Contacts of the helix formed by residues 338 - 364 (chain F) in PDB entry 5KRA
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 338 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F PHE* 1.3 71.5 - - - +
339F GLU* 1.3 63.8 + - - +
340F ALA* 3.2 10.3 + - - +
341F SER* 2.4 56.2 + - - -
342F MET* 3.1 16.5 + - - +
415F GLY* 4.7 2.3 - - - +
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Residues in contact with GLU 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F SER* 1.3 75.5 - - - +
340F ALA* 1.3 63.5 + - - +
342F MET* 4.0 2.1 - - - +
343F MET* 3.4 28.4 + - - +
415F GLY 3.3 26.1 + - - +
416F LYS* 4.2 3.8 - - - +
417F CYS 4.0 31.4 + - - +
524F HIS* 6.2 0.3 - - - -
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Residues in contact with ALA 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F SER* 3.2 8.6 + - - +
339F GLU* 1.3 80.1 + - - +
341F SER* 1.3 60.8 + - - +
343F MET* 3.2 7.5 + - - +
344F GLY* 2.9 24.1 + - - -
533F VAL* 4.0 26.0 - - + -
534F VAL* 4.2 12.6 - - + +
535F PRO* 5.6 0.7 - - - +
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Residues in contact with SER 341 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F PHE* 3.0 18.3 - - - +
338F SER* 2.4 44.7 + - - -
340F ALA* 1.3 70.4 - - - +
342F MET* 1.3 64.6 + - - +
344F GLY* 3.2 4.0 + - - +
345F LEU* 3.2 27.2 + - - +
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Residues in contact with MET 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F TYR* 4.1 30.7 - - + -
337F PHE 6.4 1.8 - - - -
338F SER 3.1 15.7 + - - +
339F GLU* 4.0 5.4 - - - +
341F SER* 1.3 81.8 + - - +
343F MET* 1.3 63.5 + - - +
345F LEU* 3.1 26.8 + - + +
346F LEU* 3.3 18.7 + - + +
408F LEU* 4.4 11.9 - - + -
410F LEU* 4.0 30.1 - - + -
414F GLN 5.0 2.5 - - - +
415F GLY* 4.8 19.5 - - - +
416F LYS* 5.9 3.6 - - + -
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Residues in contact with MET 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339F GLU* 3.4 22.8 + - - +
340F ALA* 3.2 11.1 + - - +
342F MET* 1.3 81.0 - - - +
344F GLY* 1.3 56.1 - - - +
346F LEU* 3.3 16.8 + - - +
347F THR* 3.1 32.7 + - - +
416F LYS* 5.5 5.4 - - - -
421F MET* 3.8 35.4 - - + +
524F HIS* 5.0 2.9 - - + +
528F MET* 3.5 40.6 - - + -
534F VAL* 3.9 9.2 - - + -
601F 6WT 3.6 28.9 - - + -
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Residues in contact with GLY 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340F ALA 2.9 12.3 + - - -
341F SER* 3.2 6.0 + - - -
342F MET 3.1 0.4 - - - -
343F MET* 1.3 75.4 - - - +
345F LEU* 1.3 59.3 + - - +
347F THR* 3.0 19.6 + - - -
348F ASN* 3.0 19.6 + - - +
534F VAL* 3.7 11.8 - - - +
535F PRO* 4.9 10.8 - - - +
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Residues in contact with LEU 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329F SER* 3.9 12.9 + - - +
330F GLU* 3.8 35.0 - - + +
331F TYR* 3.8 37.7 - - + +
341F SER* 3.2 14.7 + - - +
342F MET* 3.1 23.3 + - + +
344F GLY* 1.3 78.8 - - - +
346F LEU* 1.3 61.7 + - - +
348F ASN* 3.7 6.5 - - + +
349F LEU* 3.1 24.3 + - - +
352F ARG* 5.2 0.7 + - - -
408F LEU* 4.7 6.3 - - + -
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Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F MET* 3.3 20.3 + - + +
343F MET* 3.7 22.2 - - - +
344F GLY 3.3 0.4 - - - -
345F LEU* 1.3 77.9 - - - +
347F THR* 1.3 57.8 + - - +
349F LEU* 3.4 5.5 + - + +
350F ALA* 3.0 27.9 + - - +
404F PHE* 3.7 37.5 - - + -
408F LEU* 3.7 21.8 - - + -
410F LEU* 4.8 6.5 - - + -
421F MET* 6.3 0.2 - - + -
425F PHE* 6.4 0.2 - - + -
601F 6WT 3.6 50.4 - - + -
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Residues in contact with THR 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F MET* 3.1 15.2 + - + +
344F GLY* 3.0 16.6 + - - -
346F LEU* 1.3 73.9 - - - +
348F ASN* 1.3 65.6 + - - +
350F ALA* 3.3 7.3 + - - +
351F ASP* 3.0 24.6 + - - +
525F LEU* 4.8 1.6 - - + -
528F MET* 3.7 18.6 - - + -
534F VAL* 3.9 1.1 - - + +
535F PRO 3.4 15.2 + - - -
536F LEU* 3.6 30.3 - - + -
537F SER 5.9 0.6 + - - -
540F LEU* 3.8 11.1 - - + +
601F 6WT 3.8 14.4 - - + -
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Residues in contact with ASN 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F GLU* 4.8 18.4 + - - +
344F GLY 3.0 19.7 + - - +
345F LEU* 3.7 7.6 - - + +
347F THR* 1.3 76.9 + - - +
349F LEU* 1.3 61.0 + - - +
351F ASP* 3.3 10.1 + - - +
352F ARG* 2.9 61.3 + - - +
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Residues in contact with LEU 349 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F LEU* 3.9 27.1 - - + +
328F TYR 3.9 13.5 - - - +
329F SER* 5.0 6.1 - - - -
345F LEU 3.1 14.7 + - - +
346F LEU* 3.6 5.8 - - - +
348F ASN* 1.3 79.4 + - - +
350F ALA* 1.3 57.9 + - - +
352F ARG* 3.2 24.7 + - - +
353F GLU* 2.9 42.5 + - - +
404F PHE* 3.2 41.5 - - + +
405F ALA* 4.3 5.6 - - + -
408F LEU* 5.4 1.3 - - + -
601F 6WT 4.2 10.8 - - + -
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Residues in contact with ALA 350 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F LEU 3.0 17.4 + - - +
347F THR* 3.7 6.5 - - - +
348F ASN 3.3 0.2 - - - -
349F LEU* 1.3 75.6 - - - +
351F ASP* 1.3 57.9 + - - +
353F GLU* 3.4 5.1 + - - +
354F LEU* 2.9 30.5 + - - +
387F LEU* 3.9 15.9 - - + +
540F LEU* 4.7 8.1 - - + -
601F 6WT 3.6 39.9 - - + -
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Residues in contact with ASP 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F THR 3.0 12.7 + - - +
348F ASN* 3.5 13.3 + - - +
350F ALA* 1.3 78.0 - - - +
352F ARG* 1.3 67.2 + - - +
354F LEU* 3.4 18.1 + - - +
355F VAL* 3.5 15.8 + - - +
537F SER* 2.6 39.4 + - - +
539F LEU* 4.0 16.6 - - - +
540F LEU* 4.6 9.3 + - + +
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Residues in contact with ARG 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F LEU* 3.7 25.3 - - + +
328F TYR 2.8 31.1 + - - +
329F SER* 4.1 9.3 - - - +
330F GLU* 4.6 7.3 + - - +
345F LEU 5.2 0.6 + - - -
348F ASN* 2.9 39.6 + - - +
349F LEU* 3.8 22.3 - - - +
351F ASP* 1.3 80.5 - - - +
353F GLU* 1.3 65.6 + - - +
354F LEU 3.4 0.2 + - - -
355F VAL* 3.4 13.7 + - - +
356F HIS* 3.1 21.4 + - + -
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Residues in contact with GLU 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325F PRO 5.6 4.3 - - - +
326F ILE* 6.5 0.2 - - - -
327F LEU* 3.9 23.3 + - + +
349F LEU* 2.9 30.7 + - + +
350F ALA 3.8 1.6 - - - +
352F ARG* 1.3 76.7 - - - +
354F LEU* 1.3 58.6 + - - +
356F HIS* 3.1 7.0 + - - +
357F MET* 2.9 28.9 + - - +
387F LEU* 3.3 28.8 - - + +
390F GLY* 6.2 0.2 - - - -
394F ARG* 2.9 37.3 + - - -
404F PHE 4.3 0.2 - - - +
601F 6WT 3.1 17.3 - - - +
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Residues in contact with LEU 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F ALA 2.9 15.6 + - - +
351F ASP* 3.5 8.5 - - - +
352F ARG 3.2 0.6 - - - -
353F GLU* 1.3 77.0 - - - +
355F VAL* 1.3 60.8 + - - +
357F MET* 3.5 32.5 + - + -
358F ILE* 3.2 37.0 + - + +
379F LEU* 6.1 0.4 - - + -
383F TRP* 3.8 28.3 - - + -
387F LEU* 4.7 1.3 - - + +
539F LEU* 4.2 17.5 - - + -
540F LEU* 3.7 28.7 - - + -
543F MET* 4.0 24.0 - - + -
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Residues in contact with VAL 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351F ASP* 3.5 18.4 - - - +
352F ARG* 3.4 9.6 + - - +
353F GLU 3.2 0.4 - - - -
354F LEU* 1.3 75.5 - - - +
356F HIS* 1.3 63.1 + - + +
358F ILE* 3.5 8.9 + - - +
359F ASN* 2.7 44.5 + - - +
539F LEU* 4.5 13.9 - - + -
693H LEU* 4.6 18.6 - - + -
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Residues in contact with HIS 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F PRO* 4.2 17.6 - - + +
325F PRO* 3.6 30.0 - - + +
327F LEU* 3.5 29.0 - - + +
352F ARG* 3.1 24.0 - - + +
353F GLU* 3.1 8.3 + - - +
355F VAL* 1.3 79.6 - - + +
357F MET* 1.3 60.2 + - - +
359F ASN* 3.4 7.1 + - - +
360F TRP* 2.9 28.9 + - - +
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Residues in contact with MET 357 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F PRO* 5.1 4.2 - - - +
353F GLU 2.9 13.4 + - - +
354F LEU* 3.6 24.2 - - + +
355F VAL 3.3 0.2 - - - -
356F HIS* 1.3 76.7 - - - +
358F ILE* 1.3 53.1 + - - +
360F TRP* 3.0 24.0 + - + +
361F ALA* 2.8 32.9 + - - +
379F LEU* 4.2 13.2 - - + -
383F TRP* 3.3 37.5 - - - +
386F ILE* 3.7 27.1 - - + -
387F LEU* 3.6 27.8 - - + -
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Residues in contact with ILE 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F LEU* 3.2 26.4 + - + +
355F VAL* 3.7 6.1 - - - +
356F HIS 3.3 0.2 - - - -
357F MET* 1.3 77.2 - - + +
359F ASN* 1.3 63.1 + - - +
361F ALA* 3.4 11.4 + - - +
362F LYS* 3.5 15.7 + - - +
379F LEU* 4.3 12.8 - - + -
539F LEU* 4.2 12.8 - - + -
543F MET* 6.0 0.7 - - + -
690H LEU* 3.6 27.1 - - + -
693H LEU* 3.6 50.3 - - + +
694H LEU* 3.6 24.9 - - + +
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Residues in contact with ASN 359 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355F VAL* 2.7 35.8 + - - +
356F HIS* 3.4 7.6 + - - +
357F MET 3.2 0.4 - - - -
358F ILE* 1.3 79.4 - - - +
360F TRP* 1.3 64.1 + - - +
362F LYS* 3.6 41.0 + - + +
363F ARG* 3.7 13.7 - - - +
693H LEU* 4.6 5.1 + - - +
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Residues in contact with TRP 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F LEU* 4.8 6.6 + - + +
322F ALA* 3.0 39.9 - - + +
323F GLU* 4.0 11.1 + - - -
324F PRO* 3.8 18.6 - - + -
356F HIS 2.9 14.8 + - - +
357F MET* 3.0 27.3 + - + +
359F ASN* 1.3 76.1 - - - +
361F ALA* 1.3 72.2 + - + +
363F ARG* 2.9 23.7 + - - +
364F VAL* 3.3 31.1 + - + +
386F ILE* 3.7 25.6 - - + -
446F VAL* 5.2 0.9 - - - +
449F LYS* 3.6 46.9 - - + +
450F SER* 4.0 11.2 + - - -
453F LEU* 4.0 16.8 - - + -
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Residues in contact with ALA 361 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F MET 2.8 15.4 + - - +
358F ILE 3.6 11.0 - - - +
359F ASN 3.4 0.2 - - - -
360F TRP* 1.3 81.7 - - + +
362F LYS* 1.3 61.7 + - - +
364F VAL* 3.1 15.9 + - - +
367F PHE* 3.1 43.1 - - + +
379F LEU* 4.0 15.9 - - + -
453F LEU* 4.0 13.0 - - + -
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Residues in contact with LYS 362 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358F ILE* 3.6 12.3 - - - +
359F ASN* 3.6 28.6 + - - +
360F TRP 3.1 0.6 - - - -
361F ALA* 1.3 77.2 - - - +
363F ARG* 1.3 62.2 + - + +
364F VAL 3.6 4.5 + - - +
367F PHE* 4.3 3.4 - - + -
368F VAL* 3.3 35.7 - - + +
375F GLN* 5.8 0.9 - - - +
693H LEU 3.0 25.7 + - - -
694H LEU* 3.4 35.9 + - + +
696H ASP 3.6 23.8 - - - -
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Residues in contact with ARG 363 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F ALA* 4.9 7.4 + - - +
319F LEU* 5.1 0.2 - - - +
321F ASP* 2.8 52.4 + - - +
322F ALA* 3.7 30.8 + - + +
359F ASN 3.7 14.4 - - - +
360F TRP* 2.9 10.7 + - - +
362F LYS* 1.3 79.6 - - + +
364F VAL* 1.3 64.4 + - - +
365F PRO* 3.4 9.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F LEU* 4.5 3.1 - - + -
322F ALA* 5.9 0.4 - - + -
360F TRP* 3.3 51.8 + - + +
361F ALA* 3.1 14.1 + - - +
362F LYS 4.1 3.9 - - - +
363F ARG* 1.3 76.8 - - - +
365F PRO* 1.3 80.8 - - + +
366F GLY 3.3 0.2 + - - -
367F PHE* 3.1 20.7 + - + +
368F VAL* 4.5 1.2 + - - +
450F SER* 3.7 25.1 - - - +
453F LEU* 4.0 13.7 - - + -
454F LEU* 5.0 9.6 - - + -
482F ILE* 5.6 1.6 - - + -
----------------------------------------------------------
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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