Contacts of the helix formed by residues 730 - 760 (chain E) 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 GLN 730 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717E GLN* 4.7 9.9 + - - -
729E THR* 1.3 79.9 + - - +
731E ARG* 1.3 65.4 + - - +
733E ILE* 2.9 28.9 + - - +
734E ASP* 3.0 45.4 + - - +
33F VAL 5.6 1.6 + - - -
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Residues in contact with ARG 731 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729E THR* 3.4 12.1 + - + +
730E GLN* 1.3 78.6 - - - +
732E GLU* 1.3 57.9 + - - +
734E ASP* 3.4 3.4 + - - +
735E ARG* 2.9 28.4 + - - +
894E LYS 3.7 18.1 + - - -
895E HIS* 3.8 41.2 + - + +
896E THR 3.8 15.8 + - - -
897E GLU* 2.8 32.9 + - - +
898E GLY 5.0 1.0 - - - +
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Residues in contact with GLU 732 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728E LEU* 3.9 25.2 - - + +
729E THR* 3.5 25.7 - - + +
730E GLN 3.2 0.6 - - - -
731E ARG* 1.3 78.9 - - - +
733E ILE* 1.3 60.6 + - - +
735E ARG* 2.6 47.0 + - - -
736E GLN* 3.1 33.8 + - + +
805E ILE* 5.1 2.5 - - + +
806E ILE 4.2 1.0 - - - +
807E LYS* 5.6 2.6 - - - -
895E HIS 4.8 1.4 - - - +
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Residues in contact with ILE 733 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716E TRP* 4.5 9.8 - - + -
717E GLN* 3.8 36.6 - - + +
725E VAL* 3.4 35.7 - - + +
728E LEU* 3.8 24.5 - - + +
729E THR 3.2 19.7 + - - +
730E GLN* 2.9 24.6 + - - +
732E GLU* 1.3 73.7 - - - +
734E ASP* 1.3 68.4 + - - +
735E ARG 3.2 0.9 - - - -
736E GLN* 3.2 5.6 + - - +
737E GLU* 3.0 26.4 + - + +
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Residues in contact with ASP 734 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717E GLN* 5.2 1.7 - - - +
730E GLN* 3.0 34.8 + - - +
731E ARG* 3.6 3.7 - - - +
733E ILE* 1.3 76.0 - - - +
735E ARG* 1.3 63.4 + - - +
737E GLU* 3.0 26.7 + - - +
738E VAL* 3.2 11.2 + - + +
895E HIS* 3.2 35.7 + - + +
33F VAL 4.6 10.4 - - - +
34F TYR* 5.1 7.9 - - + -
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Residues in contact with ARG 735 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731E ARG 2.9 18.2 + - - +
732E GLU* 2.6 47.3 + - - +
734E ASP* 1.3 76.1 - - - +
736E GLN* 1.3 78.4 + - - +
737E GLU 3.1 1.4 + - - -
738E VAL* 3.2 7.5 + - - +
739E ILE* 3.1 40.1 + - + +
806E ILE 3.5 1.2 + - - -
807E LYS* 2.6 30.9 + - - +
808E GLU* 4.5 0.2 - - - +
809E ILE* 4.5 1.8 - - - +
892E ILE* 4.8 7.9 - - + +
895E HIS* 3.3 36.9 - - + +
896E THR* 3.6 17.5 + - - +
902E GLU* 3.7 20.0 + - - +
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Residues in contact with GLN 736 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716E TRP* 3.9 36.0 + - + -
728E LEU* 5.0 0.9 - - + -
732E GLU* 3.1 39.1 + - + +
733E ILE 3.2 6.0 + - - +
735E ARG* 1.3 83.5 - - - +
737E GLU* 1.3 56.8 + - - +
739E ILE* 3.9 8.2 - - - +
740E ASN* 3.1 26.2 + - - +
804E PRO 3.9 4.5 - - - +
805E ILE* 3.7 13.6 - - + +
806E ILE* 2.5 56.9 + - - +
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Residues in contact with GLU 737 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715E ASN* 3.5 9.6 + - - +
716E TRP* 2.8 38.0 + - + +
717E GLN* 2.6 40.0 + - - +
733E ILE* 3.0 24.7 + - + +
734E ASP* 3.0 13.6 + - - +
736E GLN* 1.3 76.0 - - - +
738E VAL* 1.3 54.3 + - - +
740E ASN* 2.9 7.7 + - - +
741E GLU* 2.8 32.1 + - - +
33F VAL* 4.4 0.5 - - - +
34F TYR* 3.9 38.1 - - + -
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Residues in contact with VAL 738 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734E ASP 3.2 13.1 + - - +
735E ARG* 3.7 5.8 - - - +
737E GLU* 1.3 75.2 - - - +
739E ILE* 1.3 61.2 + - - +
741E GLU* 3.2 2.8 + - - +
742E LEU* 3.1 21.1 + - - +
888E LEU* 3.9 12.4 - - + +
891E SER* 3.6 31.4 - - - +
892E ILE* 3.5 26.6 - - + +
895E HIS* 4.5 15.7 - - + +
34F TYR* 3.4 32.8 - - + +
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Residues in contact with ILE 739 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735E ARG* 3.1 50.6 + - + +
736E GLN* 4.0 9.2 - - - +
738E VAL* 1.3 75.0 - - - +
740E ASN* 1.3 63.7 + - - +
742E LEU* 3.4 5.6 + - - +
743E PHE* 3.0 59.3 + - + -
806E ILE* 4.2 25.6 - - + -
809E ILE* 3.8 16.6 - - + -
892E ILE* 3.7 26.2 - - + -
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Residues in contact with ASN 740 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714E GLN 4.6 8.7 - - - +
715E ASN 4.8 0.7 - - - -
716E TRP* 3.8 39.1 + - + +
719E THR* 5.5 0.7 + - - -
720E VAL* 4.5 12.9 - - - +
736E GLN 3.1 16.2 + - - +
737E GLU* 2.9 12.9 + - - +
739E ILE* 1.3 79.8 - - - +
741E GLU* 1.3 57.9 + - - +
743E PHE* 3.4 7.7 + - - +
744E VAL* 2.9 47.4 + - - +
800E ARG* 5.3 9.7 - - - +
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Residues in contact with GLU 741 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737E GLU 2.8 11.9 + - - +
738E VAL* 3.5 8.9 - - - +
739E ILE 3.2 0.2 - - - -
740E ASN* 1.3 76.5 - - - +
742E LEU* 1.3 66.2 + - - +
744E VAL* 4.6 3.1 - - + -
745E THR* 2.9 39.3 + - + +
888E LEU* 4.1 7.5 - - + +
34F TYR* 2.5 34.7 + - + +
36F PRO* 3.7 14.5 - - + +
37F THR* 3.1 21.6 + - - -
38F VAL* 3.1 37.3 + - - +
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Residues in contact with LEU 742 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738E VAL 3.1 10.0 + - - +
739E ILE* 3.5 8.3 - - - +
741E GLU* 1.3 79.1 - - - +
743E PHE* 1.3 82.4 + - + +
745E THR* 4.0 4.0 - - - -
746E GLU* 3.2 23.2 + - - +
792E TRP* 4.6 2.5 - - + -
796E MET* 3.9 17.3 - - + -
809E ILE* 4.4 7.4 - - + -
813E MET* 3.9 26.7 - - + -
881E ARG* 3.3 5.0 + - - +
885E TYR* 4.1 28.3 - - + +
888E LEU* 4.2 29.8 - - + +
889E LEU* 6.1 2.0 - - + -
892E ILE* 4.5 7.4 - - + -
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Residues in contact with PHE 743 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739E ILE* 3.0 36.6 + - + +
740E ASN* 3.9 10.3 - - - +
741E GLU 3.1 1.0 - - - -
742E LEU* 1.3 96.0 - - + +
744E VAL* 1.3 64.9 - - + +
746E GLU* 3.0 5.7 - - - +
747E ALA* 3.0 21.7 + - - +
793E CYS* 5.1 1.2 - - - -
796E MET* 3.9 48.2 - - + +
799E LEU* 4.9 5.8 - - + -
800E ARG* 4.1 34.1 - - + +
806E ILE* 4.3 22.7 - - + -
809E ILE* 4.6 3.6 - - + -
812E LEU* 4.2 13.7 - - + -
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Residues in contact with VAL 744 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714E GLN 6.1 0.4 - - - +
740E ASN* 2.9 42.1 + - - +
741E GLU* 3.9 4.5 - - - +
743E PHE* 1.3 74.4 - - + +
745E THR* 1.3 71.9 + - + +
747E ALA* 3.1 9.8 + - - +
748E SER* 3.0 24.1 + - - -
751E ARG* 5.5 0.2 + - - -
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Residues in contact with THR 745 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741E GLU* 2.9 39.7 + - + +
742E LEU* 3.5 1.7 + - - -
744E VAL* 1.3 82.4 - - + +
746E GLU* 1.3 61.3 + - - +
748E SER* 3.2 10.4 + - - -
749E HIS* 3.0 24.9 + - - +
881E ARG* 2.5 38.9 + - - -
888E LEU* 4.9 2.1 - - + +
38F VAL* 4.0 22.8 - - + +
40F GLU* 3.8 10.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 746 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742E LEU 3.2 9.8 + - - +
743E PHE 3.0 12.3 + - - +
745E THR* 1.3 77.2 + - - +
747E ALA* 1.3 63.1 + - - +
749E HIS* 3.1 5.0 + - - +
750E LEU* 3.0 22.3 + - - +
789E HIS* 3.0 36.9 + - + +
792E TRP* 3.6 19.1 - - + -
793E CYS* 4.1 14.8 - - + -
796E MET* 3.8 21.0 - - - +
881E ARG* 2.7 35.3 + - - +
885E TYR* 2.7 18.7 + - - -
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Residues in contact with ALA 747 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743E PHE 3.0 9.1 + - - +
744E VAL* 3.5 11.4 - - - +
746E GLU* 1.3 80.2 - - - +
748E SER* 1.3 57.6 + - - +
750E LEU* 3.6 4.4 + - - +
751E ARG* 3.1 37.1 + - - +
793E CYS* 3.8 20.8 - - - -
----------------------------------------------------------
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Residues in contact with SER 748 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744E VAL* 3.0 14.6 + - - -
745E THR* 3.3 8.0 + - - -
746E GLU 3.1 0.2 - - - -
747E ALA* 1.3 76.0 - - - +
749E HIS* 1.3 59.2 + - - +
751E ARG* 3.3 34.4 - - - +
752E THR* 3.2 25.5 + - - -
40F GLU* 2.8 31.5 + - - +
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Residues in contact with HIS 749 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745E THR 3.0 16.5 + - - +
746E GLU* 3.5 5.2 - - - +
748E SER* 1.3 76.1 - - - +
750E LEU* 1.3 62.5 + - - +
751E ARG 3.1 1.3 - - - -
752E THR* 3.2 6.8 + - - -
753E LEU* 2.9 40.9 + - + +
789E HIS* 3.6 32.9 + + + -
877E SER* 3.5 22.8 + - - -
878E GLU* 2.7 31.9 + - - -
881E ARG* 3.2 39.6 - - + +
40F GLU* 5.0 6.5 - - - +
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Residues in contact with LEU 750 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746E GLU 3.0 15.0 + - - +
747E ALA* 3.7 9.6 - - - +
749E HIS* 1.3 79.7 - - - +
751E ARG* 1.3 60.1 + - - +
753E LEU* 3.7 11.4 + - + -
754E ARG* 3.2 60.1 + - + +
786E ILE* 3.8 30.5 - - + +
789E HIS* 3.8 18.2 - - + -
790E ASN* 3.9 21.3 - - + +
793E CYS* 4.6 12.6 - - + -
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Residues in contact with ARG 751 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747E ALA* 3.1 32.4 + - - +
748E SER* 3.3 33.5 - - - +
750E LEU* 1.3 78.5 - - - +
752E THR* 1.3 59.0 + - - +
754E ARG* 3.2 8.4 + - - +
755E VAL* 3.0 33.0 + - + +
865E GLN* 6.0 2.2 - - - +
867E ARG* 6.4 0.4 - - - +
----------------------------------------------------------
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Residues in contact with THR 752 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748E SER 3.2 16.3 + - - -
749E HIS* 3.2 12.8 + - - +
751E ARG* 1.3 74.2 - - - +
753E LEU* 1.3 62.9 + - + +
754E ARG 2.9 4.5 - - - -
755E VAL* 3.0 20.3 + - + +
756E LEU* 3.1 14.7 + - + +
867E ARG* 3.6 21.4 + - - +
874E LEU* 4.6 23.1 - - + +
877E SER* 3.4 29.6 - - - +
40F GLU* 4.4 4.5 + - - -
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Residues in contact with LEU 753 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749E HIS* 2.9 36.2 + - + +
750E LEU* 4.0 11.2 - - + +
752E THR* 1.3 72.5 - - - +
754E ARG* 1.3 57.0 + - - +
756E LEU* 3.4 23.1 - - + +
757E ASP 3.1 19.2 + - - -
782E LEU* 4.3 4.6 - - + +
785E LEU* 4.0 23.8 - - + +
786E ILE* 3.6 32.1 - - + +
789E HIS* 3.7 32.3 - - + -
832E PHE* 5.7 0.7 - - + -
877E SER* 4.9 6.1 - - - +
878E GLU* 4.0 16.4 - - + +
----------------------------------------------------------
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Residues in contact with ARG 754 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750E LEU* 3.2 43.0 + - + +
751E ARG* 3.2 11.5 + - - +
752E THR 2.9 0.6 - - - -
753E LEU* 1.3 78.2 - - + +
755E VAL* 1.3 60.1 + - - +
756E LEU 3.2 0.7 - - - -
757E ASP* 3.7 7.2 + - + +
758E LEU* 2.9 42.6 + - + +
786E ILE* 3.9 26.0 - - + +
790E ASN* 3.4 21.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 755 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751E ARG* 3.0 23.5 + - + +
752E THR* 3.0 12.2 + - + +
754E ARG* 1.3 76.2 - - - +
756E LEU* 1.3 59.5 + - - +
758E LEU* 5.0 0.9 - - - -
759E ILE* 2.9 47.7 + - + +
760E PHE* 3.8 0.7 + - + -
865E GLN* 3.4 46.7 - - + +
866E CYS* 4.3 6.5 - - - -
867E ARG* 6.2 0.4 - - - +
874E LEU* 3.5 28.7 - - + -
----------------------------------------------------------
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Residues in contact with LEU 756 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752E THR* 3.1 13.2 + - + +
753E LEU* 3.4 24.0 - - + +
755E VAL* 1.3 73.8 - - - +
757E ASP* 1.3 66.3 + - - +
760E PHE* 3.3 12.7 + - + +
761E TYR* 2.9 23.6 + - - +
779E PHE* 4.4 9.8 - - + -
782E LEU* 4.0 26.0 - - + -
832E PHE* 4.6 4.5 - - + -
871E LEU* 3.8 28.9 - - + -
874E LEU* 3.8 28.0 - - + +
875E ILE* 4.3 22.7 - - + +
877E SER* 5.4 0.9 - - - +
----------------------------------------------------------
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Residues in contact with ASP 757 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753E LEU 3.1 14.1 + - - +
754E ARG* 3.3 8.5 + - + +
756E LEU* 1.3 79.5 - - - +
758E LEU* 1.3 71.6 + - + +
761E TYR* 3.3 11.6 - - - -
762E GLN* 2.8 65.2 + - - +
782E LEU* 3.6 9.7 - - + +
783E PRO* 6.1 0.3 - - - +
786E ILE* 3.8 20.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 758 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754E ARG* 2.9 32.1 + - + +
755E VAL* 4.4 0.9 - - - +
757E ASP* 1.3 90.1 - - + +
759E ILE* 1.3 76.5 + - + +
762E GLN* 4.4 9.1 - - + +
763E ARG* 3.4 21.7 + - - +
----------------------------------------------------------
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Residues in contact with ILE 759 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755E VAL* 2.9 35.2 + - + +
758E LEU* 1.3 82.2 - - + +
760E PHE* 1.3 72.5 + - + +
763E ARG* 3.5 24.2 - - - +
856E PHE* 4.1 1.4 - - - -
860E ALA* 3.5 47.1 - - + +
863E HIS* 4.0 37.5 - - + +
865E GLN* 5.3 7.0 - - + +
866E CYS* 4.2 4.0 - - - -
----------------------------------------------------------
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Residues in contact with PHE 760 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755E VAL 3.9 7.2 - - - -
756E LEU* 3.3 13.6 + - + +
759E ILE* 1.3 96.0 - - + +
761E TYR* 1.3 69.1 + - - +
762E GLN 3.2 2.0 - - - -
763E ARG* 2.9 17.0 + - - +
764E MET* 2.9 18.9 + - + -
779E PHE* 4.2 13.9 - - + -
856E PHE* 4.6 4.0 - + - -
857E MET* 3.9 24.0 - - + -
860E ALA* 3.9 15.7 - - + -
861E GLU* 4.0 23.6 - - + -
866E CYS* 4.0 11.7 - - - -
870E GLN 5.3 0.2 - - - -
871E LEU* 3.8 37.7 - - + -
874E LEU* 4.0 22.4 - - + -
----------------------------------------------------------
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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