Contacts of the helix formed by residues 276 - 302 (chain B) in PDB entry 1KNU
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 GLU 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS* 1.3 78.9 - - - +
277B VAL* 1.3 73.3 + - + +
278B ALA* 3.3 29.3 + - - +
279B ILE* 3.2 40.9 + - + +
280B ARG* 3.4 8.3 + - - +
357B ARG* 2.8 40.0 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 3.9 34.1 - - + -
255B LEU* 3.5 29.8 - - + -
275B LYS 2.9 8.3 + - - -
276B GLU* 1.3 77.0 - - + +
278B ALA* 1.3 73.5 + - + +
280B ARG* 2.8 31.7 + - - +
281B ILE* 3.0 24.2 + - + +
352B PHE* 4.8 0.9 - - + -
356B LEU* 4.7 6.5 - - + -
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 3.3 15.8 + - - +
277B VAL* 1.3 82.6 - - + +
279B ILE* 1.3 59.8 + - - +
281B ILE* 3.7 5.8 + - - +
282B PHE* 3.3 19.1 + - - +
356B LEU* 3.5 30.9 - - + +
357B ARG* 4.1 10.1 - - + -
360B PHE* 3.5 34.1 - - + +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 3.2 36.6 - - + +
277B VAL 2.8 4.6 + - - -
278B ALA* 1.3 70.1 - - - +
280B ARG* 1.3 55.3 + - - +
281B ILE 3.1 1.6 - - - -
282B PHE* 2.8 13.5 + - + +
283B GLN* 2.8 37.8 + - + +
360B PHE* 4.4 5.4 - - + -
460B GLU* 2.8 55.4 - - + +
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.0 19.4 - - - +
256B MET* 6.0 2.2 - - - +
259B GLU* 3.2 35.9 + - - +
266B HIS* 3.7 27.3 - - + +
267B ILE* 4.5 14.1 - - + -
275B LYS* 2.8 47.2 + - - +
276B GLU 3.4 5.4 + - - +
277B VAL* 2.8 24.4 + - - +
279B ILE* 1.3 76.0 - - - +
281B ILE* 1.3 63.2 + - + +
283B GLN* 3.4 13.0 + - - +
284B GLY 3.1 15.9 + - - -
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.3 11.9 - - + -
266B HIS* 5.6 1.3 - - - -
277B VAL* 3.0 36.0 + - + +
278B ALA 3.8 6.7 - - - +
280B ARG* 1.3 78.9 - - + +
282B PHE* 1.3 62.0 + - - +
284B GLY* 3.1 3.9 + - - -
285B CYS* 3.1 20.4 + - + +
348B MET* 4.3 25.4 - - + -
352B PHE* 3.7 28.7 - - + -
353B LEU* 4.5 11.2 - - + -
356B LEU* 4.3 20.6 - - + -
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA 3.3 11.0 + - - +
279B ILE* 2.8 14.8 + - + +
281B ILE* 1.3 76.4 - - - +
283B GLN* 1.3 64.6 + - - +
284B GLY 2.9 4.5 - - - -
285B CYS* 2.9 17.3 + - - +
286B GLN* 2.9 40.7 + - + +
360B PHE* 4.2 24.5 - + + -
363B PHE* 3.5 45.3 - + - -
453B LEU* 3.7 18.4 - - + -
456B ILE* 3.7 25.4 - - + -
460B GLU* 6.5 1.6 - - + -
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B HIS* 3.2 30.0 + - + +
267B ILE* 5.3 0.8 - - - +
268B THR* 5.2 7.2 + - - +
279B ILE* 2.8 22.5 + - + +
280B ARG* 3.9 11.7 + - - +
282B PHE* 1.3 77.3 - - + +
284B GLY* 1.3 56.4 + - - +
286B GLN* 3.7 6.3 - - - +
287B PHE* 3.0 27.9 + - - +
469B LEU* 3.3 34.7 - - - +
473B TYR* 4.1 19.4 + - + -
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B HIS* 3.8 30.4 + - - -
280B ARG 3.1 7.5 + - - -
281B ILE 3.1 8.0 + - - -
282B PHE 2.9 1.2 - - - -
283B GLN* 1.3 77.9 - - - +
285B CYS* 1.3 64.7 + - - +
287B PHE* 3.2 3.8 + - - +
288B ARG* 3.1 23.9 + - - +
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Residues in contact with CYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 3.1 11.9 + - + +
282B PHE* 2.9 10.4 + - - +
284B GLY* 1.3 75.2 - - - +
286B GLN* 1.3 62.9 + - - +
288B ARG* 3.6 5.7 + - - +
289B SER* 2.9 33.3 + - - -
327B TYR* 6.3 3.4 - - - -
330B LEU* 6.2 2.2 - - - -
363B PHE* 3.7 32.3 - - + -
364B MET* 4.5 17.3 - - - -
367B LYS* 6.4 0.2 - - - -
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 2.9 54.6 + - + +
283B GLN* 3.7 11.0 - - - +
285B CYS* 1.3 79.6 + - - +
287B PHE* 1.3 64.9 + - - +
289B SER* 3.1 13.7 + - - -
290B VAL* 3.1 26.2 + - - +
363B PHE* 4.2 11.7 - - - -
449B HIS* 4.7 5.5 - - - -
453B LEU* 4.7 7.1 - - - +
473B TYR* 4.3 23.9 - - + +
475B ASP 3.8 19.9 - - - +
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS* 4.0 43.5 - - + -
266B HIS* 4.1 24.2 - + + -
283B GLN 3.0 18.5 + - - +
284B GLY 3.6 5.4 - - - +
286B GLN* 1.3 76.4 - - - +
288B ARG* 1.3 65.0 + - + +
290B VAL* 3.4 4.9 + - - +
291B GLU* 3.3 50.4 + - + +
473B TYR* 3.5 30.2 - + - +
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 5.7 1.0 - - - -
227B PRO* 5.8 3.0 - - - +
228B LEU* 6.3 1.4 - - - +
284B GLY 3.1 15.1 + - - +
285B CYS* 3.9 6.7 - - - +
287B PHE* 1.3 81.0 - - + +
289B SER* 1.3 60.8 + - - +
291B GLU* 3.1 34.1 + - - +
292B ALA* 2.8 37.2 + - + +
295B GLU* 2.8 35.5 + - - -
330B LEU* 6.5 0.9 - - + -
343B GLU* 6.2 1.8 - - - +
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B CYS* 2.9 22.9 + - - -
286B GLN* 3.1 22.2 + - - -
288B ARG* 1.3 77.0 - - - +
290B VAL* 1.3 58.4 + - - +
292B ALA* 3.0 9.5 + - - +
293B VAL* 2.8 34.9 + - - +
326B ILE* 4.2 23.9 - - - +
327B TYR* 5.6 2.6 + - - -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLN* 3.1 8.3 + - - +
287B PHE 3.6 7.9 - - - +
288B ARG 3.3 0.4 - - - -
289B SER* 1.3 75.7 - - - +
291B GLU* 1.3 63.9 + - + +
293B VAL* 3.4 17.3 + - + +
294B GLN* 3.5 18.3 + - + +
472B ILE* 4.5 16.8 - - + +
473B TYR* 3.5 35.0 - - + -
475B ASP 5.9 2.0 - - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS* 5.5 4.0 - - - +
287B PHE* 3.3 42.3 + - + +
288B ARG* 3.1 33.5 + - - +
290B VAL* 1.3 77.2 - - + +
292B ALA* 1.3 68.1 + - - +
294B GLN* 3.0 17.8 + - - +
295B GLU* 3.2 17.8 + - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 6.4 0.2 - - + -
288B ARG* 2.8 28.7 + - + +
289B SER* 3.3 13.7 - - - +
291B GLU* 1.3 77.7 - - - +
293B VAL* 1.3 55.7 - - - +
295B GLU* 3.2 14.8 + - - +
296B ILE* 2.9 38.0 + - + +
326B ILE* 4.1 20.2 - - + -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER* 2.8 22.6 + - - +
290B VAL* 3.6 12.3 - - + +
291B GLU 3.1 0.2 - - - -
292B ALA* 1.3 78.3 - - - +
294B GLN* 1.3 63.1 + - - +
296B ILE* 3.9 7.6 - - - +
297B THR* 2.8 38.9 + - - +
322B VAL* 4.0 28.2 - - + +
326B ILE* 4.2 15.9 - - + -
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Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 3.5 15.3 + - + +
291B GLU* 3.0 10.4 + - - +
293B VAL* 1.3 83.0 - - - +
295B GLU* 1.3 65.4 - - + +
297B THR* 3.3 16.9 + - - +
298B GLU* 3.0 22.9 + - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER* 3.5 23.0 - - - +
226B PHE* 3.5 20.6 - - + -
227B PRO* 2.9 33.4 - - - +
288B ARG* 2.8 39.4 + - - -
291B GLU* 3.2 11.6 + - + +
292B ALA* 3.2 6.4 + - - +
294B GLN* 1.3 75.0 - - + +
296B ILE* 1.3 65.6 + - - +
298B GLU* 3.1 8.0 + - - +
299B TYR* 3.0 22.3 + - - +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 3.9 19.7 - - + -
292B ALA* 2.9 25.9 + - + +
293B VAL* 3.9 4.0 - - - +
295B GLU* 1.3 75.1 - - - +
297B THR* 1.3 58.1 + - - +
299B TYR* 3.2 3.1 + - + +
300B ALA* 2.9 28.4 + - - +
318B LEU* 4.7 6.1 - - + -
322B VAL* 4.0 24.7 - - + +
325B ILE* 3.6 50.9 - - + -
326B ILE* 3.8 27.1 - - + +
329B MET* 5.0 1.3 - - - -
388B ILE* 5.4 0.7 - - + -
392B ILE* 4.5 7.4 - - + -
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Residues in contact with THR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B VAL* 2.8 32.7 + - - +
294B GLN* 3.5 20.0 + - - +
295B GLU 3.2 0.4 - - - -
296B ILE* 1.3 77.8 - - - +
298B GLU* 1.3 62.2 + - - +
300B ALA* 3.6 3.0 + - - +
301B LYS* 3.4 40.1 + - - +
318B LEU* 3.9 30.6 - - + +
322B VAL* 5.3 1.0 - - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LYS* 3.9 19.1 - - - +
225B SER* 3.2 20.4 + - - +
294B GLN 3.0 13.4 + - - +
295B GLU* 3.1 10.3 + - - +
297B THR* 1.3 78.7 - - - +
299B TYR* 1.3 64.4 + - - +
301B LYS* 3.4 21.9 - - - +
302B SER* 3.6 6.4 + - - -
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 3.3 39.5 - - + +
221B SER* 3.5 17.7 - - - -
222B TYR* 3.5 22.4 - + + -
225B SER* 3.6 8.6 + - - +
226B PHE* 3.9 18.4 - + + -
295B GLU 3.0 12.8 + - - +
296B ILE* 3.5 7.4 - - - +
298B GLU* 1.3 74.9 - - - +
300B ALA* 1.3 68.6 + - - +
302B SER* 2.9 25.4 + - - -
303B ILE* 3.6 16.7 + - + +
385B ALA* 2.7 42.9 + - - +
388B ILE* 4.1 24.7 - - + -
389B ALA* 4.5 1.6 - - + -
392B ILE* 4.4 7.4 - - + -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE 2.9 17.3 + - - +
297B THR 3.8 4.9 - - - +
298B GLU 3.4 0.2 - - - -
299B TYR* 1.3 76.3 - - - +
301B LYS* 1.3 56.2 + - - +
303B ILE* 2.7 42.6 + - - +
306B PHE* 3.4 28.1 - - + +
318B LEU* 3.9 23.3 - - + -
392B ILE* 4.1 12.1 - - + -
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B THR* 3.4 34.6 + - + +
298B GLU* 3.4 15.0 - - + +
300B ALA* 1.3 78.0 - - - +
302B SER* 1.3 60.2 + - - +
303B ILE 3.5 3.5 + - - +
306B PHE* 4.0 13.4 - - + -
307B VAL* 3.3 40.6 - - + +
314B GLN* 4.9 4.3 - - - +
318B LEU* 6.0 0.9 - - + -
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B HIS* 2.9 34.7 - - - -
218B LEU* 4.8 2.0 - - - +
221B SER* 2.6 35.9 + - - -
298B GLU 3.6 4.9 + - - -
299B TYR* 2.9 15.7 + - - -
301B LYS* 1.3 77.8 - - - +
303B ILE* 1.3 64.0 + - - +
304B PRO* 3.2 1.1 - - - +
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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