Contacts of the helix formed by residues 783 - 808 (chain B) in PDB entry 5MBV
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 ALA 783 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B ASP* 4.5 10.3 - - - +
781B ASN* 3.2 9.9 - - + +
782B ALA* 1.3 77.1 - - - +
784B PRO* 1.3 72.7 - - + +
785B GLU* 3.1 19.5 + - + +
786B SER* 3.6 10.2 + - - +
787B VAL* 3.4 9.5 + - - +
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Residues in contact with PRO 784 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B ALA 3.9 4.9 - - - +
783B ALA* 1.3 81.1 - - + +
785B GLU* 1.3 73.7 + - - +
787B VAL* 3.2 13.7 + - + +
788B ASP* 3.0 35.8 + - - +
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Residues in contact with GLU 785 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 6.1 1.6 - - - +
783B ALA* 3.1 23.3 + - + +
784B PRO* 1.3 79.6 - - - +
786B SER* 1.3 65.6 + - - +
788B ASP* 3.0 18.5 + - - +
789B LEU* 3.2 24.2 + - + +
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Residues in contact with SER 786 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 4.4 8.3 + - - +
766B ALA* 3.8 19.0 - - - +
768B TYR* 3.2 39.6 + - - -
779B ASP* 3.7 23.2 + - - +
783B ALA* 3.6 5.0 + - - +
784B PRO 3.5 0.2 - - - -
785B GLU* 1.3 77.9 - - - +
787B VAL* 1.3 57.6 + - - +
789B LEU* 3.9 4.8 - - - +
790B ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 787 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B VAL* 6.4 1.3 - - + -
763B GLN 5.0 8.8 - - - +
764B GLU* 4.6 16.8 - - - +
765B GLN 5.3 1.3 - - - +
766B ALA* 4.2 15.0 - - + -
782B ALA* 4.0 11.7 - - - +
783B ALA 3.4 17.5 - - - +
784B PRO* 3.5 13.7 - - + +
785B GLU 3.1 0.8 - - - -
786B SER* 1.3 78.5 - - - +
788B ASP* 1.3 63.2 + - - +
790B ALA* 3.4 5.4 + - + +
791B GLU* 3.0 30.1 + - + +
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Residues in contact with ASP 788 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B PRO* 3.0 22.9 + - - +
785B GLU* 3.0 10.3 + - - +
787B VAL* 1.3 81.7 - - - +
789B LEU* 1.3 68.7 + - + +
791B GLU* 3.4 9.3 + - - +
792B ALA* 3.2 22.5 + - - +
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Residues in contact with LEU 789 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768B TYR* 4.2 20.4 - - + -
771B ARG* 3.4 42.5 + - - +
785B GLU* 3.2 26.2 + - + +
786B SER* 4.2 4.9 - - - +
788B ASP* 1.3 84.0 - - + +
790B ALA* 1.3 61.1 + - - +
792B ALA* 3.7 4.2 + - + -
793B GLU* 3.3 27.5 + - - +
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Residues in contact with ALA 790 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B GLN* 2.5 31.5 + - + +
765B GLN 4.2 9.2 - - - +
766B ALA* 4.3 0.4 - - - -
767B PHE 3.2 37.7 - - - +
768B TYR* 4.2 1.5 - - - +
786B SER 3.0 20.7 + - - +
787B VAL* 3.7 4.0 - - - +
788B ASP 3.2 0.2 - - - -
789B LEU* 1.3 76.7 - - - +
791B GLU* 1.3 61.7 + - - +
793B GLU* 3.3 4.6 + - - +
794B ARG 3.2 9.5 + - - -
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Residues in contact with GLU 791 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B VAL* 4.5 21.1 - - + -
763B GLN* 4.4 5.3 + - + +
787B VAL* 3.0 19.5 + - + +
788B ASP* 3.4 9.1 + - - +
789B LEU 3.4 0.2 - - - -
790B ALA* 1.3 74.7 - - - +
792B ALA* 1.3 65.7 + - - +
794B ARG* 3.4 24.1 + - - +
795B LEU* 2.9 35.7 + - - +
835B GLN* 2.9 29.3 - - - +
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Residues in contact with ALA 792 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B MET* 4.2 23.0 - - + +
470B PHE* 5.1 2.3 - - + -
771B ARG* 4.1 15.3 - - - +
788B ASP 3.2 16.4 + - - +
789B LEU* 3.9 9.0 - - + +
790B ALA 3.2 0.4 - - - -
791B GLU* 1.3 82.4 + - - +
793B GLU* 1.3 58.2 + - - +
795B LEU* 3.8 6.2 - - - +
796B ALA* 3.1 27.2 + - - +
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Residues in contact with GLU 793 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ILE* 6.3 1.6 - - + -
428B PHE* 3.2 35.9 - - + -
470B PHE* 4.8 4.5 - - + -
763B GLN* 5.2 2.0 - - - +
767B PHE* 3.9 4.7 - - - +
768B TYR* 3.3 28.9 - - - +
769B HIS* 2.8 35.9 + - - +
771B ARG* 3.5 8.8 + - - +
789B LEU 3.3 10.3 - - - +
790B ALA 3.3 6.2 + - - +
791B GLU 3.3 0.6 - - - -
792B ALA* 1.3 75.9 - - - +
794B ARG* 1.3 59.7 + - - +
796B ALA* 3.4 6.3 + - - +
797B GLU* 3.0 28.4 + - - +
800B ARG* 4.1 3.9 + - - +
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Residues in contact with ARG 794 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ARG* 5.6 6.5 + - - +
760B PHE* 3.2 43.4 - - - +
761B ARG* 2.3 29.9 + - + +
762B VAL* 3.7 17.0 - - - +
763B GLN* 3.5 35.1 - - + +
790B ALA 3.2 5.4 + - - +
791B GLU* 3.6 29.4 + - - +
792B ALA 3.3 0.2 - - - -
793B GLU* 1.3 75.0 - - - +
795B LEU* 1.3 81.4 + - - +
797B GLU* 3.2 13.2 + - + +
798B ASP* 2.9 36.6 + - + +
835B GLN* 3.6 14.7 + - - +
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Residues in contact with LEU 795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B MET* 3.7 19.7 - - + -
791B GLU* 2.9 28.7 + - - +
792B ALA* 3.8 5.6 - - - +
794B ARG* 1.3 85.8 - - - +
796B ALA* 1.3 57.4 + - - +
798B ASP* 3.3 4.1 + - + +
799B LEU* 3.0 33.6 + - + +
834B HIS* 4.6 7.0 - - - +
835B GLN* 3.3 26.7 - - - +
836B SER 3.9 16.2 - - - +
837B ALA* 4.3 7.0 - - + +
840B ARG* 3.7 27.6 - - - +
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Residues in contact with ALA 796 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B PHE* 3.8 13.7 - - - +
469B MET* 4.5 4.7 - - - -
470B PHE* 3.5 32.5 - - + -
792B ALA 3.1 15.8 + - - +
793B GLU 3.8 4.3 - - - +
794B ARG 3.3 0.2 - - - -
795B LEU* 1.3 76.3 - - - +
797B GLU* 1.3 61.9 + - - +
799B LEU* 3.4 13.1 + - - +
800B ARG* 3.1 34.3 + - - +
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Residues in contact with GLU 797 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 3.1 33.2 - - - +
421B ALA* 3.5 28.3 + - + +
422B PHE* 4.1 7.3 + - - +
559B ARG* 6.1 1.6 - - - +
742B HIS* 5.5 1.0 + - - -
793B GLU 3.0 17.0 + - - +
794B ARG* 3.2 11.5 + - - +
796B ALA* 1.3 75.9 - - - +
798B ASP* 1.3 61.0 + - - +
800B ARG* 3.2 22.7 + - - +
801B LEU* 2.9 36.2 + - + +
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Residues in contact with ASP 798 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ARG* 2.6 38.1 + - - +
757B ILE* 5.2 11.8 - - - +
759B ASN 4.4 1.7 - - - +
760B PHE* 4.4 13.2 - - - +
794B ARG* 2.9 19.5 + - - +
795B LEU* 3.3 12.3 + - + +
797B GLU* 1.3 73.2 - - - +
799B LEU* 1.3 60.6 + - - +
801B LEU* 3.1 13.7 + - - +
802B LEU 3.0 22.0 + - - -
837B ALA* 3.3 28.4 + - + +
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Residues in contact with LEU 799 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B PHE* 5.0 4.5 - - + -
467B ALA 3.4 25.1 - - - +
468B PHE* 4.2 21.4 - - + -
469B MET* 4.2 14.4 - - + -
795B LEU* 3.0 21.4 + - + +
796B ALA* 3.5 15.5 - - - +
797B GLU 3.2 0.4 - - - -
798B ASP* 1.3 77.3 - - - +
800B ARG* 1.3 56.9 + - - +
802B LEU* 3.2 4.8 + - - +
803B TYR* 3.1 26.3 + - - +
837B ALA* 3.3 35.9 - - + +
840B ARG* 4.4 12.3 - - - +
841B LEU* 3.9 24.0 - - + -
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Residues in contact with ARG 800 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO 3.3 18.2 - - - -
416B LYS* 3.3 21.3 - - - +
418B ALA* 3.2 33.4 + - - +
419B ILE* 3.8 2.4 - - - +
421B ALA* 5.5 6.2 - - - +
427B ILE* 3.2 48.8 - - - +
468B PHE* 3.8 22.0 - - + -
470B PHE* 5.3 2.1 - - - -
473B ILE* 5.3 3.4 - - - -
793B GLU* 4.1 5.7 + - - +
796B ALA* 3.1 22.4 + - - +
797B GLU* 3.2 35.8 + - - +
799B LEU* 1.3 73.9 - - - +
801B LEU* 1.3 64.7 + - - +
803B TYR 3.8 0.9 - - - +
804B VAL* 3.2 30.1 + - - +
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Residues in contact with LEU 801 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 3.6 24.7 - - + -
559B ARG* 3.5 39.3 - - + +
741B ILE* 3.7 31.9 - - + +
742B HIS* 3.7 29.6 - - + +
757B ILE* 5.2 4.6 - - + +
797B GLU* 2.9 28.1 + - + +
798B ASP* 3.1 15.2 + - - +
800B ARG* 1.3 78.1 - - - +
802B LEU* 1.3 60.0 + - - +
804B VAL* 4.3 0.4 - - - +
805B ALA* 3.3 23.2 + - - +
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Residues in contact with LEU 802 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LEU* 4.8 1.3 - - + -
461B PHE* 5.1 0.7 - - + -
754B LEU* 4.3 4.3 - - + -
757B ILE* 3.6 33.2 - - + -
798B ASP* 3.0 11.3 + - - +
799B LEU 3.6 8.1 - - - +
800B ARG 3.2 0.4 - - - -
801B LEU* 1.3 77.0 - - - +
803B TYR* 1.3 60.4 + - - +
805B ALA* 3.3 1.9 + - - -
806B LEU* 2.8 63.1 + - + +
837B ALA* 4.3 6.5 - - + -
838B LEU* 3.7 37.9 - - + +
841B LEU* 3.7 30.3 - - + -
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Residues in contact with TYR 803 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 3.6 7.4 - - - -
25B ALA* 3.0 41.3 + - + +
414B ASP* 3.3 18.8 + - - -
416B LYS* 3.4 49.1 - - + +
417B GLN* 4.1 4.3 - - + -
457B VAL* 4.6 5.6 - - + -
461B PHE* 3.4 39.9 - + + -
468B PHE* 4.2 9.4 - + + -
475B PHE* 5.0 4.3 - + - -
799B LEU 3.1 16.0 + - - +
800B ARG 4.0 3.4 - - - +
801B LEU 3.5 0.4 - - - -
802B LEU* 1.3 76.9 - - - +
804B VAL* 1.3 63.1 + - + +
806B LEU* 3.4 2.3 + - - +
807B THR* 2.9 41.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL 804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LYS 4.0 1.6 - - - +
417B GLN* 3.9 38.8 - - + +
419B ILE* 4.4 9.6 - - + -
741B ILE* 4.8 12.3 - - + +
745B LYS* 3.8 30.3 - - + -
800B ARG 3.2 18.1 + - - +
801B LEU 4.3 2.7 - - - +
802B LEU 3.3 0.4 - - - -
803B TYR* 1.3 78.1 - - + +
805B ALA* 1.3 62.4 + - - +
807B THR* 3.0 17.5 + - - -
808B ARG* 3.1 36.7 + - + +
----------------------------------------------------------
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Residues in contact with ALA 805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B LEU* 4.2 11.2 - - + -
741B ILE* 3.8 25.7 - - + +
752B VAL* 4.2 14.7 - - - +
754B LEU* 3.6 27.9 - - + +
757B ILE* 5.1 1.3 - - + -
801B LEU 3.3 17.6 + - - +
802B LEU* 3.3 5.4 + - - +
804B VAL* 1.3 79.9 - - - +
806B LEU* 1.3 61.2 + - - +
808B ARG* 3.8 11.5 + - - +
809B SER* 4.7 1.0 + - - -
813B CYS* 5.7 0.5 - - - +
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Residues in contact with LEU 806 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B MET* 3.7 12.4 - - + +
457B VAL* 4.4 17.6 - - + +
460B LEU* 4.3 29.4 - - + -
461B PHE* 4.3 10.1 - - + -
499B MET* 4.7 6.7 - - + -
754B LEU* 4.4 6.7 - - + -
802B LEU* 2.8 44.2 + - + +
803B TYR* 3.8 4.5 - - - +
804B VAL 3.2 0.2 - - - -
805B ALA* 1.3 77.4 - - - +
807B THR* 1.3 60.0 + - + +
808B ARG 3.3 0.2 - - - -
809B SER* 3.1 22.3 + - - -
813B CYS* 4.6 14.0 - - - -
815B LEU* 3.6 31.0 - - + -
838B LEU* 5.6 0.2 - - + -
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Residues in contact with THR 807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.3 32.4 - - + +
446B ASN* 5.9 3.1 - - - +
448B ARG* 3.5 20.8 + - - -
449B SER* 5.5 0.9 - - - -
457B VAL* 4.4 17.3 - - + -
803B TYR* 2.9 42.2 + - + +
804B VAL* 3.0 12.5 + - - -
806B LEU* 1.3 76.2 - - - +
808B ARG* 1.3 70.3 + - - +
809B SER* 3.2 7.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.4 31.7 - - - +
26B GLY 4.7 0.2 - - - +
417B GLN* 4.1 9.5 - - - +
448B ARG* 3.8 14.6 - - - +
557B LEU* 4.2 18.2 - - + -
744B SER* 3.3 26.9 - - - +
745B LYS* 5.1 0.2 - - - +
746B GLY* 3.0 31.0 - - - +
747B LEU 3.2 22.7 + - - +
748B GLU* 4.2 2.8 - - - -
749B TYR* 3.1 36.3 + - + +
752B VAL* 4.0 10.5 - - + -
804B VAL* 3.1 33.8 + - + +
805B ALA* 4.0 7.0 - - - +
806B LEU 3.3 1.2 - - - -
807B THR* 1.3 88.6 + - - +
809B SER* 1.3 60.1 + - - +
810B VAL* 4.3 2.3 - - - +
----------------------------------------------------------
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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