Contacts of the helix formed by residues 675 - 702 (chain A) in PDB entry 5UBT
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 675 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 4.2 7.1 + - - +
165A TYR* 4.2 14.5 + - - -
637A ALA 4.9 0.9 + - - -
638A LEU* 3.2 13.9 - - - +
671A TYR* 2.8 46.4 + - - -
672A CYS* 3.2 7.9 + - - -
674A GLY* 1.3 80.6 - - - +
676A THR* 1.3 54.5 + - - +
677A HIS* 3.2 3.6 - - - -
678A HIS* 3.1 6.3 + - - -
679A MET* 2.9 30.9 + - - +
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Residues in contact with THR 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.3 29.4 - - + -
151A ALA* 5.9 2.3 - - - +
154A ARG* 5.3 1.6 + - - +
672A CYS 3.4 9.3 + - - +
673A ARG 4.1 13.2 - - - +
674A GLY 5.4 0.5 - - - -
675A SER* 1.3 74.2 - - - +
677A HIS* 1.4 73.6 + - - +
679A MET* 3.3 24.6 - - - +
680A LYS* 3.5 16.3 + - - +
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Residues in contact with HIS 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 5.0 11.7 + - - -
155A GLN* 3.4 25.8 - - - -
162A TRP* 3.9 27.6 + + + -
165A TYR* 5.3 8.0 + + + +
285A MET 4.0 9.9 - - - -
286A ARG 2.8 25.3 + - - -
287A ASP* 4.9 4.2 + - - -
641A ARG* 4.1 18.8 + - - +
675A SER 3.1 1.5 + - - -
676A THR* 1.4 86.5 + - - +
678A HIS* 1.4 57.3 + - - +
680A LYS* 3.0 31.7 + - - +
681A VAL* 3.6 4.0 + - - +
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Residues in contact with HIS 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 4.9 1.7 + - - +
641A ARG* 3.2 45.5 + - + +
645A HIS* 3.2 41.7 + - + +
671A TYR* 3.0 28.0 - - - +
675A SER* 3.1 11.2 + - - +
677A HIS* 1.4 76.1 - - - +
679A MET* 1.3 54.4 + - - +
681A VAL* 2.9 25.8 + - + +
682A LEU* 2.8 56.5 + - + +
732A GLN* 4.2 7.9 - - - -
737A PRO* 4.6 5.2 - - + -
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Residues in contact with MET 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.8 21.5 - - + +
116A GLN* 3.8 21.1 - - + +
117A ILE* 3.5 40.4 - - + +
120A LEU* 3.7 20.8 - - + +
671A TYR* 6.1 0.7 - - + -
672A CYS* 3.6 31.6 - - + +
675A SER 2.9 13.7 + - - +
676A THR* 3.3 20.9 - - - +
678A HIS* 1.3 76.3 - - - +
680A LYS* 1.4 57.4 + - + +
682A LEU* 3.7 5.5 + - - +
683A MET* 3.2 33.4 + - - +
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Residues in contact with LYS 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 6.0 1.6 - - - +
676A THR 3.8 13.5 - - - +
677A HIS* 3.0 14.3 + - - +
679A MET* 1.4 76.0 - - + +
681A VAL* 1.3 64.7 + - + +
683A MET* 3.4 13.7 + - - +
684A LYS* 3.2 37.3 + - - +
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Residues in contact with VAL 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A ARG* 3.8 20.9 - - - +
677A HIS 4.4 2.5 - - - +
678A HIS* 2.9 22.0 + - + +
680A LYS* 1.3 77.0 - - + +
682A LEU* 1.3 61.7 + - - +
684A LYS* 3.1 22.5 + - + +
685A GLN* 3.1 33.0 + - + +
732A GLN* 3.4 48.7 - - + +
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Residues in contact with LEU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.5 23.0 - - + +
645A HIS* 3.8 3.6 - - - +
648A PHE* 3.5 48.5 - - + -
649A TRP* 3.7 10.6 - - + +
671A TYR* 3.7 13.7 - - + -
672A CYS* 5.6 0.2 - - - -
678A HIS* 2.8 56.9 + - + +
679A MET* 4.1 6.5 - - - +
681A VAL* 1.3 70.8 - - - +
683A MET* 1.4 55.4 + - - +
685A GLN* 3.6 22.1 + - - +
686A GLY* 3.0 23.9 + - - -
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Residues in contact with MET 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.9 13.0 - - - +
116A GLN* 3.5 55.0 - - + +
119A LEU* 6.4 2.2 - - + -
120A LEU* 3.8 21.3 - - + -
679A MET* 3.2 24.0 + - - +
680A LYS* 3.5 15.7 - - - +
681A VAL 3.2 0.4 - - - -
682A LEU* 1.4 72.7 - - - +
684A LYS* 1.4 64.6 + - - +
686A GLY* 3.4 1.4 + - - -
687A GLU* 3.1 35.3 + - + +
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Residues in contact with LYS 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LYS* 3.2 25.1 + - - +
681A VAL* 3.1 13.8 + - + +
683A MET* 1.4 76.6 - - - +
685A GLN* 1.4 59.3 + - - +
687A GLU* 3.9 5.7 + - - +
688A ALA* 3.5 20.4 + - - +
727A ALA 4.1 5.6 - - - +
730A HIS 4.1 18.6 - - - +
731A LEU* 3.9 19.5 - - + +
732A GLN 5.7 0.7 - - - +
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Residues in contact with GLN 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A HIS* 3.5 19.5 - - - -
649A TRP* 2.9 36.2 + - + -
681A VAL* 3.1 32.3 + - + +
682A LEU* 3.6 12.2 - - - +
684A LYS* 1.4 73.6 - - - +
686A GLY* 1.3 60.0 + - - +
687A GLU 3.2 1.6 - - - -
688A ALA* 3.2 5.4 + - - +
689A LEU* 3.0 33.5 + - - +
731A LEU* 3.9 8.9 - - + +
732A GLN* 3.1 34.1 + - - +
733A SER 3.8 1.4 + - - -
734A PRO* 3.7 21.0 - - + +
737A PRO* 4.9 0.6 - - - +
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Residues in contact with GLY 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 5.7 2.7 - - - -
649A TRP* 4.4 8.2 - - - -
682A LEU 3.0 13.4 + - - -
683A MET* 3.9 2.0 - - - -
685A GLN* 1.3 77.4 - - - +
687A GLU* 1.4 55.0 + - - +
689A LEU* 3.9 13.1 - - - +
690A SER* 3.1 27.4 + - - -
----------------------------------------------------------
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Residues in contact with GLU 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.3 18.0 + - - -
91A ASP* 4.4 22.2 - - - +
683A MET* 3.1 25.7 + - + +
684A LYS* 4.0 7.0 - - - +
685A GLN 3.2 0.2 - - - -
686A GLY* 1.4 73.5 - - - +
688A ALA* 1.4 63.9 + - - +
690A SER* 3.1 9.1 + - - -
691A LYS* 3.1 44.6 + - - +
727A ALA* 4.7 11.8 - - + +
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Residues in contact with ALA 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A LYS 3.5 7.8 + - - +
685A GLN 3.2 9.0 + - - +
687A GLU* 1.4 76.7 - - - +
689A LEU* 1.3 57.5 + - + +
691A LYS* 3.4 1.4 + - - -
692A LEU* 3.1 37.8 + - + +
727A ALA 3.3 24.3 + - - +
728A LEU* 3.4 20.1 - - + +
731A LEU* 3.8 17.7 - - + -
763A TYR* 5.7 0.9 - - - +
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Residues in contact with LEU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A TRP* 3.6 33.2 - - + -
685A GLN 3.0 23.5 + - - +
686A GLY* 3.9 6.5 - - - +
687A GLU 3.2 0.2 - - - -
688A ALA* 1.3 77.1 - - + +
690A SER* 1.3 56.1 + - - +
692A LEU* 3.5 8.3 + - + +
693A LYS* 3.1 26.7 + - - +
734A PRO* 4.6 10.1 - - + -
778A PHE* 4.0 17.5 - - + -
818A THR* 3.9 34.8 - - + +
822A THR* 6.1 0.9 - - + -
824A LEU* 3.9 28.3 - - + -
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Residues in contact with SER 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A GLY 3.1 19.2 + - - -
687A GLU* 3.1 10.1 + - - -
689A LEU* 1.3 73.5 - - - +
691A LYS* 1.4 64.3 + - - +
693A LYS* 3.7 7.0 + - - +
694A ALA* 3.6 18.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A CYS* 4.9 9.1 + - - +
91A ASP* 3.5 25.2 + - - +
93A GLN* 5.7 3.0 - - - +
687A GLU* 3.1 29.9 + - - +
688A ALA 3.7 6.5 - - - +
689A LEU 3.3 0.2 - - - -
690A SER* 1.4 78.3 - - - +
692A LEU* 1.3 53.5 + - - +
694A ALA* 3.2 9.0 + - + +
695A LEU* 2.8 33.1 + - - +
723A ALA* 4.1 21.7 + - - +
724A TYR* 3.7 38.8 - - + -
727A ALA* 3.9 17.0 - - + -
728A LEU* 3.9 12.6 - - + -
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Residues in contact with LEU 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A ALA* 3.1 27.6 + - + +
689A LEU* 3.5 7.6 + - + +
691A LYS* 1.3 73.8 - - - +
693A LYS* 1.4 55.3 + - - +
695A LEU* 3.9 18.6 - - + -
696A ASN* 2.7 35.7 + - - +
728A LEU* 3.7 18.4 - - + -
759A LEU* 3.6 7.8 - - + +
761A ILE* 3.8 32.8 - - + -
763A TYR* 5.6 3.1 - - - +
776A ILE* 4.6 18.8 - - + -
778A PHE* 3.6 33.6 - - + -
824A LEU* 5.0 2.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A LEU 3.1 17.1 + - - +
690A SER* 3.8 8.7 - - - +
691A LYS 3.3 0.2 - - - -
692A LEU* 1.4 73.3 - - - +
694A ALA* 1.4 52.1 + - - +
696A ASN* 3.2 3.6 + - - +
697A ASP* 2.7 72.0 + - - +
778A PHE* 3.7 14.3 - - + -
780A ASN* 3.6 36.8 + - + +
822A THR* 4.8 5.6 - - + +
----------------------------------------------------------
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Residues in contact with ALA 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A SER 3.6 9.5 + - - +
691A LYS* 3.2 10.4 + - + +
693A LYS* 1.4 76.1 - - - +
695A LEU* 1.3 59.0 + - - +
697A ASP* 3.8 8.6 - - - +
698A PHE* 3.0 28.4 + - - +
724A TYR* 3.5 15.7 - - - +
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Residues in contact with LEU 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A LYS 2.8 19.7 + - - +
692A LEU* 3.6 26.5 - - + +
694A ALA* 1.3 73.0 - - - +
696A ASN* 1.4 56.7 + - - +
698A PHE* 3.4 9.4 - - + +
699A VAL* 3.2 27.0 + - - +
715A MET* 3.8 31.4 - - + +
718A CYS* 4.0 20.6 - - + -
719A MET* 3.6 38.1 - - + -
724A TYR* 3.9 10.0 + - + -
728A LEU* 4.6 5.6 - - + -
759A LEU* 4.1 10.1 - - + -
761A ILE* 4.7 2.2 - - + -
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Residues in contact with ASN 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A LEU 2.7 22.1 + - - +
693A LYS 3.4 4.7 - - - +
695A LEU* 1.4 72.1 - - - +
697A ASP* 1.4 56.8 + - - +
698A PHE 3.2 0.2 - - - -
699A VAL* 3.3 2.6 + - - +
700A LYS* 2.8 53.7 + - - +
756A MET 4.0 0.2 - - - +
757A LYS 3.2 21.8 + - - +
758A PRO* 4.3 0.2 - - - +
759A LEU* 3.5 20.1 - - + +
778A PHE* 3.2 41.4 + - + -
780A ASN* 4.1 12.0 - - + +
----------------------------------------------------------
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Residues in contact with ASP 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A LYS* 2.7 56.4 + - - +
694A ALA* 3.8 9.3 - - - +
695A LEU 3.4 0.2 - - - -
696A ASN* 1.4 70.9 - - - +
698A PHE* 1.4 62.4 - - - +
700A LYS* 3.7 14.6 + - - +
701A LEU* 3.5 18.5 + - - +
780A ASN* 3.8 9.5 - - - +
----------------------------------------------------------
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Residues in contact with PHE 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ALA 3.0 16.7 + - - +
695A LEU* 3.4 13.5 - - + +
696A ASN 3.2 0.2 - - - -
697A ASP* 1.4 75.2 - - - +
699A VAL* 1.4 72.8 + - + +
701A LEU* 3.1 7.2 + - - +
702A SER* 2.8 50.4 + - - -
711A THR 4.7 0.9 - - - -
714A LEU* 3.3 55.4 - - + -
715A MET* 3.6 9.4 - - - -
718A CYS* 4.7 12.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LEU 3.2 16.4 + - - +
696A ASN 3.3 4.0 + - - +
698A PHE* 1.4 83.4 - - + +
700A LYS* 1.4 63.3 + - - +
702A SER* 3.8 5.7 - - - -
703A SER* 3.2 24.6 + - - -
711A THR* 4.1 6.5 - - + +
715A MET* 3.7 39.9 - - + -
751A PHE* 3.7 43.3 - - + -
757A LYS* 4.7 7.8 - - + +
759A LEU* 4.2 8.7 - - + -
----------------------------------------------------------
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Residues in contact with LYS 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A ASN* 2.8 36.0 + - - +
697A ASP* 3.8 16.9 + - - +
698A PHE 3.3 0.2 - - - -
699A VAL* 1.4 72.4 - - + +
701A LEU* 1.4 60.9 + - - +
703A SER* 3.9 2.3 - - - -
704A GLN* 3.6 14.9 - - - +
756A MET* 3.4 33.3 - - - +
757A LYS* 3.6 32.6 + - + -
780A ASN* 3.2 38.9 + - - -
781A GLY* 4.2 6.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ASP 3.5 9.3 + - - +
698A PHE* 3.1 8.7 + - - +
700A LYS* 1.4 74.8 - - - +
702A SER* 1.4 56.0 + - - +
703A SER 3.1 4.7 - - - -
704A GLN* 3.0 38.5 + - + +
705A LYS* 3.8 35.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A PHE* 2.8 42.5 + - - -
699A VAL* 4.2 0.2 - - - -
701A LEU* 1.4 69.1 - - - +
703A SER* 1.3 52.2 + - - +
705A LYS* 4.3 11.9 - - - -
706A THR* 3.4 18.4 + - - +
711A THR* 2.7 40.6 + - - +
714A LEU* 4.1 13.7 - - - +
----------------------------------------------------------
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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