Contacts of the helix formed by residues 702 - 726 (chain A) in PDB entry 5ZR1
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 702 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A PRO 3.3 24.6 - - - +
482A GLY* 3.3 14.4 - - - +
483A VAL* 4.7 1.1 - - + -
627A TYR* 4.8 0.4 - - - -
632A LEU* 4.7 3.4 - - - +
696A VAL* 3.8 15.6 - - - +
700A SER* 2.7 23.8 + - - +
701A GLY* 1.3 76.3 - - - +
703A ALA* 1.3 63.4 + - - +
704A ARG* 3.5 1.2 + - - +
705A ARG* 3.3 37.0 + - - +
706A ALA* 3.9 3.6 + - - +
266D SER* 3.6 18.5 + - - -
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Residues in contact with ALA 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLY 2.9 9.3 + - - +
627A TYR* 4.1 11.5 - - + -
632A LEU* 5.4 3.1 - - - -
635A ILE* 4.1 18.6 - - + -
701A GLY 4.1 0.6 + - - -
702A ASP* 1.3 72.1 - - - +
704A ARG* 1.3 63.7 + - - +
706A ALA* 4.0 6.4 - - - +
707A LEU* 3.2 29.7 + - - +
2001A AGS 3.5 39.3 - - + +
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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
----------------------------------------------------------
432A SER* 4.2 13.3 + - - +
482A GLY* 4.3 4.8 + - - -
702A ASP* 3.3 3.2 - - - +
703A ALA* 1.3 77.4 - - - +
705A ARG* 1.3 59.6 + - - +
706A ALA 3.2 0.2 + - - -
707A LEU* 3.2 5.3 + - - +
708A LYS* 3.0 40.3 + - - +
2001A AGS 3.1 65.2 + - - -
2002A MG 4.0 1.2 - - - -
239D GLU* 5.4 4.7 - - - +
240D HIS* 4.2 16.1 + - - -
266D SER* 3.3 44.8 + - - +
267D ARG* 3.1 58.4 - - - +
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Residues in contact with ARG 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A VAL* 3.9 16.7 - - + +
699A VAL* 5.8 5.8 - - - +
700A SER* 4.7 7.8 + - - +
702A ASP* 3.3 35.1 + - - +
703A ALA 3.5 0.4 - - - -
704A ARG* 1.3 76.7 - - + +
706A ALA* 1.3 56.9 + - - +
708A LYS* 4.0 10.7 - - - +
709A VAL* 3.3 25.8 + - - +
785A THR* 4.9 15.8 + - - -
786A LEU* 5.1 8.9 - - - +
265D LYS* 3.7 32.9 - - - +
266D SER* 5.3 4.2 - - - +
270D GLN* 3.7 40.3 - - - +
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Residues in contact with ALA 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LEU* 3.7 35.0 - - + -
636A ILE* 3.8 17.3 - - + +
692A ALA 4.7 1.6 - - - +
696A VAL* 4.0 7.4 - - + +
702A ASP 3.9 4.2 + - - +
703A ALA* 3.7 6.8 + - - +
704A ARG 3.2 0.6 - - - -
705A ARG* 1.3 77.9 - - - +
707A LEU* 1.3 64.6 + - + +
708A LYS 3.3 0.7 - - - -
709A VAL* 3.4 11.3 - - + +
710A CYS* 3.4 26.5 + - - -
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 3.7 43.7 - - + +
432A SER* 4.7 9.4 - - - +
635A ILE* 4.4 14.8 - - + -
636A ILE* 4.3 17.7 - - + -
639A ARG* 3.4 40.6 - - - +
703A ALA 3.2 21.3 + - - +
704A ARG* 3.2 4.5 + - - +
706A ALA* 1.3 78.1 - - + +
708A LYS* 1.3 58.7 + - + +
709A VAL 3.5 0.2 - - - -
710A CYS* 3.9 2.8 - - - +
711A LYS* 3.0 25.2 + - - +
2001A AGS 4.1 17.9 - - - +
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Residues in contact with LYS 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A SER* 5.6 1.1 - - - -
704A ARG* 3.0 29.5 + - - +
705A ARG* 4.0 11.0 - - - +
707A LEU* 1.3 75.1 - - - +
709A VAL* 1.3 61.0 + - - +
710A CYS 3.4 0.7 - - - -
711A LYS* 3.9 16.3 - - + +
712A ARG* 3.3 21.0 + - - +
239D GLU* 3.1 28.5 + - - -
266D SER 3.0 23.5 + - - -
267D ARG 3.2 2.0 + - - -
268D PHE 2.9 29.0 + - - +
269D SER* 3.7 25.9 - - - +
270D GLN* 4.2 11.4 - - + +
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Residues in contact with VAL 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ALA* 3.9 23.8 - - + -
696A VAL* 4.3 8.5 - - + -
705A ARG 3.3 17.5 + - - +
706A ALA* 3.4 18.2 - - - +
708A LYS* 1.3 78.1 - - - +
710A CYS* 1.3 60.8 + - - +
712A ARG* 4.0 3.6 - - - -
713A ALA* 3.3 22.7 + - - +
778A VAL* 4.7 4.9 - - + +
781A ALA* 3.7 12.9 - - + +
782A LEU* 3.8 43.1 - - + -
785A THR* 5.5 2.9 - - + +
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Residues in contact with CYS 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 3.6 19.9 - - + +
636A ILE* 3.8 33.2 - - + -
684A MET* 5.0 12.2 - - + +
688A ALA 5.6 0.4 - - - -
689A ILE* 5.1 8.5 - - - -
692A ALA* 4.2 17.0 - - - -
706A ALA 3.4 18.0 + - - +
707A LEU 4.2 1.6 - - - +
709A VAL* 1.3 79.0 - - - +
711A LYS* 1.3 59.3 + - - +
712A ARG 3.4 0.2 - - - -
713A ALA* 3.8 6.4 - - - +
714A ALA* 3.1 26.2 + - - +
778A VAL* 5.6 5.4 - - - -
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Residues in contact with LYS 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 4.0 33.2 - - + +
430A LEU* 3.8 15.8 - - + +
431A ASN* 3.1 30.6 - - - +
707A LEU 3.0 20.3 + - - +
708A LYS* 3.9 12.8 - - + +
710A CYS* 1.3 75.0 - - - +
712A ARG* 1.3 64.3 + - - +
714A ALA* 3.2 5.5 + - - +
715A GLU* 3.2 27.2 + - - +
94D GLU* 4.7 13.3 + - - +
95D SER* 5.6 3.6 - - - +
96D HIS* 4.6 23.3 + - - +
238D VAL* 6.2 1.4 - - - +
269D SER* 6.3 0.8 - - - -
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Residues in contact with ARG 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A LYS 3.3 19.8 + - - +
709A VAL* 4.0 2.9 - - - +
710A CYS 3.4 0.2 - - - -
711A LYS* 1.3 79.8 - - - +
713A ALA* 1.3 60.4 + - - +
715A GLU* 3.0 39.1 + - - +
716A ILE* 3.1 55.3 + - - +
719A LYS* 5.9 3.0 - - - +
781A ALA* 3.7 20.9 - - + +
784A GLU* 2.5 38.9 + - - +
785A THR* 6.1 1.3 - - + -
81D GLU* 4.4 4.2 + - - -
269D SER 5.7 3.6 - - - +
270D GLN 6.5 0.2 - - - -
271D ARG* 3.6 46.5 - - - +
273D ILE* 6.0 0.4 - - - +
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Residues in contact with ALA 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A MET* 6.2 0.4 - - + -
709A VAL 3.3 17.3 + - - +
710A CYS* 4.0 6.5 - - - +
711A LYS 3.3 0.2 - - - -
712A ARG* 1.3 79.0 - - - +
714A ALA* 1.3 61.3 + - - +
716A ILE* 3.9 3.1 - - - +
717A ALA* 3.2 23.6 + - - +
773A VAL* 3.9 11.5 - - + +
777A HIS* 3.7 22.0 - - - +
778A VAL* 3.7 25.6 - - + -
781A ALA* 3.6 6.4 - - + +
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Residues in contact with ALA 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PHE* 3.6 22.5 - - + +
426A VAL* 4.3 22.0 - - + -
427A LYS* 3.8 18.7 - - + -
430A LEU* 5.0 0.2 - - + -
684A MET* 5.5 0.9 - - + -
710A CYS 3.1 20.3 + - - +
711A LYS* 3.2 7.8 + - - +
713A ALA* 1.3 78.8 - - - +
715A GLU* 1.3 55.8 + - - +
717A ALA 4.0 0.7 - - - -
718A GLU 3.3 15.1 + - - -
773A VAL* 4.6 13.7 - - + +
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Residues in contact with GLU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 3.7 23.4 - - + +
711A LYS* 3.2 14.1 + - - +
712A ARG* 3.0 49.1 + - - +
714A ALA* 1.3 76.3 - - - +
716A ILE* 1.3 63.6 + - - +
717A ALA 3.3 0.9 - - - -
718A GLU* 3.6 10.5 - - - +
719A LYS* 3.2 26.0 + - - +
84D ARG* 3.9 8.4 + - - +
88D GLN* 3.7 18.9 + - - +
94D GLU* 5.5 1.0 - - - +
96D HIS* 5.4 6.1 + - - -
271D ARG* 3.5 19.3 + - - -
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Residues in contact with ILE 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ARG* 3.1 43.7 + - - +
713A ALA* 3.9 5.2 - - - +
715A GLU* 1.3 76.4 - - - +
717A ALA* 1.3 56.5 + - - +
719A LYS* 3.3 15.4 - - + +
720A HIS* 2.6 43.8 + - + -
777A HIS* 3.6 24.0 - - + +
780A LYS* 4.1 28.7 - - + +
781A ALA* 3.7 35.0 - - + +
784A GLU* 4.7 1.3 - - - +
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Residues in contact with ALA 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PHE* 3.7 32.0 - - + -
713A ALA 3.2 16.5 + - - +
714A ALA 4.1 0.4 - - - +
716A ILE* 1.3 77.6 - - - +
718A GLU* 1.3 60.9 + - - +
720A HIS* 3.9 3.0 + - - +
721A TYR* 3.3 20.6 + - - +
771A GLN* 5.5 0.2 + - - -
772A THR 4.4 4.7 - - - +
773A VAL* 4.1 9.9 - - + -
777A HIS* 3.6 25.3 - - + +
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Residues in contact with GLU 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A THR* 3.3 28.5 - - + +
423A PHE* 3.7 21.1 - - + -
424A SER* 3.3 8.3 + - - -
427A LYS* 3.2 26.4 + - - -
714A ALA 3.3 18.3 + - - +
715A GLU* 3.4 3.0 + - - +
716A ILE 3.2 1.0 - - - -
717A ALA* 1.3 76.0 - - - +
719A LYS* 1.3 53.2 + - - +
721A TYR* 3.0 5.7 + - + +
722A MET* 2.6 52.5 + - + +
729A TYR* 5.6 0.7 + - - -
84D ARG* 2.7 23.1 + - - +
88D GLN* 3.9 6.4 - - - +
92D GLN* 4.8 5.9 + - - +
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Residues in contact with LYS 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ARG* 5.9 2.5 - - - +
715A GLU 3.2 11.9 + - - +
716A ILE* 3.3 20.4 - - + +
718A GLU* 1.3 78.4 - - - +
720A HIS* 1.3 78.7 + - + +
722A MET* 3.7 7.5 - - - +
723A ALA* 3.0 27.2 + - - +
780A LYS* 6.0 1.2 - - - +
81D GLU* 6.5 1.1 - - - -
84D ARG* 3.7 32.3 - - - +
271D ARG* 5.9 6.1 - - - +
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Residues in contact with HIS 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ILE* 2.6 43.8 + - + +
717A ALA* 4.3 4.9 - - - +
718A GLU 3.2 0.8 - - - -
719A LYS* 1.3 97.0 + - + +
721A TYR* 1.3 58.9 + - - +
722A MET 3.2 0.2 - - - -
723A ALA* 4.1 4.4 - - + +
724A LYS* 3.0 41.8 + - + +
777A HIS* 4.4 12.4 + + - +
780A LYS* 4.1 18.3 + - + -
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Residues in contact with TYR 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A THR* 3.2 29.7 + - + -
422A ILE* 4.1 11.7 - - + +
423A PHE* 3.9 16.4 - + + -
650A VAL* 3.7 19.4 - - - +
655A GLY 4.8 0.3 + - - -
717A ALA 3.3 13.1 + - - +
718A GLU* 3.0 9.7 + - + +
720A HIS* 1.3 79.9 - - - +
722A MET* 1.3 62.4 + - + +
723A ALA 3.6 0.2 + - - -
724A LYS* 4.8 4.7 - - + -
725A HIS* 3.5 50.9 + + - +
727A TYR* 3.4 38.5 + + - -
771A GLN* 3.3 35.9 - - + +
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Residues in contact with MET 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL* 5.5 3.8 - - + -
421A THR* 4.6 12.3 - - + -
718A GLU* 2.6 47.7 + - + +
719A LYS* 3.9 10.1 - - - +
720A HIS 3.2 0.2 - - - -
721A TYR* 1.3 76.7 - - + +
723A ALA* 1.3 58.0 + - - +
726A GLY* 3.1 25.1 + - - +
727A TYR* 3.7 16.4 - - + +
728A GLY* 3.3 43.5 + - - +
729A TYR* 5.1 11.7 - - + -
84D ARG* 4.2 15.0 - - - +
92D GLN* 5.3 3.8 - - - +
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Residues in contact with ALA 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A LYS* 3.0 19.7 + - - +
720A HIS* 3.4 6.5 + - + +
721A TYR 3.3 0.2 - - - -
722A MET* 1.3 78.8 - - - +
724A LYS* 1.3 65.1 + - - +
725A HIS 3.4 0.2 - - - -
726A GLY* 4.0 5.6 + - - -
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Residues in contact with LYS 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A HIS* 3.0 25.5 + - + +
721A TYR* 4.3 3.4 - - + +
722A MET 3.6 0.2 - - - -
723A ALA* 1.3 78.7 - - + +
725A HIS* 1.3 83.2 + - + +
771A GLN* 6.0 0.4 + - - -
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Residues in contact with HIS 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A ARG* 5.8 5.4 - - - -
721A TYR* 3.5 45.8 + + - +
724A LYS* 1.3 98.4 + - + +
726A GLY* 1.3 64.9 + - - +
727A TYR* 3.5 35.4 + - + -
771A GLN* 5.4 2.0 + - - -
----------------------------------------------------------
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Residues in contact with GLY 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A MET 3.1 17.2 + - - -
723A ALA* 4.0 4.9 + - - -
724A LYS 3.5 2.4 + - - -
725A HIS* 1.3 80.0 - - - +
727A TYR* 1.3 64.9 + - - +
728A GLY 3.6 1.6 - - - -
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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