Contacts of the helix formed by residues 758 - 783 (chain A) in PDB entry 6VSB
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 SER 758 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A TYR 3.3 1.0 + - - -
757A GLY* 1.3 70.7 - - - -
759A PHE* 1.3 66.3 + - - +
760A CYS 3.2 3.4 - - - -
761A THR* 2.9 21.0 + - - +
762A GLN* 2.9 33.7 + - - +
961C THR* 3.7 10.7 + - - +
964C LYS* 5.7 3.3 - - - +
965C GLN* 2.9 21.8 + - - +
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Residues in contact with PHE 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU* 6.1 0.4 - - + -
756A TYR* 3.1 35.1 + + + +
757A GLY 3.4 4.2 + - - -
758A SER* 1.3 75.7 + - - +
760A CYS* 1.3 64.8 + - - +
762A GLN* 3.3 18.2 + - - +
763A LEU* 2.9 32.4 + - + +
1001A LEU* 4.0 23.6 - - + -
1005A GLN* 3.8 19.7 - - - -
965C GLN* 3.9 14.8 - - - -
970C PHE* 4.1 14.6 - + - -
999C GLY 4.7 0.7 - - - -
1002C GLN* 3.7 39.7 - - + -
1003C SER* 4.3 14.6 - - - -
1006C THR* 4.1 20.6 - - - -
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Residues in contact with CYS 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A CYS* 2.0 57.7 - - + +
739A THR* 4.5 2.5 - - - +
753A LEU* 3.6 24.2 - - - -
757A GLY 5.5 4.3 - - - -
758A SER 3.2 0.8 - - - -
759A PHE* 1.3 78.2 - - - +
761A THR* 1.3 53.5 + - - +
763A LEU* 3.2 5.2 + - - +
764A ASN* 2.5 41.5 + - + +
1001A LEU* 6.3 0.2 - - - -
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Residues in contact with THR 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A SER* 2.9 21.2 + - - -
760A CYS* 1.3 78.6 - - - +
762A GLN* 1.3 58.9 + - - +
764A ASN* 3.8 5.1 - - - +
765A ARG* 2.7 46.6 + - + +
302C THR 5.8 4.3 - - - +
304C LYS* 6.4 0.2 - - - +
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Residues in contact with GLN 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A SER* 2.9 34.7 + - - +
759A PHE* 3.9 14.5 - - - +
761A THR* 1.3 75.8 - - - +
763A LEU* 1.3 57.3 + - + +
765A ARG* 3.7 22.7 + - - +
766A ALA* 2.7 37.3 + - - +
1005A GLN* 5.5 0.3 + - - -
961C THR* 3.3 29.1 - - + +
965C GLN* 3.5 19.0 - - - +
1003C SER* 5.0 2.3 + - - -
1006C THR* 4.0 23.6 - - + +
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Residues in contact with LEU 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A VAL* 6.2 2.5 - - + -
738A CYS* 5.9 2.2 - - + -
759A PHE* 2.9 28.5 + - + +
760A CYS* 3.6 5.4 - - - +
762A GLN* 1.3 77.6 - - + +
764A ASN* 1.3 65.1 + - - +
766A ALA* 3.3 4.2 + - + +
767A LEU* 3.1 29.2 + - + +
1001A LEU* 5.0 5.8 - - + +
1004A LEU* 4.3 35.2 - - + +
1005A GLN* 3.2 45.8 - - - +
1008A VAL* 4.0 28.5 - - + +
1010C GLN* 5.8 2.7 - - - +
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Residues in contact with ASN 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A SER* 5.1 2.9 + - - -
736A VAL* 4.5 19.2 + - - +
737A ASP* 5.5 4.6 + - - +
738A CYS* 5.6 4.1 - - + +
760A CYS* 2.5 24.7 + - + +
761A THR* 3.8 5.8 - - - +
763A LEU* 1.3 71.8 - - - +
765A ARG* 1.3 58.3 + - - +
767A LEU* 3.2 7.6 + - - +
768A THR* 2.9 35.5 + - - -
314C GLN* 3.5 31.8 + - - +
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Residues in contact with ARG 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A THR* 2.7 30.0 + - + +
762A GLN* 3.7 23.4 + - - +
764A ASN* 1.3 74.5 - - - +
766A ALA* 1.3 53.5 + - - +
768A THR* 3.0 10.1 + - + -
769A GLY* 2.7 33.3 + - - -
957C GLN* 3.6 34.2 - - - +
958C ALA* 5.2 3.0 - - - +
961C THR* 3.4 24.7 + - - +
1014C ARG* 5.6 6.1 - - - +
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Residues in contact with ALA 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A GLN 2.7 22.3 + - - +
763A LEU* 3.7 5.2 - - + +
764A ASN 3.3 0.2 - - - -
765A ARG* 1.3 75.3 - - - +
767A LEU* 1.3 63.7 + - - +
769A GLY* 3.2 9.9 + - - -
770A ILE* 3.3 19.6 + - - +
1008A VAL* 3.8 19.5 - - + -
1012A LEU* 4.4 10.8 - - + +
1010C GLN* 4.3 18.6 - - - +
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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
----------------------------------------------------------
734A THR* 3.8 26.5 - - + +
735A SER* 4.9 4.0 - - - -
736A VAL* 3.5 37.2 - - + +
763A LEU 3.1 18.6 + - - +
764A ASN* 3.7 4.7 - - - +
766A ALA* 1.3 73.9 - - - +
768A THR* 1.3 66.3 + - - +
770A ILE* 3.0 42.0 - - + +
771A ALA* 3.1 10.7 + - - +
1007A TYR* 4.0 12.8 - - + -
1008A VAL* 3.8 28.0 - - + +
1011A GLN* 4.2 14.8 - - + -
1012A LEU* 6.3 0.4 - - + -
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Residues in contact with THR 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A THR 5.7 0.2 - - - -
735A SER* 5.4 2.9 + - - -
764A ASN* 2.9 25.5 + - - -
765A ARG* 3.3 13.4 - - + -
767A LEU* 1.3 76.9 - - - +
769A GLY* 1.3 61.7 + - - +
771A ALA* 4.0 5.9 - - + +
772A VAL* 3.0 43.5 + - + +
861A LEU* 6.3 0.9 - - - -
314C GLN* 4.8 8.7 + - + +
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Residues in contact with GLY 769 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ARG* 2.7 18.7 + - - -
766A ALA* 3.2 4.9 + - - -
767A LEU 3.1 0.8 - - - -
768A THR* 1.3 74.2 - - - +
770A ILE* 1.3 62.3 + - - +
772A VAL* 4.2 5.7 - - - +
773A GLU* 3.7 21.0 + - - +
----------------------------------------------------------
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Residues in contact with ILE 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A MET* 5.2 3.8 - - + -
732A THR 6.1 0.2 - - - +
734A THR* 4.1 7.0 - - + -
766A ALA 3.6 6.3 - - - +
767A LEU* 3.0 45.3 - - + +
769A GLY* 1.3 78.1 - - - +
771A ALA* 1.3 70.7 + - + +
772A VAL 3.1 1.6 - - - -
773A GLU* 2.9 18.0 + - - +
774A GLN* 2.9 29.3 + - + +
1011A GLN* 3.8 31.6 - - + +
1012A LEU* 3.6 33.4 - - + -
1015A ALA* 4.0 18.8 - - + -
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Residues in contact with ALA 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A LYS* 3.2 54.1 + - + +
734A THR 4.3 6.5 - - - +
767A LEU 3.1 12.4 + - - +
768A THR* 4.1 4.9 - - + +
770A ILE* 1.3 83.5 - - + +
772A VAL* 1.3 63.1 + - + +
774A GLN* 3.3 19.1 + - - +
775A ASP* 3.8 2.4 + - - +
861A LEU* 4.1 12.6 - - + -
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Residues in contact with VAL 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A LYS* 5.3 2.2 - - - +
768A THR* 3.0 33.6 + - + +
769A GLY* 4.2 6.5 - - - +
770A ILE 3.1 0.2 - - - -
771A ALA* 1.3 77.3 - - + +
773A GLU* 1.3 63.2 + - + +
774A GLN 3.2 0.9 + - - -
775A ASP* 3.4 15.5 + - - +
776A LYS* 3.6 8.8 + - - +
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Residues in contact with GLU 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A GLY 3.7 11.5 + - - +
770A ILE* 2.9 36.7 + - - +
772A VAL* 1.3 79.7 - - + +
774A GLN* 1.3 72.2 + - - +
775A ASP 3.2 0.4 - - - -
776A LYS* 3.2 22.7 + - + +
777A ASN* 3.1 24.4 + - - +
1012A LEU* 5.6 0.7 - - - +
1015A ALA* 4.2 14.4 - - - +
1016A ALA* 6.0 0.2 - - - -
1019A ARG* 3.5 34.9 + - - +
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Residues in contact with GLN 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A VAL 4.4 2.3 - - - +
730A SER* 3.5 12.5 - - - -
731A MET* 3.1 58.9 + - + +
732A THR 5.6 0.7 - - - +
733A LYS* 4.2 15.0 - - + -
770A ILE* 2.9 31.2 + - + +
771A ALA* 3.6 11.9 - - - +
772A VAL 3.1 1.0 - - - -
773A GLU* 1.3 92.7 + - - +
775A ASP* 1.3 63.6 + - - +
777A ASN* 3.4 24.7 + - - +
778A THR* 3.5 15.4 + - - -
1015A ALA* 4.4 10.1 + - - +
1018A ILE* 4.2 2.7 - - - +
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Residues in contact with ASP 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A LYS* 3.0 31.4 + - - +
771A ALA 3.8 1.4 + - - +
772A VAL* 3.4 10.1 + - - +
773A GLU 3.2 0.4 - - - -
774A GLN* 1.3 79.4 - - - +
776A LYS* 1.3 57.7 + - - +
778A THR* 3.6 6.4 + - - +
779A GLN* 3.0 29.9 + - - +
863A PRO* 4.0 7.8 - - - +
864A LEU* 3.1 54.1 + - + +
865A LEU* 4.5 4.6 + - - +
665C PRO* 5.6 1.6 - - - +
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Residues in contact with LYS 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A VAL* 3.6 5.1 + - - +
773A GLU* 3.2 22.8 + - + +
774A GLN 3.2 0.6 - - - -
775A ASP* 1.3 77.6 - - - +
777A ASN* 1.3 55.4 + - - +
779A GLN* 3.0 6.9 + - - +
780A GLU* 2.5 47.3 + - + +
1019A ARG* 3.5 31.6 - - - +
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Residues in contact with ASN 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A VAL* 3.3 17.5 - - - +
773A GLU 3.1 14.7 + - - +
774A GLN* 3.7 17.7 + - - +
775A ASP 3.4 0.4 - - - -
776A LYS* 1.3 75.4 - - - +
778A THR* 1.3 58.1 + - - +
780A GLU* 3.1 8.0 + - - +
781A VAL* 2.9 36.4 + - - +
1015A ALA 5.6 0.2 + - - -
1018A ILE* 4.0 19.0 - - - +
1019A ARG* 3.1 37.8 + - - +
1022A ALA* 3.4 26.9 - - + +
1023A ASN* 5.0 0.2 - - - +
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Residues in contact with THR 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A VAL* 3.9 16.3 + - - +
730A SER* 4.1 9.4 - - - -
774A GLN 3.5 10.8 + - - -
775A ASP* 4.0 9.4 + - - -
776A LYS 3.2 0.4 - - - -
777A ASN* 1.3 77.5 - - - +
779A GLN* 1.3 62.0 + - - +
782A PHE* 3.0 48.7 + - + +
865A LEU* 3.6 24.5 - - + +
870A ILE* 3.8 20.5 - - + +
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Residues in contact with GLN 779 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A ASP 3.0 18.5 + - - +
776A LYS* 3.0 8.9 + - + +
778A THR* 1.3 78.9 - - - +
780A GLU* 1.3 57.5 + - - +
783A ALA* 3.1 48.8 + - + +
864A LEU* 4.8 9.8 - - - +
865A LEU* 3.8 23.7 - - - +
873A TYR* 5.4 3.4 + - - -
661C GLU* 5.4 6.5 + - - -
697C MET* 5.2 6.4 - - - +
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Residues in contact with GLU 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A LYS* 2.5 28.6 + - + +
777A ASN* 3.7 7.0 - - - +
779A GLN* 1.3 74.6 - - - +
781A VAL* 1.3 64.2 + - + +
784A GLN* 3.4 23.7 + - - +
1019A ARG* 3.8 23.2 + - - -
1022A ALA* 5.8 1.3 - - - -
1023A ASN* 3.9 18.5 - - - +
1026A ALA* 4.0 16.1 - - + +
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Residues in contact with VAL 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A VAL* 3.8 19.1 - - + -
777A ASN 2.9 19.5 + - - +
778A THR 4.5 0.7 - - - +
780A GLU* 1.3 78.1 - - + +
782A PHE* 1.3 70.1 + - + +
784A GLN* 3.1 23.2 - - - +
1022A ALA* 3.4 28.3 - - + +
1025A ALA* 4.2 9.6 - - + -
1026A ALA* 3.6 22.4 - - + +
1029A MET* 3.1 30.8 - - + +
1060A VAL* 4.5 10.1 - - + -
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Residues in contact with PHE 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A VAL* 4.4 17.3 - - + -
778A THR* 3.0 36.1 + - + +
781A VAL* 1.3 80.5 - - + +
783A ALA* 1.3 52.4 + - - +
784A GLN* 2.7 18.5 + - - +
785A VAL* 4.4 2.4 + - - +
865A LEU* 5.6 0.4 - - + -
870A ILE* 3.6 28.0 - - + -
873A TYR* 3.9 27.5 - - + +
874A THR* 3.5 33.2 - - + -
877A LEU* 4.1 16.6 - - + +
1029A MET* 4.3 10.8 - - + -
1055A SER* 5.0 5.8 - - - -
1056A ALA 5.7 1.3 - - - -
1059A GLY 4.1 8.7 - - - -
1060A VAL* 3.7 35.0 - - + -
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Residues in contact with ALA 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A GLN* 3.1 44.5 + - + +
782A PHE* 1.3 72.6 - - - +
784A GLN* 1.3 61.6 + - - +
785A VAL 3.5 5.7 + - - +
873A TYR* 3.8 33.7 - - + +
----------------------------------------------------------
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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