +
262D TYR* 1.3 67.2 + - - +
264D PHE* 3.1 9.4 + - - +
265D TYR* 3.0 48.1 + - + -
302D PHE* 4.5 20.6 - - + -
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Residues in contact with TYR 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D LEU* 4.2 17.7 - - + -
234D HIS* 4.1 14.8 - + - -
235D ILE* 3.1 49.2 - - + +
238D ASN* 3.8 26.9 - - - +
258D ILE* 3.0 26.4 + - + -
259D PHE* 3.2 16.1 + + + +
261D ILE* 1.3 75.2 - - - +
263D LEU* 1.3 63.4 + - - +
265D TYR* 3.1 7.6 + - - +
266D PHE* 3.0 21.9 + - - +
198E PRO 4.6 2.7 - - - -
203E PRO* 3.8 41.8 - - + +
206E PHE* 4.3 23.2 - + + -
207E ILE* 5.3 1.8 - - + -
237E PHE* 4.0 1.7 - - - -
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Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D PHE* 3.0 39.4 + - + +
260D MET* 2.9 22.0 + - + +
262D TYR* 1.3 76.6 - - - +
264D PHE* 1.3 62.0 + - + +
266D PHE* 3.2 6.9 + - - +
267D VAL* 3.0 36.8 + - + +
206E PHE* 3.5 32.5 - - + -
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Residues in contact with PHE 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D LEU* 4.9 10.5 - - + -
212D TRP* 4.2 18.7 - + + -
260D MET* 2.9 35.8 + - + +
261D ILE* 3.1 11.4 + - - +
263D LEU* 1.3 78.8 - - + +
265D TYR* 1.3 61.3 + - - +
267D VAL* 3.2 15.0 - - + +
268D ALA* 3.0 28.4 + - - +
298D PHE* 4.2 8.9 - + + -
301D VAL* 3.7 30.3 - - + -
302D PHE* 3.3 48.7 - + + -
305D ALA* 4.6 2.5 - - + -
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Residues in contact with TYR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D ILE* 3.3 27.7 + - - +
208D LEU* 3.6 18.7 + - + +
211D SER* 3.7 13.0 - - - -
227D VAL* 3.9 13.9 - - + +
230D THR* 3.3 32.2 + - - -
231D LEU* 3.3 49.4 - - + -
234D HIS* 4.1 9.7 - + + +
261D ILE* 3.0 47.2 + - + -
262D TYR 3.5 7.4 - - - +
264D PHE* 1.3 73.5 - - - +
266D PHE* 1.3 67.1 + - - +
268D ALA* 3.2 7.4 + - + +
269D VAL* 3.0 27.7 + - - +
210E ILE* 5.1 1.6 - - - -
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Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D TYR 3.0 12.7 + - - +
263D LEU* 3.2 11.2 + - + +
265D TYR* 1.3 77.5 - - - +
267D VAL* 1.3 66.4 + - + +
269D VAL* 3.3 5.3 + - + +
270D ILE* 3.0 50.0 + - + +
206E PHE* 4.3 29.6 - + + -
209E PHE* 3.9 33.4 - + + -
210E ILE* 3.6 37.0 - - + +
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D LEU* 3.0 19.3 + - + +
264D PHE* 3.2 28.0 - - + +
266D PHE* 1.3 84.3 - - + +
268D ALA* 1.3 56.9 + - - +
270D ILE* 3.4 13.2 - - + +
271D GLU* 2.9 26.2 + - - +
298D PHE* 3.9 21.4 - - + -
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Residues in contact with ALA 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D SER* 5.7 3.1 - - - +
212D TRP* 5.4 8.3 - - + -
215D PHE* 5.1 7.3 - - + -
227D VAL* 4.4 15.5 - - + -
264D PHE 3.0 20.3 + - - +
265D TYR* 3.4 8.5 - - + +
266D PHE 3.2 0.2 - - - -
267D VAL* 1.3 74.4 - - - +
269D VAL* 1.3 66.6 + - - +
271D GLU* 3.0 14.5 + - - +
272D VAL* 3.1 18.3 + - - +
298D PHE* 4.0 20.0 - - + -
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Residues in contact with VAL 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D VAL* 6.5 0.7 - - - -
227D VAL* 3.4 29.6 - - + +
228D VAL* 5.6 4.7 - - + +
231D LEU* 6.0 0.7 - - + -
265D TYR 3.0 10.8 + - - +
266D PHE* 3.6 9.0 - - + +
268D ALA* 1.3 74.7 - - - +
270D ILE* 1.3 67.4 + - + +
272D VAL* 3.2 10.4 - - + +
273D THR* 3.0 36.6 + - - +
210E ILE* 4.1 41.1 - - + -
213E THR* 4.4 15.3 - - + +
226E LEU* 5.8 2.0 - - + -
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Residues in contact with ILE 270 (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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266D PHE* 3.0 42.8 + - + +
267D VAL* 3.4 15.3 - - + +
269D VAL* 1.3 80.0 - - + +
271D GLU* 1.3 65.6 + - - +
273D THR* 3.4 8.2 - - + +
274D VAL* 3.0 30.2 + - + +
213E THR* 4.7 13.5 - - - +
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Residues in contact with GLU 271 (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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215D PHE* 3.5 20.9 - - + -
267D VAL 2.9 14.2 + - - +
268D ALA* 3.0 11.8 + - - +
270D ILE* 1.3 77.9 - - - +
272D VAL* 1.3 90.4 + - - +
274D VAL* 3.1 10.2 + - - +
275D GLN* 3.0 22.8 + - - +
290D ILE* 4.4 14.9 - - + +
291D THR* 3.2 31.1 + - - +
294D SER* 3.1 29.5 + - - +
298D PHE* 4.8 4.3 - - + -
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D ALA* 4.6 13.0 - - + +
215D PHE* 5.4 3.1 - - + -
220D TYR* 3.5 17.2 - - + -
223D ASN* 3.7 49.6 - - + +
224D VAL* 5.2 4.7 - - + -
227D VAL* 4.7 4.9 - - + -
268D ALA 3.1 10.5 + - - +
269D VAL* 3.2 22.0 - - + +
271D GLU* 1.3 90.9 + - - +
273D THR* 1.3 63.5 + - - +
275D GLN* 3.1 11.5 + - - +
276D HIS 3.0 19.2 + - - -
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Residues in contact with THR 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D TYR* 3.4 23.9 + - - +
269D VAL* 3.0 24.5 + - - +
270D ILE* 3.4 11.2 - - + +
272D VAL* 1.3 80.3 - - - +
274D VAL* 1.3 64.9 + - + +
276D HIS* 3.4 9.2 + - - +
277D TYR* 3.5 12.8 + - - +
213E THR* 3.6 32.1 + - - +
216E TRP* 4.2 27.7 - - + +
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ILE* 3.0 19.8 + - + +
271D GLU* 3.7 9.9 - - - +
273D THR* 1.3 79.3 - - + +
275D GLN* 1.3 66.7 + - - +
277D TYR* 3.6 3.6 + - - +
278D LEU* 3.0 33.9 + - + +
290D ILE* 3.9 32.5 - - + -
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Residues in contact with GLN 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D SER 3.8 7.8 + - - +
218D THR* 3.8 41.0 + - - +
219D SER 5.6 0.2 - - - -
220D TYR* 5.8 3.2 - - - +
223D ASN* 4.2 7.4 - - - +
271D GLU* 3.0 14.9 + - - +
272D VAL* 3.1 13.9 + - - +
274D VAL* 1.3 81.6 - - - +
276D HIS* 1.3 58.9 + - - +
278D LEU* 3.4 5.8 + - - +
279D LYS* 2.9 32.8 + - + +
287D ALA* 3.8 23.7 - - + +
288D ALA* 5.4 0.7 - - - -
290D ILE* 6.0 2.5 - - + -
291D THR* 2.4 36.6 + - - +
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Residues in contact with HIS 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D TYR* 3.4 52.4 - + + +
272D VAL 3.0 5.9 + - - -
273D THR 3.9 2.9 - - - +
274D VAL 3.3 0.2 - - - -
275D GLN* 1.3 79.5 - - - +
277D TYR* 1.3 67.3 + - - +
279D LYS* 2.9 31.7 + - - +
280D VAL* 2.9 38.1 + - + +
216E TRP 4.5 2.2 - - - -
217E SER* 4.0 31.2 + - - -
218E THR* 4.3 10.7 + - - -
219E SER* 4.9 6.9 + - - -
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Residues in contact with TYR 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D THR 3.5 11.8 + - - +
274D VAL* 4.3 2.9 - - - +
276D HIS* 1.3 79.9 - - - +
278D LEU* 1.3 60.8 + - + +
280D VAL* 3.2 17.2 - - + +
281D GLU* 2.9 66.5 + - + +
216E TRP* 3.8 39.5 - + + +
218E THR* 6.1 0.9 - - - -
295E ARG* 4.4 25.6 + - - -
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Residues in contact with LEU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D VAL* 3.0 25.3 + - + +
275D GLN* 3.5 5.6 - - - +
277D TYR* 1.3 79.8 - - + +
279D LYS* 1.3 55.4 + - - +
281D GLU* 3.2 18.3 + - + +
283D GLN* 3.1 41.9 + - + +
286D ARG* 3.5 21.5 - - + +
287D ALA* 3.5 34.8 - - + +
290D ILE* 3.9 18.6 - - + -
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Residues in contact with LYS 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D THR* 3.8 40.8 - - + -
220D TYR 5.8 1.3 - - - +
275D GLN* 2.9 22.7 + - + +
276D HIS* 2.9 28.2 + - - +
278D LEU* 1.3 77.2 - - - +
280D VAL* 1.3 62.0 + - - +
281D GLU 3.2 2.5 - - - -
282D SER* 3.3 16.2 + - - +
284D PRO* 4.1 30.0 - - + +
287D ALA* 5.0 4.7 - - + -
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D HIS* 2.9 44.1 + - + +
277D TYR* 3.2 34.5 - - + +
279D LYS* 1.3 81.6 - - - +
281D GLU* 1.3 61.0 + - - +
282D SER* 3.0 11.4 + - - -
218E THR* 5.3 9.2 - - - +
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D TYR* 2.9 62.9 + - + +
278D LEU* 3.2 18.1 + - + +
280D VAL* 1.3 79.8 - - - +
282D SER* 1.3 69.2 + - - +
283D GLN* 3.2 11.0 + - + +
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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