Contacts of the helix formed by residues 806 - 843 (chain K) in PDB entry 6D6Q
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 ASP 806 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802K PRO* 3.0 32.2 + - - +
803K GLU* 4.1 4.9 + - - +
804K LEU 3.8 1.0 - - - +
805K THR* 1.3 76.6 + - - +
807K LYS* 1.3 66.9 + - - +
808K HIS* 2.9 5.0 + - + +
809K LYS* 3.1 40.1 + - + +
810K LEU* 3.2 11.9 + - - +
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Residues in contact with LYS 807 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684K GLU* 3.3 56.1 + - - +
685K HIS* 4.2 5.2 - - + +
755K CYS* 4.5 10.3 - - - -
757K GLY* 3.9 16.8 + - - -
758K MET* 3.5 32.7 - - + +
805K THR 2.8 16.2 + - - +
806K ASP* 1.3 71.6 - - - +
808K HIS* 1.3 58.9 + - + +
810K LEU* 3.8 7.7 - - - +
811K ALA* 2.9 32.1 + - - +
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Residues in contact with HIS 808 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758K MET* 3.7 25.2 - - + +
806K ASP* 2.9 3.7 + - + -
807K LYS* 1.3 78.5 - - + +
809K LYS* 1.3 61.0 + - + +
811K ALA* 3.3 4.9 + - - +
812K ASP* 2.9 28.3 + - - +
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Residues in contact with LYS 809 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802K PRO* 5.6 3.4 - - - +
803K GLU* 3.2 51.0 + - + +
806K ASP* 3.1 27.0 + - + +
808K HIS* 1.3 81.7 - - + +
810K LEU* 1.3 57.3 + - - +
812K ASP* 3.2 7.1 + - - +
813K ILE* 2.9 39.4 + - + +
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Residues in contact with LEU 810 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685K HIS* 4.5 7.2 - - + -
686K ALA* 3.3 38.8 - - - +
687K LEU* 3.3 25.7 - - + +
755K CYS* 3.4 22.2 - - + -
786K ILE* 5.0 9.2 - - + -
790K LEU* 5.5 2.0 - - + -
803K GLU 5.4 7.7 + - - +
804K LEU* 4.2 21.8 - - + +
806K ASP 3.2 15.4 + - - +
807K LYS* 3.8 4.7 - - - +
809K LYS* 1.3 78.0 - - - +
811K ALA* 1.3 56.6 + - - +
813K ILE* 2.9 19.1 - - + +
814K CYS* 2.9 29.5 + - + +
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Residues in contact with ALA 811 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755K CYS* 5.2 6.3 - - + +
758K MET* 5.0 14.6 - - + -
807K LYS 2.9 19.3 + - - +
808K HIS* 3.6 5.8 - - - +
810K LEU* 1.3 79.8 - - - +
812K ASP* 1.3 58.5 + - - +
814K CYS* 3.2 7.2 + - - +
815K LYS* 2.9 29.1 + - - +
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Residues in contact with ASP 812 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808K HIS 2.9 14.7 + - - +
809K LYS* 3.6 10.8 - - - +
811K ALA* 1.3 76.2 - - - +
813K ILE* 1.3 59.8 + - + +
815K LYS* 3.2 25.3 + - - +
816K ASN* 3.0 27.6 + - - +
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Residues in contact with ILE 813 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524K ALA* 6.0 6.3 - - + -
687K LEU* 5.4 1.3 - - + -
782K TYR* 4.5 12.1 - - + -
786K ILE* 3.5 32.3 - - + -
803K GLU 5.9 2.7 - - - +
809K LYS* 2.9 22.0 + - + +
810K LEU* 2.9 35.4 - - + +
812K ASP* 1.3 77.3 - - + +
814K CYS* 1.3 57.9 + - + +
816K ASN* 3.3 11.8 + - - +
817K LEU* 2.9 29.4 + - - +
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Residues in contact with CYS 814 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687K LEU* 4.2 15.0 - - + -
753K TYR* 3.2 40.4 - - - -
754K PHE* 3.2 27.4 - - - -
810K LEU 2.9 18.6 + - - +
811K ALA* 3.5 9.0 - - - +
813K ILE* 1.3 75.6 - - - +
815K LYS* 1.3 61.3 + - - +
817K LEU* 3.1 9.5 + - - +
818K ASN* 2.9 34.0 + - - -
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Residues in contact with LYS 815 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811K ALA 2.9 13.6 + - - +
812K ASP* 3.5 25.1 + - - +
814K CYS* 1.3 73.4 - - - +
816K ASN* 1.3 69.3 + - - +
818K ASN* 3.2 10.9 + - + +
819K PHE* 2.9 24.7 + - + +
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Residues in contact with ASN 816 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524K ALA* 4.5 9.3 + - - +
525K ARG* 4.5 19.6 - - - +
812K ASP* 3.0 14.7 + - - +
813K ILE* 3.4 14.3 - - - +
815K LYS* 1.3 81.0 - - - +
817K LEU* 1.3 56.2 + - - +
819K PHE* 3.3 12.1 + - - +
820K ARG* 2.9 45.8 + - - +
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Residues in contact with LEU 817 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527K GLY* 4.2 20.6 - - - +
528K THR* 6.3 0.2 - - - -
687K LEU* 5.9 1.1 - - + -
753K TYR* 3.4 39.3 - - + -
781K ARG* 5.9 4.7 - - + -
782K TYR* 4.3 17.9 - - + +
783K ALA* 3.5 37.2 - - + +
786K ILE* 6.0 0.7 - - + -
813K ILE 2.9 17.8 + - - +
814K CYS* 3.1 10.0 + - - +
816K ASN* 1.3 76.1 - - - +
818K ASN* 1.3 58.4 + - - +
820K ARG* 3.2 7.3 + - - +
821K HIS* 2.9 28.9 + - + +
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Residues in contact with ASN 818 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752K VAL* 3.0 31.6 - - + +
753K TYR* 3.0 44.7 + - - -
814K CYS* 2.9 27.5 + - - -
815K LYS* 3.6 9.7 - - + +
817K LEU* 1.3 75.0 - - - +
819K PHE* 1.3 66.7 + - - +
820K ARG 3.1 0.2 + - - -
821K HIS* 3.2 6.8 + - - +
822K LYS* 3.0 23.5 + - - +
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Residues in contact with PHE 819 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438K ASP* 4.6 18.4 - - + -
815K LYS* 2.9 15.0 + - + +
816K ASN* 3.4 19.1 - - - +
818K ASN* 1.3 75.2 - - - +
820K ARG* 1.3 71.0 + - - +
822K LYS* 3.3 25.5 + - - +
823K MET* 2.9 65.9 + - + +
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Residues in contact with ARG 820 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437K HIS 4.8 3.0 + - - -
438K ASP* 3.5 19.6 + - - +
439K VAL* 4.0 9.7 - - - +
440K PRO* 3.2 27.7 - - - +
525K ARG* 2.9 36.1 + - - +
526K ARG* 5.0 1.6 - - - +
527K GLY* 3.7 24.7 - - - +
528K THR* 4.0 13.7 - - + -
816K ASN* 2.9 31.3 + - - +
817K LEU* 3.5 9.2 - - - +
818K ASN 3.1 0.2 - - - -
819K PHE* 1.3 87.0 - - - +
821K HIS* 1.3 60.9 + - - +
823K MET* 3.3 12.2 + - - +
824K ALA* 2.9 28.0 + - - +
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Residues in contact with HIS 821 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528K THR* 4.5 15.5 + - + +
689K ARG* 5.9 3.5 + - - -
751K ALA 5.6 6.5 - - - -
753K TYR* 5.8 6.7 - + + -
774K HIS* 6.5 0.7 - + - -
781K ARG* 6.2 2.7 - - - -
817K LEU* 2.9 21.4 + - + +
818K ASN* 3.7 7.2 - - - +
820K ARG* 1.3 76.7 - - - +
822K LYS* 1.3 57.9 - - - +
824K ALA* 3.3 8.3 + - - +
825K GLN* 3.0 65.9 + - + +
58O A 4.8 10.3 + - - -
59O A 5.9 0.4 + - - -
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Residues in contact with LYS 822 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750K GLN* 4.8 13.5 - - - +
818K ASN 3.0 12.1 + - - +
819K PHE* 3.5 30.3 - - - +
821K HIS* 1.3 76.4 - - - +
823K MET* 1.3 88.4 + - - +
825K GLN* 3.3 9.2 + - - +
826K TYR* 3.0 57.0 + - + +
57O A 5.7 6.3 - - + +
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Residues in contact with MET 823 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437K HIS* 3.0 47.6 - - + +
438K ASP* 5.1 0.2 - - - -
439K VAL* 4.2 9.9 - - + -
819K PHE* 2.9 47.2 + - + +
820K ARG* 3.6 14.8 - - - +
822K LYS* 1.3 103.7 - - - +
824K ALA* 1.3 56.8 + - - +
826K TYR* 3.3 20.5 + - + +
827K ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 824 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439K VAL* 4.8 2.2 - - - +
528K THR* 4.2 13.2 - - + -
530K VAL* 4.0 30.6 - - + +
820K ARG* 2.9 13.8 + - - +
821K HIS* 3.5 12.1 - - - +
822K LYS 3.2 0.2 - - - -
823K MET* 1.3 74.3 - - - +
825K GLN* 1.3 68.5 + - + +
827K ALA* 3.2 6.0 + - - +
828K GLN* 2.9 26.1 + - - +
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Residues in contact with GLN 825 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821K HIS* 3.0 53.2 + - + +
822K LYS* 3.3 9.2 + - - +
824K ALA* 1.3 79.8 - - - +
826K TYR* 1.3 69.5 + - + +
828K GLN* 3.3 13.0 + - - +
829K ARG* 3.0 44.0 + - - +
57O A 5.1 11.0 - - - +
58O A 5.5 4.0 - - - +
62O A 5.3 7.7 - - - +
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Residues in contact with TYR 826 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437K HIS* 3.5 25.5 + + + +
822K LYS* 3.0 55.6 + - + +
823K MET* 3.6 19.1 - - + +
825K GLN* 1.3 80.2 - - + +
827K ALA* 1.3 64.0 + - - +
829K ARG* 3.3 28.0 + - - +
830K ALA* 3.0 22.9 + - - +
56O A 5.2 10.1 + - - -
57O A 4.3 25.3 + - - -
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Residues in contact with ALA 827 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433K LEU* 4.1 21.8 - - + +
434K LEU* 4.6 4.5 - - + -
437K HIS* 4.3 16.1 + - - +
439K VAL* 4.5 13.5 - - + -
530K VAL* 5.2 3.8 - - + -
532K LEU* 4.2 6.4 - - + +
823K MET 2.9 17.0 + - - +
824K ALA* 3.7 6.5 - - - +
826K TYR* 1.3 77.2 - - - +
828K GLN* 1.3 63.3 + - - +
830K ALA* 3.1 5.5 + - - +
831K SER* 2.9 22.3 + - - -
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Residues in contact with GLN 828 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530K VAL* 5.5 2.6 - - + +
531K TYR* 3.4 29.4 + - - +
532K LEU* 4.1 18.2 - - + +
533K CYS* 5.6 1.2 - - - +
654K LYS* 5.9 0.8 - - - +
824K ALA 2.9 17.1 + - - +
825K GLN* 3.9 12.7 + - - +
827K ALA* 1.3 74.7 - - - +
829K ARG* 1.3 63.9 + - + +
831K SER* 3.2 2.4 + - - -
832K VAL* 3.0 34.4 + - + +
62O A 4.0 32.8 + - - -
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Residues in contact with ARG 829 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825K GLN* 3.0 35.0 + - - +
826K TYR* 3.5 28.3 - - - +
828K GLN* 1.3 77.3 - - + +
830K ALA* 1.3 61.0 + - - +
832K VAL* 2.8 27.6 - - + +
833K ALA* 2.9 11.0 + - - +
56O A 2.7 42.9 + - - +
57O A 3.1 30.5 + - - -
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Residues in contact with ALA 830 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433K LEU* 4.4 15.7 - - + -
437K HIS* 4.6 12.3 - - + -
826K TYR 3.0 12.9 + - - +
827K ALA* 3.1 10.5 + - - +
829K ARG* 1.3 75.0 - - - +
831K SER* 1.3 58.1 + - - +
833K ALA* 3.3 8.3 + - - +
834K PHE* 2.9 27.7 + - - +
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Residues in contact with SER 831 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433K LEU* 4.4 11.4 - - - +
532K LEU* 3.8 21.9 - - - +
533K CYS* 3.8 13.7 + - - -
827K ALA 2.9 13.6 + - - -
828K GLN 3.5 7.9 - - - -
829K ARG 3.2 0.2 - - - -
830K ALA* 1.3 74.4 - - - +
832K VAL* 1.3 63.3 + - - +
834K PHE* 3.1 7.4 + - - +
835K HIS* 2.7 50.0 + - - -
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Residues in contact with VAL 832 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533K CYS* 3.3 26.0 - - - -
637K VAL* 4.6 18.2 - - + +
639K PHE* 3.8 8.6 - - + -
828K GLN* 3.0 25.7 + - + +
829K ARG* 2.8 31.9 - - + +
831K SER* 1.3 75.0 - - - +
833K ALA* 1.3 63.6 + - + +
835K HIS* 3.2 3.3 + - - +
836K THR* 2.9 29.7 + - + +
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Residues in contact with ALA 833 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829K ARG 2.9 14.5 + - - +
830K ALA* 3.4 12.6 - - - +
832K VAL* 1.3 78.4 - - + +
834K PHE* 1.3 60.2 + - - +
836K THR* 2.5 24.3 + - - -
837K GLN* 2.9 23.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 834 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424K GLY* 3.5 27.8 - - - -
426K LYS* 4.2 24.2 - - + -
429K GLU* 3.6 37.5 - - + -
433K LEU* 6.0 3.4 - - + -
830K ALA 2.9 13.5 + - - +
831K SER* 3.1 10.7 + - - +
833K ALA* 1.3 77.0 - - - +
835K HIS* 1.3 71.6 + + - +
837K GLN* 3.2 22.0 + - + +
838K LEU* 2.9 50.5 + - + +
921K GLN* 6.0 2.2 - - - -
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Residues in contact with HIS 835 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426K LYS* 4.0 31.3 + - + +
533K CYS* 3.5 25.9 - - + +
534K GLU* 4.9 9.9 - - + +
639K PHE* 3.6 33.2 - + + -
648K PRO* 5.9 7.0 - - + -
831K SER* 2.7 46.0 + - - -
832K VAL 3.7 1.3 - - - +
834K PHE* 1.3 88.6 - + - +
836K THR* 1.3 58.6 + - - +
838K LEU* 3.3 12.2 + - + +
839K PHE* 2.9 28.8 + - - +
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Residues in contact with THR 836 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637K VAL* 5.5 6.1 - - + -
639K PHE* 3.5 22.7 - - + -
651K LEU* 5.4 3.8 - - + -
832K VAL* 2.9 17.3 + - + +
833K ALA* 2.5 29.4 + - - -
835K HIS* 1.3 73.7 - - - +
837K GLN* 1.3 64.0 + - - +
839K PHE* 3.2 4.8 + - - +
840K PHE* 2.9 44.1 + - + -
867K TYR 5.7 2.5 - - - +
869K LEU* 4.9 15.3 - - + +
923K ILE* 5.5 4.1 - - - +
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Residues in contact with GLN 837 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833K ALA* 2.9 24.8 + - - +
834K PHE* 3.4 24.7 - - + +
836K THR* 1.3 75.9 + - - +
838K LEU* 1.3 58.7 + - - +
840K PHE* 3.3 4.8 + - - +
841K LYS* 2.9 29.2 + - - +
913K LEU* 3.8 16.8 - - + +
920K HIS* 5.1 1.0 - - - +
921K GLN* 2.3 51.9 + - - +
922K LYS* 4.6 1.4 - - - +
923K ILE* 4.5 19.5 - - + +
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Residues in contact with LEU 838 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424K GLY 5.2 3.4 - - - +
426K LYS* 5.1 12.6 - - + -
648K PRO* 5.5 12.3 - - + -
834K PHE* 2.9 43.7 + - + +
835K HIS* 3.6 11.0 - - + +
836K THR 3.2 0.2 - - - -
837K GLN* 1.3 76.0 - - - +
839K PHE* 1.3 59.9 + - - +
841K LYS* 3.1 14.6 + - + +
842K SER* 2.9 41.3 + - - +
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Residues in contact with PHE 839 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639K PHE* 5.0 11.4 - + + -
648K PRO* 3.7 17.9 - - + -
649K ILE 3.1 24.5 - - - -
650K ASP* 3.7 20.4 - - - -
651K LEU* 5.0 10.5 - - + -
835K HIS 2.9 17.4 + - - +
836K THR* 3.7 6.7 - - - +
838K LEU* 1.3 81.2 - - + +
840K PHE* 1.3 73.9 + + - +
842K SER* 3.2 6.3 + - - +
843K ASN* 2.7 57.1 + - + +
845K ILE* 5.6 1.8 - - + -
867K TYR* 3.8 31.0 - + - -
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Residues in contact with PHE 840 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836K THR* 2.9 27.9 + - + +
837K GLN* 3.8 4.3 - - - +
839K PHE* 1.3 91.2 - + - +
841K LYS* 1.3 62.1 + - - +
843K ASN 2.7 20.6 - - - +
844K GLY* 3.5 7.9 + - - -
845K ILE* 4.0 28.0 - - + +
867K TYR* 4.5 21.5 - + + -
869K LEU* 4.3 25.6 - - + -
911K ILE* 3.6 34.8 - - + +
913K LEU* 4.3 20.1 - - + +
923K ILE* 3.6 25.6 - - + -
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Residues in contact with LYS 841 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424K GLY* 5.5 8.9 - - - -
837K GLN 2.9 15.1 + - - +
838K LEU* 3.3 17.2 - - + +
839K PHE 3.1 0.2 - - - -
840K PHE* 1.3 78.9 - - - +
842K SER* 1.3 63.7 + - - +
843K ASN* 4.5 0.7 - - - -
844K GLY* 4.7 1.0 + - - -
913K LEU* 4.5 18.1 - - + +
915K SER* 6.5 0.4 - - - -
921K GLN* 4.2 24.3 + - - +
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Residues in contact with SER 842 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838K LEU* 2.9 26.3 + - - +
839K PHE* 3.8 7.2 - - - -
841K LYS* 1.3 78.4 - - - +
843K ASN* 1.3 73.9 + - - +
844K GLY 4.1 0.9 + - - -
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Residues in contact with ASN 843 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649K ILE 4.5 2.8 - - - +
650K ASP* 5.1 0.8 - - - +
839K PHE* 2.7 48.5 + - + +
840K PHE* 2.7 30.3 - - - +
842K SER* 1.3 83.2 + - - +
844K GLY* 1.3 57.2 + - - +
845K ILE* 3.0 13.2 + - + +
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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) + - + + + + + -
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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