Contacts of the helix formed by residues 697 - 729 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B ARG* 3.2 29.1 + - + -
584B ILE 5.0 2.9 + - - -
586B TRP* 3.9 22.3 + + + +
587B ASP 4.1 8.7 - - - -
588B PRO* 4.1 7.2 - - + -
593B ILE* 3.8 32.5 - - + +
659C TYR* 3.1 33.6 + + - +
693C ILE* 3.4 22.9 - - + +
695C TYR* 3.3 23.8 - + + +
696C ASN* 1.3 79.1 + - + +
698C LYS* 1.3 65.1 + - - +
699C PHE 3.2 4.5 + - - +
700C ILE* 3.5 6.3 + - + -
701C GLU* 3.5 8.3 + - - +
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Residues in contact with LYS 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B PRO* 5.6 0.6 + - - +
692C VAL* 5.3 1.2 - - - +
693C ILE* 3.7 10.5 + - - +
694C ASN 5.2 0.2 - - - -
695C TYR 3.2 26.1 + - - -
696C ASN* 3.2 21.3 + - - +
697C HIS* 1.3 73.4 - - - +
699C PHE* 1.3 59.9 + - - +
701C GLU* 2.7 37.9 + - - +
702C ASN* 2.9 38.0 + - - +
1001C Y01 3.7 28.7 + - + +
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Residues in contact with PHE 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B PRO 4.8 13.9 + - - +
593B ILE* 3.3 33.0 - - + +
594B ILE* 3.8 43.7 - - + -
597B GLY* 3.9 12.8 - - - -
598B LEU* 4.6 8.7 - - + -
697C HIS 3.2 0.4 - - - -
698C LYS* 1.3 76.7 - - - +
700C ILE* 1.3 58.4 + - - +
702C ASN* 3.2 4.2 + - - +
703C ILE* 3.0 38.7 + - + +
1001C Y01 3.5 66.2 + - + +
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Residues in contact with ILE 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B ILE* 4.0 35.0 - - + +
596B GLU* 4.6 12.3 - - + +
597B GLY* 4.7 1.8 - - - -
655C LEU* 3.8 33.1 - - + +
656C TYR* 3.7 18.6 + - + -
659C TYR* 3.4 41.7 - - + +
693C ILE* 4.5 6.7 - - + -
697C HIS* 3.5 10.3 + - + +
698C LYS 3.4 0.2 - - - -
699C PHE* 1.3 77.9 - - + +
701C GLU* 1.3 59.9 + - - +
703C ILE* 3.3 9.6 + - - +
704C GLY* 2.9 23.2 + - - -
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Residues in contact with GLU 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B LYS* 5.7 0.5 + - - -
656C TYR* 3.8 9.5 + - - -
691C VAL 3.6 14.4 - - - +
692C VAL* 4.2 18.5 - - - +
693C ILE* 3.8 18.8 + - + +
697C HIS 3.5 10.1 + - - +
698C LYS* 2.7 46.1 + - - +
699C PHE 3.3 0.6 - - - -
700C ILE* 1.3 79.2 - - - +
702C ASN* 1.3 60.9 + - - +
704C GLY* 3.3 1.6 + - - -
705C TYR* 2.9 54.9 + - + -
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Residues in contact with ASN 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672B GLU* 5.0 3.0 + - - +
676B LYS* 5.4 1.6 + - - -
1004B SBJ 3.4 37.4 + - - +
698C LYS* 2.9 25.6 + - - +
699C PHE 3.2 3.3 + - - +
701C GLU* 1.3 78.5 - - - +
703C ILE* 1.3 62.6 + - - +
705C TYR* 3.6 10.8 - - - +
706C VAL* 3.0 34.9 + - - +
1001C Y01 2.6 48.3 + - + +
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Residues in contact with ILE 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B GLY* 3.7 22.9 - - - +
600B ALA* 4.8 0.9 - - + -
601B ILE* 3.7 31.4 - - + -
655C LEU* 3.8 19.7 - - + -
699C PHE* 3.0 34.4 + - + +
700C ILE* 3.6 9.2 - - - +
702C ASN* 1.3 76.0 - - - +
704C GLY* 1.3 55.7 + - - +
706C VAL* 3.4 4.0 + - - +
707C LEU* 2.9 36.3 + - + +
1001C Y01 3.6 40.2 - - + -
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Residues in contact with GLY 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652C MET* 4.3 4.1 - - - +
655C LEU* 3.7 12.0 - - - +
656C TYR* 3.6 23.8 - - - -
691C VAL* 4.0 8.6 - - - +
700C ILE 2.9 12.3 + - - -
701C GLU 3.3 0.2 + - - -
702C ASN 3.3 0.2 - - - -
703C ILE* 1.3 76.9 - - - +
705C TYR* 1.3 56.4 + - - +
707C LEU* 3.9 3.8 - - - +
708C TYR* 3.0 31.9 + - - +
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Residues in contact with TYR 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B LYS* 4.4 26.7 + - + +
680B TRP* 4.0 14.0 - + - -
1004B SBJ 3.7 42.3 - - + +
688C VAL* 3.6 26.7 + - + +
691C VAL* 3.8 19.7 - - + +
692C VAL* 3.6 17.1 - - + +
701C GLU* 2.9 54.3 + - + +
702C ASN* 3.6 13.5 - - - +
704C GLY* 1.3 75.3 - - - +
706C VAL* 1.3 57.5 + - - +
708C TYR* 3.9 2.9 - - - +
709C GLY* 3.0 23.7 + - - -
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Residues in contact with VAL 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B ILE* 6.4 0.9 - - + -
1004B SBJ 4.2 57.7 - - + +
702C ASN 3.0 20.4 + - - +
703C ILE* 3.9 4.5 - - + +
705C TYR* 1.3 76.1 - - - +
707C LEU* 1.3 65.1 + - + +
709C GLY* 3.4 1.2 + - - -
710C VAL* 3.0 39.3 + - + +
1001C Y01 3.8 39.3 - - + -
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Residues in contact with LEU 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B ALA* 4.3 22.9 - - + +
601B ILE* 4.7 18.8 - - + -
604B VAL* 4.3 31.2 - - + -
648C PHE* 3.6 15.6 - - + -
651C GLY 4.4 1.3 - - - +
652C MET* 3.9 30.5 - - + -
655C LEU* 4.6 4.7 - - + -
703C ILE* 2.9 29.7 + - + +
704C GLY 4.0 2.5 - - - +
706C VAL* 1.3 82.2 - - + +
708C TYR* 1.3 58.8 + - - +
710C VAL* 3.5 4.8 + - + -
711C TYR* 2.9 28.8 + - - +
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Residues in contact with TYR 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B TRP* 3.5 27.8 - + + -
685B LEU* 4.8 4.5 - - + +
652C MET* 3.9 19.4 - - + +
668C PHE* 4.5 8.5 - + - -
677C THR* 4.1 2.2 + - + +
678C LEU* 4.1 19.1 - - + -
681C ALA* 3.4 14.9 - - + +
686C SER* 3.3 35.4 + - - -
687C GLU 4.0 15.8 + - - -
688C VAL* 4.7 8.7 - - + -
690C SER* 4.5 7.1 + - - -
691C VAL* 4.1 18.4 - - + -
704C GLY 3.0 18.6 + - - +
705C TYR* 3.9 3.4 - - - +
707C LEU* 1.3 77.0 - - - +
709C GLY* 1.3 53.9 + - - +
711C TYR* 3.3 5.3 + + - +
712C ASN* 2.6 49.5 + - - -
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Residues in contact with GLY 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B PHE* 3.9 15.9 - - - -
680B TRP* 3.6 17.1 - - - -
1004B SBJ 4.3 7.2 - - - -
705C TYR 3.0 15.2 + - - -
706C VAL 3.8 2.0 - - - -
708C TYR* 1.3 75.7 - - - +
710C VAL* 1.3 57.8 + - - +
712C ASN* 3.3 3.2 + - - +
713C VAL* 3.0 35.3 + - - +
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Residues in contact with VAL 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B VAL* 6.1 0.4 - - + -
1003B S9Y 5.5 6.3 - - + -
1004B SBJ 4.0 54.9 - - + +
648C PHE* 3.7 21.3 - - + -
706C VAL* 3.0 30.9 + - + +
707C LEU* 3.9 7.2 - - + +
709C GLY* 1.3 74.8 - - - +
711C TYR* 1.3 54.1 + - - +
713C VAL* 3.5 5.5 + - - +
714C THR* 2.5 43.8 + - - +
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Residues in contact with TYR 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C VAL* 4.9 0.7 - - + -
645C PHE* 3.4 17.9 - + - -
648C PHE* 3.8 39.4 - + + -
652C MET* 4.6 1.6 - - + -
678C LEU* 2.5 59.7 + - + -
681C ALA* 4.1 15.7 - - + -
682C ILE* 3.9 9.1 - - + +
707C LEU 2.9 18.7 + - - +
708C TYR* 3.5 9.0 - + - +
710C VAL* 1.3 77.4 - - - +
712C ASN* 1.3 71.2 + - - +
714C THR* 3.4 2.0 + - - -
715C MET* 3.0 62.0 + - + +
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Residues in contact with ASN 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B TRP* 3.7 18.0 - - - -
683B PHE* 3.8 34.7 - - + +
685B LEU* 5.0 4.9 - - - +
681C ALA* 4.0 19.9 - - - +
708C TYR* 2.6 52.5 + - - +
709C GLY* 3.3 4.9 + - - +
711C TYR* 1.3 83.1 - - - +
713C VAL* 1.3 62.5 + - - +
715C MET* 3.4 5.1 + - - +
716C VAL* 3.0 28.1 + - - +
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Residues in contact with VAL 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B MET* 5.0 9.4 - - + -
679B PHE* 4.1 14.8 - - + -
683B PHE* 4.0 17.9 - - + -
1004B SBJ 3.8 33.0 - - + -
709C GLY 3.0 18.9 + - - +
710C VAL 4.0 2.9 - - - +
712C ASN* 1.3 75.3 - - - +
714C THR* 1.3 58.5 + - - +
716C VAL* 3.3 7.0 + - + +
717C ILE* 3.0 45.1 + - + +
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Residues in contact with THR 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B S9Y 5.1 8.6 - - + +
1004B SBJ 3.7 31.1 - - + +
644C VAL* 3.8 32.8 - - + -
648C PHE* 4.5 4.8 - - + -
710C VAL* 2.5 31.0 + - - +
711C TYR* 3.8 5.3 - - - -
713C VAL* 1.3 76.9 - - - +
715C MET* 1.3 57.2 + - - +
717C ILE* 3.3 9.4 + - - +
718C VAL* 3.0 33.2 + - + +
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Residues in contact with MET 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641C PHE* 3.5 65.1 - - + +
644C VAL* 3.7 21.5 - - + -
645C PHE* 3.9 7.2 - - + +
682C ILE* 5.4 6.7 - - + -
711C TYR* 3.0 58.2 + - + +
712C ASN* 4.0 4.7 - - - +
714C THR* 1.3 73.5 - - - +
716C VAL* 1.3 61.6 + - + +
718C VAL* 3.9 5.4 - - - +
719C LEU* 3.0 39.4 + - + +
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Residues in contact with VAL 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B PHE* 3.9 23.8 - - + -
722B MET* 6.3 2.5 - - + -
712C ASN 3.0 20.6 + - - +
713C VAL* 3.6 7.2 - - - +
715C MET* 1.3 78.0 - - + +
717C ILE* 1.3 60.3 + - + +
719C LEU* 3.9 5.6 - - + +
720C LEU* 3.0 37.8 + - + +
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Residues in contact with ILE 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627B LEU* 5.1 9.0 - - + -
630B THR* 4.9 9.6 + - - +
631B VAL* 4.6 20.0 - - + -
634B ILE* 3.7 31.4 - - + -
638B MET* 5.1 2.0 - - + -
1004B SBJ 3.8 34.8 - - + -
713C VAL* 3.0 34.7 + - + +
714C THR* 3.6 4.9 - - - +
715C MET 3.3 0.2 - - - -
716C VAL* 1.3 80.0 - - + +
718C VAL* 1.3 60.0 + - + +
720C LEU* 3.4 8.9 + - + +
721C ASN* 2.9 29.0 + - + +
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Residues in contact with VAL 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627B LEU* 4.7 23.6 - - + -
1004B SBJ 6.3 0.7 - - + -
637C PHE* 5.1 11.1 - - + +
640C ILE* 4.9 7.6 - - + -
641C PHE* 4.0 34.5 - - + +
644C VAL* 4.9 13.0 - - + -
714C THR* 3.0 30.2 + - + +
715C MET* 3.9 9.0 - - - +
716C VAL 3.4 0.2 - - - -
717C ILE* 1.3 77.8 - - + +
719C LEU* 1.3 57.2 - - + +
721C ASN* 3.4 9.3 + - - +
722C MET* 3.0 28.3 + - + +
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Residues in contact with LEU 719 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641C PHE* 3.6 27.6 - - + -
682C ILE* 4.2 25.1 - - + +
715C MET* 3.0 23.5 + - + +
716C VAL* 4.1 5.4 - - - +
718C VAL* 1.3 76.6 - - + +
720C LEU* 1.3 58.1 + - - +
722C MET* 3.3 31.8 + - + +
723C LEU* 3.0 28.9 + - - +
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Residues in contact with LEU 720 (chain C).
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* 5.5 2.7 - - - +
634B ILE* 5.0 6.1 - - + -
719B LEU 5.9 0.2 - - - +
722B MET* 4.0 22.7 - - + -
723B LEU* 4.2 25.1 - - + -
726B MET* 3.7 33.2 - - + -
716C VAL* 3.0 26.2 + - + +
717C ILE* 3.9 9.6 - - + +
719C LEU* 1.3 73.6 - - - +
721C ASN* 1.3 62.0 + - + +
723C LEU* 3.4 8.0 + - - +
724C ILE* 3.0 43.1 + - + +
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Residues in contact with ASN 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B LEU 4.8 0.2 + - - -
626B SER* 3.3 26.4 + - - +
627B LEU* 3.5 37.2 - - + +
630B THR* 3.9 22.8 - - - +
637C PHE* 3.9 19.1 - - - -
717C ILE* 2.9 18.8 + - + +
718C VAL* 3.7 5.0 + - - +
720C LEU* 1.3 80.0 - - - +
722C MET* 1.3 56.1 + - - +
724C ILE* 3.5 6.8 + - - +
725C ALA* 2.9 30.1 + - - +
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Residues in contact with MET 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634C ILE* 4.2 24.7 - - + +
637C PHE* 3.9 43.7 - - + -
641C PHE* 6.4 0.9 - - - -
718C VAL* 3.0 17.9 + - + +
719C LEU* 3.6 34.1 - - + +
721C ASN* 1.3 77.2 - - - +
723C LEU* 1.3 56.2 + - - +
725C ALA* 3.4 1.6 + - - +
726C MET* 2.9 46.0 + - - +
716D VAL* 6.3 2.0 - - + -
720D LEU* 4.0 26.7 - - + -
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Residues in contact with LEU 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723B LEU* 4.1 31.2 - - + -
727B ILE* 5.6 0.4 - - + -
719C LEU 3.0 17.8 + - - +
720C LEU* 3.8 6.5 - - + +
722C MET* 1.3 77.8 - - - +
724C ILE* 1.3 58.4 + - - +
726C MET* 3.4 4.7 + - - +
727C ILE* 2.9 50.5 + - + +
720D LEU* 4.2 25.1 - - + -
723D LEU* 4.1 25.4 - - + -
724D ILE* 4.4 9.2 - - + -
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Residues in contact with ILE 724 (chain C).
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* 5.5 9.2 - - + -
723B LEU* 4.4 11.4 - - + -
726B MET* 3.8 47.8 - - + +
727B ILE* 3.9 20.9 - - + +
730B SER* 3.8 25.1 - - - +
720C LEU* 3.0 32.2 + - + +
721C ASN* 4.0 5.8 - - - +
722C MET 3.3 0.2 - - - -
723C LEU* 1.3 75.7 - - + +
725C ALA* 1.3 59.4 + - - +
727C ILE* 3.3 8.4 + - + +
728C ASN* 2.9 28.3 + - + +
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Residues in contact with ALA 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B SER* 5.4 7.4 - - - +
637C PHE* 3.8 26.7 - - + -
721C ASN* 2.9 22.1 + - - +
722C MET 3.8 0.9 - - - +
724C ILE* 1.3 76.9 - - - +
726C MET* 1.3 58.8 + - - +
728C ASN* 3.3 6.3 + - - +
729C SER* 2.9 30.1 + - - -
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Residues in contact with MET 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630C THR* 3.7 35.4 - - + +
633C ASP* 4.2 24.6 - - + +
634C ILE* 3.6 22.4 - - + -
637C PHE* 5.0 4.3 - - + -
722C MET* 2.9 34.6 + - + +
723C LEU 4.0 1.3 - - - +
725C ALA* 1.3 73.3 - - - +
727C ILE* 1.3 65.5 + - - +
728C ASN 3.3 0.2 - - - -
729C SER* 3.6 12.2 + - - +
730C SER* 3.2 20.1 + - - -
720D LEU* 3.7 29.2 - - + -
724D ILE* 3.8 18.9 - - + +
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Residues in contact with ILE 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B ILE* 3.8 37.5 - - + -
731B PHE* 4.5 9.0 - - + -
723C LEU* 2.9 37.3 + - + +
724C ILE* 3.7 5.4 - - - +
726C MET* 1.3 77.0 - - - +
728C ASN* 1.3 62.7 + - - +
730C SER* 3.5 7.8 + - - -
731C PHE* 3.4 31.9 - - + -
723D LEU* 5.6 0.4 - - + -
724D ILE* 3.9 24.2 - - + -
727D ILE* 3.8 35.7 - - + -
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Residues in contact with ASN 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B SER* 4.0 27.4 + - - +
731B PHE* 3.4 35.3 - - + -
724C ILE* 2.9 17.5 + - + +
725C ALA* 3.7 6.5 - - - +
726C MET 3.3 0.2 - - - -
727C ILE* 1.3 79.5 - - - +
729C SER* 1.3 57.0 + - - +
730C SER 3.1 5.0 + - - -
731C PHE* 3.6 4.7 + - - +
732C GLN* 3.4 27.7 + - - +
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Residues in contact with SER 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C ASP* 3.9 19.7 + - - +
725C ALA 2.9 20.0 + - - -
726C MET* 3.6 10.9 - - - +
727C ILE 3.4 0.2 - - - -
728C ASN* 1.3 73.7 - - - +
730C SER* 1.3 63.3 + - - +
732C GLN* 4.3 14.4 - - - -
733C GLU 5.8 0.2 - - - -
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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) + - + + + + + -
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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