Contacts of the helix formed by residues 697 - 729 (chain B) in PDB entry 6UZA
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 HIS 697 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A ARG* 3.2 29.1 + - + -
584A ILE 5.0 2.3 + - - -
586A TRP* 3.9 22.7 + + + +
587A ASP 4.1 8.1 - - - -
588A PRO* 4.1 7.0 - - + -
593A ILE* 3.8 32.3 - - + +
659B TYR* 3.1 34.4 + + - +
693B ILE* 3.4 23.4 - - + +
695B TYR* 3.3 25.2 - + + +
696B ASN* 1.3 78.5 - - + +
698B LYS* 1.3 64.9 + - - +
699B PHE 3.2 4.2 + - - +
700B ILE* 3.5 6.2 + - + -
701B GLU* 3.5 8.0 + - - +
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Residues in contact with LYS 698 (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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588A PRO* 5.6 0.6 + - - +
692B VAL* 5.3 1.2 - - - +
693B ILE* 3.7 10.3 + - - +
695B TYR 3.2 27.3 + - - -
696B ASN* 3.2 21.1 + - - +
697B HIS* 1.3 73.1 - - - +
699B PHE* 1.3 59.3 + - - +
700B ILE 3.4 0.2 - - - -
701B GLU* 2.7 37.2 + - - +
702B ASN* 2.9 38.3 + - - +
1001B Y01 3.7 28.3 + - + +
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Residues in contact with PHE 699 (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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588A PRO 4.8 13.2 + - - +
593A ILE* 3.3 33.9 - - + +
594A ILE* 3.8 44.2 - - + -
597A GLY* 3.9 14.1 - - - -
598A LEU* 4.6 8.7 - - + -
697B HIS 3.2 0.4 - - - -
698B LYS* 1.3 76.2 - - - +
700B ILE* 1.3 58.9 + - - +
702B ASN* 3.2 4.0 + - - +
703B ILE* 3.0 37.9 + - + +
1001B Y01 3.5 67.2 + - + +
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Residues in contact with ILE 700 (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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593A ILE* 4.0 34.1 - - + +
596A GLU* 4.6 13.2 - - + +
597A GLY* 4.7 2.5 - - - -
655B LEU* 3.8 33.7 - - + +
656B TYR* 3.7 18.4 + - + -
659B TYR* 3.4 42.0 - - + +
693B ILE* 4.5 5.8 - - + -
697B HIS* 3.5 9.9 + - + +
698B LYS 3.4 0.2 - - - -
699B PHE* 1.3 76.5 - - + +
701B GLU* 1.3 57.1 + - - +
703B ILE* 3.3 9.0 + - - +
704B GLY* 2.9 23.4 + - - -
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Residues in contact with GLU 701 (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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676A LYS* 5.7 0.2 + - - -
656B TYR* 3.8 9.3 + - - -
691B VAL 3.6 14.4 - - - +
692B VAL* 4.2 18.5 - - - +
693B ILE* 3.8 18.1 + - + +
697B HIS 3.5 10.4 + - - +
698B LYS* 2.7 45.8 + - + +
699B PHE 3.3 0.4 - - - -
700B ILE* 1.3 80.5 - - - +
702B ASN* 1.3 59.2 + - - +
704B GLY* 3.3 1.6 + - - -
705B TYR* 2.9 55.6 + - + -
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Residues in contact with ASN 702 (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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672A GLU* 5.0 2.6 + - - +
676A LYS* 5.4 1.7 + - - -
1003A SBJ 3.4 36.1 + - - +
698B LYS* 2.9 25.5 + - - +
699B PHE 3.7 3.6 - - - +
701B GLU* 1.3 78.3 - - - +
703B ILE* 1.3 61.7 + - - +
705B TYR* 3.4 11.5 + - - +
706B VAL* 3.0 34.1 + - - +
1001B Y01 2.6 47.4 + - + +
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Residues in contact with ILE 703 (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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597A GLY* 3.7 23.3 - - - +
600A ALA* 4.8 0.9 - - + -
601A ILE* 3.7 31.9 - - + -
655B LEU* 3.8 17.9 - - + -
699B PHE* 3.0 33.4 + - + +
700B ILE* 3.6 10.3 - - - +
702B ASN* 1.3 75.5 - - - +
704B GLY* 1.3 56.6 + - - +
706B VAL* 3.4 3.8 + - - +
707B LEU* 2.9 35.8 + - + +
1001B Y01 3.6 40.2 - - + -
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Residues in contact with GLY 704 (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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652B MET* 4.3 3.1 - - - +
655B LEU* 3.7 12.3 - - - +
656B TYR* 3.6 23.1 - - - -
691B VAL* 4.0 9.9 - - - +
700B ILE 2.9 11.9 + - - -
701B GLU 3.3 0.2 + - - -
702B ASN 3.3 0.2 - - - -
703B ILE* 1.3 77.7 - - - +
705B TYR* 1.3 53.9 + - - +
707B LEU* 3.5 3.4 + - - +
708B TYR* 3.0 31.7 + - - +
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Residues in contact with TYR 705 (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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676A LYS* 4.4 26.2 + - + +
680A TRP* 4.0 13.6 - + - -
1003A SBJ 3.7 43.6 - - + +
688B VAL* 3.6 28.0 + - + +
691B VAL* 3.8 19.5 - - + +
692B VAL* 3.6 17.3 - - + +
701B GLU* 2.9 53.7 + - + +
702B ASN* 3.6 13.9 - - - +
703B ILE 3.3 0.2 - - - -
704B GLY* 1.3 76.9 - - - +
706B VAL* 1.3 56.3 + - - +
708B TYR* 3.5 2.9 + - - +
709B GLY 3.0 23.2 + - - -
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Residues in contact with VAL 706 (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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601A ILE* 6.4 1.1 - - + -
1003A SBJ 4.2 55.5 - - + +
702B ASN 3.0 21.1 + - - +
703B ILE* 3.9 4.0 - - - +
705B TYR* 1.3 75.1 - - - +
707B LEU* 1.3 65.5 + - + +
709B GLY* 3.4 0.7 + - - -
710B VAL* 3.0 39.7 + - + +
1001B Y01 3.8 39.5 - - + -
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Residues in contact with LEU 707 (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 ALA* 4.3 23.1 - - + +
601A ILE* 4.7 18.2 - - + -
604A VAL* 4.3 32.1 - - + -
648B PHE* 3.6 15.7 - - + -
651B GLY 4.4 1.3 - - - +
652B MET* 3.9 30.7 - - + -
655B LEU* 4.6 4.5 - - + -
703B ILE* 2.9 28.8 + - + +
704B GLY 4.0 3.1 - - - +
706B VAL* 1.3 81.7 - - + +
708B TYR* 1.3 57.2 + - - +
710B VAL* 3.5 4.6 + - + -
711B TYR* 2.9 28.8 + - - +
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Residues in contact with TYR 708 (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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680A TRP* 3.5 26.5 - + + -
685A LEU* 4.8 4.4 - - + +
652B MET* 3.9 19.9 - - + +
668B PHE* 4.5 7.6 - + - -
677B THR* 4.1 1.6 + - + -
678B LEU* 4.1 18.4 - - + -
681B ALA* 3.4 15.9 - - + +
686B SER* 3.3 35.3 + - - -
687B GLU 4.0 16.4 + - - -
688B VAL* 4.7 8.5 - - + -
690B SER* 4.5 7.2 + - - -
691B VAL* 4.1 17.9 - - + -
704B GLY 3.0 19.0 + - - +
705B TYR* 3.9 4.0 - - - +
707B LEU* 1.3 77.9 - - - +
709B GLY* 1.3 54.8 + - - +
711B TYR* 3.3 5.0 + + - +
712B ASN* 2.6 50.4 + - - -
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Residues in contact with GLY 709 (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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679A PHE* 3.9 16.9 - - - -
680A TRP* 3.6 16.9 - - - -
1003A SBJ 4.3 7.2 - - - -
705B TYR 3.0 14.6 + - - -
706B VAL 3.8 2.2 - - - -
708B TYR* 1.3 75.7 - - - +
710B VAL* 1.3 57.5 + - - +
712B ASN* 3.3 3.1 + - - +
713B VAL* 3.0 34.8 + - - +
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Residues in contact with VAL 710 (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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604A VAL* 6.1 0.2 - - + -
1002A S9Y 5.5 5.8 - - + -
1003A SBJ 4.0 54.0 - - + +
648B PHE* 3.7 21.1 - - + -
706B VAL* 3.0 30.7 + - + +
707B LEU* 3.9 7.0 - - + +
709B GLY* 1.3 75.7 - - - +
711B TYR* 1.3 54.0 + - - +
713B VAL* 3.5 5.8 + - - +
714B THR* 2.5 43.7 + - - +
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Residues in contact with TYR 711 (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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644B VAL* 4.9 0.4 - - + -
645B PHE* 3.4 17.4 - + - -
648B PHE* 3.8 40.1 - + + -
652B MET* 4.6 1.8 - - + -
678B LEU* 2.5 59.3 + - + -
681B ALA* 4.1 15.9 - - + -
682B ILE* 3.9 9.2 - - + +
707B LEU 2.9 18.5 + - - +
708B TYR* 3.5 9.2 - + - +
709B GLY 3.3 0.2 - - - -
710B VAL* 1.3 78.1 - - - +
712B ASN* 1.3 72.2 + - - +
714B THR* 3.4 1.6 + - - -
715B MET* 3.0 63.2 + - + +
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Residues in contact with ASN 712 (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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680A TRP* 3.7 17.9 - - - -
683A PHE* 3.8 34.1 - - + +
685A LEU* 5.0 5.0 - - - +
681B ALA* 4.0 20.1 - - - +
708B TYR* 2.6 52.8 + - - +
709B GLY* 3.3 4.9 + - - +
711B TYR* 1.3 81.3 - - - +
713B VAL* 1.3 63.3 + - - +
715B MET* 3.4 4.6 + - - +
716B VAL* 3.0 28.6 + - - +
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Residues in contact with VAL 713 (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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638A MET* 5.0 8.7 - - + -
679A PHE* 4.1 15.5 - - + -
683A PHE* 4.0 17.0 - - + -
1003A SBJ 3.8 32.8 - - + -
709B GLY 3.0 18.2 + - - +
710B VAL 4.0 3.4 - - - +
712B ASN* 1.3 75.2 - - - +
714B THR* 1.3 57.4 + - - +
716B VAL* 3.3 8.0 + - + +
717B ILE* 3.0 45.5 + - + +
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Residues in contact with THR 714 (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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1002A S9Y 5.1 8.4 - - + +
1003A SBJ 3.7 31.2 - - + +
644B VAL* 3.8 33.0 - - + -
648B PHE* 4.5 4.8 - - + -
710B VAL* 2.5 30.1 + - - +
711B TYR* 3.8 4.7 - - - -
713B VAL* 1.3 76.4 - - - +
715B MET* 1.3 58.2 + - - +
717B ILE* 3.3 9.5 + - - +
718B VAL* 3.0 33.4 + - + +
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Residues in contact with MET 715 (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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641B PHE* 3.5 62.8 - - + +
644B VAL* 3.7 21.3 - - + -
645B PHE* 3.9 7.4 - - + +
682B ILE* 5.4 6.5 - - + -
711B TYR* 3.0 58.6 + - + +
712B ASN* 4.0 4.9 - - - +
714B THR* 1.3 73.5 - - - +
716B VAL* 1.3 62.0 + - + +
718B VAL* 3.9 5.6 - - - +
719B LEU* 3.0 40.0 + - + +
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Residues in contact with VAL 716 (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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683A PHE* 3.9 23.8 - - + -
722A MET* 6.3 2.7 - - + -
712B ASN 3.0 20.5 + - - +
713B VAL* 3.6 8.3 - - + +
715B MET* 1.3 77.3 - - + +
717B ILE* 1.3 59.2 + - + +
719B LEU* 3.5 5.3 + - + +
720B LEU* 3.0 37.2 + - + +
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Residues in contact with ILE 717 (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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627A LEU* 5.1 9.2 - - + -
630A THR* 4.9 9.9 - - - +
631A VAL* 4.6 19.7 - - + -
634A ILE* 3.7 31.4 - - + -
638A MET* 5.1 2.0 - - + -
1003A SBJ 3.8 34.8 - - + -
713B VAL* 3.0 36.3 + - + +
714B THR* 3.6 4.5 - - - +
716B VAL* 1.3 80.4 - - + +
718B VAL* 1.3 58.8 + - + +
720B LEU* 3.4 10.2 + - + +
721B ASN* 2.9 28.6 + - + +
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Residues in contact with VAL 718 (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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627A LEU* 4.7 23.3 - - + -
1003A SBJ 6.3 0.4 - - + -
637B PHE* 5.1 11.5 - - + +
640B ILE* 4.9 7.2 - - + -
641B PHE* 4.0 34.8 - - + +
644B VAL* 4.9 12.6 - - + -
714B THR* 3.0 30.9 + - + +
715B MET* 3.9 9.4 - - - +
716B VAL 3.4 0.2 - - - -
717B ILE* 1.3 78.2 - - + +
719B LEU* 1.3 58.3 + - + +
721B ASN* 3.4 8.3 + - - +
722B MET* 3.0 29.2 + - + +
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Residues in contact with LEU 719 (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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641B PHE* 3.6 28.7 - - + -
682B ILE* 4.2 25.8 - - + +
715B MET* 3.0 24.3 + - + +
716B VAL* 4.1 4.9 - - + +
718B VAL* 1.3 75.4 - - + +
720B LEU* 1.3 58.7 + - - +
722B MET* 3.3 31.1 + - + +
723B LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 720 (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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630A THR* 5.5 2.9 - - - +
634A ILE* 5.0 6.5 - - + -
722A MET* 4.0 22.9 - - + -
723A LEU* 4.2 24.9 - - + -
726A MET* 3.7 33.4 - - + -
716B VAL* 3.0 27.4 + - + +
717B ILE* 3.9 9.2 - - + +
719B LEU* 1.3 72.7 - - - +
721B ASN* 1.3 63.5 + - + +
723B LEU* 3.4 8.5 + - + +
724B ILE* 3.0 42.9 + - + +
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Residues in contact with ASN 721 (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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626A SER* 3.3 27.1 + - - +
627A LEU* 3.5 38.2 - - + +
630A THR* 3.9 23.1 - - - +
637B PHE* 3.9 18.9 - - - -
717B ILE* 2.9 19.3 + - + +
718B VAL* 3.7 5.4 + - - +
720B LEU* 1.3 80.7 - - - +
722B MET* 1.3 55.8 + - - +
724B ILE* 3.5 6.1 + - - +
725B ALA* 2.9 30.0 + - - +
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Residues in contact with MET 722 (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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634B ILE* 4.2 24.2 - - + -
637B PHE* 3.9 44.2 - - + -
641B PHE* 6.4 1.1 - - - -
718B VAL* 3.0 18.5 + - + +
719B LEU* 3.6 32.1 - - + +
720B LEU 3.3 0.2 - - - -
721B ASN* 1.3 77.2 - - - +
723B LEU* 1.3 57.2 + - - +
725B ALA* 3.4 1.2 + - - +
726B MET* 2.9 46.8 + - - +
716C VAL* 6.3 2.9 - - + -
720C LEU* 4.0 26.5 - - + -
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Residues in contact with LEU 723 (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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723A LEU* 4.1 31.0 - - + -
727A ILE* 5.6 0.2 - - + -
719B LEU 3.0 17.0 + - - +
720B LEU* 3.8 7.2 - - - +
722B MET* 1.3 76.5 - - - +
724B ILE* 1.3 58.9 + - - +
726B MET* 3.4 3.9 + - - +
727B ILE* 2.9 50.0 + - + +
720C LEU* 4.2 27.4 - - + -
723C LEU* 4.1 24.9 - - + -
724C ILE* 4.4 8.5 - - + -
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Residues in contact with ILE 724 (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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630A THR* 5.5 8.1 - - + -
723A LEU* 4.4 11.2 - - + -
726A MET* 3.8 47.8 - - + +
727A ILE* 3.9 21.5 - - + +
730A SER* 3.8 25.4 - - - +
720B LEU* 3.0 32.2 + - + +
721B ASN* 4.0 6.5 - - - +
723B LEU* 1.3 76.0 - - + +
725B ALA* 1.3 57.7 + - - +
727B ILE* 3.3 8.1 + - - +
728B ASN* 2.9 27.6 + - + +
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Residues in contact with ALA 725 (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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626A SER* 5.4 7.0 - - - +
637B PHE* 3.8 26.9 - - + -
721B ASN* 2.9 23.0 + - - +
722B MET 3.8 1.1 - - - +
724B ILE* 1.3 77.4 - - - +
726B MET* 1.3 58.9 + - - +
728B ASN* 3.3 6.5 + - - +
729B SER* 2.9 30.0 + - - -
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Residues in contact with MET 726 (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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630B THR* 3.7 35.7 - - + +
633B ASP* 4.2 25.5 - - + +
634B ILE* 3.6 22.4 - - + -
637B PHE* 5.0 4.0 - - + -
722B MET* 2.9 33.4 + - + +
723B LEU* 4.0 2.0 - - - +
725B ALA* 1.3 74.8 - - - +
727B ILE* 1.3 64.7 + - - +
729B SER* 3.6 12.0 + - - +
730B SER* 3.2 19.9 + - - -
720C LEU* 3.7 28.5 - - + -
724C ILE* 3.8 19.1 - - + +
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Residues in contact with ILE 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ILE* 3.8 37.7 - - + -
731A PHE* 4.5 9.2 - - + -
723B LEU* 2.9 36.7 + - + +
724B ILE* 3.7 6.3 - - - +
726B MET* 1.3 77.9 - - - +
728B ASN* 1.3 61.5 + - - +
730B SER* 3.5 7.8 + - - -
731B PHE* 3.4 30.7 - - + -
723C LEU* 5.6 0.2 - - + -
724C ILE* 3.9 23.1 - - + -
727C ILE* 3.8 36.6 - - + -
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Residues in contact with ASN 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A SER* 4.0 28.5 + - - +
731A PHE* 3.4 34.9 - - + -
724B ILE* 2.9 17.7 + - + +
725B ALA* 3.7 7.0 - - - +
726B MET 3.3 0.2 - - - -
727B ILE* 1.3 78.6 - - - +
729B SER* 1.3 57.6 + - - +
730B SER 3.1 4.9 + - - -
731B PHE* 3.6 5.0 + - - +
732B GLN* 3.4 27.3 + - - +
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Residues in contact with SER 729 (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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633B ASP* 3.9 19.5 + - - +
725B ALA 2.9 19.8 + - - -
726B MET* 3.6 11.3 - - - +
727B ILE 3.4 0.4 - - - -
728B ASN* 1.3 72.3 - - - +
730B SER* 1.3 62.8 + - - +
732B GLN* 4.3 13.7 - - - -
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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) + - + + + + + -
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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