Contacts of the helix formed by residues 764 - 789 (chain A) in PDB entry 2YEV
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 764 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A HIS* 3.6 23.1 + + - -
681A LEU* 3.8 17.6 - - + +
682A ARG* 5.9 6.4 - - - +
759A ILE* 3.7 26.7 - - + -
760A THR 3.1 21.6 + - - +
761A LEU* 3.3 24.2 + - + -
762A HIS* 4.1 1.5 - - - -
763A ASN* 1.3 74.8 + - - +
765A GLY* 1.3 64.6 + - - +
766A THR 3.5 2.0 - - - -
767A LEU* 3.3 7.3 + - + +
768A GLU* 3.2 42.2 + - + +
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Residues in contact with GLY 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A SER* 4.5 3.1 - - - -
617A ALA* 3.4 29.8 - - - +
763A ASN* 3.8 4.8 + - - +
764A HIS* 1.3 72.4 - - - +
766A THR* 1.3 66.7 + - - +
768A GLU* 2.9 22.8 + - - +
769A ALA* 3.0 11.1 + - - +
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Residues in contact with THR 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A ALA* 5.2 4.2 - - + +
617A ALA* 4.4 1.0 - - - +
746A GLY 4.4 3.6 - - - +
749A LEU* 4.3 14.8 - - + -
750A ALA* 4.1 18.2 - - + +
753A GLN* 3.1 43.0 + - - +
764A HIS 3.5 0.4 - - - -
765A GLY* 1.3 73.7 - - - +
767A LEU* 1.3 56.2 + - - +
769A ALA* 3.5 5.9 + - - +
770A ALA* 2.9 28.9 + - + +
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Residues in contact with LEU 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A VAL* 5.2 3.4 - - + +
677A ALA* 6.4 1.1 - - + -
678A HIS* 4.4 20.0 - - + +
681A LEU* 3.4 23.1 - - + -
689A PHE* 3.2 33.9 - - + -
693A LEU* 4.0 27.4 - - + -
747A LEU* 5.0 3.1 - - + -
750A ALA* 4.1 14.3 - - + +
753A GLN* 4.6 1.4 + - - -
759A ILE* 4.1 14.8 - - + -
764A HIS* 3.3 10.8 + - + +
765A GLY 3.1 1.0 - - - -
766A THR* 1.3 76.4 - - - +
768A GLU* 1.3 62.6 + - - +
770A ALA* 4.7 0.4 - - - -
771A SER* 2.9 43.0 + - - -
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Residues in contact with GLU 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LYS* 5.8 2.3 - - - +
615A SER* 3.0 33.9 + - - +
618A TRP* 4.3 30.3 - - + +
678A HIS* 4.1 17.6 - - + -
764A HIS* 3.2 45.5 + - + +
765A GLY* 2.9 11.1 + - - +
767A LEU* 1.3 77.9 - - - +
769A ALA* 1.3 62.8 + - - +
771A SER* 3.9 4.0 - - - -
772A MET* 3.1 24.4 + - - +
35C ASP* 4.8 2.7 - - - +
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Residues in contact with ALA 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ALA* 4.0 15.7 - - + +
618A TRP* 5.1 1.3 - - - +
621A MET* 3.5 40.6 - - + +
765A GLY 3.0 14.4 + - - +
766A THR* 3.9 5.8 - - - +
768A GLU* 1.3 75.5 - - - +
770A ALA* 1.3 60.1 + - - +
772A MET* 3.2 1.6 + - - -
773A TYR* 3.0 29.1 + - - +
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Residues in contact with ALA 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A MET* 5.1 1.8 - - - -
743A GLY* 5.0 2.8 - - - +
746A GLY* 3.5 37.7 - - - +
747A LEU* 3.9 14.8 - - + +
750A ALA* 5.1 0.7 - - + -
766A THR* 2.9 19.5 + - + +
767A LEU* 4.2 3.4 - - - +
769A ALA* 1.3 75.8 - - - +
771A SER* 1.3 58.5 + - - +
773A TYR* 3.3 7.7 + - - +
774A TRP* 2.9 29.5 + - - +
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Residues in contact with SER 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A VAL* 3.5 34.1 + - - +
675A HIS* 5.5 0.5 - - - -
678A HIS* 4.7 11.8 + - - -
747A LEU* 4.3 1.9 - - - +
767A LEU* 2.9 26.5 + - - -
768A GLU* 3.9 4.9 - - - -
770A ALA* 1.3 77.5 - - - +
772A MET* 1.3 62.5 + - - +
774A TRP* 3.1 6.0 + - - +
775A HIS* 3.0 37.1 + - - -
35C ASP* 5.3 3.7 + - - -
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Residues in contact with MET 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A TRP* 3.5 39.9 - - + +
621A MET* 3.6 13.2 - - + -
622A ALA* 3.3 42.8 - - + +
625A ILE* 3.9 11.8 - - + +
768A GLU 3.1 15.5 + - - +
769A ALA 3.8 2.5 - - - +
771A SER* 1.3 79.5 + - - +
773A TYR* 1.3 60.9 + - - +
775A HIS* 3.5 10.0 + - - +
776A LEU* 3.2 20.6 + - - +
35C ASP* 4.3 16.8 - - + +
38C PHE* 4.2 12.6 - - + -
39C VAL* 4.1 14.8 - - + +
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Residues in contact with TYR 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A MET* 3.8 29.8 - - + -
624A PHE* 4.6 7.6 - + - -
625A ILE* 4.3 14.3 - - + +
628A GLU* 3.1 26.3 + - + -
739A HIS* 3.0 36.1 - + - -
742A ILE* 3.9 20.8 - - + +
743A GLY* 3.7 36.1 - - - -
769A ALA 3.0 16.5 + - - +
770A ALA* 3.7 5.8 - - - +
772A MET* 1.3 75.8 - - - +
774A TRP* 1.3 62.0 - - - +
776A LEU* 3.3 8.2 + - + +
777A VAL* 3.1 26.9 + - + +
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Residues in contact with TRP 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU* 3.9 15.8 + - + +
670A SER* 2.7 37.7 + - - -
671A SER* 4.2 10.7 + - - -
674A VAL* 4.4 7.4 - - + -
696A THR* 3.7 16.4 - - + +
697A ILE* 6.2 0.7 - - - -
700A GLY* 3.7 31.0 - - - -
740A VAL* 3.6 26.7 - - + -
743A GLY* 3.7 18.6 - - - -
744A GLY* 3.5 25.1 - - - -
747A LEU* 3.6 19.1 - - + -
770A ALA 2.9 14.7 + - - +
771A SER* 3.1 11.2 + - - +
773A TYR* 1.3 75.6 - - - +
775A HIS* 1.3 66.3 + - - +
777A VAL* 3.1 13.6 + - + +
778A ASP* 2.9 19.2 + - + +
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Residues in contact with HIS 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A SER* 3.0 53.4 + - - -
674A VAL* 3.3 17.6 - - + +
675A HIS* 4.4 10.0 - - + +
771A SER* 3.0 30.1 + - - -
772A MET* 3.7 11.7 - - - +
774A TRP* 1.3 75.2 - - - +
776A LEU* 1.3 57.1 + - - +
778A ASP* 3.2 4.5 + - - +
779A ALA* 2.9 26.7 + - - +
35C ASP* 5.0 9.2 - - + -
36C LEU* 3.8 29.0 - - + +
39C VAL* 3.8 20.7 - - + +
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Residues in contact with LEU 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A ILE* 3.9 32.5 - - + -
628A GLU* 3.5 37.7 - - + -
629A VAL* 4.9 5.8 - - + -
632A PHE* 6.4 0.4 - - + -
739A HIS* 6.0 1.8 - - + -
772A MET 3.2 11.0 + - - +
773A TYR* 3.4 17.5 - - + +
774A TRP 3.1 0.4 - - - -
775A HIS* 1.3 76.5 - - - +
777A VAL* 1.3 66.8 + - + +
779A ALA* 3.1 8.9 + - + +
780A VAL* 2.9 37.8 + - + +
39C VAL* 4.3 10.3 - - + +
42C MET* 4.3 19.1 - - + -
46C ILE* 5.3 2.7 - - + -
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Residues in contact with VAL 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU* 4.4 8.1 - - + -
736A HIS* 3.0 40.9 + - + +
739A HIS* 3.8 35.0 - - + +
740A VAL* 3.6 25.1 - - + +
773A TYR* 3.1 28.9 + - + +
774A TRP* 3.1 21.8 + - + +
776A LEU* 1.3 78.0 - - + +
778A ASP* 1.3 62.5 + - - +
780A VAL* 3.6 3.5 + - - -
781A TRP* 3.2 8.5 + - - +
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Residues in contact with ASP 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU* 3.9 27.8 - - + +
668A VAL* 3.7 30.4 + - - +
671A SER* 2.9 34.6 + - - +
774A TRP* 2.9 10.1 + - + +
775A HIS 3.2 10.1 - - - +
776A LEU 3.1 0.2 - - - -
777A VAL* 1.3 79.0 - - - +
779A ALA* 1.3 62.9 + - - +
781A TRP* 3.3 16.1 + - - +
782A LEU* 3.4 13.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A HIS 2.9 12.7 + - - +
776A LEU* 3.1 12.3 + - + +
778A ASP* 1.3 76.6 - - - +
780A VAL* 1.3 62.5 + - + +
782A LEU* 3.0 23.9 + - - +
783A VAL 3.4 1.2 + - - -
39C VAL* 4.0 18.8 - - + +
43C LEU* 3.2 42.7 - - + +
46C ILE* 6.2 0.4 - - + -
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Residues in contact with VAL 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A GLU 5.8 0.7 - - - +
632A PHE* 3.7 50.0 - - + -
736A HIS* 3.9 12.6 - - + -
776A LEU* 2.9 30.4 + - + +
777A VAL* 4.0 4.7 - - - +
779A ALA* 1.3 75.8 - - + +
781A TRP* 1.3 64.5 + - - +
783A VAL* 3.1 12.8 + - + +
784A ILE* 3.0 24.1 + - + +
43C LEU* 5.0 0.4 - - - -
46C ILE* 3.9 24.2 - - + -
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Residues in contact with TRP 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A ALA* 3.8 16.2 - - + -
663A ASN* 4.0 5.8 - - + -
664A THR* 3.0 43.3 + - + +
667A LEU* 3.5 27.8 - - + -
703A PHE* 3.6 16.7 - + - -
707A GLN* 3.3 33.9 - - - -
733A VAL* 4.3 3.6 - - + -
736A HIS* 3.6 23.7 + + - +
777A VAL 3.2 5.6 + - - +
778A ASP* 3.3 12.1 - - - +
780A VAL* 1.3 78.4 - - - +
782A LEU* 1.3 53.8 + - + +
784A ILE* 3.0 25.4 + - + +
785A VAL* 2.7 47.9 + - + +
789A TYR* 3.6 21.3 - + - -
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Residues in contact with LEU 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A THR* 3.8 29.2 - - + +
668A VAL* 4.6 12.1 - - + -
778A ASP* 3.7 19.7 - - - +
779A ALA* 3.0 17.2 + - + +
781A TRP* 1.3 81.1 - - + +
783A VAL* 1.3 60.0 + - - +
785A VAL* 3.7 6.8 + - + +
786A THR* 2.8 28.2 + - - -
43C LEU* 4.9 15.3 - - + -
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Residues in contact with VAL 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 3.8 30.1 - - + -
779A ALA 4.0 2.0 - - - +
780A VAL* 3.1 11.8 + - + +
782A LEU* 1.3 76.1 - - - +
784A ILE* 1.3 63.9 + - - +
786A THR* 3.2 8.3 + - - -
787A ILE* 3.0 31.1 + - + +
43C LEU* 3.3 29.8 - - + -
46C ILE* 4.7 13.7 - - + -
47C LEU* 4.2 30.5 - - + -
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Residues in contact with ILE 784 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A PHE* 4.5 0.4 - - + -
636A ILE* 5.4 5.8 - - + -
732A ILE* 4.1 27.6 - - + +
733A VAL* 3.7 22.9 - - + -
736A HIS* 3.4 44.4 - - + +
780A VAL* 3.0 22.0 + - + +
781A TRP* 3.0 28.5 + - + +
783A VAL* 1.3 74.2 - - + +
785A VAL* 1.3 68.4 + - - +
787A ILE* 3.1 6.1 + - - -
788A PHE* 2.8 28.4 + - + +
789A TYR* 4.0 5.4 - - + -
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Residues in contact with VAL 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU* 4.8 4.5 - - + -
660A ALA* 4.3 8.3 - - + +
661A LEU* 4.8 9.4 - - + -
664A THR* 3.4 13.2 - - + +
781A TRP* 2.7 63.0 + - + +
782A LEU* 3.9 8.3 - - + +
784A ILE* 1.3 70.6 - - - +
786A THR* 1.3 58.8 + - - +
789A TYR* 3.0 23.7 + - + +
790A VAL* 2.9 41.0 + - + -
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Residues in contact with THR 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A LEU 2.8 17.4 + - - -
783A VAL* 3.2 12.2 + - - -
784A ILE 3.1 0.4 - - - -
785A VAL* 1.3 79.5 - - - +
787A ILE* 1.3 66.8 + - + +
790A VAL* 3.4 14.3 - - + +
791A TRP* 3.0 30.1 + - + +
----------------------------------------------------------
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Residues in contact with ILE 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 3.7 45.5 - - + -
639A TYR* 2.9 35.3 + - + -
640A LEU* 4.7 8.7 - - + -
643A ARG* 3.5 10.9 + - - -
783A VAL* 3.0 25.4 + - + +
784A ILE* 3.9 2.0 - - + +
786A THR* 1.3 88.2 - - + +
788A PHE* 1.3 85.7 + - + +
791A TRP* 3.6 21.0 - - + +
47C LEU* 6.2 1.8 - - + -
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Residues in contact with PHE 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A TYR* 3.5 37.2 - + - -
654A ARG* 2.8 21.8 + - - -
655A PRO* 5.4 0.9 - - - +
725A TRP* 3.5 32.0 - + - -
728A ALA* 3.8 9.2 - - + -
729A PHE* 3.6 36.7 - + + -
732A ILE* 3.7 39.5 - - + -
733A VAL* 4.0 12.8 - - + -
784A ILE* 2.8 17.1 + - + +
787A ILE* 1.3 106.8 - - + +
789A TYR* 1.3 72.6 + - + +
----------------------------------------------------------
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Residues in contact with TYR 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ARG* 3.7 12.5 + - - +
655A PRO* 3.7 24.5 - - + -
656A ALA 3.8 11.9 - - - -
657A LEU* 4.0 25.2 + - + +
660A ALA* 3.4 27.1 - - + -
707A GLN* 3.6 15.2 + - - -
710A GLU* 2.7 31.9 + - - -
729A PHE* 3.3 24.5 - + - -
733A VAL* 3.7 1.4 - - - +
781A TRP* 3.6 21.1 - + - -
784A ILE* 3.9 15.0 - - + -
785A VAL* 3.0 24.3 + - - +
788A PHE* 1.3 83.7 - - + +
790A VAL* 1.3 66.0 + - - +
----------------------------------------------------------
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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