Contacts of the helix formed by residues 832 - 860 (chain B) in PDB entry 1DQ8
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 GLY 832 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ASP* 5.2 0.4 - - - -
652B GLY* 3.1 24.1 - - - -
653B ASP* 2.9 25.7 + - - -
704B LYS* 4.8 0.3 - - - -
831B PRO* 1.3 70.6 - - - +
833B GLU* 1.3 55.4 + - - +
835B ALA* 3.3 4.2 + - - +
836B ARG* 2.9 46.9 + - - +
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Residues in contact with GLU 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ASP* 3.3 0.2 + - - -
827B CYS* 3.8 11.9 - - - -
830B ASN* 3.1 43.2 + - + +
832B GLY* 1.3 75.0 - - - +
834B ASN* 1.3 61.8 + - - +
836B ARG* 3.2 20.5 + - - +
837B GLN* 3.0 29.3 + - + +
840B ARG* 2.8 31.4 + - - -
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Residues in contact with ASN 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ASP* 2.8 14.3 + - - +
804B THR* 3.5 10.1 - - - +
822B GLY 3.9 6.3 + - - +
823B VAL* 3.4 43.3 + - - +
824B GLN 3.6 12.3 + - - -
825B GLY 2.9 18.6 + - - +
826B ALA 3.5 17.0 + - - -
827B CYS* 3.6 13.8 - - - +
833B GLU* 1.3 76.2 - - - +
835B ALA* 1.3 59.0 + - - +
837B GLN* 3.4 1.6 + - - +
838B LEU 3.0 21.8 + - - -
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Residues in contact with ALA 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B GLY 4.5 0.4 - - - +
653B ASP* 3.0 35.7 + - + +
704B LYS* 3.9 21.3 - - - +
802B ILE* 3.8 7.4 - - - +
803B GLY* 4.2 10.1 - - - -
804B THR* 3.8 9.6 - - - +
832B GLY 3.7 6.7 - - - +
834B ASN* 1.3 74.8 - - - +
836B ARG* 1.3 60.0 + - - +
838B LEU* 3.3 4.4 + - - +
839B ALA* 3.0 27.2 + - - +
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Residues in contact with ARG 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B VAL* 4.1 28.7 - - + +
586B ASP* 3.3 16.2 + - - +
650B ARG* 3.0 31.2 - - - +
652B GLY* 5.2 1.2 + - - +
704B LYS* 4.1 16.8 - - - +
830B ASN* 4.2 7.1 + - - -
831B PRO 3.2 20.6 + - - -
832B GLY* 2.9 37.5 + - - +
833B GLU* 3.2 28.8 + - - +
834B ASN 3.4 0.2 - - - -
835B ALA* 1.3 75.0 - - - +
837B GLN* 1.3 63.5 + - - +
839B ALA* 3.2 7.0 + - - +
840B ARG* 3.1 29.6 + - - +
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Residues in contact with GLN 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B LEU* 4.7 2.0 - - - +
547B ASP* 5.5 1.4 + - - +
549B LYS* 3.2 19.8 + - - +
551B PHE* 3.2 32.7 - - + -
821B LEU 5.2 0.7 - - - +
823B VAL* 3.4 20.4 - - + -
833B GLU* 3.0 20.6 + - + +
834B ASN* 3.6 4.9 - - - +
836B ARG* 1.3 77.9 - - - +
838B LEU* 1.3 61.3 + - - +
840B ARG* 3.1 38.4 + - - +
841B ILE* 3.0 28.9 + - + +
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Residues in contact with LEU 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760B ILE* 4.7 8.1 - - + -
764B CYS* 4.7 4.0 - - + -
766B GLN* 3.9 19.5 - - + +
802B ILE* 3.5 30.5 - - + -
803B GLY 4.2 5.2 - - - +
804B THR* 4.3 3.6 - - + -
818B LEU* 3.9 15.7 - - + -
821B LEU* 3.5 31.6 - - + -
823B VAL* 4.1 11.6 - - + +
834B ASN 3.0 14.8 + - - +
835B ALA* 3.7 8.5 - - - +
837B GLN* 1.3 74.9 - - - +
839B ALA* 1.3 57.4 + - - +
841B ILE* 3.2 10.0 + - + +
842B VAL* 2.9 38.7 + - + +
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Residues in contact with ALA 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B VAL* 5.4 0.4 - - + -
704B LYS* 3.8 33.7 - - + -
706B VAL* 4.1 11.0 - - + -
800B ILE* 3.8 13.7 - - + +
802B ILE* 4.2 6.9 - - + +
835B ALA 3.0 14.6 + - - +
836B ARG 3.4 8.5 - - - +
838B LEU* 1.3 76.8 - - - +
840B ARG* 1.3 56.0 + - - +
842B VAL* 3.2 8.8 + - - +
843B CYS* 2.9 29.6 + - - +
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Residues in contact with ARG 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B LEU* 3.5 11.6 - - + +
547B ASP* 4.1 10.5 + - - +
549B LYS* 4.6 9.4 - - - +
581B SER* 3.2 38.0 + - - +
582B ARG* 4.8 1.8 - - - +
583B VAL* 3.8 24.1 - - + +
706B VAL* 4.4 11.9 - - + +
833B GLU* 2.8 28.7 + - - -
836B ARG* 3.1 18.7 + - - +
837B GLN* 3.1 45.6 + - - +
839B ALA* 1.3 75.3 - - - +
841B ILE* 1.3 58.1 + - - +
843B CYS* 3.3 1.7 + - - +
844B GLY* 2.8 24.4 + - - -
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Residues in contact with ILE 841 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 3.8 3.8 - - + +
546B LEU* 3.8 7.4 - - + -
551B PHE* 3.6 41.1 - - + -
553B VAL* 4.3 12.6 - - + -
760B ILE* 5.1 2.5 - - + -
821B LEU* 4.0 42.2 - - + +
823B VAL* 4.6 0.9 - - + -
837B GLN* 3.0 36.9 + - + +
838B LEU* 3.4 14.1 - - + +
840B ARG* 1.3 76.1 - - - +
842B VAL* 1.3 56.8 + - - +
844B GLY* 3.3 0.5 + - - -
845B THR* 2.7 46.7 + - - +
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Residues in contact with VAL 842 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756B ILE* 4.4 0.5 - - - +
757B VAL* 4.1 26.5 - - + -
760B ILE* 4.1 34.3 - - + -
761B TYR* 4.4 10.5 - - + +
800B ILE* 4.3 16.2 - - + -
802B ILE* 3.7 22.4 - - + -
838B LEU* 2.9 20.0 + - + +
839B ALA* 3.2 9.2 + - - +
841B ILE* 1.3 77.5 - - - +
843B CYS* 1.3 59.6 + - - +
845B THR* 3.8 1.6 - - - -
846B VAL* 2.9 31.4 + - + +
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Residues in contact with CYS 843 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B SER* 5.7 0.2 - - - -
706B VAL* 3.4 37.9 - - + -
708B CYS* 3.8 10.9 - - + +
795B CYS* 3.5 27.8 - - - +
797B MET* 3.8 30.5 - - - -
800B ILE* 4.4 2.5 - - + -
839B ALA 2.9 10.9 + - - +
840B ARG 3.7 3.1 - - - +
842B VAL* 1.3 76.0 - - - +
844B GLY* 1.3 62.9 + - - +
846B VAL* 3.3 4.3 + - - +
847B MET* 3.1 21.8 + - - +
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Residues in contact with GLY 844 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 3.9 18.2 - - - +
546B LEU* 4.6 4.7 - - - -
573B ILE* 4.4 2.4 - - - +
579B ALA* 5.8 0.2 - - - -
708B CYS* 3.6 22.6 - - - -
840B ARG 2.8 15.8 + - - -
841B ILE 3.7 1.3 - - - -
843B CYS* 1.3 77.7 - - - +
845B THR* 1.3 56.7 + - - +
847B MET* 3.2 6.4 + - - +
848B ALA* 3.0 24.6 + - - +
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Residues in contact with THR 845 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 3.3 15.3 - - + +
553B VAL* 3.6 25.7 - - + +
555B MET* 4.7 2.9 - - - -
566B THR* 3.4 25.8 - - + -
570B CYS* 5.3 2.5 - - - -
756B ILE* 3.7 18.3 - - + +
760B ILE* 4.0 9.4 - - + -
841B ILE* 2.7 23.1 + - - +
842B VAL 3.8 3.4 - - - -
844B GLY* 1.3 73.9 - - - +
846B VAL* 1.3 60.8 + - - +
848B ALA* 3.1 7.3 + - + +
849B GLY* 2.8 24.9 + - - -
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Residues in contact with VAL 846 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B ALA* 3.7 38.4 - - + +
756B ILE* 3.7 22.2 - - + +
757B VAL* 3.9 10.1 - - + -
777B CYS* 4.1 9.2 - - - -
795B CYS* 4.3 2.9 - - - -
797B MET* 3.7 24.5 - - + -
842B VAL 2.9 17.4 + - - +
843B CYS 3.5 8.7 - - - +
845B THR* 1.3 74.9 - - - +
847B MET* 1.3 52.3 + - - +
849B GLY* 3.0 2.1 + - - -
850B GLU* 2.7 49.7 + - + +
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Residues in contact with MET 847 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ILE* 4.1 12.3 - - + -
579B ALA* 3.4 32.5 - - + -
708B CYS* 3.6 18.4 - - + +
709B GLU* 3.6 30.3 - - - -
710B ALA* 3.7 8.3 - - + -
793B ILE* 3.8 34.7 - - + +
794B SER* 4.5 1.6 - - - -
795B CYS* 3.6 21.3 - - + -
843B CYS 3.1 12.3 + - - +
844B GLY 3.4 7.2 - - - +
845B THR 3.2 0.2 - - - -
846B VAL* 1.3 77.4 - - - +
848B ALA* 1.3 56.7 + - - +
850B GLU* 3.3 2.0 + - - +
851B LEU* 2.9 29.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 4.7 0.4 - - + -
566B THR* 3.9 9.0 - - + +
569B GLY* 3.3 14.9 + - - -
570B CYS* 3.7 29.6 - - - +
573B ILE* 3.7 25.1 - - + +
844B GLY 3.0 10.7 + - - +
845B THR* 3.1 11.0 + - - +
847B MET* 1.3 76.0 - - - +
849B GLY* 1.3 63.0 + - - +
851B LEU* 3.3 1.8 + - - +
852B SER* 3.2 17.8 + - - -
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Residues in contact with GLY 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B SER* 4.4 1.0 + - - -
566B THR* 4.4 14.7 - - - +
752B HIS* 3.0 28.5 - - - -
756B ILE* 3.9 10.5 - - - -
845B THR 2.8 14.8 + - - -
846B VAL 3.0 3.3 + - - -
848B ALA* 1.3 77.7 - - - +
850B GLU* 1.3 61.2 + - - +
852B SER* 3.3 3.6 + - - -
853B LEU 3.1 15.4 + - - -
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Residues in contact with GLU 850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B ASN* 4.0 1.6 + - - -
750B ASN* 3.3 6.2 - - - +
751B ALA* 2.8 26.3 + - - +
752B HIS* 2.8 40.4 + - - -
753B ALA 3.6 5.6 + - - -
779B THR* 2.7 42.6 + - + +
781B MET* 4.8 1.1 - - - -
793B ILE* 4.5 2.2 - - + -
795B CYS* 4.0 4.0 - - - -
846B VAL* 2.7 33.7 + - + +
847B MET* 3.6 7.4 - - - +
849B GLY* 1.3 71.5 - - - +
851B LEU* 1.3 63.4 + - - +
853B LEU* 4.2 0.8 - - - +
854B MET* 2.9 32.8 + - + +
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Residues in contact with LEU 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B GLY* 4.0 9.9 - - - +
572B ALA* 4.5 3.4 - - + -
573B ILE* 3.8 22.2 - - + -
712B ILE* 3.8 32.5 - - + -
721B LEU* 4.1 16.1 - - + +
728B MET* 3.4 18.0 - - + +
781B MET* 4.9 0.2 - - - -
791B LEU* 3.6 31.2 - - + -
793B ILE* 3.7 24.2 - - + +
847B MET 2.9 15.3 + - - +
848B ALA 3.4 5.6 - - - +
850B GLU* 1.3 76.6 - - - +
852B SER* 1.3 56.4 + - - +
855B ALA* 3.1 28.1 + - - +
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Residues in contact with SER 852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B COA 3.0 6.7 + - - -
565B SER* 2.9 39.6 + - - -
568B ARG* 2.9 39.6 + - - +
569B GLY* 4.0 4.9 - - - -
721B LEU* 4.5 3.4 - - - -
848B ALA 3.2 9.0 + - - -
849B GLY 3.3 1.3 + - - -
851B LEU* 1.3 78.0 - - - +
853B LEU* 1.3 63.2 + - - +
855B ALA* 3.3 2.3 + - - -
856B ALA* 3.0 20.3 + - - +
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Residues in contact with LEU 853 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B COA 3.5 26.2 - - - +
201B MAH 3.7 29.6 - - + +
565B SER* 3.9 0.6 + - - -
751B ALA* 3.7 10.8 - - + -
752B HIS* 3.4 45.5 - - + +
849B GLY 3.1 6.7 + - - +
850B GLU 4.2 1.8 - - - +
852B SER* 1.3 76.0 - - - +
854B MET* 1.3 60.3 + - + +
856B ALA* 3.1 3.6 + - + +
857B LEU* 2.9 41.6 + - + +
862B LEU* 3.6 28.7 - - + -
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Residues in contact with MET 854 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B MET* 3.8 10.8 - - + +
731B VAL* 4.5 13.8 - - + +
732B ASN* 4.3 6.5 - - - +
735B LYS* 3.4 12.6 - - + -
736B ASN* 3.4 27.1 - - - +
751B ALA* 3.3 24.5 - - + -
781B MET* 3.6 27.6 - - + -
850B GLU* 2.9 27.5 + - + +
851B LEU 4.0 2.5 - - - +
853B LEU* 1.3 77.1 - - - +
855B ALA* 1.3 56.5 - - - +
857B LEU* 3.1 32.8 - - + +
858B ALA* 3.0 30.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 855 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ARG* 4.0 4.5 - - - +
721B LEU* 3.6 39.4 - - + +
723B THR* 3.9 5.9 - - + -
728B MET* 3.5 16.1 - - - -
851B LEU 3.1 18.8 + - - +
852B SER 3.5 5.6 - - - +
853B LEU 3.2 0.2 - - - -
854B MET* 1.3 75.2 - - - +
856B ALA* 1.3 63.5 + - - +
858B ALA* 3.4 2.3 + - - +
859B ALA* 3.1 26.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 856 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B COA 3.7 28.5 - - - +
568B ARG* 4.1 6.0 - - - +
852B SER 3.0 13.4 + - - +
853B LEU* 3.1 9.4 + - + +
855B ALA* 1.3 76.8 - - - +
857B LEU* 1.3 57.0 + - - +
859B ALA* 3.3 0.7 + - - -
860B GLY 2.9 7.8 + - - -
861B HIS* 2.7 47.7 + - + -
862B LEU* 3.7 10.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 857 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU 3.7 13.2 - - - +
682A ALA* 4.2 12.9 - - + -
683A VAL* 3.7 33.5 + - + +
684A SER* 4.1 13.7 - - - +
201B MAH 4.0 2.0 - - - +
731B VAL* 4.5 4.0 - - + -
735B LYS* 3.6 24.5 - - + +
853B LEU* 2.9 26.7 + - + +
854B MET* 3.1 35.0 - - + +
856B ALA* 1.3 76.7 - - - +
858B ALA* 1.3 60.4 + - - +
859B ALA 3.5 0.3 + - - -
860B GLY* 3.5 9.9 + - - -
862B LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU 4.5 2.5 - - - +
723B THR* 3.8 19.6 + - - +
727B ALA* 4.1 19.6 - - + +
728B MET* 4.4 3.1 - - - +
731B VAL* 3.6 26.0 - - + +
854B MET 3.0 19.5 + - - +
855B ALA* 3.8 4.0 - - - +
856B ALA 3.3 0.2 - - - -
857B LEU* 1.3 76.2 - - - +
859B ALA* 1.3 59.1 + - - +
860B GLY 3.5 0.4 + - - -
----------------------------------------------------------
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Residues in contact with ALA 859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B LYS 3.7 17.5 - - - +
723B THR* 4.4 4.7 - - - -
855B ALA 3.1 17.8 + - - +
856B ALA 4.1 0.2 - - - +
858B ALA* 1.3 78.8 - - - +
860B GLY* 1.3 59.9 + - - +
861B HIS* 3.5 37.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY 860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A GLU* 5.5 3.8 - - - -
856B ALA 2.9 4.8 + - - -
857B LEU 3.5 7.1 + - - -
858B ALA 3.5 2.8 + - - -
859B ALA* 1.3 79.5 - - - +
861B HIS* 1.3 61.7 + - - +
862B LEU* 3.6 2.9 - - - -
863B VAL* 3.2 20.9 - - - +
----------------------------------------------------------
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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