Contacts of the helix formed by residues 695 - 718 (chain A) in PDB entry 1OFD
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 695 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A TRP* 3.4 14.0 + - + +
693A ARG 4.1 1.2 + - - -
694A ILE* 1.3 78.6 - - - +
696A LEU* 1.3 63.8 + - - +
697A PRO* 3.5 15.5 - - + +
698A THR* 2.7 34.7 + - - -
699A ALA* 3.2 15.1 + - - +
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Residues in contact with LEU 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A GLU* 3.7 47.6 - - + +
673A VAL 4.7 0.4 - - - +
674A ARG* 4.0 20.2 - - + +
677A TRP* 3.5 54.9 - - + +
678A LEU* 4.8 9.6 - - + -
695A ASP* 1.3 71.6 - - - +
697A PRO* 1.3 72.8 - - + +
699A ALA* 3.1 6.3 + - + +
700A LEU* 3.0 38.2 + - + +
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Residues in contact with PRO 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 4.6 8.8 - - + +
433A GLU* 3.6 28.3 - - + +
695A ASP* 3.5 19.3 - - + +
696A LEU* 1.3 95.4 - - + +
698A THR* 1.3 56.5 + - - +
700A LEU* 3.6 8.5 + - + +
701A LYS* 3.0 30.4 + - - +
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Residues in contact with THR 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ARG 4.3 14.6 + - - +
694A ILE* 4.1 7.9 - - + -
695A ASP* 2.7 29.9 + - - -
697A PRO* 1.3 75.8 - - - +
699A ALA* 1.3 55.4 + - - +
701A LYS* 3.3 23.5 + - - +
702A ASN* 2.7 57.4 + - - +
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Residues in contact with ALA 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ALA* 3.5 24.2 - - + +
673A VAL* 4.0 17.5 - - + -
676A TRP* 4.2 14.1 - - + -
677A TRP* 4.3 8.5 - - + -
694A ILE* 3.5 15.6 - - + +
695A ASP 3.2 8.3 + - - +
696A LEU* 3.1 10.4 + - + +
698A THR* 1.3 75.2 - - - +
700A LEU* 1.3 56.9 + - - +
702A ASN* 3.5 2.6 - - - +
703A TYR* 3.0 24.4 + - - +
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 3.6 49.0 - - + -
432A ALA 3.9 14.4 - - - +
433A GLU* 4.9 2.5 - - + -
670A LEU* 3.9 37.9 - - + +
673A VAL* 3.9 19.5 - - + -
674A ARG* 4.3 8.3 - - + +
696A LEU* 3.0 40.6 + - + +
697A PRO* 4.0 3.6 - - + +
699A ALA* 1.3 74.0 - - - +
701A LYS* 1.3 65.0 + - - +
703A TYR* 3.2 7.1 + - - +
704A ARG 3.1 17.5 + - - -
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Residues in contact with LYS 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ASP 5.8 1.8 - - - +
431A PHE* 3.8 16.9 - - + -
697A PRO 3.0 18.1 + - - +
698A THR* 3.6 27.2 + - - +
700A LEU* 1.3 75.5 - - - +
702A ASN* 1.3 62.0 + - - +
704A ARG* 3.3 6.8 + - + +
705A GLN* 2.8 42.4 + - + +
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Residues in contact with ASN 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A MET 3.4 9.0 - - - +
465A ALA 3.0 29.3 + - - +
466A SER 3.8 6.9 + - - -
467A GLN 4.4 2.0 - - - +
468A GLY* 3.7 14.9 - - - +
694A ILE* 3.6 21.4 - - - +
698A THR* 2.7 33.1 + - - +
699A ALA 3.5 0.4 - - - +
701A LYS* 1.3 78.1 + - - +
703A TYR* 1.3 62.8 + - - +
705A GLN* 3.2 15.3 + - - +
706A SER* 2.9 26.9 + - - -
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Residues in contact with TYR 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A VAL* 4.4 15.5 - - + -
464A MET* 3.6 32.7 + - + -
465A ALA* 4.3 2.7 - - - -
545A LEU* 4.2 9.0 - - + -
648A TRP* 2.8 41.6 + - - -
653A PHE* 3.6 7.8 - - - -
666A PRO* 4.5 3.8 - - + -
669A ALA* 3.4 17.3 - - + +
670A LEU* 3.8 29.2 - - + -
673A VAL* 4.0 23.1 - - + -
699A ALA 3.0 13.9 + - - +
700A LEU* 3.2 9.8 + - - +
702A ASN* 1.3 76.3 - - - +
704A ARG* 1.3 65.2 - - - +
706A SER* 3.2 5.9 + - - -
707A VAL* 3.1 36.7 + - + +
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Residues in contact with ARG 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A SER 3.2 23.0 + - - -
429A ASP* 5.1 1.4 + - - +
431A PHE* 3.9 23.5 - - + -
542A ARG* 4.2 10.8 - - - +
543A SER* 5.7 2.4 - - - -
545A LEU* 3.1 43.4 + - + +
547A ASN* 3.5 20.2 - - - +
550A GLU* 2.5 36.2 + - - -
700A LEU 3.1 12.4 + - - +
701A LYS* 3.3 9.2 + - - +
703A TYR* 1.3 77.9 - - + +
705A GLN* 1.3 63.8 + - - +
707A VAL* 3.2 2.4 + - - +
708A GLU* 3.0 48.9 + - - +
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Residues in contact with GLN 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A GLN 4.7 2.0 + - - -
468A GLY* 3.0 32.7 + - - +
701A LYS* 2.8 29.1 + - + +
702A ASN* 3.6 12.2 + - - +
704A ARG* 1.3 75.5 - - - +
706A SER* 1.3 57.3 + - - +
708A GLU* 3.4 11.0 + - - +
709A ALA* 2.9 35.3 + - + +
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Residues in contact with SER 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A MET* 2.9 40.9 + - - -
468A GLY 2.9 31.6 - - - -
469A LYS* 3.0 11.2 + - - +
470A GLU* 4.1 6.8 + - - +
650A THR* 3.9 4.5 + - - -
702A ASN 2.9 5.7 + - - -
703A TYR 3.2 10.3 + - - -
705A GLN* 1.3 78.3 - - - +
707A VAL* 1.3 56.1 + - - +
709A ALA* 3.8 3.5 - - - +
710A GLY* 3.0 24.9 + - - -
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Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A MET* 5.1 4.5 - - - -
545A LEU* 3.9 19.3 - - + -
648A TRP 4.7 2.7 - - - +
650A THR* 4.1 11.0 + - - +
653A PHE* 3.6 53.6 - - + -
703A TYR* 3.1 34.2 + - + +
704A ARG 3.2 7.4 + - - +
706A SER* 1.3 74.2 - - - +
708A GLU* 1.3 54.1 + - + +
710A GLY* 3.1 2.1 + - - -
711A LEU* 2.8 43.0 + - + +
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Residues in contact with GLU 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A LEU* 3.6 22.0 - - + +
543A SER* 2.6 38.0 + - - +
544A PRO* 5.4 1.1 - - + -
545A LEU* 5.5 1.3 - - + -
704A ARG* 3.0 43.9 + - + +
705A GLN* 3.9 9.3 - - - +
707A VAL* 1.3 78.6 - - + +
709A ALA* 1.3 61.5 + - - +
711A LEU* 3.1 6.5 + - + +
712A PHE* 3.0 34.5 + - + -
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Residues in contact with ALA 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A GLY 5.5 2.2 - - - +
469A LYS* 6.1 3.1 - - + -
470A GLU* 5.0 0.7 - - - +
509A PRO* 5.4 0.5 - - - +
510A LEU* 6.4 2.0 - - + -
705A GLN* 2.9 22.2 + - + +
706A SER* 3.8 6.1 - - - +
708A GLU* 1.3 75.4 - - - +
710A GLY* 1.3 57.2 + - - +
712A PHE* 3.3 12.4 + - - +
713A LYS* 3.0 28.2 + - - +
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Residues in contact with GLY 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLU* 3.5 19.8 + - - +
650A THR* 3.3 26.5 - - - -
706A SER 3.0 11.4 + - - -
707A VAL 3.1 1.5 + - - -
709A ALA* 1.3 76.4 - - - +
711A LEU* 1.3 57.3 + - - +
713A LYS* 3.4 2.9 + - - +
714A ILE* 3.0 34.1 + - - +
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Residues in contact with LEU 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A LEU* 4.1 19.1 - - + -
544A PRO* 3.6 30.3 - - + -
650A THR 4.1 7.9 - - - +
653A PHE* 4.1 16.6 - - + +
654A ALA* 3.7 40.8 - - + +
657A VAL* 5.6 1.8 - - + -
707A VAL* 2.8 23.4 + - + +
708A GLU* 3.1 9.1 + - + +
710A GLY* 1.3 75.4 - - - +
712A PHE* 1.3 64.5 + - - +
714A ILE* 3.3 2.0 + - + +
715A LEU* 3.0 33.4 + - + +
723A LEU* 4.6 16.4 - - + -
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Residues in contact with PHE 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A PRO* 3.6 8.0 - - + +
513A ASN* 3.4 26.0 - - - +
516A MET* 3.3 47.8 - - + +
517A SER* 3.9 10.8 - - - -
518A LEU* 3.7 42.4 - - + -
708A GLU* 3.0 27.2 + - + -
709A ALA* 3.6 10.8 - - - +
711A LEU* 1.3 74.5 - - - +
713A LYS* 1.3 61.8 + - - +
715A LEU* 3.6 6.5 + - + +
716A SER* 3.0 27.2 + - - -
721A SER 5.2 1.1 - - - -
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Residues in contact with LYS 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLU* 3.4 26.7 - - - +
509A PRO* 4.0 15.3 - - + +
709A ALA 3.0 14.4 + - - +
710A GLY 3.5 8.7 - - - +
711A LEU 3.2 0.2 - - - -
712A PHE* 1.3 76.3 - - - +
714A ILE* 1.3 64.3 + - + +
716A SER* 2.7 23.2 + - - +
717A LYS* 3.1 27.2 + - - +
975A GLU* 2.9 38.1 + - + +
978A GLN* 5.9 0.8 - - - +
1069A PRO* 3.8 18.0 - - + +
1071A SER* 4.9 1.8 - - - +
1072A SER* 4.3 2.5 - - - +
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Residues in contact with ILE 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A GLN* 3.4 44.0 - - + +
498A ARG 5.2 1.8 - - - +
650A THR* 3.6 42.0 - - + +
654A ALA* 3.8 13.9 - - + -
710A GLY 3.0 17.5 + - - +
711A LEU* 3.3 4.7 + - + +
713A LYS* 1.3 77.5 - - + +
715A LEU* 1.3 63.6 - - + +
717A LYS* 3.2 30.4 + - - +
718A MET* 3.9 3.6 + - - +
726A TYR* 3.4 31.8 - - + +
731A ILE* 6.0 0.5 - - - +
1071A SER* 5.8 0.7 - - - +
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Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A MET* 5.6 1.3 - - - -
518A LEU* 4.8 6.5 - - + -
711A LEU* 3.0 26.0 + - + +
712A PHE* 3.8 7.9 - - + +
714A ILE* 1.3 76.8 - - + +
716A SER* 1.3 61.6 + - - +
718A MET* 3.1 11.1 + - - +
720A ILE* 3.0 45.2 + - + +
721A SER 4.1 8.7 - - - +
722A LEU 3.6 9.6 - - - +
723A LEU* 3.4 44.9 - - + +
726A TYR* 3.3 42.4 - - + -
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Residues in contact with SER 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PRO* 3.2 4.6 - - - +
507A ILE* 3.0 59.9 + - - -
509A PRO* 3.3 27.0 - - - +
516A MET* 4.6 2.2 - - - -
712A PHE 3.0 16.1 + - - -
713A LYS* 2.7 19.2 + - - +
715A LEU* 1.3 73.5 - - - +
717A LYS* 1.3 64.7 + - - +
719A GLY 3.0 4.1 + - - -
720A ILE 4.2 0.9 - - - -
974A GLY 4.7 2.2 + - - -
975A GLU* 6.1 0.7 - - - +
1004A PRO* 5.4 0.5 - - - +
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Residues in contact with LYS 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A GLN* 2.8 34.4 + - + +
498A ARG 4.6 3.6 - - - +
499A PHE* 3.5 10.5 - - + +
500A ALA* 2.9 25.2 + - - +
506A PRO* 3.7 6.8 - - - +
713A LYS* 3.1 27.6 + - - +
714A ILE* 3.3 16.0 - - - +
715A LEU 3.2 0.2 - - - -
716A SER* 1.3 82.8 + - - +
718A MET* 1.3 57.6 + - - +
974A GLY* 3.4 38.3 - - - +
975A GLU* 3.4 20.4 + - + -
1071A SER* 5.0 2.0 + - - -
1072A SER* 3.1 23.8 + - - +
1076A ALA* 3.9 14.7 - - + +
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Residues in contact with MET 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 2.9 30.6 + - - +
498A ARG* 3.6 29.4 - - - +
499A PHE 3.5 35.7 - - - +
500A ALA* 3.8 8.7 - - - +
504A ASN* 3.0 25.0 + - - +
714A ILE 3.9 2.4 + - - +
715A LEU* 3.1 9.3 + - - +
716A SER 3.1 0.4 - - - -
717A LYS* 1.3 76.6 - - - +
719A GLY* 1.3 58.6 + - - +
720A ILE* 3.7 23.8 - - + -
726A TYR* 6.1 0.4 - - + -
731A ILE* 3.7 26.7 - - + -
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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