Contacts of the helix formed by residues 247 - 274 (chain B) in PDB entry 5FLZ
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 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 1.4 90.7 - - - +
248B PRO* 1.4 68.8 - - - +
249B MET* 3.5 15.9 - - - -
250B LYS* 3.0 15.2 + - - +
251B LYS* 3.0 22.5 + - - +
309B GLY* 4.4 2.3 - - - -
312B PHE* 3.8 13.3 - - - -
359B TYR* 3.3 10.2 - - - +
361B GLU* 3.3 21.9 + - - -
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Residues in contact with PRO 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B SER* 1.4 81.8 - - - +
249B MET* 1.3 66.0 + - + +
251B LYS* 3.4 14.4 - - + +
252B ALA* 3.1 18.4 + - - +
341B LEU* 3.5 33.1 - - + +
345B TYR* 3.7 21.1 - - + +
358B THR* 4.1 13.0 - - + +
359B TYR* 4.1 6.1 - - + -
361B GLU* 3.6 10.8 - - - +
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B SER* 3.1 7.6 - - - +
248B PRO* 1.3 76.9 - - + +
250B LYS* 1.3 61.5 + - - +
252B ALA* 3.3 9.0 + - - +
253B LEU* 3.4 6.9 + - - +
309B GLY 5.2 3.6 - - - +
312B PHE* 4.2 19.1 - - + -
313B LEU* 6.1 0.7 - - - +
338B MET* 3.4 38.2 - - + +
341B LEU* 3.5 25.8 - - + -
342B TYR* 3.5 40.6 - - + +
345B TYR* 4.1 17.5 - - + +
361B GLU* 3.4 37.2 - - + +
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 2.8 59.0 + - + +
244B LEU* 4.5 3.4 - - - +
245B ASN* 3.7 19.4 + - - +
246B ILE* 3.6 47.3 + - + +
247B SER* 3.0 14.9 + - - +
249B MET* 1.3 77.2 - - - +
251B LYS* 1.4 62.3 + - - +
253B LEU* 3.0 30.3 + - + +
254B ILE* 3.1 24.1 + - + +
304B LEU* 5.0 10.8 - - + -
312B PHE* 4.5 6.7 - - + -
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 5.9 5.1 - - - +
247B SER 3.0 7.8 + - - +
248B PRO* 3.4 20.0 - - + +
250B LYS* 1.4 77.3 - - - +
252B ALA* 1.3 62.7 + - - +
254B ILE* 3.3 19.2 + - + +
255B ILE* 3.0 48.4 + - + +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PRO 3.1 9.4 + - - +
249B MET 3.4 11.4 - - - +
251B LYS* 1.3 80.1 - - - +
253B LEU* 1.4 58.3 + - - +
255B ILE* 3.4 11.5 + - - +
256B GLU* 3.1 31.8 + - - +
337B SER* 3.4 28.2 + - - +
338B MET* 3.6 11.9 - - - -
341B LEU* 4.5 4.9 - - + -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B MET* 3.5 13.2 - - + +
250B LYS* 3.0 16.8 + - + +
252B ALA* 1.4 76.4 - - - +
254B ILE* 1.4 56.8 + - - +
256B GLU* 3.1 4.1 + - - -
257B ILE* 3.0 28.8 + - - +
297B TYR* 3.5 27.2 + - + +
300B PHE* 3.8 25.4 - - + -
304B LEU* 3.4 33.7 - - + -
312B PHE* 5.7 4.9 - - + -
316B LEU* 6.1 0.2 - - + -
334B LEU* 4.3 18.2 - - + -
338B MET* 3.7 22.9 - - + -
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Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 5.5 6.5 - - + +
241B PHE* 4.0 41.1 - - + +
242B ARG* 4.2 26.9 - - + +
244B LEU* 6.4 1.3 - - + -
250B LYS* 3.1 35.6 + - + +
251B LYS* 3.3 18.8 + - + +
253B LEU* 1.4 69.4 - - - +
255B ILE* 1.4 58.1 + - + +
257B ILE* 3.1 12.3 - - + +
258B SER* 2.8 49.0 + - - +
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LYS* 3.0 41.5 + - + +
252B ALA* 3.6 11.9 - - - +
253B LEU 3.3 0.2 - - - -
254B ILE* 1.4 76.6 - - + +
256B GLU* 1.4 56.3 + - + +
258B SER* 3.4 7.2 + - - -
259B GLU* 3.1 27.0 + - + +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA 3.1 16.7 + - - +
253B LEU 3.1 7.9 + - - +
255B ILE* 1.4 71.8 - - + +
257B ILE* 1.3 65.3 + - - +
259B GLU* 3.3 12.1 + - - +
260B GLU* 3.2 26.3 + - - +
297B TYR* 4.4 5.8 - - + +
330B ILE* 5.3 1.9 - - - +
333B ASN* 3.1 43.9 + - - +
334B LEU* 3.6 30.6 + - + +
337B SER* 4.2 10.8 + - - +
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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
----------------------------------------------------------
234B LEU* 3.8 28.7 - - + +
237B LYS* 5.7 5.6 - - + -
238B VAL* 4.3 24.2 - - + -
241B PHE* 6.2 3.1 - - + -
253B LEU 3.0 16.5 + - - +
254B ILE* 3.1 28.3 - - + +
256B GLU* 1.3 74.5 - - - +
258B SER* 1.4 57.1 + - - +
260B GLU* 2.8 29.0 + - + -
261B LEU* 3.1 25.2 + - + +
294B LEU* 5.6 3.6 - - + -
297B TYR* 4.2 31.8 + - + -
301B THR* 5.8 1.6 - - - +
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Residues in contact with SER 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 5.5 4.5 - - - +
242B ARG* 3.7 22.4 + - - -
254B ILE* 2.8 28.2 + - - +
255B ILE* 3.5 8.3 - - - -
256B GLU 3.3 0.2 - - - -
257B ILE* 1.4 76.5 - - - +
259B GLU* 1.4 58.2 + - - +
261B LEU* 3.5 20.2 + - - +
262B GLN* 3.1 24.7 + - - -
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ILE* 3.1 13.5 + - + +
256B GLU* 3.4 15.9 - - - +
258B SER* 1.4 73.5 - - - +
260B GLU* 1.4 78.6 + - - +
262B GLN* 3.0 32.9 + - + +
263B ASN* 3.9 4.2 + - - +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLU* 3.2 17.4 + - - +
257B ILE* 2.8 13.5 + - + +
259B GLU* 1.4 88.5 - - - +
261B LEU* 1.3 69.0 - - + +
263B ASN* 2.9 43.4 + - - +
264B TYR* 3.8 0.5 + - - +
293B ARG* 4.2 11.4 - - - +
294B LEU* 4.5 20.5 - - + +
297B TYR* 5.5 9.1 - - + -
330B ILE* 3.8 27.9 - - - +
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B TYR* 5.1 8.6 + - + +
234B LEU* 4.2 25.4 - - + -
238B VAL* 4.9 18.6 - - + -
257B ILE* 3.1 30.3 + - + +
258B SER* 3.8 16.6 - - - +
259B GLU 3.3 0.6 - - - -
260B GLU* 1.3 77.9 - - - +
262B GLN* 1.4 66.1 + - - +
264B TYR* 3.0 21.2 + - + +
265B THR* 3.0 15.7 + - - +
294B LEU* 5.1 7.2 - - + -
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Residues in contact with GLN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B SER* 3.1 22.2 + - - +
259B GLU* 3.0 31.9 + - + +
260B GLU 3.0 0.6 - - - -
261B LEU* 1.4 81.6 - - - +
263B ASN* 1.3 61.3 + - - +
265B THR* 3.3 11.2 + - - -
266B ALA* 3.2 19.9 + - - +
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Residues in contact with ASN 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU* 3.9 2.7 + - - +
260B GLU* 2.9 49.7 + - - +
262B GLN* 1.3 74.4 - - - +
264B TYR* 1.3 79.0 + - - +
266B ALA* 3.1 10.7 - - - +
267B PHE* 3.0 34.5 + - + -
290B ASN* 3.2 17.3 - - - +
293B ARG* 3.8 28.5 + - - +
294B LEU* 5.7 3.1 - - - +
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Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 3.7 36.9 + - + +
193B LEU* 4.7 1.8 - - + -
227B ALA* 5.8 1.6 - - - +
231B TYR* 3.3 45.7 - + + +
260B GLU 4.7 0.2 - - - +
261B LEU* 3.0 16.6 + - - +
263B ASN* 1.3 82.6 + - - +
265B THR* 1.4 59.3 + - - +
267B PHE* 2.9 7.0 + - - +
268B VAL* 2.9 41.7 + - + -
287B ILE* 3.6 29.5 - - + +
290B ASN* 3.3 26.5 - - + -
294B LEU* 4.6 14.6 - - + -
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Residues in contact with THR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 5.9 4.3 - - + +
231B TYR* 5.3 2.3 + - - -
261B LEU 3.0 16.1 + - - -
262B GLN* 3.4 13.2 + - - -
263B ASN 3.2 0.4 - - - -
264B TYR* 1.4 75.4 - - - +
266B ALA* 1.3 62.9 + - - +
268B VAL* 3.0 22.0 + - + +
269B ASN* 2.9 20.7 + - - +
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLN 3.2 9.4 + - - +
263B ASN* 3.1 14.8 + - - +
265B THR* 1.3 77.3 - - - +
267B PHE* 1.3 64.9 + - + +
269B ASN* 3.1 13.2 - - - +
270B ASN* 3.0 35.4 + - - +
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN* 3.0 30.3 + - + -
264B TYR 2.9 7.4 + - - +
266B ALA* 1.3 76.8 - - + +
268B VAL* 1.3 60.8 + - - +
270B ASN* 3.0 19.5 + - + +
271B LEU* 2.9 31.2 + - + +
286B GLU* 5.0 6.3 - - + -
287B ILE* 4.3 19.5 - - + -
289B GLU* 4.1 13.7 - - - -
290B ASN* 3.0 42.6 - - - -
293B ARG* 3.8 16.2 - - - -
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 5.4 9.6 - - - +
192B LEU* 6.3 0.2 - - + -
193B LEU* 4.0 33.2 - - + -
264B TYR* 2.9 41.1 + - + +
265B THR* 3.0 12.5 + - + +
267B PHE* 1.3 73.7 - - - +
269B ASN* 1.4 64.9 + - - +
271B LEU* 3.2 13.8 + - + +
272B VAL* 3.1 30.0 + - + +
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Residues in contact with ASN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 2.9 30.6 + - - +
266B ALA* 3.1 14.3 + - - +
268B VAL* 1.4 75.5 - - - +
270B ASN* 1.4 73.4 + - - +
272B VAL* 3.2 9.2 + - - +
273B SER* 2.7 41.2 + - - +
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Residues in contact with ASN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 3.0 27.2 + - - +
267B PHE* 3.0 24.8 + - + +
269B ASN* 1.4 90.0 + - - +
271B LEU* 1.3 63.2 + - + +
273B SER* 3.1 9.3 + - - -
274B SER* 3.0 22.3 + - - -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 5.3 4.7 - - + -
264B TYR* 6.5 0.2 - - + -
267B PHE* 2.9 23.7 + - + +
268B VAL* 3.7 16.4 - - + +
270B ASN* 1.3 72.7 - - + +
272B VAL* 1.4 64.5 + - + +
274B SER* 3.2 25.7 + - - +
275B GLY 4.4 0.2 + - - -
276B THR 5.3 0.3 - - - +
278B VAL* 4.2 23.8 - - + +
283B LEU* 3.5 33.9 - - + -
286B GLU* 4.2 28.5 - - + -
287B ILE* 4.8 14.8 - - + -
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 6.0 5.6 - - - -
268B VAL* 3.1 24.4 + - + +
269B ASN* 3.6 8.5 - - - +
271B LEU* 1.4 78.3 - - + +
273B SER* 1.4 60.1 + - - +
274B SER 3.2 1.0 + - - -
275B GLY* 3.3 12.6 + - - -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ASN* 2.7 25.1 + - - +
270B ASN* 3.1 12.8 + - - -
272B VAL* 1.4 68.3 - - - +
274B SER* 1.4 66.1 - - - +
275B GLY* 3.2 2.6 + - - -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASN 3.0 14.3 + - - -
271B LEU* 3.2 21.7 + - - +
272B VAL 3.2 0.2 - - - -
273B SER* 1.4 74.7 - - - +
275B GLY* 1.4 56.9 + - - +
276B THR* 3.1 28.6 + - - +
278B VAL* 4.3 10.0 - - - +
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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