Contacts of the helix formed by residues 587 - 613 (chain B) in PDB entry 5OC9
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 587 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B PHE* 3.4 32.3 - - - +
585B PRO* 4.6 2.4 - - - +
586B GLU* 1.4 72.5 - - - +
588B LYS* 1.3 62.3 + - - +
589B ALA* 3.3 4.7 - - - +
590B ASP* 3.7 26.9 - - - -
591B LEU 3.6 4.7 + - - -
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Residues in contact with LYS 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A ALA* 4.0 17.9 - - + -
581B ASN* 2.8 42.7 + - - +
584B PHE 2.8 26.7 + - - +
585B PRO* 3.6 14.3 + - - +
586B GLU 2.9 16.3 + - - +
587B SER* 1.3 70.6 - - - +
589B ALA* 1.3 63.3 + - - +
590B ASP 3.4 0.2 - - - -
591B LEU* 3.5 14.3 - - + +
592B ILE* 3.2 29.5 + - + +
704B CA 4.0 5.2 - - - -
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Residues in contact with ALA 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A LYS* 4.0 13.7 - - + -
589A ALA* 4.0 21.3 - - - +
592A ILE* 3.6 26.5 - - + +
587B SER* 5.1 1.8 - - - -
588B LYS* 1.3 75.5 - - - +
590B ASP* 1.4 67.8 + - - +
592B ILE* 3.5 3.7 + - - +
593B LEU* 3.1 27.5 + - + +
704B CA 3.9 5.9 - - - -
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Residues in contact with ASP 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B PHE* 4.3 12.3 - - + -
587B SER* 3.7 28.0 + - - +
588B LYS 3.4 0.2 - - - -
589B ALA* 1.4 77.4 - - - +
591B LEU* 1.3 59.3 + - - +
593B LEU* 3.1 16.9 + - - +
594B ILE* 3.0 37.9 + - + +
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Residues in contact with LEU 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B GLY 3.9 15.0 - - - +
580B VAL* 3.6 32.5 - - + +
581B ASN* 3.4 25.8 - - - +
584B PHE* 3.6 40.3 - - + -
587B SER 3.6 2.5 + - - +
588B LYS* 3.5 25.4 - - + +
590B ASP* 1.3 76.7 - - - +
592B ILE* 1.4 63.3 + - + +
594B ILE* 3.2 5.9 + - - +
595B VAL* 3.0 40.3 + - + +
708B 79M 5.1 1.1 - - + -
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Residues in contact with ILE 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A ALA* 3.7 35.4 - - + +
592A ILE* 3.7 22.4 - - + -
593A LEU* 3.9 33.4 - - + -
596A VAL* 5.1 0.2 - - + -
588B LYS* 3.2 18.8 + - + +
589B ALA 3.8 5.8 - - - +
591B LEU* 1.4 81.8 - - + +
593B LEU* 1.3 53.7 + - - +
595B VAL* 3.2 8.0 + - + +
596B VAL* 2.8 50.3 + - + +
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Residues in contact with LEU 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 3.9 32.1 - - + -
589B ALA* 3.1 22.9 + - + +
590B ASP* 3.1 16.6 + - - +
592B ILE* 1.3 76.0 - - - +
594B ILE* 1.4 57.9 + - + +
596B VAL* 4.0 7.9 - - + +
597B ALA* 3.0 29.6 + - - +
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Residues in contact with ILE 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B PHE* 4.3 16.8 - - + -
590B ASP* 3.0 27.3 + - + +
591B LEU* 3.2 6.9 + - - +
593B LEU* 1.4 75.8 - - + +
595B VAL* 1.4 57.9 + - - +
597B ALA* 3.2 6.8 + - - +
598B VAL* 2.9 40.0 + - + +
708B 79M 3.6 32.3 - - + -
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Residues in contact with VAL 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B CYS* 3.4 33.8 - - + +
572B ALA* 4.6 4.0 - - - +
575B GLY* 3.9 17.0 - - - -
591B LEU* 3.0 25.3 + - + +
592B ILE* 3.5 9.6 - - + +
594B ILE* 1.4 73.6 - - - +
596B VAL* 1.4 55.1 + - + +
598B VAL* 3.2 5.0 + - - +
599B GLU* 2.8 34.0 + - + +
708B 79M 3.7 32.3 - - + -
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Residues in contact with VAL 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU* 6.2 0.2 - - + -
596A VAL* 3.8 43.5 - - + -
592B ILE* 2.8 35.9 + - + +
593B LEU* 4.0 8.1 - - + +
595B VAL* 1.4 71.3 - - + +
597B ALA* 1.3 58.5 + - - +
599B GLU* 3.3 10.2 + - - +
600B HIS* 2.8 60.2 + - + +
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Residues in contact with ALA 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B LEU 3.0 19.7 + - - +
594B ILE* 3.2 8.0 + - + +
596B VAL* 1.3 76.8 - - - +
598B VAL* 1.4 58.2 + - + +
600B HIS* 3.3 8.0 + - - +
601B ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B CYS* 4.4 1.1 - - - -
594B ILE* 2.9 27.8 + - + +
595B VAL* 3.5 9.9 - - - +
597B ALA* 1.4 74.2 - - + +
599B GLU* 1.3 56.3 + - - +
601B ALA* 3.3 8.6 + - - +
602B LEU* 2.9 48.6 + - + +
708B 79M 3.9 33.4 - - + -
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Residues in contact with GLU 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A HIS* 2.8 36.7 + - - -
567B VAL* 3.8 20.1 - - + +
568B VAL* 3.4 27.3 - - - +
571B CYS* 3.8 21.5 - - + -
595B VAL* 2.8 17.1 + - + +
596B VAL* 3.5 9.2 - - - +
597B ALA 3.3 0.2 - - - -
598B VAL* 1.3 77.3 - - - +
600B HIS* 1.3 75.7 + - - +
602B LEU* 3.5 2.1 + - - +
603B LEU* 3.0 38.3 + - + +
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Residues in contact with HIS 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A VAL* 4.5 7.9 - - + -
599A GLU* 2.8 41.0 + - - -
600A HIS* 4.1 4.2 + + - -
603A LEU* 4.6 6.2 - - + +
708A 79M 3.8 44.7 - - + +
596B VAL* 2.8 45.5 + - + +
597B ALA* 3.3 7.8 + - - +
599B GLU* 1.3 88.6 + - - +
601B ALA* 1.3 64.0 + - - +
603B LEU* 3.5 9.9 + - + +
604B ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B ALA 3.0 14.1 + - - +
598B VAL* 3.3 11.2 + - - +
600B HIS* 1.3 76.4 - - - +
602B LEU* 1.4 56.3 + - + +
604B ALA* 3.4 7.0 + - - +
605B LEU* 3.0 40.8 + - + +
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Residues in contact with LEU 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER* 5.7 3.1 - - - +
251B LEU* 3.8 19.1 - - + -
567B VAL* 3.8 10.3 - - + -
571B CYS* 3.8 20.0 - - - -
598B VAL* 2.9 39.9 + - + +
599B GLU 3.8 4.0 - - - +
601B ALA* 1.4 74.3 - - + +
603B LEU* 1.4 54.8 + - - +
605B LEU* 3.2 14.6 + - + +
606B LYS* 2.8 36.2 + - - +
708B 79M 3.8 22.7 - - + -
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Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A HIS* 4.8 5.6 - - - +
708A 79M 4.1 18.6 - - + -
564B VAL* 4.0 26.2 - - + +
567B VAL* 3.9 28.2 - - + +
568B VAL* 5.2 2.2 - - + -
599B GLU* 3.0 45.6 + - + +
600B HIS* 3.8 10.8 - - + +
601B ALA 3.4 0.2 - - - -
602B LEU* 1.4 74.0 - - - +
604B ALA* 1.4 60.0 + - - +
606B LYS* 3.6 4.2 + - + +
607B PHE* 3.2 17.8 + - - +
709B 79M 3.4 39.4 - - + +
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Residues in contact with ALA 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A 79M 4.5 12.7 - - + +
709A 79M 3.8 30.3 - - + +
600B HIS 3.1 13.8 + - - +
601B ALA* 3.6 10.5 - - - +
602B LEU 3.3 0.2 - - - -
603B LEU* 1.4 74.3 - - - +
605B LEU* 1.4 58.3 + - + +
607B PHE* 3.3 5.6 + - - +
608B ILE* 3.0 37.0 + - + +
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Residues in contact with LEU 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B ALA* 3.0 30.6 + - + +
602B LEU* 3.6 16.2 - - + +
604B ALA* 1.4 73.0 - - + +
606B LYS* 1.3 59.9 + - - +
608B ILE* 3.8 17.0 - - + +
609B LEU* 3.0 31.1 + - - +
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Residues in contact with LYS 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LEU* 3.3 26.3 + - - +
254B SER* 3.5 7.3 - - - -
255B THR* 2.8 36.4 + - - +
563B SER* 3.3 44.5 + - - +
564B VAL* 4.7 5.2 - - + -
567B VAL* 3.7 24.7 - - + -
602B LEU 2.8 17.5 + - - +
603B LEU* 3.7 8.1 - - + +
605B LEU* 1.3 75.3 - - - +
607B PHE* 1.4 60.7 + - - +
609B LEU* 3.7 4.8 + - - -
610B ALA* 3.2 23.0 + - - +
709B 79M 3.7 20.1 - - + +
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Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.8 4.3 - - + -
708A 79M 5.0 4.5 - - + -
709A 79M 3.2 68.6 - - + -
711A 79M 4.5 17.9 - - + -
603B LEU 3.2 14.6 + - - +
604B ALA* 3.5 9.0 - - - +
606B LYS* 1.4 74.8 - - - +
608B ILE* 1.4 62.8 + - + +
610B ALA* 3.3 3.5 + - - +
611B PHE* 2.9 44.5 + + + +
709B 79M 3.2 37.0 - - + +
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Residues in contact with ILE 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A TYR* 6.2 3.4 - - + -
709A 79M 3.8 28.0 - - + -
710A 79M 5.3 15.0 - - + -
711A 79M 4.4 23.8 - - + -
604B ALA* 3.0 26.0 + - + +
605B LEU* 3.8 19.1 - - + +
606B LYS 3.5 0.2 - - - -
607B PHE* 1.4 76.7 - - + +
609B LEU* 1.4 52.4 + - - +
611B PHE* 3.2 7.3 + - - +
612B ALA* 2.8 38.2 + - + +
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ILE* 4.4 18.6 - - + +
255B THR* 3.8 26.0 - - + +
256B VAL* 4.0 18.2 - - + -
605B LEU 3.0 17.9 + - - +
606B LYS* 3.9 6.1 - - - +
608B ILE* 1.4 75.7 - - - +
610B ALA* 1.3 57.4 + - - +
612B ALA* 3.4 8.1 + - + +
613B ILE* 3.1 51.3 + - + +
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Residues in contact with ALA 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B THR* 3.9 2.9 - - + +
259B GLU* 3.1 23.4 - - - +
560B GLU* 5.4 0.4 - - - +
606B LYS 3.2 18.2 + - - +
607B PHE* 3.3 5.1 + - + +
609B LEU* 1.3 74.2 - - - +
611B PHE* 1.3 57.8 + - - +
613B ILE 3.1 5.5 - - - +
703B CA 2.4 31.5 - - - -
709B 79M 3.7 28.7 - - - -
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Residues in contact with PHE 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 5.1 14.8 - - + -
711A 79M 3.6 37.9 - - + -
607B PHE* 2.9 34.3 + + + +
608B ILE* 3.5 9.0 - - - +
610B ALA* 1.3 76.0 - - - +
612B ALA* 1.3 65.9 + - - +
613B ILE 4.0 4.0 - - - +
614B PRO* 5.3 1.0 - - - +
703B CA 4.6 0.7 - - - -
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Residues in contact with ALA 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR* 3.4 34.9 + - + +
608B ILE* 2.8 23.9 + - + +
609B LEU* 3.7 9.9 - - + +
611B PHE* 1.3 77.4 - - + +
613B ILE* 1.3 62.3 + - + +
614B PRO* 3.4 11.3 - - - +
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Residues in contact with ILE 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 4.3 18.8 - - + +
259B GLU* 3.1 36.8 - - + +
260B LEU* 5.1 4.5 - - + +
263B ARG* 3.9 24.9 - - - +
609B LEU* 3.1 43.3 + - + +
610B ALA 3.1 0.7 - - - +
611B PHE 4.0 3.2 - - - +
612B ALA* 1.3 75.0 - - + +
614B PRO* 1.4 62.2 - - + +
703B CA 2.4 30.5 - - - -
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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