Contacts of the helix formed by residues 644 - 672 (chain A) in PDB entry 5FZ9
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* 3.5 35.7 - - + +
469A GLN* 4.1 18.1 + - - +
642A VAL 3.8 2.0 + - - -
643A LEU* 1.3 76.4 - - - +
645A VAL* 1.3 63.0 + - - +
646A VAL* 3.2 32.1 + - - +
647A VAL* 3.4 16.3 + - + +
648A ALA* 3.0 24.3 + - - +
751A ARG* 5.1 1.3 - - - +
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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 4.3 0.2 - - - -
644A ASP* 1.3 78.1 + - - +
646A VAL* 1.3 75.7 + - + +
648A ALA* 3.5 7.9 + - - +
649A SER* 3.2 21.1 + - - -
751A ARG* 3.8 39.3 - - - +
752A ALA* 4.1 9.7 - - - +
753A GLU* 5.2 6.1 - - - +
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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
----------------------------------------------------------
469A GLN* 4.7 12.1 - - - +
605A VAL* 4.6 14.6 - - + -
644A ASP* 3.2 11.8 + - - +
645A VAL* 1.3 83.6 - - + +
647A VAL* 1.3 67.5 + - + +
649A SER* 3.3 7.6 + - - -
650A THR* 3.1 34.4 + - - +
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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 3.7 23.3 - - - +
469A GLN* 4.3 10.8 - - + +
470A SER 5.2 2.0 - - - +
471A VAL* 4.8 6.5 - - + -
474A HIS* 5.2 3.8 - - + -
605A VAL* 3.8 25.1 - - + +
636A MET* 4.4 8.3 - - - -
643A LEU* 4.3 20.6 - - + -
644A ASP* 3.5 20.2 - - + +
646A VAL* 1.3 77.6 - - + +
648A ALA* 1.3 63.5 + - - +
650A THR* 3.1 2.1 + - - -
651A VAL* 2.9 44.3 + - + +
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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 15.7 - - + -
644A ASP 3.0 18.1 + - - +
645A VAL 3.7 6.1 - - - +
646A VAL 3.3 0.2 - - - -
647A VAL* 1.3 74.8 - - - +
649A SER* 1.3 63.1 + - - +
651A VAL* 3.5 1.8 + - - +
652A GLN* 3.1 24.4 + - - +
748A LEU* 4.0 24.2 - - + +
751A ARG* 3.9 26.5 - - + -
752A ALA* 4.3 4.5 - - - +
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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 3.2 11.5 + - - -
646A VAL* 3.6 11.7 - - - -
647A VAL 3.2 0.6 - - - -
648A ALA* 1.3 81.1 - - - +
650A THR* 1.3 61.6 + - - +
652A GLN* 3.5 9.0 + - - +
653A LYS* 3.5 42.7 + - - +
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* 3.4 44.0 - - + +
608A LEU* 3.9 16.9 - - + +
609A PRO* 5.3 4.5 - - + -
646A VAL* 3.1 22.3 + - - +
647A VAL 3.9 2.5 - - - -
649A SER* 1.3 73.9 - - - +
651A VAL* 1.3 66.0 + - - +
652A GLN 3.2 0.4 - - - -
653A LYS* 3.4 18.1 + - + +
654A ASP* 3.4 16.8 + - - +
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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* 5.6 0.2 - - + -
608A LEU* 3.9 15.9 - - + -
633A ILE* 4.2 32.7 - - + +
636A MET* 3.7 33.0 - - + -
643A LEU* 4.8 1.6 - - + -
647A VAL* 2.9 34.1 + - + +
648A ALA 3.9 4.0 - - - +
650A THR* 1.3 75.9 - - - +
652A GLN* 1.3 63.2 + - - +
654A ASP* 3.3 19.1 + - - +
656A ALA 5.0 0.2 + - - -
748A LEU* 3.8 25.5 - - + +
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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 3.1 17.9 + - - +
649A SER* 3.5 8.4 + - - +
650A THR 3.2 0.2 - - - -
651A VAL* 1.3 77.2 - - - +
653A LYS* 1.3 76.1 + - - +
656A ALA* 3.0 24.8 + - - +
745A MET* 4.0 38.9 - - + +
748A LEU* 3.9 16.6 - - + +
749A LYS* 3.5 35.0 - - - +
752A ALA* 5.1 4.3 - - - +
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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* 3.5 34.2 + - - +
650A THR* 3.4 15.9 + - + +
651A VAL 3.3 0.4 - - - -
652A GLN* 1.3 88.8 - - - +
654A ASP* 1.3 61.4 + - - +
656A ALA* 3.4 7.5 + - - +
657A ILE* 3.4 27.6 + - + +
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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* 4.5 17.5 - - + +
609A PRO* 4.7 7.0 - - + +
612A ARG* 2.8 46.5 + - - +
629A HIS* 3.0 27.4 + - - -
633A ILE* 3.2 22.4 - - + +
650A THR 3.4 8.7 + - - +
651A VAL 3.3 16.2 + - - +
653A LYS* 1.3 83.0 - - - +
656A ALA 3.2 14.2 + - - -
657A ILE* 3.3 33.4 + - - +
659A ILE 5.1 1.0 + - - -
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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
----------------------------------------------------------
651A VAL 5.0 0.2 + - - -
652A GLN* 3.0 27.1 + - - +
653A LYS* 3.6 11.7 - - - +
654A ASP 3.2 16.2 + - - -
657A ILE* 1.3 68.4 + - + +
659A ILE* 3.4 15.5 + - - +
660A GLU* 3.2 28.9 + - + +
745A MET* 3.8 29.1 - - + +
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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
----------------------------------------------------------
612A ARG* 4.0 25.8 - - - -
653A LYS* 3.4 15.4 + - + +
654A ASP* 3.3 22.1 + - - +
656A ALA* 1.3 79.9 - - + +
659A ILE 3.2 14.4 + - - -
660A GLU* 3.3 5.2 + - - +
661A ASP* 3.0 55.7 + - - +
1763A EDO 6.1 0.4 - - - -
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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
----------------------------------------------------------
654A ASP 5.1 1.0 + - - -
656A ALA* 3.4 14.6 + - - +
657A ILE 3.2 23.8 + - - -
660A GLU* 1.3 79.2 + - - +
661A ASP 3.3 1.9 - - - +
662A GLU* 3.2 20.6 + - - +
664A ALA 5.1 0.2 + - - -
745A MET* 4.2 34.1 - - + -
1763A EDO 5.2 2.8 + - - -
1767A NUK 3.6 30.9 - - + +
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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* 3.2 18.3 + - + +
657A ILE* 4.0 5.2 - - - +
659A ILE* 1.3 87.9 - - - +
661A ASP* 1.3 65.7 + - - +
664A ALA* 3.3 20.8 + - - +
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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* 4.9 7.7 + - - +
657A ILE* 3.0 38.0 + - - +
660A GLU* 1.3 79.1 - - - +
662A GLU* 1.3 61.5 + - - +
664A ALA* 3.4 7.5 + - - +
665A LEU* 3.1 29.1 + - + +
1763A EDO 4.1 21.0 - - - +
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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
----------------------------------------------------------
659A ILE* 3.2 13.2 + - - +
661A ASP* 1.3 82.1 - - - +
664A ALA 3.3 14.4 + - - -
665A LEU* 3.3 30.2 + - - +
667A GLU 5.0 1.0 + - - -
702A SER* 2.6 38.7 + - - -
716A LEU* 4.4 6.0 - - - +
734A TYR* 5.8 0.3 - - - +
1763A EDO 3.3 31.0 + - - +
1767A NUK 3.3 57.3 - - + +
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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 23.2 + - - +
661A ASP* 3.7 10.1 - - - +
662A GLU 3.3 16.0 + - - -
665A LEU* 1.3 68.9 + - + +
667A GLU* 3.5 25.0 + - - +
668A THR* 3.1 25.8 + - - -
1767A NUK 5.6 3.0 - - - -
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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 18.8 + - + +
662A GLU* 3.3 17.1 + - - +
664A ALA* 1.3 80.6 - - + +
667A GLU 3.3 14.4 + - - -
668A THR* 3.3 9.9 + - + +
669A VAL* 3.1 39.9 + - - +
716A LEU* 4.1 39.7 - - + +
717A HIS* 3.7 43.3 - - + +
1763A EDO 3.7 29.8 - - - -
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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
----------------------------------------------------------
662A GLU 5.0 1.8 + - - -
664A ALA* 3.5 24.1 + - - +
665A LEU 3.3 22.0 + - - -
668A THR* 1.3 67.3 + - - +
669A VAL* 3.4 3.9 - - - +
670A ARG* 3.3 15.9 + - - +
671A LYS* 3.1 41.3 + - - +
1767A NUK 5.1 21.0 + - - +
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Residues in contact with THR 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ALA* 3.1 13.8 + - - +
665A LEU* 3.3 13.7 + - + +
667A GLU* 1.3 78.4 - - - +
669A VAL* 1.3 64.3 + - + +
671A LYS* 3.3 10.9 + - - +
672A LEU* 3.3 32.1 + - + +
716A LEU 6.0 1.3 - - - +
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Residues in contact with VAL 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LEU 3.1 17.7 + - - +
667A GLU 5.2 2.0 - - - +
668A THR* 1.3 76.9 - - + +
670A ARG* 1.3 68.8 + - + +
672A LEU* 3.2 18.5 + - + +
673A GLY 3.5 0.2 + - - -
674A VAL* 3.3 28.8 + - + +
704A ILE* 4.8 4.7 - - + -
716A LEU* 4.0 33.9 - - + +
719A VAL* 3.5 30.5 - - + -
732A LEU* 4.7 13.7 - - + -
1765A EDO 4.4 10.5 - - - +
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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
----------------------------------------------------------
667A GLU* 3.3 17.2 + - - +
668A THR 3.3 0.6 - - - -
669A VAL* 1.3 83.0 - - - +
671A LYS* 1.3 59.4 + - + +
673A GLY* 3.0 21.2 + - - -
674A VAL 3.5 17.7 - - - -
675A ILE* 3.9 34.8 - - - +
1765A EDO 3.7 23.3 + - - +
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Residues in contact with LYS 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A GLU* 3.1 25.4 + - - +
668A THR* 3.7 10.3 - - - +
669A VAL 3.3 0.2 - - - -
670A ARG* 1.3 78.2 - - + +
672A LEU* 1.3 61.2 + - + +
673A GLY 3.2 1.9 + - - -
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Residues in contact with LEU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A THR* 3.3 24.0 + - + +
669A VAL* 3.2 13.8 + - + +
670A ARG 3.1 1.2 - - - -
671A LYS* 1.3 80.0 - - - +
673A GLY* 1.3 59.1 + - - +
674A VAL* 3.6 4.9 - - + +
719A VAL* 4.3 25.1 - - + -
720A LYS* 3.7 37.2 - - - +
727A PRO* 3.4 24.6 - - + +
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Residues in contact with GLY 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A ARG* 3.0 15.6 + - - -
671A LYS 3.2 1.6 - - - -
672A LEU* 1.3 82.1 - - - +
674A VAL* 1.3 62.7 + - - +
675A ILE* 3.5 14.6 + - - +
727A PRO* 3.5 21.8 - - - +
728A TYR* 3.7 7.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A VAL* 3.3 21.5 + - + +
670A ARG* 3.5 12.0 - - - -
672A LEU* 5.1 2.2 - - + -
673A GLY* 1.3 75.7 - - - +
675A ILE* 1.3 58.4 + - - +
676A ASP 4.2 4.0 - - - +
704A ILE* 4.3 11.0 - - + -
719A VAL* 4.3 15.7 - - + -
727A PRO* 3.9 16.2 - - + +
730A TYR* 4.2 33.2 - - + +
731A LYS 4.2 0.9 - - - -
732A LEU* 3.9 30.5 - - + +
1765A EDO 2.6 25.5 + - - +
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Residues in contact with ILE 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A ARG* 3.9 33.7 - - - +
673A GLY* 3.5 14.2 + - - +
674A VAL* 1.3 78.0 - - - +
676A ASP* 1.3 70.6 + - - +
677A SER* 3.6 1.6 + - - -
727A PRO 4.9 1.2 + - - -
728A TYR* 5.5 11.6 + - + +
730A TYR 4.9 1.2 + - - -
1765A EDO 2.7 27.1 + - - +
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Residues in contact with ASP 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A VAL* 4.2 2.8 - - - +
675A ILE* 1.3 82.8 - - - +
677A SER* 1.3 69.5 + - - +
728A TYR 5.4 5.5 + - - +
730A TYR 3.9 15.5 + - - +
731A LYS* 3.5 29.5 + - + -
732A LEU* 3.0 21.8 + - - +
1765A EDO 4.2 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) + - + + + + + -
------------------------------------------------------------
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