Contacts of the helix formed by residues 408 - 434 (chain B) in PDB entry 6EBT
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 PHE 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY* 4.7 0.7 - - - -
396B VAL* 5.4 3.6 - - + -
397B GLY* 3.7 36.1 - - - -
400B ASN* 3.5 45.8 - - + -
402B HIS* 4.7 9.9 - + - -
406B ASN* 2.8 13.7 + - - +
407B VAL* 1.3 89.2 - - + +
409B LYS* 1.3 64.4 + - - +
410B PRO* 3.5 5.1 - - - -
411B MET* 3.5 19.5 + - + +
412B MET* 3.2 21.9 + - + +
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Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY 2.9 13.8 + - - +
145B SER* 3.9 21.8 - - - +
188B ASN 4.1 3.8 - - - -
191B PHE* 3.7 15.7 - - + -
192B PRO* 3.7 27.8 - - + +
195B MET* 3.9 10.6 - - + +
315B LEU 3.1 19.6 + - - -
318B HIS* 2.8 33.8 + - + +
405B LEU* 3.5 18.4 - - - +
406B ASN 2.7 29.8 + - - +
408B PHE* 1.3 76.9 - - - +
410B PRO* 1.3 62.9 - - + +
412B MET* 3.1 6.2 + - - +
413B ILE* 3.1 23.9 + - - +
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Residues in contact with PRO 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 4.1 13.0 - - + +
140B VAL* 3.2 32.3 - - + +
142B GLN* 4.3 4.0 - - + +
143B THR 3.4 18.8 - - - +
144B GLY* 3.1 18.2 - - - +
146B GLY* 4.1 9.4 - - - +
191B PHE* 3.9 17.5 - - + -
408B PHE 3.7 2.7 - - - -
409B LYS* 1.3 91.0 - - + +
411B MET* 1.3 56.9 + - - +
413B ILE* 3.3 3.7 - - + +
414B LYS* 3.0 29.3 + - - +
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Residues in contact with MET 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 3.6 9.5 - - - +
141B TRP* 3.6 34.1 - - + -
393B ALA* 3.5 33.7 - - + +
396B VAL* 5.8 1.3 - - + -
397B GLY* 3.7 22.7 - - - +
408B PHE* 3.5 21.8 + - + +
409B LYS 3.4 0.6 - - - -
410B PRO* 1.3 79.5 - - - +
412B MET* 1.3 68.7 + - + +
414B LYS* 3.6 2.3 + - - +
415B ASN* 2.7 50.2 + - - +
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Residues in contact with MET 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B HIS* 3.6 38.1 - - + +
321B LEU* 4.1 13.2 - - + -
322B VAL* 3.8 7.4 - - + -
394B VAL* 3.6 25.5 - - + +
397B GLY 3.7 4.3 - - - +
398B GLY* 3.4 40.2 - - - +
406B ASN* 4.1 11.4 - - - +
408B PHE* 3.2 17.8 + - + +
409B LYS* 3.1 6.3 + - - +
411B MET* 1.3 96.0 - - + +
413B ILE* 1.3 62.8 + - - +
415B ASN 3.4 0.2 + - - -
416B VAL* 3.1 25.8 + - - +
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Residues in contact with ILE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 5.1 2.5 - - - -
89B PRO* 5.8 0.2 - - + -
92B VAL* 3.9 11.7 - - + -
191B PHE* 4.0 20.6 - - + -
195B MET* 3.2 46.0 - - + +
199B ALA* 4.1 11.9 - - + -
321B LEU* 4.2 12.3 - - + +
409B LYS 3.1 13.0 + - - +
410B PRO* 3.3 13.2 - - + +
412B MET* 1.3 74.6 - - - +
414B LYS* 1.3 64.4 + - - +
416B VAL* 4.3 5.2 - - + -
417B LEU* 2.9 56.6 + - + +
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Residues in contact with LYS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR 4.8 12.0 + - - -
86B GLU* 5.7 6.5 - - - +
87B ARG 5.5 2.7 + - - +
89B PRO* 3.6 32.0 - - + +
140B VAL* 4.0 25.6 - - + -
141B TRP* 5.5 6.1 - - + -
410B PRO 3.0 19.9 + - - +
411B MET* 3.7 5.6 - - - +
413B ILE* 1.3 78.8 - - - +
415B ASN* 1.3 63.9 + - - +
417B LEU* 3.5 0.7 + - - +
418B HIS* 2.8 58.4 + - - +
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Residues in contact with ASN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TRP* 5.4 2.0 - - - -
325B SER* 6.0 0.2 - - - -
390B ASN* 3.2 31.7 + - + +
393B ALA* 3.8 14.8 - - - +
394B VAL* 3.4 21.5 - - + -
411B MET* 2.7 48.4 + - - +
414B LYS* 1.3 80.7 - - - +
416B VAL* 1.3 65.8 + - - +
418B HIS* 3.6 6.4 + - - +
419B SER* 2.9 30.8 + - - -
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA* 4.5 9.4 - - + -
321B LEU* 3.8 43.1 - - + +
324B LEU* 3.9 27.4 - - + -
325B SER* 4.4 6.5 - - - -
328B MET* 3.4 17.1 - - + +
394B VAL* 4.1 12.6 - - + -
412B MET 3.1 18.3 + - - +
413B ILE* 3.8 8.5 - - + +
415B ASN* 1.3 77.4 - - - +
417B LEU* 1.3 58.5 + - + +
419B SER* 3.4 0.4 + - - -
420B ALA* 3.0 27.5 + - + +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 3.8 21.3 - - + -
91B PRO* 4.1 16.6 - - + -
92B VAL* 3.5 31.9 - - + -
198B ALA* 3.8 30.5 - - + +
199B ALA* 4.1 8.5 - - + +
202B GLU* 3.9 19.9 - - + +
413B ILE* 2.9 32.2 + - + +
414B LYS* 3.9 3.6 - - - +
416B VAL* 1.3 73.2 - - + +
418B HIS* 1.3 58.4 + - - +
420B ALA* 3.8 3.8 - - + +
421B ARG* 2.9 32.9 + - - +
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Residues in contact with HIS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLN* 4.0 17.9 - - + -
390B ASN* 3.1 18.2 + - - +
414B LYS* 2.8 44.9 + - - +
415B ASN* 3.6 7.3 + - - +
417B LEU* 1.3 76.0 - - - +
419B SER* 1.3 63.3 + - - +
421B ARG* 3.8 5.0 - - + +
422B LEU* 3.0 60.8 + - + +
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Residues in contact with SER 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER* 5.3 3.0 + - - -
328B MET* 3.7 21.5 - - - -
387B VAL* 3.8 27.9 + - - +
390B ASN* 3.1 30.1 + - - +
415B ASN 2.9 14.3 + - - -
418B HIS* 1.3 75.6 - - - +
420B ALA* 1.3 57.7 + - - +
422B LEU* 4.0 2.2 - - - +
423B LEU* 2.9 36.2 + - - +
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 4.1 20.6 - - + -
203B VAL* 5.2 4.9 - - + -
206B VAL* 4.1 5.4 - - - +
207B LEU* 4.1 21.9 - - + +
324B LEU* 6.5 0.2 - - + -
328B MET* 3.5 18.1 - - - -
416B VAL* 3.0 19.5 + - + +
417B LEU* 3.8 5.2 - - + +
419B SER* 1.3 76.2 - - - +
421B ARG* 1.3 63.1 + - - +
423B LEU* 4.0 0.9 - - - +
424B GLY* 3.0 21.1 + - - -
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Residues in contact with ARG 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PRO* 6.0 3.4 - - - +
202B GLU* 4.0 21.4 + - - +
206B VAL* 4.2 11.7 - - - -
417B LEU 2.9 18.3 + - - +
418B HIS* 3.8 6.3 - - + +
420B ALA* 1.3 76.4 - - - +
422B LEU* 1.3 65.5 + - + +
424B GLY* 3.3 0.7 + - - -
425B ASP* 2.7 66.3 + - - +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B VAL* 3.6 30.2 - - + +
386B GLN* 4.0 22.0 - - + -
387B VAL* 5.4 0.7 - - + -
390B ASN* 5.1 0.4 - - - +
418B HIS* 3.0 56.5 + - + +
419B SER* 4.0 5.2 - - - +
421B ARG* 1.3 81.8 - - + +
423B LEU* 1.3 57.3 + - - +
425B ASP* 4.8 2.5 - - + -
426B ALA* 2.8 35.2 + - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 3.6 18.4 - - + -
211B LEU* 5.7 0.4 - - + -
328B MET* 3.6 44.0 - - + +
331B THR* 4.4 9.6 - - + -
332B ALA* 4.6 10.5 - - + -
335B LEU* 3.7 27.8 - - + -
380B MET* 4.8 0.8 - - - +
383B VAL* 4.3 11.0 - - + -
384B ALA* 5.3 2.0 - - - -
387B VAL* 3.7 22.0 - - + -
419B SER 2.9 21.9 + - - +
422B LEU* 1.3 75.8 - - - +
424B GLY* 1.3 57.8 + - - +
426B ALA* 4.0 1.2 - - - +
427B SER* 2.9 36.1 + - - +
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Residues in contact with GLY 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.5 25.1 - - - -
207B LEU* 4.0 11.1 - - - +
210B GLY* 3.8 3.4 - - - -
420B ALA 3.0 16.7 + - - -
421B ARG 3.8 0.4 - - - -
423B LEU* 1.3 78.8 - - - +
425B ASP* 1.3 62.0 + - - +
427B SER* 3.3 3.0 + - - -
428B VAL* 3.2 27.4 + - - +
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Residues in contact with ASP 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.8 12.1 - - - +
421B ARG* 2.7 58.2 + - - +
422B LEU* 4.2 3.6 - - + +
424B GLY* 1.3 71.8 - - - -
426B ALA* 1.3 58.7 + - - +
428B VAL* 3.2 8.1 + - - +
429B SER* 2.9 29.0 + - - -
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ALA* 5.0 2.5 - - + +
380B MET* 3.4 29.6 - - + +
383B VAL* 4.1 19.1 - - + -
422B LEU 2.8 24.0 + - - +
423B LEU 4.0 1.1 - - - +
425B ASP* 1.3 74.1 - - - +
427B SER* 1.3 53.6 + - - +
429B SER* 3.9 5.3 - - - +
430B PHE* 2.7 37.6 + - - +
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLY 3.3 28.7 - - - -
211B LEU* 3.5 20.3 - - - +
214B LEU* 4.0 12.3 - - - +
335B LEU* 4.0 2.6 - - - +
380B MET* 3.5 15.3 - - - +
423B LEU 2.9 23.1 + - - -
424B GLY 3.7 1.3 - - - -
425B ASP 3.2 0.2 - - - -
426B ALA* 1.3 77.6 - - - +
428B VAL* 1.3 53.2 + - - +
430B PHE* 3.9 1.3 - - - +
431B THR* 2.7 38.4 + - - -
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL 5.7 0.2 - - - +
210B GLY* 3.8 18.6 - - - +
213B LYS* 4.4 21.1 - - + +
424B GLY 3.2 15.0 + - - +
425B ASP* 3.6 8.7 - - - +
427B SER* 1.3 75.3 - - - +
429B SER* 1.3 62.0 + - - +
431B THR* 3.1 5.8 + - - -
432B GLU* 2.8 56.7 + - + +
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Residues in contact with SER 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLN* 2.6 26.4 + - - +
425B ASP 2.9 15.9 + - - -
426B ALA* 3.9 6.1 - - - -
428B VAL* 1.3 78.1 - - - +
430B PHE* 1.3 57.4 + - - +
432B GLU* 5.1 1.1 - - - -
433B ASN* 2.9 54.2 + - - +
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Residues in contact with PHE 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.9 17.7 - - + -
338B ILE* 4.5 10.5 - - + -
339B ALA* 4.1 12.6 - - + -
342B ILE* 3.8 26.5 - - + -
376B GLN* 3.6 29.1 + - + +
377B CYS* 3.6 33.9 - - - -
380B MET* 3.9 21.1 - - + -
426B ALA 2.7 24.0 + - - +
427B SER 4.0 2.2 - - - +
429B SER* 1.3 73.1 - - - +
431B THR* 1.3 58.0 + - - +
434B CYS* 3.2 21.8 + - + +
435B VAL* 3.0 41.6 + - + +
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LYS* 3.7 17.5 - - + +
214B LEU* 3.1 28.1 + - - +
217B ALA* 3.5 25.8 - - + -
427B SER 2.7 22.8 + - - -
428B VAL* 3.4 5.8 - - - -
430B PHE* 1.3 76.5 - - - +
432B GLU* 1.3 71.2 + - + +
435B VAL* 3.2 12.1 + - - -
436B VAL* 3.1 34.9 + - + +
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Residues in contact with GLU 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LYS* 4.6 14.9 - - + -
428B VAL* 2.8 42.4 + - + +
429B SER* 5.3 0.7 - - - -
431B THR* 1.3 82.2 - - + +
433B ASN* 1.3 72.8 + - - +
436B VAL* 3.3 22.2 - - + +
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Residues in contact with ASN 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PRO* 4.2 8.8 - - - +
361B ASN* 2.7 40.2 + - - +
376B GLN* 3.5 22.5 - - - +
429B SER* 2.9 38.5 + - - +
432B GLU* 1.3 87.6 + - - +
434B CYS* 1.3 60.9 + - - +
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Residues in contact with CYS 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 4.5 2.9 - - - -
358B LEU* 4.3 22.7 - - - -
359B PRO* 3.3 14.4 - - - +
374B PRO* 6.4 0.4 - - - -
376B GLN* 4.0 17.0 - - + -
377B CYS* 4.6 2.7 - - - -
430B PHE* 3.2 32.5 + - + +
432B GLU 3.4 1.4 + - - -
433B ASN* 1.3 80.6 - - - +
435B VAL* 1.3 71.2 + - - +
436B VAL* 3.4 1.5 - - - +
437B GLY 3.1 11.9 + - - -
438B ILE* 3.1 30.3 + - - +
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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