Contacts of the helix formed by residues 644 - 672 (chain A) in PDB entry 5FY9
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 ASP 644 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLU* 5.0 18.0 - - + +
469A GLN* 5.6 7.8 - - + +
642A VAL 3.8 2.0 + - - -
643A LEU* 1.3 77.6 - - - +
645A VAL* 1.3 62.2 + - - +
646A VAL* 3.1 31.4 + - - +
647A VAL* 3.4 25.2 + - + +
648A ALA* 2.9 25.6 + - - +
751A ARG* 5.3 1.1 - - - +
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Residues in contact with VAL 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU 4.4 0.2 - - - -
644A ASP* 1.3 76.2 + - - +
646A VAL* 1.3 74.1 + - + +
648A ALA* 3.5 7.7 + - - +
649A SER* 3.1 25.5 + - - -
751A ARG* 3.5 39.7 - - - +
752A ALA* 3.9 10.3 - - - +
753A GLU* 5.1 5.2 - - - +
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Residues in contact with VAL 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A VAL* 5.0 11.2 - - + -
644A ASP* 3.1 10.6 + - - +
645A VAL* 1.3 84.2 - - + +
647A VAL* 1.3 66.9 + - + +
649A SER* 3.3 8.0 + - - -
650A THR* 3.0 34.6 + - - +
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Residues in contact with VAL 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLU 5.0 4.0 - - - +
469A GLN* 4.9 20.9 - - + -
471A VAL* 5.6 3.8 - - + -
474A HIS* 5.1 5.2 - - + -
605A VAL* 3.7 28.0 - - + -
636A MET* 4.6 7.0 - - - -
643A LEU* 4.1 21.3 - - + -
644A ASP* 3.4 28.9 + - + +
646A VAL* 1.3 77.4 - - + +
648A ALA* 1.3 63.5 + - - +
650A THR* 3.0 3.5 + - - -
651A VAL* 2.8 42.3 + - + +
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Residues in contact with ALA 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU* 4.2 7.4 - - + -
644A ASP 2.9 20.8 + - - +
645A VAL* 3.6 6.5 - - - +
646A VAL 3.3 0.2 - - - -
647A VAL* 1.3 72.0 - - - +
649A SER* 1.3 63.1 + - - +
651A VAL* 3.5 1.8 + - - +
652A GLN* 3.0 24.9 + - - +
748A LEU* 3.9 32.9 - - + +
751A ARG* 3.8 25.4 - - + -
752A ALA* 4.3 2.9 - - + -
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Residues in contact with SER 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A VAL 3.1 15.3 + - - -
646A VAL* 3.5 13.0 - - - -
648A ALA* 1.3 76.8 - - - +
650A THR* 1.3 61.9 + - - +
652A GLN* 3.5 9.9 + - - +
653A LYS* 3.3 43.2 + - - +
752A ALA* 3.8 17.2 - - - +
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Residues in contact with THR 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A VAL* 3.5 45.6 - - + +
608A LEU* 4.0 13.8 - - + +
609A PRO* 5.3 4.7 - - + -
646A VAL* 3.0 19.7 + - - +
647A VAL 3.0 4.9 + - - -
649A SER* 1.3 75.2 + - - +
651A VAL* 1.3 67.0 + - - +
652A GLN 3.2 0.4 - - - -
653A LYS* 3.2 23.8 + - + +
654A ASP* 3.3 10.4 + - - +
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Residues in contact with VAL 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A VAL* 6.1 0.2 - - + -
608A LEU* 3.9 15.9 - - + +
633A ILE* 4.0 30.5 - - + +
636A MET* 3.6 33.0 - - + -
643A LEU* 4.6 2.2 - - + -
647A VAL* 2.8 33.5 + - + +
648A ALA 3.8 4.0 - - - +
650A THR* 1.3 77.6 - - - +
652A GLN* 1.3 56.7 + - - +
654A ASP* 3.2 4.1 + - - +
655A MET* 2.8 27.9 + - - +
748A LEU* 3.7 23.3 - - + -
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Residues in contact with GLN 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ALA 3.0 17.8 + - - +
649A SER* 3.5 9.0 + - - +
650A THR 3.2 0.2 - - - -
651A VAL* 1.3 76.9 - - - +
653A LYS* 1.3 60.9 + - - +
655A MET* 3.4 3.0 + - - +
656A ALA* 3.0 28.2 + - + +
745A MET* 3.7 22.0 - - + +
748A LEU* 3.9 20.5 - - + +
749A LYS* 3.4 49.2 - - - +
752A ALA* 4.6 7.6 - - - +
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Residues in contact with LYS 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A SER* 3.3 32.7 + - - +
650A THR* 3.2 15.2 + - + +
651A VAL 3.2 0.6 - - - -
652A GLN* 1.3 78.3 - - + +
654A ASP* 1.3 64.4 + - - +
656A ALA* 3.3 14.8 + - - +
657A ILE* 3.3 20.1 + - + +
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Residues in contact with ASP 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A LEU* 4.2 17.6 - - + +
609A PRO* 4.5 7.2 - - + +
612A ARG* 2.7 49.4 + - - +
629A HIS* 2.9 18.8 + - - -
633A ILE* 3.2 16.6 - - + +
650A THR 3.3 8.2 + - - +
651A VAL 3.2 7.9 + - - +
653A LYS* 1.3 78.4 - - - +
655A MET* 1.3 59.2 + - - +
657A ILE* 3.1 12.7 + - - +
658A MET* 2.9 26.2 + - - +
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Residues in contact with MET 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A ILE* 3.9 13.6 - - + +
634A CYS* 4.4 3.6 - - - -
637A ALA* 3.7 21.8 - - + -
651A VAL 2.8 17.2 + - - +
652A GLN* 3.7 7.0 - - - +
654A ASP* 1.3 76.0 + - - +
656A ALA* 1.3 57.8 + - - +
658A MET* 3.2 21.0 + - + +
659A ILE* 2.9 44.6 + - + +
741A LEU* 4.0 23.3 - - + +
744A MET* 3.7 41.5 - - + -
745A MET* 4.0 13.9 - - - -
748A LEU* 3.8 11.4 - - - -
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Residues in contact with ALA 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A GLN* 3.0 18.3 + - + +
653A LYS* 3.6 8.5 - - - +
654A ASP 3.2 0.2 - - - -
655A MET* 1.3 77.0 - - - +
657A ILE* 1.3 62.2 + - + +
659A ILE* 3.9 2.6 - - - +
660A GLU* 3.0 30.4 + - + +
745A MET* 3.5 23.7 - - + -
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Residues in contact with ILE 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PRO* 6.2 4.3 - - + -
612A ARG* 3.9 17.9 - - - -
653A LYS* 3.3 14.1 + - + +
654A ASP* 3.1 16.4 + - - +
656A ALA* 1.3 74.6 - - + +
658A MET* 1.3 62.5 + - - +
660A GLU* 3.3 6.4 + - - +
661A ASP* 2.8 49.8 + - - +
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Residues in contact with MET 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ARG* 3.5 25.3 - - - +
630A ASP* 3.4 51.8 - - - +
633A ILE* 4.5 6.1 - - + -
634A CYS* 3.7 22.9 - - - -
654A ASP 2.9 8.6 + - - +
655A MET* 3.4 33.9 - - + +
657A ILE* 1.3 77.6 - - - +
659A ILE* 1.3 64.3 + - + +
661A ASP* 3.4 5.1 + - - +
662A GLU* 2.8 30.1 + - - +
701A MET* 3.8 25.4 - - + +
741A LEU* 4.4 1.8 - - + -
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Residues in contact with ILE 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A MET* 2.9 37.1 + - + +
656A ALA* 3.9 3.6 - - - +
658A MET* 1.3 80.5 - - + +
660A GLU* 1.3 60.0 + - + +
662A GLU* 3.1 7.3 + - - +
663A LYS* 2.8 28.9 + - - +
738A LEU* 4.1 15.2 - - + +
741A LEU* 3.9 41.3 - - + +
742A TYR* 3.7 35.0 - - + +
745A MET* 3.9 22.9 - - + -
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ALA* 3.0 19.8 + - + +
657A ILE* 3.6 6.5 - - - +
659A ILE* 1.3 78.0 - - + +
661A ASP* 1.3 65.7 + - - +
663A LYS* 3.4 23.3 + - - +
664A ALA* 3.3 21.1 + - - +
742A TYR* 4.2 13.7 + - - -
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Residues in contact with ASP 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ARG* 4.8 7.9 + - - +
657A ILE* 2.8 41.0 + - - +
658A MET* 3.8 5.9 + - - +
660A GLU* 1.3 76.1 - - - +
662A GLU* 1.3 61.0 + - - +
664A ALA* 3.4 6.9 + - - +
665A LEU* 3.1 33.8 + - + +
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Residues in contact with GLU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A MET 2.8 18.6 + - - +
659A ILE* 3.1 5.8 + - - +
661A ASP* 1.3 74.4 - - - +
663A LYS* 1.3 66.4 + - - +
665A LEU* 3.2 16.0 + - - +
666A ARG* 2.8 61.9 + - - +
701A MET* 3.5 41.7 - - + +
702A SER* 2.6 27.4 + - - -
716A LEU* 4.9 1.8 - - - -
738A LEU* 4.8 5.4 - - + -
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Residues in contact with LYS 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A ILE 2.8 16.5 + - - +
660A GLU* 3.6 24.7 + - - +
662A GLU* 1.3 77.5 - - - +
664A ALA* 1.3 62.3 + - - +
666A ARG* 3.4 3.5 + - - +
667A GLU* 3.1 50.0 + - + +
738A LEU* 4.1 31.5 - - + +
742A TYR* 4.2 17.8 + - - +
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Residues in contact with ALA 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLU 3.3 10.0 + - - +
661A ASP* 3.7 9.6 - - - +
662A GLU 3.2 0.8 - - - -
663A LYS* 1.3 80.1 - - - +
665A LEU* 1.3 62.9 + - + +
667A GLU* 3.4 11.5 + - - +
668A THR* 3.1 26.0 + - - -
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Residues in contact with LEU 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A ASP* 3.1 27.1 + - + +
662A GLU* 3.2 16.8 + - - +
664A ALA* 1.3 77.4 - - + +
666A ARG* 1.3 59.3 + - - +
668A THR* 3.3 9.3 + - + +
669A VAL* 3.0 32.9 + - - +
716A LEU* 4.0 33.9 - - + +
717A HIS* 3.7 43.7 - - + +
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Residues in contact with ARG 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A GLU* 2.8 56.5 + - - +
663A LYS* 3.9 4.7 - - - +
665A LEU* 1.3 74.6 - - - +
667A GLU* 1.3 64.2 + - - +
669A VAL* 3.3 9.5 + - + +
670A ARG* 3.0 25.3 + - - +
701A MET* 3.5 23.2 + - - +
702A SER* 4.5 2.6 + - - -
716A LEU* 4.0 10.5 - - + -
732A LEU* 4.3 10.7 - - + +
734A TYR* 3.8 12.1 - - - +
736A TYR 3.0 30.1 + - - +
737A THR* 4.0 1.8 - - - +
738A LEU* 3.9 28.9 - - + +
741A LEU* 5.1 0.6 - - - +
1760A EDO 3.3 27.9 + - - +
1764A EDO 4.8 0.9 + - - -
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Residues in contact with GLU 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A LYS* 3.1 47.9 + - + +
664A ALA* 3.6 11.5 - - - +
666A ARG* 1.3 78.0 - - + +
668A THR* 1.3 60.9 + - - +
670A ARG* 3.4 6.8 + - - +
671A LYS* 3.1 42.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ALA 3.1 15.0 + - - -
665A LEU* 3.5 14.2 - - + +
666A ARG 3.2 0.2 - - - -
667A GLU* 1.3 76.6 - - - +
669A VAL* 1.3 65.4 + - + +
671A LYS* 3.2 11.4 + - - +
672A LEU* 3.2 32.9 + - + +
716A LEU 5.9 2.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LEU 3.0 15.8 + - - +
666A ARG* 3.4 16.6 - - + +
668A THR* 1.3 77.3 - - + +
670A ARG* 1.3 70.0 + - - +
672A LEU* 3.0 20.4 + - + +
674A VAL* 3.3 24.7 + - + +
704A ILE* 4.6 10.5 - - + -
716A LEU* 3.9 29.8 - - + +
719A VAL* 3.6 31.0 - - + -
732A LEU* 4.7 5.8 - - + -
1764A EDO 4.3 11.2 - - - +
----------------------------------------------------------
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Residues in contact with ARG 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ARG 3.0 17.4 + - - +
667A GLU* 3.7 7.0 - - - +
669A VAL* 1.3 78.4 - - - +
671A LYS* 1.3 59.7 + - + +
673A GLY* 2.9 19.0 + - - -
674A VAL 3.3 18.6 + - - -
675A ILE* 3.8 35.6 - - - +
1764A EDO 3.5 24.6 + - - +
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Residues in contact with LYS 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A GLU* 3.1 27.3 + - - +
668A THR* 3.6 12.6 - - + +
669A VAL 3.2 0.2 - - - -
670A ARG* 1.3 79.4 - - + +
672A LEU* 1.3 61.5 + - + +
673A GLY 3.2 1.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A THR* 3.2 25.5 + - + +
669A VAL* 3.0 15.9 + - + +
671A LYS* 1.3 80.0 - - + +
673A GLY* 1.3 58.9 + - - +
674A VAL* 3.6 5.6 - - + +
719A VAL* 4.1 28.9 - - + -
720A LYS* 3.9 35.4 - - + +
727A PRO* 3.3 25.2 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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