Contacts of the helix formed by residues 392 - 418 (chain A) in PDB entry 3SV1
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 ASN 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 2.5 17.4 + - - +
391A LYS* 1.3 73.5 - - - +
393A ILE* 1.3 63.5 + - - +
394A ARG 3.1 1.1 - - - -
395A MET* 2.7 48.9 - - - +
396A MET* 3.6 1.0 + - - +
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Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLU* 5.9 0.7 - - - +
389A PRO* 3.3 20.4 - - + -
390A SER* 2.6 45.0 + - - +
392A ASN* 1.3 80.0 + - - +
394A ARG* 1.3 57.8 + - - +
396A MET* 3.3 45.8 - - + +
397A GLN* 3.4 13.2 + - + +
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Residues in contact with ARG 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER* 3.6 13.9 + - - -
389A PRO* 3.2 32.1 - - + +
390A SER 2.7 25.8 + - - +
391A LYS* 4.3 0.2 - - - -
393A ILE* 1.3 71.0 - - - +
395A MET* 1.3 59.0 + - - +
396A MET 2.9 4.7 - - - -
397A GLN* 2.4 55.7 + - - +
398A ALA* 2.8 32.6 + - - +
459A SER* 4.4 10.7 + - - -
460A TYR* 3.5 44.3 - - + +
471A MET* 4.0 10.9 - - - -
500A MET* 4.7 5.7 - - - -
758D GLU* 4.8 2.0 - - - -
763D LYS* 2.6 40.0 - - - +
767D GLN* 3.8 9.1 + - - +
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Residues in contact with MET 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LYS 3.4 12.7 + - - +
392A ASN* 2.7 41.5 - - - +
394A ARG* 1.3 78.3 - - - +
396A MET* 1.3 73.7 + - - +
398A ALA* 3.8 6.8 - - - +
399A GLN* 2.7 53.3 + - - +
460A TYR* 3.4 19.3 + - - +
754D GLN* 5.7 7.4 - - - +
755D ASN 6.4 0.2 - - - -
756D GLY 6.0 0.2 - - - +
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Residues in contact with MET 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ASN 4.3 2.9 - - - +
393A ILE* 3.3 38.8 + - + +
394A ARG 2.9 1.0 - - - -
395A MET* 1.3 84.4 - - - +
397A GLN* 1.3 71.0 + - + +
398A ALA 3.0 0.7 - - - -
399A GLN* 2.6 33.5 + - - +
400A GLU* 3.0 16.5 + - + +
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Residues in contact with GLN 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 3.8 38.6 - - + +
384A LEU 4.6 3.6 + - - -
385A SER* 4.4 9.9 + - - +
389A PRO* 4.9 3.4 - - - +
393A ILE* 3.4 8.3 - - + +
394A ARG* 2.4 73.3 + - - +
396A MET* 1.3 92.0 - - + +
398A ALA* 1.3 59.8 + - - +
400A GLU* 3.1 7.3 + - - +
401A ALA* 2.9 29.6 + - - +
471A MET* 4.1 10.5 - - - +
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ARG 2.8 22.3 + - - +
395A MET* 3.8 10.5 - - - +
397A GLN* 1.3 74.2 - - - +
399A GLN* 1.3 59.5 + - + +
401A ALA* 3.1 19.1 + - - +
402A VAL* 3.1 20.6 + - - +
460A TYR* 4.3 7.2 - - + -
462A ALA* 5.1 8.3 - - + -
469A VAL* 4.6 8.9 - - + +
471A MET* 3.7 24.0 - - + -
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A MET* 2.7 48.4 + - - +
396A MET* 2.6 18.8 + - - +
398A ALA* 1.3 75.7 - - + +
400A GLU* 1.3 56.9 + - - +
401A ALA 3.2 0.2 - - - -
402A VAL* 2.8 30.9 - - + +
403A SER* 3.0 10.6 + - - -
464A ILE* 5.0 24.4 - - + +
754D GLN* 6.0 3.0 - - - +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 6.1 0.9 - - + -
396A MET* 3.0 16.2 + - + +
397A GLN* 3.6 10.8 - - - +
399A GLN* 1.3 77.3 - - - +
401A ALA* 1.3 61.9 + - - +
402A VAL 3.2 0.7 - - - -
403A SER* 3.6 9.8 + - - -
404A ARG* 3.3 21.1 + - - +
407A ARG* 3.5 24.9 + - - -
447B GLN* 5.9 1.7 - - - +
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A THR* 3.1 39.5 - - + +
383A LEU* 4.7 5.2 - - + -
397A GLN 2.9 12.2 + - - +
398A ALA* 3.1 13.9 + - - +
400A GLU* 1.3 81.2 - - - +
402A VAL* 1.3 57.6 + - - +
404A ARG* 3.5 4.8 - - - +
405A VAL* 3.2 15.4 - - - +
469A VAL* 4.8 2.9 - - + -
502A CYS* 3.8 23.3 - - + -
504A VAL* 3.8 2.0 - - + +
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ALA* 3.1 16.2 - - + +
399A GLN* 2.8 31.6 - - + +
401A ALA* 1.3 76.7 - - - +
403A SER* 1.3 64.1 + - - +
404A ARG 3.2 1.6 - - - -
405A VAL* 3.3 8.8 - - - +
406A LYS* 2.8 46.6 + - + +
464A ILE* 5.0 11.4 - - + -
467A ILE* 4.6 10.8 - - + -
469A VAL* 3.4 31.0 - - + -
504A VAL* 4.3 4.7 - - + -
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Residues in contact with SER 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLN 3.0 15.4 + - - -
400A GLU* 3.6 15.1 + - - -
401A ALA 3.5 0.2 - - - -
402A VAL* 1.3 79.9 - - - +
404A ARG* 1.3 67.2 + - - +
406A LYS* 3.5 18.3 + - - +
407A ARG* 2.8 60.3 + - - +
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Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER 3.8 13.6 + - - -
381A THR* 2.8 40.7 + - - +
382A GLN 5.0 0.4 - - - +
400A GLU* 3.3 18.1 + - - +
401A ALA 3.5 4.7 - - - +
403A SER* 1.3 79.9 - - - +
405A VAL* 1.3 56.5 + - - +
407A ARG* 4.5 0.9 - - - +
408A MET* 2.9 49.7 + - - +
372B ILE* 3.7 21.1 - - - +
431B ASP* 2.6 41.5 + - - -
442B LEU* 6.1 0.4 - - - -
444B ALA* 4.0 18.8 + - - +
447B GLN* 3.1 17.8 + - + +
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 3.4 44.2 - - + +
379A GLY* 4.0 3.1 - - - +
380A SER 4.1 13.2 - - - +
401A ALA 3.2 18.4 - - - +
402A VAL* 3.3 10.3 - - - +
404A ARG* 1.3 74.5 - - - +
406A LYS* 1.3 60.4 + - + +
408A MET* 2.8 21.0 - - + +
409A GLN* 2.7 26.9 + - + +
504A VAL* 3.3 27.8 - - + -
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 5.9 7.9 - - + -
402A VAL* 2.8 35.6 + - + +
403A SER* 3.5 32.7 + - - +
405A VAL* 1.3 72.7 - - + +
407A ARG* 1.3 59.7 + - - +
409A GLN* 2.8 24.8 + - - +
410A LYS* 2.9 21.7 + - + +
467A ILE* 6.4 2.7 - - + -
504A VAL* 6.1 1.3 - - + -
369B ASP* 3.9 20.8 + - - -
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Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLU* 3.5 12.9 + - - -
403A SER* 2.8 54.0 + - - +
404A ARG* 4.5 1.2 - - - +
406A LYS* 1.3 77.5 - - - +
408A MET* 1.3 60.2 + - - +
410A LYS* 3.5 6.0 + - - +
411A ALA 3.3 13.0 + - - -
369B ASP* 3.1 46.0 + - - +
370B GLY 3.2 24.0 - - - +
371B ILE* 3.4 2.8 - - - -
372B ILE* 3.2 37.1 + - + +
433B PHE* 3.5 25.6 - - - -
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Residues in contact with MET 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU 3.4 20.6 - - - +
379A GLY* 4.5 7.4 - - - -
380A SER 4.5 5.8 - - - +
404A ARG* 2.9 36.5 + - - +
405A VAL* 2.8 34.5 - - + +
406A LYS 3.1 0.2 - - - -
407A ARG* 1.3 76.7 - - - +
409A GLN* 1.3 65.8 + - + +
411A ALA* 3.7 4.4 - - - +
412A ALA* 3.1 27.5 + - + +
372B ILE* 3.7 19.8 - - + +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 2.9 43.1 - - + +
405A VAL* 2.7 21.7 + - + +
406A LYS* 2.8 13.1 + - - +
408A MET* 1.3 79.9 - - + +
410A LYS* 1.3 55.5 + - + +
411A ALA 3.0 1.1 - - - -
412A ALA* 2.5 28.1 + - - +
413A LYS* 2.6 56.6 + - - +
426A THR* 3.6 31.2 - - - +
427A LEU* 4.1 3.9 - - - +
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 2.9 23.6 + - + +
407A ARG* 3.9 6.3 - - - +
409A GLN* 1.3 76.3 - - + +
411A ALA* 1.3 62.3 + - - +
413A LYS* 3.2 13.3 + - + +
414A ILE* 3.1 30.7 + - + +
366B ASP* 3.9 24.5 + - - +
369B ASP* 2.5 48.9 + - - +
370B GLY 3.5 18.1 + - - +
371B ILE* 3.8 13.9 - - + -
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG 3.3 2.8 + - - -
408A MET 3.7 4.7 - - - +
409A GLN 3.0 0.4 - - - -
410A LYS* 1.3 78.4 - - - +
412A ALA* 1.3 61.9 + - - +
414A ILE* 3.8 3.4 - - - +
415A LYS* 3.2 21.8 + - - +
371B ILE* 3.9 9.7 - - + +
372B ILE 3.3 42.6 - - - +
373B PHE* 3.8 29.5 - - + -
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A MET* 3.1 23.1 + - + +
409A GLN* 2.5 28.3 + - + +
411A ALA* 1.3 69.6 - - - +
413A LYS* 1.3 64.5 + - - +
415A LYS* 3.0 21.6 + - - +
416A LYS* 3.3 5.2 + - - +
426A THR* 4.5 17.2 - - - +
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Residues in contact with LYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A GLN* 2.6 51.3 + - - +
410A LYS* 3.4 14.8 - - + +
412A ALA* 1.3 71.4 - - - +
414A ILE* 1.3 57.2 + - + +
416A LYS* 2.4 41.2 + - - +
417A LYS 3.4 2.4 + - - -
425A GLN* 5.8 2.8 - - + +
426A THR* 4.0 22.0 - - - +
427A LEU* 4.9 4.6 - - - +
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Residues in contact with ILE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LYS 3.2 18.2 - - - +
411A ALA* 3.8 7.6 - - - +
413A LYS* 1.3 80.7 - - + +
415A LYS* 1.3 56.6 + - - +
417A LYS* 2.8 35.3 + - + +
418A ALA* 3.9 2.6 + - - +
366B ASP* 4.3 22.2 - - + +
367B LEU* 6.1 0.7 - - + -
371B ILE* 4.0 32.8 - - + -
373B PHE* 4.7 10.3 - - + -
512B LEU* 5.8 9.9 - - + +
516B SER* 5.1 5.6 - - - +
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ALA 3.2 11.6 + - - +
412A ALA* 3.0 17.6 + - - +
413A LYS 2.9 0.8 + - - -
414A ILE* 1.3 78.6 - - - +
416A LYS* 1.3 57.7 + - - +
417A LYS 3.8 0.2 + - - -
418A ALA* 3.9 17.4 + - - +
373B PHE* 5.2 7.4 - - + -
509B ASP* 5.6 6.7 - - - +
512B LEU* 5.7 9.6 - - + -
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ALA 3.3 5.4 + - - +
413A LYS* 2.4 35.2 + - - +
415A LYS* 1.3 65.7 - - - +
417A LYS* 1.3 51.1 + - - -
418A ALA 3.1 2.7 - - - -
419A ASN* 2.7 48.7 - - + +
425A GLN* 6.2 4.9 - - + -
426A THR* 6.2 3.4 - - - -
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Residues in contact with LYS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LYS 3.4 3.0 + - - -
414A ILE* 2.8 21.1 + - + +
416A LYS* 1.3 76.5 - - - +
418A ALA* 1.3 57.9 + - + +
419A ASN* 2.6 25.0 + - - +
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE 3.9 1.9 + - - +
415A LYS* 3.9 14.0 + - - +
416A LYS 3.1 2.0 - - - -
417A LYS* 1.3 81.0 - - + +
419A ASN* 1.3 57.9 + - - +
512B LEU* 5.1 16.2 - - + -
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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