Contacts of the helix formed by residues 790 - 825 (chain C) in PDB entry 5VOT
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 790 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C LYS* 6.1 3.8 - - - -
512C PRO 3.0 25.6 + - - -
513C GLY* 4.0 7.3 + - - +
516C SER* 3.6 11.1 + - - -
788C SER* 3.0 18.7 + - - -
789C LEU* 1.3 75.4 - - - +
791C ASN* 1.3 70.9 + - - +
792C VAL 3.0 3.0 + - - -
793C ALA* 3.4 7.6 + - - +
794C GLY* 3.2 13.6 + - - -
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Residues in contact with ASN 791 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B ILE* 5.0 19.3 - - + +
612B ILE* 6.1 2.5 - - + -
615B SER* 5.3 4.6 + - - -
513C GLY 4.4 0.4 - - - +
516C SER* 3.2 42.0 + - - -
517C PHE* 3.3 10.1 + - + +
620C LEU* 6.1 2.0 - - - +
624C LEU* 4.6 20.4 - - - +
788C SER* 5.3 4.4 - - - -
790C SER* 1.3 80.9 - - - +
792C VAL* 1.3 58.6 + - + +
794C GLY* 2.7 22.1 + - - +
795C VAL* 3.0 17.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 792 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 5.9 5.2 - - + +
525B ILE* 4.1 27.8 - - + +
528B CYS* 5.0 15.9 - - + -
529B ILE* 6.5 0.7 - - + -
608B PHE* 4.9 4.1 - - + -
612B ILE* 5.4 12.3 - - + +
788C SER 4.9 3.8 - - - +
789C LEU* 4.2 26.0 - - + +
790C SER 3.0 0.6 + - - -
791C ASN* 1.3 76.3 - - + +
793C ALA* 1.3 52.1 + - + +
795C VAL* 4.0 4.7 - - - +
796C PHE* 2.4 47.3 + - + +
154G ILE* 6.0 4.3 - - + -
----------------------------------------------------------
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Residues in contact with ALA 793 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789C LEU 4.8 2.1 + - - +
790C SER 3.4 6.2 + - - +
792C VAL* 1.3 76.1 - - + +
794C GLY* 1.3 65.3 + - - +
795C VAL 3.0 3.1 - - - -
796C PHE* 3.6 9.6 - - + -
797C TYR* 2.9 66.8 + - + +
154G ILE* 6.0 2.9 - - + +
158G SER* 5.2 11.7 - - - -
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Residues in contact with GLY 794 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C GLY 4.0 5.2 - - - -
514C VAL* 3.3 54.4 - - - +
517C PHE* 4.3 7.1 - - - +
790C SER 3.2 9.9 + - - -
791C ASN* 2.7 19.5 + - - -
793C ALA* 1.3 72.5 - - - +
795C VAL* 1.3 56.7 + - - +
797C TYR* 5.5 0.4 - - - -
798C ILE* 4.5 4.7 - - - +
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Residues in contact with VAL 795 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B VAL* 6.6 0.2 - - + -
607B PHE* 4.1 33.4 - - + +
608B PHE* 3.9 23.1 - - + -
611B ILE* 3.7 33.0 - - + -
612B ILE* 5.0 2.7 - - + -
517C PHE* 4.6 12.3 - - + -
791C ASN 3.0 15.4 + - - +
792C VAL 4.0 2.7 - - - +
794C GLY* 1.3 75.0 - - - +
796C PHE* 1.3 64.4 + - - +
797C TYR 3.2 2.2 - - - -
798C ILE* 2.9 29.7 + - + +
799C LEU* 3.0 9.4 + - - +
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Residues in contact with PHE 796 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B CYS* 4.9 9.9 - - + -
531B PHE* 6.1 0.9 - - + -
532B ALA* 3.4 35.2 - - + -
608B PHE* 4.2 14.4 - + + -
792C VAL* 2.4 40.7 + - + +
793C ALA* 3.0 4.2 + - - -
795C VAL* 1.3 82.1 - - + +
797C TYR* 1.3 70.6 + + - +
799C LEU* 2.9 32.0 + - + +
800C VAL* 3.0 35.9 + - + +
150G ILE* 5.5 6.5 - - + -
151G ILE* 4.5 9.2 - - + -
154G ILE* 4.0 28.3 - - + -
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Residues in contact with TYR 797 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C VAL* 4.4 19.1 - - + -
793C ALA* 2.9 42.5 + - + +
794C GLY 5.5 0.2 - - - -
796C PHE* 1.3 85.0 - + - +
798C ILE* 1.3 58.3 + - + +
800C VAL* 3.3 5.4 + - + +
801C GLY* 2.9 27.9 + - - -
151G ILE 5.9 0.4 - - - -
154G ILE* 5.9 3.6 - - + -
155G VAL* 4.6 23.6 - - + +
158G SER* 4.4 12.5 + - - -
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Residues in contact with ILE 798 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B VAL* 3.8 12.9 - - + +
607B PHE* 4.8 24.0 - - + -
514C VAL* 4.8 13.0 - - + -
517C PHE* 5.7 4.9 - - + -
794C GLY 4.5 13.7 - - - +
795C VAL* 2.9 17.3 + - + +
797C TYR* 1.3 79.1 - - + +
799C LEU* 1.3 61.1 + - - +
801C GLY* 4.6 1.1 - - - +
802C GLY* 2.9 21.1 + - - -
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Residues in contact with LEU 799 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ALA* 3.7 15.9 - - + -
536B VAL* 4.2 21.1 - - + -
604B VAL* 3.7 37.1 - - + +
605B TRP* 4.5 15.3 - - + +
608B PHE* 4.6 12.6 - - + -
795C VAL* 3.0 6.7 + - + +
796C PHE* 2.9 48.4 + - + +
798C ILE* 1.3 75.9 - - - +
800C VAL* 1.3 64.4 + - - +
802C GLY* 3.0 4.5 + - - -
803C LEU* 2.9 32.2 + - + +
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Residues in contact with VAL 800 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796C PHE* 3.0 42.4 + - + +
797C TYR* 4.0 5.4 - - + +
799C LEU* 1.3 73.4 - - + +
801C GLY* 1.3 60.5 + - - +
803C LEU* 2.8 37.0 + - + +
804C GLY* 3.0 12.0 + - - -
147G LEU* 5.2 9.2 - - + +
148G SER* 5.7 1.6 - - - -
151G ILE* 4.0 26.0 - - + +
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Residues in contact with GLY 801 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C TYR 2.9 16.1 + - - -
798C ILE* 3.9 2.0 - - - -
800C VAL* 1.3 78.5 - - - +
802C GLY* 1.3 56.6 + - - +
804C GLY* 3.5 1.5 + - - -
805C LEU* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 802 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ILE* 4.4 8.0 - - - +
601B VAL* 5.6 0.6 - - - +
604B VAL* 4.8 14.4 - - - -
798C ILE 2.9 16.3 + - - -
799C LEU 3.5 4.0 - - - -
801C GLY* 1.3 75.3 - - - +
803C LEU* 1.3 63.6 + - - +
805C LEU* 3.2 14.1 - - - +
806C ALA* 2.9 24.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 803 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ALA* 6.5 0.7 - - - -
535B GLY* 5.7 1.6 - - - -
536B VAL* 3.9 37.5 - - + +
539B VAL* 4.8 21.6 - - + +
601B VAL* 5.2 10.1 - - + -
604B VAL* 5.3 4.0 - - + -
796C PHE* 6.4 0.2 - - + -
799C LEU* 2.9 25.9 + - + +
800C VAL* 2.8 32.7 + - + +
802C GLY* 1.3 79.6 - - - +
804C GLY* 1.3 63.3 + - - +
806C ALA* 3.1 4.8 + - - +
807C MET* 2.9 27.0 + - + +
147G LEU* 4.9 17.0 - - + -
----------------------------------------------------------
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Residues in contact with GLY 804 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800C VAL 3.0 9.0 + - - -
801C GLY* 4.0 2.0 - - - -
803C LEU* 1.3 78.9 - - - +
805C LEU* 1.3 62.2 - - - +
807C MET* 3.2 13.0 + - - +
808C LEU* 2.9 24.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 805 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ILE* 4.2 26.2 - - + -
801C GLY 2.9 15.2 + - - +
802C GLY* 3.2 12.6 - - - +
803C LEU 3.1 0.2 - - - -
804C GLY* 1.3 77.7 - - - +
806C ALA* 1.3 63.9 + - - +
808C LEU* 3.1 9.8 + - + +
809C VAL* 2.9 37.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 806 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B VAL* 5.6 2.0 - - + -
543B VAL* 4.8 7.9 - - + +
597B SER* 4.5 14.7 - - - +
600B ILE* 4.5 8.5 - - + -
601B VAL* 3.8 28.5 - - + -
802C GLY 2.9 18.6 + - - +
803C LEU* 3.7 3.6 - - - +
805C LEU* 1.3 74.1 - - - +
807C MET* 1.3 64.8 + - - +
809C VAL* 3.1 10.6 + - - +
810C ALA* 2.9 25.6 + - - +
----------------------------------------------------------
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Residues in contact with MET 807 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B VAL* 3.6 32.1 - - + -
542B LEU* 5.2 13.5 - - + -
543B VAL* 4.7 8.3 - - - -
803C LEU* 2.9 20.3 + - + +
804C GLY* 3.2 15.2 + - - +
806C ALA* 1.3 77.5 - - - +
808C LEU* 1.3 64.5 + - - +
810C ALA* 3.9 3.4 - - - +
811C LEU* 3.0 40.6 + - + +
140G ILE* 4.1 31.6 - - + +
143G VAL* 6.3 1.3 - - + -
144G SER* 4.2 22.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 808 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804C GLY 2.9 12.6 + - - +
805C LEU* 3.6 12.3 - - + +
807C MET* 1.3 75.0 - - - +
809C VAL* 1.3 68.4 + - + +
811C LEU* 4.3 9.6 - - - +
812C ILE* 2.9 50.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 809 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 4.8 7.4 - - + +
597B SER* 3.6 26.0 - - - -
600B ILE* 4.3 16.6 - - + -
805C LEU* 2.9 33.8 + - + +
806C ALA* 3.1 11.2 + - - +
808C LEU* 1.3 81.6 - - + +
810C ALA* 1.3 66.0 + - - +
812C ILE* 4.3 1.4 - - - +
813C GLU* 2.9 34.0 + - + +
----------------------------------------------------------
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Residues in contact with ALA 810 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 6.3 1.3 - - + -
543B VAL* 4.0 33.9 - - + +
597B SER* 4.3 3.1 - - - +
806C ALA 2.9 17.6 + - - +
807C MET 4.0 2.2 - - - +
809C VAL* 1.3 73.6 - - - +
811C LEU* 1.3 66.9 + - + +
814C PHE* 2.9 48.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 811 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 6.1 4.3 - - + -
807C MET* 3.0 40.8 + - + +
808C LEU* 3.7 7.9 - - - +
810C ALA* 1.3 77.0 - - + +
812C ILE* 1.3 64.6 + - + +
815C CYS* 2.9 39.6 + - + +
140G ILE* 4.5 21.3 - - + -
141G PHE* 6.0 4.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 812 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808C LEU* 2.9 44.4 + - + +
809C VAL* 4.3 0.9 - - - +
811C LEU* 1.3 78.3 - - + +
813C GLU* 1.3 52.3 + - - +
815C CYS* 5.0 2.0 - - + -
816C TYR* 2.6 46.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 813 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 4.5 23.3 - - + +
809C VAL* 2.9 23.7 + - + +
810C ALA 4.2 1.1 - - - +
812C ILE* 1.3 79.9 - - - +
814C PHE* 1.3 71.8 + - + +
816C TYR* 3.1 17.7 - - - +
817C LYS* 2.9 27.0 + - + +
----------------------------------------------------------
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Residues in contact with PHE 814 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B VAL 5.4 6.3 - - - -
546B PHE 5.2 4.0 - - - +
547B SER* 3.9 39.2 - - - +
595B SER* 4.1 21.1 - - - -
596B LEU* 5.4 5.8 - - + -
597B SER* 4.4 11.4 - - - -
810C ALA* 2.9 45.6 + - + +
811C LEU* 5.4 0.2 - - - -
813C GLU* 1.3 88.6 - - + +
815C CYS* 1.3 61.4 + - - +
816C TYR 3.1 1.1 - - - -
817C LYS* 3.8 6.5 - - + +
818C SER* 2.9 33.3 + - - -
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Residues in contact with CYS 815 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811C LEU* 2.9 22.5 + - + +
812C ILE* 4.6 2.2 - - + +
814C PHE* 1.3 76.1 - - - +
816C TYR* 1.3 57.9 + - - +
818C SER* 4.9 3.4 - - - -
819C ARG* 2.9 39.1 + - - +
----------------------------------------------------------
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Residues in contact with TYR 816 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812C ILE* 2.6 30.7 + - + +
813C GLU* 3.1 19.1 - - - +
815C CYS* 1.3 77.9 - - - +
817C LYS* 1.3 69.6 + - + +
819C ARG* 3.6 3.1 - - - +
820C ALA* 2.9 35.0 + - + +
----------------------------------------------------------
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Residues in contact with LYS 817 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813C GLU* 2.9 17.3 + - + +
814C PHE* 3.2 10.3 + - + +
816C TYR* 1.3 82.8 - - + +
818C SER* 1.3 64.1 + - - +
820C ALA* 3.1 5.3 + - - +
821C GLU* 2.9 28.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 818 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B SER 5.2 9.9 - - - -
548B PRO 6.0 1.3 - - - -
814C PHE 2.9 19.5 + - - -
815C CYS* 4.4 3.4 - - - -
817C LYS* 1.3 73.2 - - - +
819C ARG* 1.3 50.9 + - - +
821C GLU* 5.3 1.8 - - - -
822C ALA* 2.5 45.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 819 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815C CYS* 2.9 28.5 + - - +
816C TYR* 3.6 4.5 - - - +
818C SER* 1.3 79.1 - - - +
820C ALA* 1.3 57.5 + - - +
822C ALA* 3.6 3.6 - - - +
823C LYS* 2.9 30.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 820 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C TYR* 2.9 29.8 + - + +
817C LYS* 3.7 4.5 - - - +
819C ARG* 1.3 76.3 - - - +
821C GLU* 1.3 59.6 + - - +
823C LYS* 3.1 8.2 + - - +
824C ARG* 2.9 25.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 821 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817C LYS 2.9 16.6 + - - +
818C SER* 4.8 1.6 - - - +
820C ALA* 1.3 74.0 - - - +
822C ALA* 1.3 52.9 + - - +
824C ARG* 3.1 12.0 + - + +
825C MET* 2.7 34.7 + - + +
----------------------------------------------------------
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Residues in contact with ALA 822 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818C SER* 2.5 27.9 + - - +
819C ARG* 3.6 5.2 - - - +
821C GLU* 1.3 77.3 - - - +
823C LYS* 1.3 58.3 + - - +
825C MET* 2.9 32.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 823 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C ARG 2.9 18.6 + - - +
820C ALA* 3.5 5.8 - - - +
822C ALA* 1.3 74.8 - - - +
824C ARG* 1.3 62.8 + - - +
825C MET 3.0 8.4 - - - +
----------------------------------------------------------
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Residues in contact with ARG 824 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820C ALA 2.9 12.6 + - - +
821C GLU* 3.1 18.4 + - + +
823C LYS* 1.3 76.5 - - - +
825C MET* 1.3 60.9 + - - +
----------------------------------------------------------
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Residues in contact with MET 825 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821C GLU* 2.7 18.1 + - + +
822C ALA* 2.9 24.5 + - - +
823C LYS 3.0 11.1 - - - +
824C ARG* 1.3 74.4 - - - +
----------------------------------------------------------
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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