Contacts of the helix formed by residues 252 - 281 (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 THR 252 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 3.3 34.8 - - + +
116B ARG* 4.1 4.0 - - - +
245B LEU* 5.0 10.8 - - + -
248B ALA* 4.5 16.6 - - + -
250B TYR* 3.8 3.6 + - + -
251B MET* 1.3 80.0 - - - +
253B TYR* 1.3 60.9 + - - +
254B THR* 4.2 7.2 - - - +
255B GLY* 3.1 25.9 + - - -
256B ALA* 2.9 28.1 + - - +
313B PHE* 3.7 1.3 - - - -
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Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE 4.7 0.2 + - - -
116B ARG 3.2 22.1 + - - +
117B ARG* 4.7 3.1 - - - -
118B TYR 3.9 16.4 - - - +
120B PHE* 4.2 19.5 - + - -
201B ILE* 6.0 2.9 - - + -
252B THR* 1.3 69.7 - - - +
254B THR* 1.3 71.6 + - + +
256B ALA* 3.0 4.7 + - - +
257B ILE* 3.0 56.1 + - + +
306B ASN* 4.4 13.4 + - - -
309B LEU* 4.4 1.6 - - + -
310B ALA* 3.8 35.7 - - - +
313B PHE* 3.6 33.1 - + + -
314B PHE* 4.2 18.6 - + - -
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 3.3 42.6 + - + +
119B PRO* 4.1 13.5 - - + -
200B ILE* 6.4 1.6 - - + -
201B ILE* 4.7 16.8 - - + -
241B VAL* 5.2 8.1 - - + +
245B LEU* 5.3 0.5 - - - +
252B THR* 4.2 7.1 - - - -
253B TYR* 1.3 85.1 - - + +
255B GLY* 1.3 57.2 + - - +
257B ILE* 3.8 8.3 - - + +
258B ILE* 2.9 44.2 + - + +
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 4.4 9.1 - - - +
252B THR* 3.1 24.4 + - - -
254B THR* 1.3 74.7 + - - +
256B ALA* 1.3 65.8 + - - +
258B ILE* 3.7 11.1 - - - +
259B PHE* 3.4 19.6 + - - +
198C PRO* 4.6 6.1 - - - +
199C ASN* 5.8 2.9 - - - -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 4.3 15.9 - - + -
252B THR 2.9 15.3 + - - +
253B TYR 3.0 10.3 + - - +
255B GLY* 1.3 75.2 - - - +
257B ILE* 1.3 68.3 + - - +
259B PHE* 2.9 17.2 + - - +
260B MET* 3.0 11.3 + - - +
309B LEU* 3.6 23.1 - - + -
313B PHE* 4.2 11.4 - - + -
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Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 5.0 13.9 - - + -
204B MET* 4.2 20.0 - - + -
205B LEU* 6.0 2.7 - - + -
253B TYR* 3.0 44.5 + - + +
254B THR* 3.8 12.8 - - + +
256B ALA* 1.3 74.0 - - - +
258B ILE* 1.3 62.0 + - + +
260B MET* 3.5 12.4 - - + +
261B ILE* 2.9 42.9 + - + +
302B PHE* 5.9 2.2 - - + -
306B ASN* 4.4 21.8 - - - +
309B LEU* 3.6 22.2 - - + -
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ILE* 5.7 1.8 - - + -
204B MET* 3.4 37.5 - - + -
234B HIS* 3.0 27.7 + - + +
238B ASN* 3.6 33.2 - - - +
241B VAL* 5.3 17.0 - - + -
254B THR* 2.9 31.2 + - + +
255B GLY* 3.7 15.5 - - - +
257B ILE* 1.3 79.5 - - + +
259B PHE* 1.3 64.1 + - + +
261B ILE* 3.4 0.8 + - - -
262B TYR* 3.0 25.4 + - + -
198C PRO* 5.0 2.9 - - + +
199C ASN* 5.0 5.4 - - - +
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 5.5 8.7 - - + -
255B GLY 3.4 16.6 + - - +
256B ALA* 2.9 4.6 + - - +
258B ILE* 1.3 79.3 - - + +
260B MET* 1.3 62.0 + - - +
262B TYR* 3.1 15.5 - + + +
263B LEU* 2.9 45.6 + - + +
197C ILE* 5.4 3.6 - - + -
198C PRO* 4.0 33.0 - - + +
202C LEU* 3.7 35.4 - - + -
203C PRO* 4.9 1.3 - - + -
206C PHE* 3.7 21.5 - + - -
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Residues in contact with MET 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ALA 3.0 10.4 + - - +
257B ILE* 3.5 14.4 - - + +
259B PHE* 1.3 77.6 - - - +
261B ILE* 1.3 61.7 + - - +
263B LEU* 2.9 25.3 + - + +
264B PHE* 2.9 26.5 + - + -
302B PHE* 3.9 26.2 - - + -
305B ALA* 3.5 38.6 - - + +
306B ASN* 3.8 15.9 - - - +
309B LEU* 3.6 28.5 - - + -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B MET* 3.6 35.9 - - + +
205B LEU* 5.1 2.9 - - + -
208B LEU* 3.6 17.9 - - + -
234B HIS* 3.3 27.4 - - + +
257B ILE* 2.9 32.3 + - + +
259B PHE 3.3 0.2 - - - -
260B MET* 1.3 74.3 - - - +
262B TYR* 1.3 63.2 + - - +
264B PHE* 3.1 10.3 + - - +
265B TYR* 3.0 48.4 + - + -
302B PHE* 3.8 29.4 - - + -
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Residues in contact with TYR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 3.9 17.9 - - + -
234B HIS* 3.4 20.4 + + - -
235B ILE* 3.0 46.8 - - + +
238B ASN* 3.7 25.4 - - - +
258B ILE* 3.0 27.1 + - + -
259B PHE* 3.1 18.2 - + + +
261B ILE* 1.3 76.1 - - - +
263B LEU* 1.3 61.1 + - - +
265B TYR* 3.1 9.0 + - - +
266B PHE* 3.0 21.1 + - - +
198C PRO 4.8 1.8 - - - -
203C PRO* 3.7 41.2 - - + +
206C PHE* 4.2 22.1 - + + -
207C ILE* 5.1 1.8 - - + -
237C PHE* 4.0 1.4 - - - -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 2.9 33.6 + - + +
260B MET* 2.9 17.7 + - + +
262B TYR* 1.3 75.0 - - - +
264B PHE* 1.3 65.0 + - + +
266B PHE* 3.0 10.7 + - + +
267B VAL* 2.9 36.7 + - + +
206C PHE* 3.4 33.7 - - + -
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Residues in contact with PHE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 4.5 6.3 - - + -
211B SER* 5.9 0.7 - - - -
212B TRP* 3.7 29.7 - + + -
260B MET* 2.9 31.1 + - + +
261B ILE* 3.1 10.5 + - - +
263B LEU* 1.3 79.7 - - + +
265B TYR* 1.3 59.8 + - - +
267B VAL* 3.7 13.8 - - + +
268B ALA* 3.0 30.7 + - - +
298B PHE* 4.1 10.7 - + + -
301B VAL* 3.4 33.9 - - + -
302B PHE* 3.4 48.0 - + + -
305B ALA* 4.6 1.1 - - + -
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.1 42.6 + - - +
208B LEU* 3.6 10.2 - - + -
211B SER* 3.7 16.2 - - - -
227B VAL* 3.6 13.5 - - + +
230B THR* 3.1 27.3 + - - -
231B LEU* 3.1 45.1 - - + -
234B HIS* 3.9 9.6 - + + -
261B ILE* 3.0 50.5 + - + -
262B TYR* 3.1 7.8 + - - +
264B PHE* 1.3 76.7 - - - +
266B PHE* 1.3 57.4 + - - +
268B ALA* 3.5 5.3 - - - +
269B VAL* 3.0 35.9 + - + +
210C ILE* 4.5 1.6 - - + -
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR 3.0 12.4 + - - +
263B LEU* 3.2 14.4 - - + +
265B TYR* 1.3 76.0 - - - +
267B VAL* 1.3 70.4 + - + +
269B VAL* 3.1 7.7 + - + +
270B ILE* 3.0 44.8 + - + +
206C PHE* 4.0 34.1 - + + -
209C PHE* 3.9 31.6 - + + -
210C ILE* 3.5 36.5 - - + +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 2.9 29.2 + - + +
264B PHE* 3.7 19.7 - - + +
266B PHE* 1.3 81.3 - - + +
268B ALA* 1.3 67.0 + - - +
270B ILE* 3.7 10.9 - - + +
271B GLU* 3.0 22.7 + - - +
298B PHE* 3.9 19.7 - - + -
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER* 4.9 7.2 - - - +
212B TRP* 5.7 3.4 - - + -
215B PHE* 4.7 8.7 - - + -
227B VAL* 4.2 16.2 - - + -
264B PHE 3.0 21.9 + - - +
265B TYR* 3.5 6.1 - - - +
267B VAL* 1.3 78.3 - - - +
269B VAL* 1.3 63.0 + - - +
271B GLU* 3.1 6.6 + - - +
272B VAL* 3.0 27.4 + - - +
298B PHE* 3.5 22.7 - - + -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 3.6 20.0 - - + -
228B VAL* 5.4 5.6 - - + -
231B LEU* 5.9 2.0 - - + -
265B TYR* 3.0 18.1 + - + +
266B PHE* 3.2 9.4 - - + +
268B ALA* 1.3 76.1 - - - +
270B ILE* 1.3 67.8 + - + +
272B VAL* 3.1 12.9 - - + +
273B THR* 3.0 22.6 + - - +
210C ILE* 3.6 46.9 - - + -
213C THR* 4.3 20.0 - - + +
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 3.0 36.8 + - + +
267B VAL* 3.7 12.6 - - + +
268B ALA 3.3 0.2 - - - -
269B VAL* 1.3 79.4 - - + +
271B GLU* 1.3 66.1 + - - +
273B THR* 3.3 7.0 + - + +
274B VAL* 2.9 33.1 + - + +
213C THR* 4.5 14.4 - - - +
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 3.8 11.2 - - - -
267B VAL 3.0 14.7 + - - +
268B ALA* 3.1 11.4 + - - +
270B ILE* 1.3 79.3 - - - +
272B VAL* 1.3 97.6 + - - +
274B VAL* 3.1 9.1 + - - +
275B GLN* 2.9 22.5 + - - +
290B ILE* 4.3 15.7 - - + +
291B THR* 3.2 33.5 + - - +
294B SER* 2.8 30.9 + - - +
298B PHE* 4.6 7.4 - - + -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 5.3 1.6 - - + -
215B PHE* 4.7 13.0 - - + -
220B TYR* 3.8 15.8 - - + -
223B ASN* 3.7 44.2 - - + +
224B VAL* 5.9 2.9 - - + -
227B VAL* 4.7 13.7 - - + -
268B ALA 3.0 12.2 + - - +
269B VAL* 3.1 24.0 - - + +
271B GLU* 1.3 90.4 + - - +
273B THR* 1.3 62.8 + - - +
275B GLN* 3.1 10.2 + - - +
276B HIS 3.0 18.4 + - - -
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 3.3 24.0 + - - +
269B VAL* 3.0 18.0 + - - +
270B ILE* 3.5 9.2 - - + +
272B VAL* 1.3 78.8 - - - +
274B VAL* 1.3 66.1 + - + +
276B HIS* 3.1 5.0 + - - +
277B TYR* 3.0 21.5 + - - +
213C THR* 2.9 35.1 + - - +
216C TRP* 3.9 31.0 - - + +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 2.9 26.0 + - + +
271B GLU* 3.5 7.2 - - - +
273B THR* 1.3 79.1 - - + +
275B GLN* 1.3 60.9 + - - +
277B TYR* 3.9 4.6 - - - +
278B LEU* 2.9 38.1 + - + +
290B ILE* 3.9 33.2 - - + -
216C TRP* 6.4 2.0 - - + -
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B SER 4.1 7.2 + - - +
218B THR* 3.9 24.5 + - - +
219B SER 5.4 1.0 - - - -
220B TYR* 5.5 3.6 - - - +
223B ASN* 3.8 23.5 + - - +
271B GLU* 2.9 15.3 + - - +
272B VAL* 3.1 14.9 + - - +
274B VAL* 1.3 81.5 - - - +
276B HIS* 1.3 57.7 + - - +
278B LEU* 3.6 8.0 - - - +
279B LYS* 2.9 34.5 + - + +
287B ALA* 4.1 17.6 - - + +
290B ILE* 6.0 3.4 - - + -
291B THR* 2.4 39.1 + - - +
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 3.5 45.5 - + + +
272B VAL 3.0 7.3 + - - -
273B THR 3.1 6.7 + - - +
275B GLN* 1.3 78.8 - - - +
277B TYR* 1.3 64.7 + - - +
279B LYS* 3.0 18.9 + - - +
280B VAL* 2.9 50.5 + - + +
216C TRP 4.0 4.0 - - - -
217C SER* 3.4 40.2 + - - -
218C THR* 4.2 5.5 + - - -
219C SER* 4.7 7.3 + - - -
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B THR 3.0 12.9 + - - +
274B VAL* 4.1 4.7 - - - +
276B HIS* 1.3 78.5 - - - +
278B LEU* 1.3 69.0 + - + +
280B VAL* 3.4 12.3 - - + +
281B GLU* 3.0 61.4 + - + +
216C TRP* 3.6 44.8 + + + +
295C ARG* 3.9 31.5 + - - -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 2.9 22.7 + - + +
275B GLN* 3.6 6.1 - - - +
277B TYR* 1.3 84.2 - - + +
279B LYS* 1.3 57.3 + - - +
281B GLU* 3.3 20.8 + - + +
283B GLN* 3.4 37.3 + - + +
286B ARG* 3.4 41.1 - - + +
287B ALA* 3.6 16.4 - - + +
290B ILE* 3.6 21.8 - - + -
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Residues in contact with LYS 279 (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 42.1 + - + -
220B TYR* 5.9 1.3 - - - +
275B GLN* 2.9 25.2 + - + +
276B HIS* 3.0 19.8 + - - +
278B LEU* 1.3 74.2 - - - +
280B VAL* 1.3 63.9 + - - +
281B GLU 3.2 4.7 - - - -
282B SER* 3.4 15.2 + - - +
283B GLN 4.5 3.1 + - - +
284B PRO* 5.1 13.4 - - + +
287B ALA* 4.3 18.8 - - + -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B HIS* 2.9 46.7 + - + +
277B TYR* 3.4 28.7 - - + +
279B LYS* 1.3 81.5 - - - +
281B GLU* 1.3 63.7 + - - +
282B SER* 3.0 10.5 + - - -
216C TRP 5.4 0.7 - - - +
218C THR* 5.5 7.6 - - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TYR* 3.0 57.3 + - + +
278B LEU* 3.4 14.4 - - + +
279B LYS 3.2 0.6 - - - -
280B VAL* 1.3 82.3 - - - +
282B SER* 1.3 70.4 + - - +
283B GLN* 3.4 10.9 + - + +
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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