Contacts of the helix formed by residues 407 - 437 (chain L) in PDB entry 2FRV
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 THR 407 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L TRP* 4.7 9.2 - - + -
271L TRP* 4.1 20.9 - - + -
274L ILE 2.6 23.2 + - - -
275L GLY* 3.5 9.4 - - - -
406L SER* 1.3 69.6 - - - +
408L LEU* 1.3 64.3 + - - +
410L ARG* 3.2 21.8 + - - +
411L THR* 2.8 30.2 + - - +
522L ARG 3.6 29.4 - - - +
523L THR* 3.5 10.5 + - - -
526L SER* 3.7 10.0 + - - +
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Residues in contact with LEU 408 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120L TRP* 5.1 10.8 - - + -
265L ALA* 4.0 39.9 - - + +
268L TYR* 3.7 26.5 - - + +
269L LYS* 4.1 7.2 - - + -
271L TRP* 3.1 28.0 + - + +
272L ALA* 3.6 22.2 - - + +
397L LEU* 4.9 11.7 - - + -
399L VAL* 6.5 0.2 - - + -
403L ALA 5.1 0.2 - - - +
406L SER* 3.1 0.4 - - - +
407L THR* 1.3 79.6 - - - +
409L GLY* 1.3 56.7 + - - +
411L THR* 3.0 15.2 + - + +
412L ALA* 2.9 27.2 + - + +
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Residues in contact with GLY 409 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372L LEU* 3.7 3.6 - - - +
403L ALA 3.8 6.4 + - - -
404L LEU* 3.5 35.2 - - - +
406L SER* 2.9 12.7 + - - -
408L LEU* 1.3 74.1 - - - +
410L ARG* 1.3 59.0 + - - +
412L ALA* 4.2 3.5 - - - +
413L ALA* 2.9 34.0 + - - +
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Residues in contact with ARG 410 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L GLY 2.7 24.4 + - - -
277L THR* 3.2 22.8 + - - +
368L GLU* 3.1 21.8 + - - +
371L PRO* 4.9 1.2 - - + +
372L LEU* 4.2 20.0 + - + +
404L LEU 4.2 0.4 + - - -
406L SER* 3.0 15.8 + - - +
407L THR* 3.2 34.6 + - - +
408L LEU 3.2 0.2 - - - -
409L GLY* 1.3 78.1 - - - +
411L THR* 1.3 59.5 + - - +
413L ALA* 4.0 2.4 + - - +
414L ARG* 3.7 26.4 + - - +
505L ALA* 4.4 1.8 - - - +
523L THR 4.7 0.4 + - - -
526L SER* 3.3 39.1 + - - +
527L TYR* 3.3 38.4 + - - -
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Residues in contact with THR 411 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L PHE* 5.0 7.9 - - + -
116L HIS* 3.5 35.8 - - + +
120L TRP* 5.1 4.8 - - + +
257L TYR* 4.8 1.4 + - - -
261L LEU* 3.6 25.3 - - + +
407L THR* 2.8 18.6 + - - +
408L LEU* 3.0 15.9 + - + -
410L ARG* 1.3 77.3 - - - +
412L ALA* 1.3 63.7 + - - +
413L ALA 3.3 0.2 - - - -
414L ARG* 3.6 17.5 + - - +
415L GLY 3.7 4.0 + - - -
526L SER* 3.7 5.5 - - - -
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Residues in contact with ALA 412 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261L LEU* 4.2 16.9 - - + +
262L LEU* 5.4 2.5 - - + -
393L VAL* 4.1 27.3 - - + +
397L LEU* 5.2 8.1 - - + -
404L LEU* 5.4 4.3 - - + -
408L LEU* 2.9 15.9 + - + +
409L GLY* 4.2 6.1 - - - +
411L THR* 1.3 75.3 - - - +
413L ALA* 1.3 53.2 + - - +
415L GLY* 2.7 24.3 + - - -
416L ILE* 3.0 17.1 + - + +
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Residues in contact with ALA 413 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371L PRO* 3.6 5.9 - - - +
372L LEU* 3.6 38.1 - - + +
375L VAL* 3.7 10.7 - - + +
404L LEU* 5.5 2.6 - - + +
409L GLY 2.9 18.7 + - - +
410L ARG 4.1 2.2 - - - +
411L THR 3.3 0.2 - - - -
412L ALA* 1.3 76.3 - - - +
414L ARG* 1.3 55.1 + - - +
416L ILE* 3.6 14.0 - - + +
417L GLN* 2.8 30.8 + - - +
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Residues in contact with ARG 414 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L HIS* 3.5 26.9 + - + +
111L HIS* 3.5 32.9 - - - -
112L PHE* 5.5 0.7 - - - +
116L HIS* 5.2 1.0 + - - -
257L TYR* 3.8 13.1 + - - +
371L PRO* 3.6 36.9 - - + +
410L ARG* 3.7 18.6 + - - +
411L THR* 3.6 15.8 + - - +
412L ALA 3.2 0.8 - - - -
413L ALA* 1.3 77.1 - - - +
415L GLY* 1.3 57.8 + - - +
417L GLN* 4.4 0.4 - - - +
418L CYS* 3.0 30.5 + - - +
462L PRO 5.3 0.4 + - - -
463L ARG* 5.7 1.2 - - - +
526L SER* 2.6 36.3 + - - +
527L TYR* 3.8 5.3 + - - +
528L ASP* 3.4 32.5 + - - +
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Residues in contact with GLY 415 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257L TYR* 3.7 10.5 + - - -
258L ILE* 3.2 24.8 - - - +
261L LEU* 3.6 23.3 - - - -
411L THR 3.7 2.4 + - - -
412L ALA 2.7 10.0 + - - -
414L ARG* 1.3 80.9 - - - +
416L ILE* 1.3 59.8 + - - +
418L CYS* 3.5 3.1 + - - +
419L LEU* 3.3 16.5 + - - +
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Residues in contact with ILE 416 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375L VAL* 4.0 20.9 - - + -
386L THR* 4.7 9.0 - - + +
389L ALA* 3.8 26.2 - - + +
390L VAL* 3.9 28.5 - - + -
393L VAL* 4.1 28.0 - - + -
404L LEU* 5.3 6.7 - - + -
412L ALA* 3.0 17.4 + - + +
413L ALA* 3.7 14.1 - - - +
415L GLY* 1.3 75.5 - - - +
417L GLN* 1.3 64.8 + - - +
419L LEU* 3.0 16.5 + - + +
420L THR* 3.2 20.7 + - + +
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Residues in contact with GLN 417 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L TYR* 3.7 23.6 - - + -
108L HIS* 2.8 30.9 + - + -
370L GLY 4.5 0.5 - - - -
371L PRO* 3.5 26.5 - - + +
374L SER* 3.7 18.1 + - - -
375L VAL* 4.1 10.8 - - + -
413L ALA 2.8 20.6 + - - +
416L ILE* 1.3 74.3 - - - +
418L CYS* 1.3 61.4 + - - +
419L LEU 3.4 0.5 + - - -
420L THR* 3.9 8.0 + - - -
421L ALA* 3.4 22.9 + - - +
460L ASN* 4.2 5.5 - - - +
461L ALA 4.5 1.0 + - - -
462L PRO* 3.1 24.2 + - - +
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Residues in contact with CYS 418 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L TYR* 4.1 4.9 - - - -
105L MET* 4.0 14.2 - - - +
108L HIS* 3.1 39.9 - - + +
253L ILE* 4.0 27.4 - - - -
257L TYR* 4.0 15.0 - - + -
414L ARG 3.0 14.8 + - - +
415L GLY 3.7 5.2 - - - +
416L ILE 3.1 0.4 - - - -
417L GLN* 1.3 79.8 - - - +
419L LEU* 1.3 56.6 + - - +
421L ALA* 4.0 4.0 - - - +
422L ALA* 3.4 21.5 + - - +
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Residues in contact with LEU 419 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253L ILE* 4.5 12.6 - - + -
254L GLU* 3.5 41.1 - - + +
258L ILE* 4.6 17.0 - - + -
389L ALA* 4.7 19.3 - - + -
392L LEU* 5.6 8.1 - - + -
415L GLY 3.3 14.1 + - - +
416L ILE* 3.0 6.1 + - - +
418L CYS* 1.3 77.9 - - - +
420L THR* 1.3 55.5 + - + +
421L ALA 3.3 1.6 - - - -
422L ALA* 3.3 8.3 + - + +
423L GLN* 2.8 58.0 + - + +
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Residues in contact with THR 420 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297L TYR* 3.2 27.0 + - - -
298L THR* 4.7 10.4 - - - +
383L HIS* 4.9 0.9 - - - -
385L PRO* 3.9 34.1 - - + +
386L THR* 4.0 14.1 + - - +
389L ALA* 4.5 4.7 - - + -
416L ILE* 3.5 22.5 + - + +
417L GLN* 3.9 8.8 + - - -
419L LEU* 1.3 76.5 - - + +
421L ALA* 1.3 66.8 + - - +
423L GLN* 3.2 11.1 + - - +
424L GLU* 3.0 19.1 + - - +
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Residues in contact with ALA 421 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L GLY* 4.7 5.8 - - - +
104L TYR* 3.7 33.7 - - + -
105L MET* 5.3 0.2 - - - -
286L PHE* 4.6 15.0 - - + -
297L TYR* 4.9 4.0 - - - -
417L GLN 3.4 17.1 + - - +
418L CYS 4.0 2.7 - - - +
420L THR* 1.3 80.6 + - - +
422L ALA* 1.3 62.9 + - - +
424L GLU* 3.0 16.7 + - - +
425L VAL* 3.2 18.2 + - - +
428L TRP* 4.6 1.0 - - - -
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Residues in contact with ALA 422 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L MET* 4.1 28.2 - - + +
246L TYR* 2.6 33.1 + - - -
250L ARG* 4.0 22.3 - - + +
253L ILE* 4.7 4.9 - - + -
418L CYS 3.4 15.0 + - - +
419L LEU* 3.3 15.4 + - + +
421L ALA* 1.3 79.5 - - - +
423L GLN* 1.3 57.3 + - - +
425L VAL* 3.6 3.4 + - - -
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Residues in contact with GLN 423 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246L TYR* 4.0 0.5 + - - -
250L ARG* 3.5 32.0 + - - +
254L GLU* 4.6 1.4 - - - +
297L TYR* 4.7 2.2 + - - +
385L PRO* 3.9 28.1 + - - +
388L LYS* 5.6 3.2 - - - +
389L ALA* 6.0 0.3 - - - +
419L LEU* 2.8 53.0 + - + +
420L THR* 3.6 12.1 + - - +
421L ALA 3.1 0.4 - - - -
422L ALA* 1.3 77.4 - - - +
424L GLU* 1.3 64.1 - - - +
425L VAL 3.4 0.2 + - - -
426L GLU* 3.7 16.8 + - - +
427L VAL* 4.5 1.9 + - - +
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Residues in contact with GLU 424 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297L TYR* 3.5 38.9 + - + -
420L THR 3.0 10.8 + - - +
421L ALA 3.0 9.6 + - - +
423L GLN* 1.3 76.6 - - - +
425L VAL* 1.3 64.0 + - - +
426L GLU 3.1 2.9 - - - -
427L VAL* 3.1 51.1 + - - +
428L TRP* 3.2 41.1 + - + +
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Residues in contact with VAL 425 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L LEU* 3.6 21.1 - - + +
101L GLY* 3.8 31.2 - - - -
102L ALA* 4.4 2.2 - - - +
105L MET* 4.5 6.1 - - - -
242L PHE* 3.9 15.5 - - + -
246L TYR* 3.7 35.4 - - + -
421L ALA 3.2 15.8 + - - +
422L ALA 4.0 1.3 - - - +
423L GLN 3.3 1.2 - - - -
424L GLU* 1.3 76.6 - - - +
426L GLU* 1.3 61.4 + - - +
428L TRP* 3.5 14.0 + - + -
429L LEU* 3.1 22.5 + - + +
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Residues in contact with GLU 426 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243L ARG* 3.4 23.4 + - - -
246L TYR* 2.9 42.9 + - - +
247L LYS* 3.9 22.6 + - - -
250L ARG* 4.0 11.4 + - - +
423L GLN 3.7 10.1 - - - +
425L VAL* 1.3 77.4 - - - +
427L VAL* 1.3 60.1 + - + +
429L LEU* 3.6 4.5 - - - +
430L ASP* 3.2 40.3 + - - +
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Residues in contact with VAL 427 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423L GLN 5.3 1.3 - - - +
424L GLU* 3.1 42.4 + - - +
426L GLU* 1.3 82.3 - - + +
428L TRP* 1.3 73.1 + - + +
430L ASP* 3.5 5.8 + - - +
431L LYS* 3.2 31.5 + - + +
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Residues in contact with TRP 428 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L LEU* 4.0 29.7 - - + +
97L ASN* 3.3 44.4 - - + +
98L LEU* 3.8 20.9 - - + +
101L GLY* 4.4 1.6 - - - -
286L PHE* 3.1 52.8 + + + +
297L TYR* 4.6 4.5 - + + +
421L ALA 4.6 2.2 - - - -
424L GLU* 3.2 40.1 + - + +
425L VAL* 3.7 32.1 - - + -
427L VAL* 1.3 83.7 - - + +
429L LEU* 1.3 60.5 + - - +
431L LYS* 3.7 2.2 - - + +
432L LEU* 2.8 30.7 + - - +
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Residues in contact with LEU 429 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L LEU* 4.0 21.0 - - + +
213L PHE* 4.3 8.1 - - + -
239L ILE* 4.1 18.6 - - + +
242L PHE* 3.9 28.5 - - + -
243L ARG* 3.4 53.6 - - + +
246L TYR* 4.9 6.7 - - + -
425L VAL 3.1 17.7 + - - +
426L GLU* 3.6 7.2 - - - +
427L VAL 3.2 0.2 - - - -
428L TRP* 1.3 78.5 - - - +
430L ASP* 1.3 54.4 + - - +
432L LEU* 3.2 3.0 + - + +
433L GLU* 2.7 38.0 + - - +
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Residues in contact with ASP 430 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243L ARG* 2.9 32.9 + - - -
426L GLU* 3.2 27.4 - - - +
427L VAL* 3.5 7.2 - - - +
429L LEU* 1.3 80.4 - - - +
431L LYS* 1.3 55.6 + - - +
433L GLU* 3.3 8.3 + - - +
434L ALA* 3.0 28.7 + - - +
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Residues in contact with LYS 431 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L GLU* 5.2 14.4 - - - +
94L LEU* 3.9 28.3 - - + -
288L THR* 6.1 5.6 - - - -
427L VAL* 3.2 23.8 + - + +
428L TRP* 3.7 6.5 - - + +
430L ASP* 1.3 69.9 - - - +
432L LEU* 1.4 71.7 + - - +
433L GLU 3.0 1.3 - - - -
434L ALA* 3.1 6.8 + - + +
435L ASN* 2.9 32.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 432 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L ASN* 3.7 46.7 - - + +
94L LEU* 3.8 15.0 - - + +
95L MET* 4.4 5.6 - - + +
98L LEU* 4.5 10.1 - - + -
213L PHE* 4.4 17.9 - - + -
234L LEU* 3.9 23.1 - - + -
239L ILE* 3.6 26.2 - - + -
428L TRP 2.8 23.5 + - - +
429L LEU* 3.6 7.0 - - + +
431L LYS* 1.4 75.3 - - - +
433L GLU* 1.3 58.3 - - - +
435L ASN* 3.3 4.7 + - - +
436L VAL* 3.0 24.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 433 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236L PRO* 5.1 8.5 - - + +
239L ILE* 3.7 30.5 - - + +
243L ARG* 3.0 25.5 + - - -
429L LEU 2.7 18.7 + - - +
430L ASP* 3.3 7.5 - - - +
432L LEU* 1.3 78.4 - - - +
434L ALA* 1.3 55.6 + - - +
436L VAL* 3.4 4.9 + - + +
437L LYS* 3.0 62.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 434 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430L ASP 3.0 15.6 + - - +
431L LYS* 3.1 8.0 + - - +
433L GLU* 1.3 73.6 - - - +
435L ASN* 1.3 69.2 + - - +
437L LYS* 3.3 10.0 + - - +
438L ALA* 3.0 24.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 435 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L GLU* 2.9 29.0 + - - +
91L ASN* 2.8 26.9 + - - +
94L LEU* 3.9 8.7 - - - +
431L LYS* 2.9 20.1 + - - +
432L LEU 3.4 8.5 - - - +
434L ALA* 1.3 78.9 - - - +
436L VAL* 1.3 64.9 + - - +
438L ALA* 3.4 3.9 + - - -
439L GLY 3.4 3.6 + - - -
440L LYS* 2.8 49.5 + - + +
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Residues in contact with VAL 436 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L ASN* 4.1 5.2 - - - +
234L LEU* 3.3 56.5 - - + +
236L PRO* 5.6 6.3 - - + -
239L ILE* 5.3 2.2 - - + -
432L LEU* 3.0 20.0 + - + +
433L GLU* 3.4 6.9 + - + +
434L ALA 3.2 0.2 - - - -
435L ASN* 1.3 80.1 - - - +
437L LYS* 1.3 58.8 + - - +
439L GLY* 3.0 19.8 + - - -
440L LYS 3.9 13.7 - - - +
441L ASP* 4.9 6.7 - - + +
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Residues in contact with LYS 437 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236L PRO* 4.8 18.0 - - - +
433L GLU* 3.0 54.1 + - - +
434L ALA* 3.7 9.4 - - - +
435L ASN 3.2 0.2 - - - -
436L VAL* 1.3 73.7 - - + +
438L ALA* 1.3 56.4 + - - +
439L GLY* 3.0 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