Contacts of the helix formed by residues 276 - 301 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS* 1.3 94.3 - - - +
277A VAL* 1.3 70.1 + - + +
278A ALA* 3.6 15.8 + - - +
279A ILE* 3.1 28.5 + - + +
280A ARG* 3.1 18.2 + - - +
357A ARG* 2.7 50.3 + - - +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET* 3.5 29.8 - - + -
255A LEU* 3.4 31.9 - - + -
275A LYS 3.6 1.2 + - - -
276A GLU* 1.3 73.9 - - + +
278A ALA* 1.3 73.1 + - + +
280A ARG* 3.1 19.4 + - - +
281A ILE* 2.9 45.4 + - + +
352A PHE* 4.0 11.0 - - + -
356A LEU* 4.5 4.9 - - + -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 3.2 19.8 + - - +
277A VAL* 1.3 83.8 - - + +
279A ILE* 1.3 57.3 + - - +
281A ILE* 3.5 3.6 + - - +
282A PHE* 2.9 27.6 + - - +
356A LEU* 4.1 17.5 - - + +
357A ARG 4.2 14.8 - - - +
360A PHE* 3.8 31.9 - - + +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS 4.5 16.2 - - - +
276A GLU* 3.1 32.3 + - + +
278A ALA* 1.3 74.2 - - - +
280A ARG* 1.3 57.3 + - - +
282A PHE* 3.4 5.9 - - - +
283A GLN* 2.7 52.6 + - - +
357A ARG* 3.9 3.6 - - - +
360A PHE* 3.9 22.0 - - + -
460A GLU* 3.6 25.1 - - - +
462A ASP* 5.7 3.6 - - - +
463A MET* 4.2 15.7 - - + -
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 3.5 30.5 - - - +
256A MET* 5.8 6.5 - - - +
259A GLU* 3.5 22.5 + - - +
266A HIS* 5.3 8.6 + - + -
275A LYS* 3.0 31.4 + - - +
276A GLU* 3.1 8.4 + - - +
277A VAL* 3.1 20.1 + - - +
279A ILE* 1.3 77.6 - - - +
281A ILE* 1.3 58.3 + - + +
283A GLN* 3.3 8.6 + - - +
284A GLY* 3.0 22.3 + - - -
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.1 11.0 - - + -
277A VAL* 2.9 30.1 + - + +
278A ALA 3.7 4.3 - - - +
280A ARG* 1.3 73.5 - - + +
282A PHE* 1.3 62.2 + - - +
284A GLY* 2.9 16.8 + - - +
285A CYS* 3.1 22.4 + - - -
348A MET* 4.2 23.3 - - + -
352A PHE* 3.5 32.3 - - + -
353A LEU* 4.4 11.7 - - + -
356A LEU* 3.8 20.2 - - + -
1001A YPA 4.5 10.1 - - + -
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA 2.9 18.8 + - - +
279A ILE 3.2 4.7 + - - +
281A ILE* 1.3 78.0 - - - +
283A GLN* 1.3 63.2 + - - +
284A GLY 3.3 0.3 + - - -
285A CYS* 3.4 5.7 + - - -
286A GLN* 3.1 45.4 + - - +
360A PHE* 3.5 28.0 - + + -
363A PHE* 3.5 31.6 - + - -
453A LEU* 4.3 13.2 - - + -
456A ILE* 4.5 9.9 - - + -
463A MET* 3.3 34.8 - - + -
465A LEU* 4.9 5.4 - - + -
1001A YPA 3.4 34.2 - - + +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A HIS* 5.3 1.0 + - - -
279A ILE* 2.7 48.0 + - - +
280A ARG* 3.6 8.3 - - - +
282A PHE* 1.3 74.4 - - - +
284A GLY* 1.3 62.6 + - - +
286A GLN* 3.5 11.9 + - + +
287A PHE* 3.3 21.7 + - - +
463A MET* 3.4 33.5 - - - +
464A SER* 3.8 15.1 + - - +
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A HIS* 3.9 24.2 - - - -
280A ARG 3.0 10.4 + - - -
281A ILE 2.9 9.1 + - - -
283A GLN* 1.3 76.4 - - - +
285A CYS* 1.3 65.9 + - - +
287A PHE* 3.2 7.3 + - - +
288A ARG* 3.0 21.5 + - - +
1001A YPA 4.0 14.8 - - - -
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 3.1 25.4 + - - -
282A PHE* 3.8 2.7 - - - +
284A GLY* 1.3 73.8 - - - +
286A GLN* 1.3 53.3 + - - +
288A ARG* 3.3 2.2 + - - +
289A SER* 2.6 39.6 + - - -
353A LEU* 6.4 1.3 - - - -
364A MET* 5.2 4.7 - - - -
1001A YPA 3.5 81.2 - - + -
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.1 33.2 + - - +
283A GLN* 3.6 16.6 - - + +
284A GLY 3.2 0.2 - - - -
285A CYS* 1.3 79.1 - - - +
287A PHE* 1.3 56.8 + - - +
289A SER* 3.2 2.8 + - - -
290A VAL* 2.8 35.8 + - - +
463A MET* 3.5 7.6 - - - +
464A SER 3.6 3.4 + - - -
465A LEU* 2.8 37.4 - - + +
466A HIS* 3.0 27.2 - - + +
469A LEU* 3.6 19.5 - - + +
1001A YPA 3.7 18.4 - - + -
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE 4.7 0.7 - - - -
265A LYS* 3.4 39.5 - - + -
266A HIS* 3.5 26.5 - + + +
283A GLN 3.3 9.2 + - - +
284A GLY 3.2 7.2 + - - +
286A GLN* 1.3 80.3 - - - +
288A ARG* 1.3 64.0 + - + +
290A VAL* 3.3 11.1 + - + +
291A GLU* 2.8 65.5 + - + +
466A HIS* 5.6 5.6 - + - -
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 5.9 0.4 - - - -
227A PRO* 5.9 2.2 - - - +
228A LEU* 6.2 2.2 - - - +
284A GLY 3.0 15.5 + - - +
285A CYS* 3.7 4.0 - - - +
287A PHE* 1.3 79.3 - - + +
289A SER* 1.3 59.7 + - - +
291A GLU* 3.2 38.6 + - - +
292A ALA* 2.9 38.7 + - + +
295A GLU* 3.3 31.3 + - - -
333A LEU* 6.0 2.6 - - - +
343A GLU* 6.4 0.2 - - - +
1001A YPA 3.2 69.0 - - + +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A CYS 2.6 22.1 + - - -
286A GLN* 3.5 4.9 - - - -
288A ARG* 1.3 74.7 - - - +
290A VAL* 1.3 62.9 + - - +
292A ALA* 3.0 9.5 + - - +
293A VAL* 2.9 25.3 + - - +
323A HIS* 4.4 0.2 + - - -
326A ILE* 3.2 19.7 - - - +
469A LEU* 4.3 5.5 - - - +
1001A YPA 2.8 46.1 + - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN 2.8 21.8 + - - +
287A PHE* 3.5 10.8 - - + +
289A SER* 1.3 75.9 - - - +
291A GLU* 1.3 61.5 + - + +
293A VAL* 3.2 8.7 + - - +
294A GLN* 3.2 34.0 + - - +
466A HIS* 3.5 48.5 - - + +
468A LEU* 3.7 18.6 - - + +
469A LEU* 3.8 21.7 - - + +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 4.7 9.5 - - - -
287A PHE* 2.8 60.1 + - + +
288A ARG* 3.3 34.2 + - - +
290A VAL* 1.3 74.1 - - + +
292A ALA* 1.3 65.1 + - - +
294A GLN* 3.0 31.8 + - - +
295A GLU* 3.0 20.2 + - - +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 6.2 0.2 - - - -
288A ARG* 2.9 35.1 + - - +
289A SER* 3.3 10.3 - - - +
291A GLU* 1.3 75.1 - - - +
293A VAL* 1.3 64.1 + - - +
295A GLU* 3.1 6.7 + - - +
296A ILE* 2.8 33.4 + - + +
326A ILE* 3.9 24.5 - - + -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER* 2.9 20.8 + - - +
290A VAL* 3.3 11.9 - - - +
291A GLU 3.2 0.2 - - - -
292A ALA* 1.3 78.0 - - - +
294A GLN* 1.3 56.9 + - + +
296A ILE* 3.3 1.6 + - - +
297A THR* 2.8 43.6 + - - +
318A LEU* 6.1 0.9 - - + -
322A VAL* 3.2 34.1 - - + -
323A HIS* 5.7 0.4 - - - +
326A ILE* 4.1 6.5 - - + -
468A LEU* 4.2 20.4 - - + -
469A LEU* 4.6 5.8 - - + -
472A ILE* 4.0 23.1 - - + -
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 3.2 31.3 + - + +
291A GLU* 3.0 21.3 + - - +
293A VAL* 1.3 77.0 - - - +
295A GLU* 1.3 64.1 + - + +
297A THR* 3.3 7.0 + - - -
298A GLU* 3.0 23.6 + - - +
468A LEU* 5.0 7.5 - - + +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 3.0 25.6 - - - +
226A PHE* 3.8 20.8 - - + +
227A PRO* 3.7 26.5 - - + +
288A ARG* 3.3 35.7 + - - -
291A GLU* 3.0 19.1 + - - +
292A ALA* 3.1 7.8 + - - +
294A GLN* 1.3 77.3 - - - +
296A ILE* 1.3 56.1 + - - +
298A GLU* 3.0 11.2 + - - +
299A TYR* 2.9 27.2 + - - +
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 4.1 14.4 - - + -
292A ALA* 2.8 22.0 + - + +
293A VAL* 3.8 4.3 - - - +
295A GLU* 1.3 72.3 - - - +
297A THR* 1.3 66.4 + - - +
299A TYR* 3.2 8.1 + - + +
300A ALA* 2.9 22.9 + - - +
318A LEU* 4.7 9.0 - - + -
322A VAL* 3.8 30.3 - - + +
325A ILE* 3.5 49.8 - - + -
326A ILE* 3.8 16.6 - - + +
329A MET* 5.1 2.5 - - - -
388A ILE* 5.4 0.9 - - + -
392A ILE* 4.2 8.3 - - + -
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Residues in contact with THR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 2.8 33.5 + - - +
294A GLN* 3.6 7.7 - - - -
296A ILE* 1.3 77.4 - - - +
298A GLU* 1.3 63.4 + - - +
299A TYR 3.4 0.2 + - - -
300A ALA* 3.4 2.4 + - - +
301A LYS* 3.3 32.1 + - + +
318A LEU* 3.8 35.6 - - + +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LYS 4.1 11.6 - - - +
225A SER* 4.0 20.1 + - - +
294A GLN 3.0 13.4 + - - +
295A GLU* 3.4 10.8 - - - +
297A THR* 1.3 80.0 - - - +
299A TYR* 1.3 60.0 + - - +
301A LYS* 3.6 27.4 + - - +
302A SER* 3.9 5.4 + - - -
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 3.5 43.4 - - + +
221A SER* 3.9 12.6 - - - -
222A TYR* 3.6 25.4 - + + -
225A SER* 3.7 9.6 + - - +
226A PHE* 3.9 19.3 - + + -
295A GLU 2.9 12.6 + - - +
296A ILE* 3.2 7.2 + - + +
298A GLU* 1.3 75.0 - - - +
300A ALA* 1.3 65.9 + - - +
302A SER* 2.8 28.6 + - - -
303A ILE* 3.6 15.8 + - + +
385A ALA* 2.6 33.4 + - - -
388A ILE* 3.8 30.5 - - + -
389A ALA* 4.2 1.2 - - - +
392A ILE* 4.5 7.9 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE 2.9 17.0 + - - +
297A THR 3.8 5.6 - - - +
299A TYR* 1.3 76.7 - - - +
301A LYS* 1.3 57.9 + - - +
303A ILE* 2.9 35.9 + - - +
306A PHE* 3.5 36.5 - - + +
318A LEU* 4.3 9.2 - - + -
392A ILE* 3.7 18.2 - - + -
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A THR* 3.3 25.1 - - + +
298A GLU* 3.8 21.3 - - - +
299A TYR 3.1 1.0 - - - -
300A ALA* 1.3 76.4 - - - +
302A SER* 1.3 59.4 + - - +
303A ILE 3.3 3.5 + - - +
306A PHE* 4.4 8.5 - - + -
307A VAL* 3.7 35.5 - - + +
314A GLN* 6.1 0.2 - - - +
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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