Contacts of the helix formed by residues 510 - 537 (chain B) in PDB entry 4L6V
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 GLY 510 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B GLU* 3.8 3.8 - - - -
455B PRO* 3.4 11.1 - - - +
508B THR* 4.3 0.8 + - - +
509B ILE* 1.3 73.7 - - - +
511B PRO* 1.3 73.2 - - - +
512B GLY 3.1 3.4 - - - -
513B ASP* 2.9 31.5 + - - +
514B PHE 3.4 4.2 + - - -
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Residues in contact with PRO 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU* 3.6 46.9 - - + -
453B ILE 3.3 25.2 + - - +
454B GLU* 3.6 16.4 - - + +
510B GLY* 1.3 84.6 - - - +
512B GLY* 1.3 62.5 + - - +
514B PHE* 3.2 16.5 + - - +
515B LEU* 3.6 14.5 + - - +
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Residues in contact with GLY 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TYR* 4.1 5.9 + - - -
510B GLY* 3.1 1.8 - - - -
511B PRO* 1.3 78.9 - - - +
513B ASP* 1.3 61.1 + - - +
515B LEU* 3.8 6.3 + - - +
516B VAL* 3.0 25.9 + - - +
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Residues in contact with ASP 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PRO* 4.6 1.8 - - + -
508B THR 4.5 3.4 - - - +
509B ILE* 3.6 31.5 - - + +
510B GLY* 2.9 29.3 + - - +
512B GLY* 1.3 79.9 - - - +
514B PHE* 1.3 64.9 + - - +
515B LEU 3.2 1.0 + - - -
516B VAL* 3.5 8.7 + - - +
517B HIS* 3.0 38.2 + - + +
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Residues in contact with PHE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 4.6 4.5 - - + -
453B ILE* 3.2 69.8 - - + +
454B GLU 4.4 7.2 - - - -
455B PRO* 3.8 19.2 - - + +
510B GLY 3.4 2.6 + - - -
511B PRO 3.2 6.2 + - - +
513B ASP* 1.3 79.9 - - - +
515B LEU* 1.3 82.8 + - + +
517B HIS* 3.7 4.1 + - - +
518B HIS* 3.3 56.8 + + - -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B THR* 4.1 9.1 - - + +
434B LEU* 3.4 39.0 - - + -
435B TYR* 3.0 48.0 - - + +
438B ASN* 4.7 15.0 - - - +
451B ILE 4.9 5.8 - - - +
452B LEU* 6.4 0.9 - - + -
453B ILE* 4.5 3.4 - - + -
511B PRO* 3.6 14.7 + - + +
512B GLY* 3.8 6.3 + - - +
513B ASP 3.2 0.4 - - - -
514B PHE* 1.3 91.2 - - + +
516B VAL* 1.3 58.7 + - - +
517B HIS 3.1 2.0 - - - -
518B HIS* 3.2 7.4 + - + +
519B ALA* 2.9 26.3 + - - +
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Residues in contact with VAL 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TYR* 3.5 9.8 + - - +
512B GLY 3.0 22.7 - - - +
513B ASP* 3.8 12.6 - - - +
515B LEU* 1.3 74.8 - - - +
517B HIS* 1.3 57.0 + - - +
519B ALA* 3.4 11.9 + - + +
520B ILE* 2.9 40.1 + - + +
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Residues in contact with HIS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B ILE* 5.6 8.1 - - + -
513B ASP* 3.0 34.2 + - + +
514B PHE* 3.8 6.3 - - - +
515B LEU 3.1 0.2 - - - -
516B VAL* 1.3 78.7 - - - +
518B HIS* 1.3 65.5 + - + +
520B ILE* 3.1 17.4 + - + +
521B ALA* 2.8 28.2 + - - +
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Residues in contact with HIS 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B PHE* 6.5 0.9 - + - -
427B LEU* 4.1 21.1 - - + +
431B THR* 3.5 20.8 + - + +
514B PHE* 3.3 49.5 + + + +
515B LEU* 3.2 10.0 + - + +
517B HIS* 1.3 77.3 - - + +
519B ALA* 1.3 61.8 + - - +
521B ALA* 3.5 8.4 - - + +
522B LEU* 2.9 27.0 + - - +
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B THR* 4.0 18.5 - - + +
435B TYR* 5.2 3.8 - - + -
515B LEU 2.9 13.2 + - - +
516B VAL* 3.4 18.8 - - + +
518B HIS* 1.3 78.8 - - - +
520B ILE* 1.3 56.3 + - + +
522B LEU* 3.4 12.4 - - + +
523B GLY* 3.1 20.1 + - - -
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Residues in contact with ILE 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B VAL* 2.9 26.6 + - + +
517B HIS* 3.4 20.2 - - + +
519B ALA* 1.3 75.7 - - + +
521B ALA* 1.3 58.5 + - - +
522B LEU 3.1 0.2 - - - -
523B GLY* 2.7 21.1 + - - +
524B LEU* 2.8 34.7 + - + +
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Residues in contact with ALA 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 3.8 16.6 - - + -
517B HIS 2.8 12.9 + - - +
518B HIS* 3.3 13.7 + - - +
520B ILE* 1.3 77.1 - - - +
522B LEU* 1.3 57.2 + - - +
524B LEU* 3.8 7.1 - - - +
525B HIS* 2.9 45.2 + - + +
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Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B SER* 3.3 30.5 - - - +
427B LEU* 3.7 15.2 - - + +
428B GLY* 3.6 25.6 - - - +
431B THR* 5.3 5.6 - - + +
432B LEU* 6.5 0.2 - - + -
518B HIS 2.9 14.0 + - - +
519B ALA* 3.4 15.0 - - + +
520B ILE 3.1 0.2 - - - -
521B ALA* 1.3 76.0 - - - +
523B GLY* 1.3 62.6 + - - +
525B HIS* 4.8 0.7 - - - -
526B THR* 2.9 44.3 + - - +
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Residues in contact with GLY 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ALA 3.1 10.3 + - - -
520B ILE* 2.7 16.4 + - - -
522B LEU* 1.3 73.6 - - - +
524B LEU* 1.3 58.3 + - - +
526B THR* 4.7 1.5 - - - -
527B THR* 2.6 31.5 + - - -
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ILE* 2.8 36.6 + - + +
521B ALA* 3.2 6.9 + - - +
523B GLY* 1.3 76.1 - - - +
525B HIS* 1.3 63.1 + - + +
527B THR* 3.6 4.3 + - - -
528B ALA* 3.0 29.7 + - - +
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Residues in contact with HIS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU* 3.2 25.4 - - + +
423B VAL* 3.4 34.8 - - + +
424B SER* 3.7 14.4 - - - +
427B LEU* 4.2 9.1 - - + +
521B ALA* 2.9 34.3 + - + +
522B LEU 4.2 1.1 - - - +
524B LEU* 1.3 79.2 - - + +
526B THR* 1.3 55.1 + - - +
528B ALA* 3.1 3.6 + - - +
529B LEU 2.7 30.8 + - - -
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Residues in contact with THR 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B SER* 3.2 22.7 + - - +
522B LEU* 2.9 27.6 + - - +
523B GLY* 4.7 1.8 - - - -
525B HIS* 1.3 76.6 - - - +
527B THR* 1.3 62.3 + - - +
529B LEU* 3.3 15.6 + - + +
530B ILE* 3.1 34.9 + - + +
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Residues in contact with THR 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 4.8 11.9 - - + -
523B GLY 2.6 24.1 + - - -
524B LEU* 3.9 5.2 - - - -
525B HIS 3.3 0.4 - - - -
526B THR* 1.3 78.2 - - - +
528B ALA* 1.3 60.4 + - - +
530B ILE* 3.6 11.8 + - + +
531B LEU* 3.2 41.7 + - + +
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Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PHE* 5.1 9.4 - - + -
420B LEU* 4.2 5.2 - - + -
524B LEU 3.0 18.8 + - - +
525B HIS* 3.5 6.7 - - - +
527B THR* 1.3 74.7 - - - +
529B LEU* 1.3 57.9 + - - +
531B LEU* 4.6 6.5 - - - +
532B ILE* 2.7 56.9 + - + +
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 4.6 3.8 - - - +
696A LEU* 4.1 23.8 - - + -
417B ILE* 3.8 39.2 - - + +
420B LEU* 3.9 25.3 - - + +
421B SER* 4.2 17.0 - - - +
424B SER* 4.5 9.0 - - - +
525B HIS 2.7 17.4 + - - +
526B THR* 3.3 20.2 + - + +
528B ALA* 1.3 72.7 - - - +
530B ILE* 1.3 59.1 + - + +
532B ILE* 4.2 0.3 - - - +
533B LYS* 2.9 33.3 + - - +
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Residues in contact with ILE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 3.5 37.5 - - + +
526B THR* 3.1 30.6 + - + +
527B THR* 3.9 11.4 - - + +
528B ALA 3.3 0.2 - - - -
529B LEU* 1.3 79.3 - - + +
531B LEU* 1.3 62.7 + - + +
533B LYS* 3.7 1.4 - - - +
534B GLY* 2.9 28.6 + - - -
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Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET* 4.4 1.1 - - + +
382B VAL* 3.9 38.1 - - + +
385B PHE* 3.6 50.8 - - + +
386B ALA* 4.9 4.5 - - + +
389B ALA* 5.2 1.2 - - - +
527B THR* 3.2 35.5 + - + +
528B ALA* 4.0 1.3 - - - +
530B ILE* 1.3 84.5 - - + +
532B ILE* 1.3 63.1 + - - +
534B GLY* 3.6 1.6 + - - -
535B ALA* 3.2 22.5 + - - +
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Residues in contact with ILE 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PHE* 3.9 29.8 - - + -
416B LEU* 5.3 7.6 - - + -
417B ILE* 5.2 4.3 - - + -
420B LEU* 3.7 25.1 - - + -
528B ALA* 2.7 36.6 + - + +
529B LEU 4.2 1.3 - - - +
531B LEU* 1.3 70.0 - - - +
533B LYS* 1.3 65.5 + - - +
535B ALA* 3.1 6.6 + - - +
536B LEU* 2.9 45.2 + - + +
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Residues in contact with LYS 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 3.4 56.0 + - + +
695A GLU* 3.2 34.6 + - - +
696A LEU* 3.6 26.0 - - + +
417B ILE* 3.8 28.4 - - + +
529B LEU 2.9 20.2 + - - +
530B ILE 3.7 1.6 - - - +
532B ILE* 1.3 76.8 - - - +
534B GLY* 1.3 71.4 - - - +
535B ALA 2.9 0.7 + - - -
536B LEU* 2.9 2.4 + - - +
537B ASP* 2.9 40.2 + - - +
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Residues in contact with GLY 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 5.7 1.3 - - - -
389B ALA* 4.1 7.2 - - - +
530B ILE 2.9 15.9 + - - -
531B LEU* 4.0 2.0 - - - -
533B LYS* 1.3 87.7 - - - +
535B ALA* 1.3 56.3 + - - +
537B ASP* 4.2 1.5 - - - -
538B ALA* 3.2 24.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PHE* 4.7 6.5 - - + +
388B GLY 4.5 5.4 - - - +
389B ALA* 3.6 31.6 - - + +
392B PHE* 3.1 22.8 - - + +
531B LEU 3.2 13.3 + - - +
532B ILE* 3.1 12.0 + - + +
533B LYS 3.0 0.8 - - - -
534B GLY* 1.3 77.2 - - - +
536B LEU* 1.3 62.4 + - + +
538B ALA* 3.0 20.1 - - - +
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PHE* 4.2 10.8 - - + -
409B MET* 4.5 18.6 - - + +
410B LEU* 3.8 33.6 - - + +
413B LYS* 3.8 44.8 + - + +
416B LEU* 3.9 17.0 - - + -
417B ILE* 4.2 9.6 - - + -
532B ILE* 2.9 41.0 + - + +
533B LYS* 3.7 3.4 - - - +
535B ALA* 1.3 79.6 - - + +
537B ASP* 1.3 59.6 + - - +
538B ALA 3.1 3.3 + - - -
539B ARG* 4.1 7.8 + - - +
540B GLY 4.6 0.3 - - - +
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Residues in contact with ASP 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A GLU* 3.6 37.2 - - - +
698A GLU* 5.8 0.2 - - - -
699A SER* 4.6 2.3 + - - -
413B LYS* 2.5 41.2 + - - +
417B ILE* 4.0 8.7 - - - +
533B LYS* 2.9 34.9 + - - +
534B GLY* 4.2 2.9 - - - +
536B LEU* 1.3 72.0 - - - +
538B ALA* 1.3 62.4 - - - +
539B ARG 3.2 2.2 - - - -
540B GLY* 3.2 20.2 + - - +
541B SER* 4.1 11.8 - - - -
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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