Contacts of the helix formed by residues 729 - 760 (chain A) in PDB entry 3T06
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 THR 729 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A LEU* 1.3 74.5 - - + +
730A GLN* 1.3 70.3 + - - +
731A ARG* 3.3 13.2 + - + +
732A GLU* 3.3 32.5 + - + +
733A ILE* 3.0 30.7 + - - +
897A GLU* 6.0 2.0 - - - +
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Residues in contact with GLN 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLN* 5.4 2.1 + - - -
729A THR* 1.3 74.7 + - - +
731A ARG* 1.3 58.7 + - - +
733A ILE* 3.3 13.4 + - - +
734A ASP* 2.8 61.2 + - - +
33B VAL 5.7 0.7 - - - +
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Residues in contact with ARG 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A THR* 3.3 10.6 + - + +
730A GLN* 1.3 78.3 - - - +
732A GLU* 1.3 58.1 + - - +
734A ASP* 4.5 4.3 - - - +
735A ARG* 3.0 29.9 + - - +
894A LYS 3.8 15.4 + - - -
895A HIS* 3.8 39.2 + - + +
896A THR 4.3 12.5 + - - -
897A GLU* 3.3 40.5 + - - +
898A GLY 5.1 1.8 - - - +
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Residues in contact with GLU 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A LEU* 3.5 30.1 - - + -
729A THR* 3.3 29.9 + - + +
731A ARG* 1.3 78.4 - - - +
733A ILE* 1.3 60.1 + - - +
735A ARG* 3.1 36.6 + - - +
736A GLN* 3.1 36.4 + - + +
805A ILE* 5.5 4.0 - - + -
806A ILE 5.5 0.2 - - - -
897A GLU* 6.1 0.9 - - - +
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Residues in contact with ILE 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A TRP* 3.8 26.0 - - + -
717A GLN* 3.8 33.7 - - + +
725A VAL* 4.2 22.2 - - + +
728A LEU* 4.0 26.9 - - + +
729A THR 3.0 21.6 + - - +
730A GLN* 3.7 14.4 - - - +
731A ARG 3.1 0.2 - - - -
732A GLU* 1.3 76.0 - - - +
734A ASP* 1.3 72.1 + - - +
735A ARG 3.0 1.3 - - - -
736A GLN* 3.0 5.0 + - - +
737A GLU* 2.9 22.6 + - + +
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Residues in contact with ASP 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLN* 5.2 1.6 + - - -
730A GLN* 2.8 47.1 + - - +
731A ARG* 4.0 1.8 - - - +
733A ILE* 1.3 80.7 - - - +
735A ARG* 1.3 59.5 + - - +
737A GLU* 3.8 7.6 - - - +
738A VAL* 3.1 31.5 + - - +
895A HIS* 3.6 34.0 + - + +
33B VAL 5.2 5.4 - - - +
34B TYR* 4.7 10.3 - - + +
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Residues in contact with ARG 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A ARG 3.0 18.5 + - - +
732A GLU* 3.1 31.0 + - - +
733A ILE 3.0 0.2 - - - -
734A ASP* 1.3 75.8 - - - +
736A GLN* 1.3 64.2 + - - +
738A VAL* 3.3 5.8 + - - +
739A ILE* 3.0 44.5 + - + +
806A ILE 3.1 23.2 + - - -
807A LYS* 2.8 21.4 + - - +
809A ILE* 4.4 2.0 - - - +
892A ILE* 4.7 7.6 - - + +
895A HIS* 3.1 32.0 - - + +
896A THR* 2.9 18.8 + - - +
902A GLU* 2.5 30.3 + - - +
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Residues in contact with GLN 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A TRP* 3.7 39.8 - - + -
728A LEU* 5.4 1.1 - - + -
732A GLU* 3.1 33.7 + - + +
733A ILE 3.0 6.9 + - - +
735A ARG* 1.3 79.8 - - - +
737A GLU* 1.3 65.9 + - - +
739A ILE* 3.9 7.3 - - - +
740A ASN* 3.1 24.8 + - - +
804A PRO 3.8 1.9 - - - +
805A ILE* 3.6 16.6 - - + +
806A ILE* 2.7 59.5 + - - +
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Residues in contact with GLU 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A ASN* 3.6 15.7 + - - +
716A TRP* 3.1 27.9 + - + +
717A GLN* 2.9 55.3 + - + +
733A ILE* 2.9 19.1 + - + +
734A ASP* 3.8 6.3 - - - +
736A GLN* 1.3 77.6 - - - +
738A VAL* 1.3 57.4 + - - +
740A ASN* 3.3 5.4 + - - +
741A GLU* 3.1 25.6 + - - +
34B TYR* 3.8 34.6 + - + -
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Residues in contact with VAL 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A ASP 3.1 17.7 - - - +
735A ARG* 3.3 5.2 + - - +
737A GLU* 1.3 73.0 - - - +
739A ILE* 1.3 65.1 + - - +
740A ASN 3.1 1.6 - - - -
741A GLU* 3.4 5.0 + - - +
742A LEU* 3.2 20.1 + - - +
888A LEU* 3.8 10.4 - - + +
891A SER* 3.5 35.4 - - - +
892A ILE* 3.7 22.3 - - + +
895A HIS* 4.1 13.2 - - + +
34B TYR* 3.4 28.9 - - + +
37B THR* 5.0 0.2 - - - +
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Residues in contact with ILE 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A ARG* 3.0 58.9 + - + +
736A GLN* 3.5 10.1 + - - +
738A VAL* 1.3 76.1 - - - +
740A ASN* 1.3 59.3 + - - +
742A LEU* 3.4 6.3 + - - +
743A PHE* 3.1 42.0 + - + -
806A ILE* 4.2 26.0 - - + -
809A ILE* 3.7 33.2 - - + -
892A ILE* 3.8 21.3 - - + -
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Residues in contact with ASN 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A ASN* 4.8 4.0 - - - -
716A TRP* 4.0 35.7 + - + +
720A VAL* 5.0 5.1 - - - +
736A GLN 3.1 19.0 + - - +
737A GLU* 3.5 6.5 - - - +
738A VAL 3.1 0.4 - - - -
739A ILE* 1.3 78.5 - - - +
741A GLU* 1.3 66.4 + - - +
743A PHE* 3.2 10.0 + - - +
744A VAL* 2.9 39.2 + - - +
800A ARG* 5.4 8.9 - - - +
806A ILE* 6.4 1.1 - - + +
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Residues in contact with GLU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A GLU 3.1 12.2 + - - +
738A VAL* 3.7 8.0 - - - +
740A ASN* 1.3 78.1 + - - +
742A LEU* 1.3 55.7 + - - +
744A VAL* 4.8 4.0 - - - -
745A THR* 2.7 50.7 + - + +
888A LEU* 4.4 9.1 - - + +
34B TYR* 2.4 36.4 + - + +
36B PRO* 3.6 12.0 - - + +
37B THR* 2.7 38.3 + - - -
38B VAL* 2.8 19.2 + - - +
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Residues in contact with LEU 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A VAL 3.2 9.8 + - - +
739A ILE* 3.5 7.6 - - - +
740A ASN 3.2 0.4 - - - -
741A GLU* 1.3 80.4 - - - +
743A PHE* 1.3 72.3 + - + +
744A VAL 3.1 0.5 + - - -
745A THR* 3.2 5.3 + - - -
746A GLU* 3.1 22.0 + - - +
792A TRP* 4.5 4.0 - - + -
796A MET* 3.8 16.2 - - + -
809A ILE* 4.5 5.4 - - + -
813A MET* 3.6 36.6 - - + -
881A ARG* 3.4 4.1 + - - +
885A TYR* 4.1 23.8 - - + -
888A LEU* 3.9 36.2 - - + +
889A LEU* 5.7 2.7 - - + -
892A ILE* 4.7 8.1 - - + -
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Residues in contact with PHE 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A ILE* 3.1 32.4 + - + +
740A ASN* 3.2 11.4 + - - +
742A LEU* 1.3 87.9 - - + +
744A VAL* 1.3 62.5 + - + +
746A GLU* 3.6 2.4 - - - +
747A ALA* 3.5 18.4 + - - +
793A CYS* 4.7 1.2 - - - -
796A MET* 3.5 48.3 - - + +
799A LEU* 4.4 10.8 - - + -
800A ARG* 3.4 50.0 + - + +
806A ILE* 4.3 18.4 - - + -
809A ILE* 4.0 27.1 - - + -
812A LEU* 4.3 4.7 - - + -
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Residues in contact with VAL 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A ASN* 2.9 34.9 + - - +
741A GLU* 4.1 3.4 - - - +
743A PHE* 1.3 77.8 - - + +
745A THR* 1.3 68.8 + - + +
746A GLU 2.9 5.1 + - - -
747A ALA* 3.2 6.9 + - - +
748A SER* 3.0 23.1 + - - -
800A ARG* 6.2 1.6 - - - +
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Residues in contact with THR 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A GLU* 2.7 40.0 + - + +
742A LEU* 3.2 3.1 + - - -
744A VAL* 1.3 81.2 - - + +
746A GLU* 1.3 57.1 + - - +
748A SER* 3.5 10.8 - - - -
749A HIS* 3.2 23.9 + - - +
881A ARG* 2.8 37.8 + - - -
888A LEU* 4.5 2.1 - - - +
38B VAL* 4.1 23.1 - - + +
40B GLU* 3.8 12.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A LEU 3.1 14.8 + - - +
743A PHE 3.6 5.8 - - - +
744A VAL 2.9 0.2 - - - -
745A THR* 1.3 76.3 - - - +
747A ALA* 1.3 57.4 + - - +
748A SER 2.9 3.8 - - - -
749A HIS* 2.8 7.0 + - - +
750A LEU* 2.8 27.6 + - + +
789A HIS* 2.6 36.9 + - + +
792A TRP* 3.4 16.8 - - + -
793A CYS* 4.2 14.4 - - + -
796A MET* 3.9 21.7 - - + +
881A ARG* 2.7 35.6 + - - +
885A TYR* 2.7 22.2 + - - -
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Residues in contact with ALA 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A PHE 3.5 8.3 + - - +
744A VAL* 3.2 9.2 + - - +
746A GLU* 1.3 78.9 - - - +
748A SER* 1.3 59.4 + - - +
750A LEU* 3.9 7.3 - - - +
751A ARG* 3.4 19.9 + - - +
793A CYS* 3.8 22.4 - - - -
800A ARG* 5.8 1.8 - - - +
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Residues in contact with SER 748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 3.0 18.5 + - - -
745A THR* 3.5 13.9 - - - -
747A ALA* 1.3 79.8 - - - +
749A HIS* 1.3 61.5 + - - +
751A ARG* 3.5 19.0 + - - +
752A THR* 3.1 25.1 + - - -
40B GLU* 3.4 22.2 + - - +
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Residues in contact with HIS 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745A THR 3.2 16.3 + - - +
746A GLU* 2.8 6.0 + - - +
748A SER* 1.3 78.1 - - - +
750A LEU* 1.3 59.9 + - - +
751A ARG 3.1 1.6 - - - -
752A THR* 3.2 7.2 + - - +
753A LEU* 2.9 45.9 + - + +
789A HIS* 3.9 26.5 + + - -
877A SER* 3.0 43.8 + - - -
878A GLU* 2.7 26.5 + - - -
881A ARG* 3.4 23.7 - - + +
40B GLU* 4.9 5.2 - - - +
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Residues in contact with LEU 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A GLU* 2.8 14.1 + - + +
747A ALA* 4.0 10.3 - - - +
749A HIS* 1.3 80.1 - - - +
751A ARG* 1.3 55.9 + - - +
753A LEU* 3.3 5.4 + - + +
754A ARG* 3.0 50.7 + - - +
786A ILE* 4.0 36.3 - - + +
789A HIS* 4.4 12.3 - - + +
790A ASN* 3.5 37.5 - - - +
793A CYS* 4.8 13.2 - - + -
----------------------------------------------------------
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Residues in contact with ARG 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ALA 3.4 16.1 + - - +
748A SER* 3.5 27.5 + - - +
749A HIS 3.1 0.6 - - - -
750A LEU* 1.3 76.4 - - - +
752A THR* 1.3 72.8 + - - +
753A LEU 3.1 1.1 - - - -
754A ARG* 3.3 8.5 + - - +
755A VAL* 3.0 27.7 + - + +
865A GLN* 4.9 18.1 + - + +
867A ARG* 3.3 41.1 - - - +
40B GLU* 5.8 0.2 + - - -
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Residues in contact with THR 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A SER 3.1 15.9 + - - -
749A HIS* 3.2 13.5 + - - +
751A ARG* 1.3 77.8 + - - +
753A LEU* 1.3 64.7 + - + +
755A VAL* 3.3 15.0 + - - +
756A LEU* 3.3 13.4 + - + +
867A ARG* 2.9 34.7 + - - +
874A LEU* 4.1 16.4 - - + +
877A SER* 3.3 30.9 - - - +
40B GLU* 5.0 4.2 + - - -
----------------------------------------------------------
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Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A HIS* 2.9 48.6 + - + +
750A LEU* 3.6 8.3 - - + +
751A ARG 3.1 0.4 - - - -
752A THR* 1.3 77.8 - - - +
754A ARG* 1.3 58.7 + - - +
756A LEU* 3.4 22.9 + - + +
757A ASP 3.1 19.4 + - - -
782A LEU* 4.5 5.7 - - + +
785A LEU* 4.2 29.2 - - + +
786A ILE* 3.6 30.5 - - + +
789A HIS* 4.0 20.2 - - + -
832A PHE* 5.5 0.9 - - + -
877A SER* 4.8 6.1 - - - +
878A GLU* 4.2 7.0 - - + +
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Residues in contact with ARG 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A LEU* 3.0 35.2 + - + +
751A ARG* 3.3 8.0 + - - +
753A LEU* 1.3 75.8 - - - +
755A VAL* 1.3 59.9 + - - +
757A ASP* 3.6 9.6 - - + +
758A LEU* 2.9 40.7 + - + +
786A ILE* 3.4 29.5 - - + +
790A ASN* 3.1 32.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A ARG* 3.0 20.2 + - + +
752A THR* 3.5 9.0 - - - +
753A LEU 3.2 0.2 - - - -
754A ARG* 1.3 73.3 - - - +
756A LEU* 1.3 70.3 + - - +
758A LEU* 4.8 1.3 - - - -
759A ILE* 2.9 39.1 + - + +
760A PHE* 4.9 1.1 - - + -
865A GLN* 3.2 46.2 - - + +
866A CYS* 4.8 4.0 - - - -
867A ARG* 5.4 1.3 - - - +
874A LEU* 3.7 36.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A THR 3.3 10.4 + - - +
753A LEU* 3.5 26.9 - - + +
755A VAL* 1.3 81.9 - - - +
757A ASP* 1.3 65.0 + - - +
760A PHE* 2.9 29.3 + - + -
761A TYR 2.9 10.2 + - - -
779A PHE* 4.4 11.7 - - + -
782A LEU* 4.2 10.5 - - + -
832A PHE* 4.6 9.0 - - + -
871A LEU* 3.8 23.3 - - + -
874A LEU* 3.7 33.0 - - + +
875A ILE* 4.1 27.4 - - + +
877A SER* 5.5 0.4 - - - +
----------------------------------------------------------
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Residues in contact with ASP 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU 3.1 3.6 + - - +
754A ARG* 3.4 8.9 + - - +
756A LEU* 1.3 77.3 - - - +
758A LEU* 1.3 66.3 + - + +
761A TYR* 3.5 11.9 - - - -
762A GLN* 2.8 63.3 + - - +
782A LEU* 3.7 16.7 - - + +
783A PRO* 5.1 4.7 - - - +
786A ILE* 3.7 27.3 - - + +
----------------------------------------------------------
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Residues in contact with LEU 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ARG* 2.9 29.2 + - + +
755A VAL* 4.2 1.3 - - - +
757A ASP* 1.3 84.2 - - + +
759A ILE* 1.3 75.3 + - + +
760A PHE 3.1 2.8 + - - -
762A GLN* 4.1 8.9 - - + +
763A ARG* 3.6 22.3 + - - +
865A GLN* 6.1 2.9 - - - +
----------------------------------------------------------
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Residues in contact with ILE 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A VAL* 2.9 33.9 + - + +
758A LEU* 1.3 85.2 - - + +
760A PHE* 1.3 73.5 + - + +
763A ARG* 3.5 29.5 + - - +
856A PHE* 4.0 3.3 - - - -
860A ALA* 3.5 40.9 - - + +
863A HIS* 3.4 43.7 - - + +
865A GLN* 5.2 1.6 - - + -
866A CYS* 4.2 6.1 - - - -
----------------------------------------------------------
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Residues in contact with PHE 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A VAL* 4.1 7.4 - - + -
756A LEU* 2.9 18.1 + - + +
759A ILE* 1.3 95.8 - - + +
761A TYR* 1.3 68.9 + - - +
762A GLN 3.4 1.6 - - - -
763A ARG* 3.2 3.3 + - - +
764A MET* 2.8 55.6 + - + +
779A PHE* 4.2 10.3 - - + -
856A PHE* 4.4 1.1 - + - -
857A MET* 4.2 13.5 - - + -
860A ALA* 3.7 22.4 - - + -
861A GLU* 4.1 22.4 - - + -
866A CYS* 4.1 7.4 - - - -
871A LEU* 4.0 31.9 - - + -
874A LEU* 3.8 22.7 - - + -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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