Contacts of the helix formed by residues 710 - 742 (chain I) in PDB entry 4P6X
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 GLN 710 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707I ASN* 2.9 21.9 + - - +
708I SER 2.7 1.4 + - - -
709I SER* 1.3 84.6 - - - +
711I ASN* 1.3 61.1 + - - +
712I TRP 3.4 2.5 - - - -
713I GLN* 3.1 20.5 - - + +
714I ARG* 2.8 31.7 + - + +
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Residues in contact with ASN 711 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701I ILE* 3.9 30.9 - - + +
702I VAL* 3.7 33.9 + - + +
704I ARG* 4.9 6.6 - - - +
705I GLU 5.8 2.0 + - - -
706I GLY 6.0 0.2 - - - -
707I ASN* 4.1 9.3 + - - +
708I SER* 2.6 49.0 + - - +
710I GLN* 1.3 71.4 - - - +
712I TRP* 1.3 62.4 + - + +
714I ARG* 3.1 5.3 + - - +
715I PHE* 2.8 28.6 + - - +
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Residues in contact with TRP 712 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708I SER* 4.1 5.5 + - - -
709I SER 5.3 0.8 + - - +
710I GLN 3.4 0.6 - - - -
711I ASN* 1.3 79.6 - - + +
713I GLN* 1.3 66.3 + - - +
715I PHE* 3.3 31.8 + + + +
716I TYR* 2.9 23.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 713 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709I SER 5.1 2.8 + - - +
710I GLN* 3.1 28.6 + - + +
712I TRP* 1.3 77.6 - - - +
714I ARG* 1.3 56.6 + - - +
716I TYR* 3.1 13.2 + - - +
717I GLN* 2.9 59.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 714 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656I LEU* 2.9 36.6 + - - +
657I GLN 3.3 11.5 + - - -
658I VAL* 3.4 8.9 - - - +
662I GLU* 2.6 44.7 + - - -
701I ILE* 3.9 9.9 - - + -
704I ARG* 3.3 37.6 - - - +
710I GLN* 2.8 17.7 + - + +
711I ASN* 3.1 9.8 + - - +
713I GLN* 1.3 70.6 - - + +
715I PHE* 1.3 56.2 + - - +
717I GLN* 3.0 17.8 + - + +
718I LEU* 2.7 48.9 + - + +
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Residues in contact with PHE 715 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694I ILE* 3.7 41.3 - - + -
697I LEU* 4.1 10.8 - - + -
698I GLY* 4.3 9.0 - - - -
701I ILE* 3.6 25.7 - - + +
711I ASN 2.8 15.4 + - - +
712I TRP* 3.5 33.0 - + + +
713I GLN 3.3 0.2 - - - -
714I ARG* 1.3 75.5 - - - +
716I TYR* 1.3 60.2 + - - +
718I LEU* 4.7 0.2 - - - -
719I THR* 2.9 55.5 + - + +
774I PHE* 5.6 1.3 - + - -
775I HIS* 6.5 0.9 - + - -
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Residues in contact with TYR 716 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712I TRP 2.9 13.4 + - - +
713I GLN* 3.1 16.8 - - - +
715I PHE* 1.3 79.4 - - - +
717I GLN* 1.3 64.6 + - + +
719I THR* 3.2 6.4 + - - -
720I LYS* 3.0 51.9 + - + +
775I HIS* 3.6 24.6 + + - -
777I LYS* 3.0 42.7 - - - +
----------------------------------------------------------
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Residues in contact with GLN 717 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655I ARG* 4.4 9.3 + - - +
656I LEU* 4.0 33.9 - - + +
713I GLN* 2.9 49.0 + - + +
714I ARG* 3.4 21.0 + - + +
716I TYR* 1.3 85.6 - - + +
718I LEU* 1.3 59.3 + - + +
720I LYS* 3.2 8.9 - - - +
721I LEU* 2.9 26.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 718 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656I LEU* 3.9 22.7 - - + -
658I VAL* 3.9 21.1 - - + -
662I GLU* 3.6 36.8 - - + +
666I MET* 3.7 18.2 - - + +
697I LEU* 4.3 13.7 - - + -
701I ILE* 3.7 20.6 - - + -
714I ARG* 2.7 33.3 + - + +
715I PHE* 4.1 2.7 - - - +
717I GLN* 1.3 71.2 - - + +
719I THR* 1.3 61.1 + - - +
721I LEU* 3.0 7.1 + - - +
722I LEU* 3.0 30.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 719 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697I LEU* 4.3 10.1 - - + -
715I PHE* 2.9 52.2 + - + +
716I TYR* 3.2 1.4 + - - -
718I LEU* 1.3 76.0 - - - +
720I LYS* 1.3 55.8 + - - +
722I LEU* 3.4 10.2 + - - +
723I ASP* 3.1 31.9 + - - -
774I PHE* 3.6 37.6 - - + -
775I HIS* 2.7 29.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 720 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716I TYR* 3.0 36.6 + - + +
717I GLN* 3.2 10.8 - - - +
719I THR* 1.3 75.7 + - - +
721I LEU* 1.3 64.5 + - - +
723I ASP* 3.3 9.3 + - + +
724I SER* 3.1 22.0 + - - -
775I HIS* 3.4 35.0 + - + +
777I LYS* 3.1 38.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 721 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606I PHE* 4.4 6.1 - - + -
648I TYR* 4.5 3.6 - - + +
649I VAL* 5.5 3.4 - - + +
652I GLU* 3.8 37.7 - - + +
653I LEU* 3.9 23.6 - - + +
656I LEU* 4.3 15.9 - - + -
658I VAL* 4.9 1.1 - - + -
666I MET* 3.6 22.2 - - + -
717I GLN 2.9 13.1 + - - +
718I LEU* 3.0 11.4 + - - +
720I LYS* 1.3 75.0 - - - +
722I LEU* 1.3 62.3 + - - +
724I SER* 2.7 31.4 + - - +
725I MET* 3.3 20.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 722 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606I PHE* 4.9 1.6 - - + -
666I MET* 3.7 42.4 - - + +
669I LEU* 3.7 26.2 - - + -
670I LEU* 3.6 33.4 - - + +
673I SER* 6.0 0.5 - - - -
697I LEU* 4.4 4.3 - - + -
718I LEU 3.0 16.3 + - - +
719I THR* 3.5 12.3 - - - +
720I LYS 3.2 0.2 - - - -
721I LEU* 1.3 74.5 - - - +
723I ASP* 1.3 66.3 + - - +
725I MET* 3.1 22.2 + - + +
726I HIS* 4.1 5.9 + - - -
774I PHE* 3.6 27.8 - - + -
----------------------------------------------------------
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Residues in contact with ASP 723 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719I THR 3.1 11.9 + - - -
720I LYS* 3.3 10.3 + - + +
722I LEU* 1.3 75.2 - - - +
724I SER* 1.3 63.0 + - - +
725I MET 3.1 1.4 + - - -
726I HIS* 3.1 30.4 + - - +
727I GLU 4.4 0.3 + - - -
772I LEU 4.1 1.9 - - - +
773I LEU* 3.4 23.3 - - + +
774I PHE* 2.8 30.9 + - - -
775I HIS* 2.9 43.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 724 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648I TYR* 3.1 29.4 + - - -
720I LYS 3.1 12.0 + - - -
721I LEU* 2.7 28.6 + - - +
723I ASP* 1.3 76.0 - - - +
725I MET* 1.3 60.6 + - - +
726I HIS 3.1 0.4 - - - -
727I GLU* 3.2 21.5 + - - +
728I VAL* 3.3 14.4 + - - +
----------------------------------------------------------
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Residues in contact with MET 725 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602I ALA* 4.1 21.3 - - + +
605I ALA* 4.3 7.9 - - + -
606I PHE* 4.0 31.9 - - + +
648I TYR* 5.5 0.4 - - - -
649I VAL* 3.8 33.7 - - + -
670I LEU* 3.9 25.4 - - + -
721I LEU* 3.3 22.6 + - + +
722I LEU* 3.1 13.8 + - - +
723I ASP 3.1 1.2 - - - -
724I SER* 1.3 75.8 - - - +
726I HIS* 1.3 59.0 + - - +
727I GLU 3.2 0.2 - - - -
728I VAL* 3.6 14.2 - - + +
729I VAL* 2.9 39.7 + - + +
----------------------------------------------------------
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Residues in contact with HIS 726 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670I LEU* 6.5 0.2 - - + -
673I SER* 3.5 30.0 - - - -
674I THR* 3.7 13.1 + - - -
722I LEU 4.5 3.2 + - - -
723I ASP* 3.1 25.2 + - - +
725I MET* 1.3 78.3 - - - +
727I GLU* 1.3 56.8 + - - +
729I VAL* 3.7 5.8 - - - +
730I GLU* 3.0 36.4 + - - +
771I LYS* 3.5 41.2 + - + +
772I LEU 2.8 25.2 + - - -
773I LEU* 3.7 16.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 727 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648I TYR* 5.9 3.8 - - - -
723I ASP 4.4 0.4 + - - -
724I SER* 3.2 14.3 + - - +
726I HIS* 1.3 76.6 - - - +
728I VAL* 1.3 68.1 + - + +
730I GLU* 3.2 17.3 + - - +
731I ASN* 3.1 41.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 728 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605I ALA* 4.7 1.1 - - + -
645I HIS* 3.9 21.8 - - + +
648I TYR* 3.4 39.0 - - + -
649I VAL* 3.9 13.0 - - + -
724I SER 3.3 9.3 + - - +
725I MET* 3.3 24.2 + - + +
727I GLU* 1.3 80.5 - - + +
729I VAL* 1.3 63.1 + - - +
731I ASN* 3.4 9.2 + - - +
732I LEU* 3.0 40.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 729 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598I TYR 4.8 8.5 - - - +
601I MET* 4.2 13.7 - - + +
602I ALA* 3.6 38.4 - - + +
605I ALA* 5.7 0.9 - - + -
725I MET* 2.9 27.3 + - + +
726I HIS* 3.7 7.2 - - - +
727I GLU 3.2 0.2 - - - -
728I VAL* 1.3 75.5 - - + +
730I GLU* 1.3 60.1 + - + +
732I LEU* 3.2 6.0 + - - +
733I LEU* 2.8 54.9 + - + +
----------------------------------------------------------
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Residues in contact with GLU 730 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726I HIS* 3.0 20.2 + - - +
727I GLU* 3.2 16.5 + - - +
729I VAL* 1.3 77.6 - - + +
731I ASN* 1.3 62.8 + - - +
733I LEU* 3.4 7.5 + - - +
734I ASN* 3.1 33.2 + - - +
771I LYS* 2.4 39.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 731 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645I HIS* 3.2 48.2 + - + +
727I GLU* 3.1 37.1 + - - +
728I VAL* 3.5 7.1 - - - +
730I GLU* 1.3 79.7 - - - +
732I LEU* 1.3 61.3 + - - +
734I ASN* 3.3 22.6 + - - +
735I TYR* 3.3 21.9 + - + -
----------------------------------------------------------
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Residues in contact with LEU 732 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601I MET* 3.9 28.3 - - + +
605I ALA* 3.7 30.1 - - + -
642I GLN 3.9 11.9 - - - +
645I HIS* 3.9 22.9 - - + +
646I MET* 4.0 27.1 - - + -
728I VAL* 3.0 27.5 + - + +
729I VAL* 3.9 3.4 - - - +
731I ASN* 1.3 77.7 - - - +
733I LEU* 1.3 56.5 + - - +
735I TYR* 3.5 9.6 + - + +
736I CYS* 2.9 27.4 + - - +
900I HCY 3.9 12.5 - - + +
----------------------------------------------------------
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Residues in contact with LEU 733 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598I TYR 5.1 6.7 - - - +
600I TRP* 4.4 15.7 - - + +
601I MET* 3.9 26.7 - - + -
729I VAL* 2.8 41.8 + - + +
730I GLU* 3.8 7.2 - - + +
732I LEU* 1.3 73.4 - - - +
734I ASN* 1.3 58.9 + - - +
736I CYS* 3.9 2.7 - - + -
737I PHE* 2.7 72.4 + - + -
760I GLN* 6.3 0.9 - - + -
764I TYR* 6.1 0.7 - - + -
----------------------------------------------------------
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Residues in contact with ASN 734 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730I GLU* 3.1 22.1 + - - +
731I ASN* 3.3 15.6 + - - +
733I LEU* 1.3 77.6 - - - +
735I TYR* 1.3 60.4 + - + +
737I PHE* 3.7 3.8 - - - +
738I GLN* 2.8 34.1 + - - +
764I TYR* 3.0 36.4 + - - -
----------------------------------------------------------
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Residues in contact with TYR 735 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641I ASP* 3.1 43.9 + - + +
642I GLN* 3.4 40.2 - - + +
644I LYS* 5.3 0.3 - - - +
645I HIS* 3.9 19.2 - + - -
731I ASN* 3.3 23.1 + - + -
732I LEU* 3.7 10.1 - - + +
734I ASN* 1.3 78.7 - - + +
736I CYS* 1.3 56.7 + - - +
738I GLN* 4.3 17.7 - - - -
739I THR* 2.8 36.0 + - + +
900I HCY 3.1 14.3 - - + +
----------------------------------------------------------
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Residues in contact with CYS 736 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600I TRP* 4.1 22.0 - - - -
601I MET* 3.9 7.6 - - + -
732I LEU 2.9 19.2 + - - +
733I LEU* 3.4 9.9 - - - +
734I ASN 3.2 0.2 - - - -
735I TYR* 1.3 77.4 - - - +
737I PHE* 1.3 68.0 + - - +
739I THR* 3.1 4.3 + - - -
740I PHE* 3.0 24.9 + - - +
749I PHE* 3.8 10.7 - - - -
757I ILE* 3.4 34.1 - - - -
900I HCY 3.2 14.5 + - + -
----------------------------------------------------------
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Residues in contact with PHE 737 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600I TRP* 6.0 0.7 - + - -
733I LEU* 2.7 54.6 + - + +
734I ASN* 3.9 3.4 - - - +
736I CYS* 1.3 78.0 - - - +
738I GLN* 1.3 64.1 + - - +
740I PHE* 3.3 4.5 + - - +
741I LEU* 3.0 35.4 + - + +
757I ILE* 3.8 30.7 - - + -
760I GLN* 4.0 35.0 - - + -
761I ILE* 3.8 22.2 - - + -
764I TYR* 3.7 36.3 - + + -
----------------------------------------------------------
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Residues in contact with GLN 738 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734I ASN 2.8 23.2 + - - +
735I TYR* 3.8 20.5 - - - +
737I PHE* 1.3 74.2 - - - +
739I THR* 1.3 59.3 + - + +
741I LEU* 3.8 4.7 - - - +
742I ASP* 2.8 38.1 + - + +
745I MET* 3.8 24.4 - - + +
----------------------------------------------------------
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Residues in contact with THR 739 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560I MET* 5.0 0.7 - - + -
642I GLN* 4.6 11.4 - - - +
735I TYR* 2.8 25.4 + - + +
736I CYS 3.1 7.8 + - - -
738I GLN* 1.3 79.1 - - + +
740I PHE* 1.3 61.1 + - - +
742I ASP 3.7 13.1 - - - +
743I LYS* 5.4 1.0 - - - +
745I MET* 3.7 23.0 - - + +
747I ILE* 3.5 35.5 - - + +
749I PHE* 3.4 9.2 - - - -
900I HCY 2.5 32.0 + - - +
----------------------------------------------------------
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Residues in contact with PHE 740 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736I CYS 3.0 18.7 + - - +
737I PHE 3.6 3.6 - - - +
738I GLN 3.2 0.2 - - - -
739I THR* 1.3 79.6 + - - +
741I LEU* 1.3 67.7 + - + +
743I LYS* 3.8 15.2 - - - +
749I PHE* 3.8 33.7 - + + -
754I ALA* 3.9 29.8 - - + -
757I ILE* 3.6 27.6 - - + -
758I THR* 3.5 33.7 - - + -
761I ILE* 4.1 14.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 741 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737I PHE* 3.0 26.8 + - + +
738I GLN* 4.1 3.6 - - - +
740I PHE* 1.3 85.8 - - + +
742I ASP* 1.3 58.9 + - - +
743I LYS* 3.1 18.8 + - - +
761I ILE* 3.6 35.7 - - + -
----------------------------------------------------------
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Residues in contact with ASP 742 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738I GLN* 2.8 22.0 + - + +
739I THR 3.7 8.8 - - - +
740I PHE 3.6 0.4 - - - -
741I LEU* 1.3 73.1 - - - +
743I LYS* 1.3 60.2 + - - +
744I THR* 2.7 42.1 + - - +
745I MET* 3.1 44.6 + - + +
----------------------------------------------------------
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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