Contacts of the helix formed by residues 657 - 683 (chain J) in PDB entry 6H25
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 ARG 657 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590J TYR* 4.9 16.2 - - + +
591J ALA* 5.6 10.7 - - - +
594J GLN* 3.8 28.1 - - + +
654J LYS* 6.2 1.0 - - - +
655J GLU* 2.7 28.8 + - - +
656J LEU* 1.3 82.8 - - - +
658J GLU* 1.3 63.7 + - - +
659J THR* 3.4 6.7 - - - +
660J ASN* 3.5 27.2 + - - +
661J SER* 4.2 4.0 + - - -
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Residues in contact with GLU 658 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594J GLN* 4.2 11.3 + - - +
614J ASN* 5.3 11.7 - - - +
657J ARG* 1.3 72.3 - - - +
659J THR* 1.3 61.1 + - + +
660J ASN 3.2 2.5 - - - -
661J SER* 3.1 11.3 + - - +
662J MET* 2.9 25.1 + - - +
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Residues in contact with THR 659 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478J VAL* 5.8 3.8 - - - -
590J TYR* 3.2 31.5 + - - +
593J ALA* 5.5 4.6 - - + +
594J GLN* 3.4 27.0 + - - +
597J ILE* 4.1 25.1 - - + -
614J ASN* 5.7 6.5 - - + +
657J ARG* 4.3 4.2 - - - +
658J GLU* 1.3 75.9 - - + +
660J ASN* 1.3 59.5 + - - +
662J MET* 3.2 11.9 + - + +
663J VAL* 2.9 35.6 + - - +
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Residues in contact with ASN 660 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590J TYR* 3.3 37.2 + - - +
656J LEU* 4.5 11.2 - - + -
657J ARG* 3.5 35.0 + - - +
658J GLU 3.2 0.2 - - - -
659J THR* 1.3 77.9 + - - +
661J SER* 1.3 55.9 + - - +
663J VAL* 3.3 9.3 - - - +
664J GLU* 2.9 30.2 + - - +
42R U 4.5 12.8 + - - +
43R U 5.0 9.1 + - - -
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Residues in contact with SER 661 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624J ARG* 2.6 33.4 + - - -
657J ARG 4.2 3.2 + - - -
658J GLU* 3.1 15.2 + - - -
660J ASN* 1.3 78.6 - - - +
662J MET* 1.3 57.4 + - - +
664J GLU* 3.3 19.6 + - - +
665J GLU* 2.9 32.4 + - - +
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Residues in contact with MET 662 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613J LEU* 5.3 2.9 - - + +
614J ASN* 5.6 4.7 - - - +
617J ALA* 3.8 30.5 - - + -
620J LEU* 5.1 0.2 - - - +
658J GLU 2.9 12.6 + - - +
659J THR* 3.2 17.2 + - + +
661J SER* 1.3 76.7 - - - +
663J VAL* 1.3 59.4 + - + +
665J GLU* 3.3 4.2 + - - +
666J PHE* 3.0 38.5 + - + -
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Residues in contact with VAL 663 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478J VAL* 5.6 11.0 - - + +
488J ASP* 4.6 13.0 - - - +
490J LEU* 3.9 26.2 - - + -
590J TYR* 4.2 17.3 - - + +
659J THR* 2.9 19.6 + - - +
660J ASN* 3.3 19.3 - - - +
662J MET* 1.3 75.5 - - + +
664J GLU* 1.3 59.3 + - - +
666J PHE* 3.9 7.0 - - + +
667J MET* 3.0 37.9 + - + +
42R U 4.8 9.6 - - - +
43R U 5.5 4.5 - - - +
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Residues in contact with GLU 664 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631J THR* 3.4 29.2 - - - +
660J ASN 2.9 17.9 + - - +
661J SER* 3.3 22.8 + - - +
663J VAL* 1.3 77.9 - - - +
665J GLU* 1.3 72.9 + - - +
667J MET* 3.2 3.3 + - - +
668J LEU* 2.9 41.3 + - + +
41R U 4.6 12.2 + - - +
42R U 3.9 37.2 - - - +
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Residues in contact with GLU 665 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617J ALA* 5.9 1.1 - - + +
620J LEU* 4.0 34.4 - - + +
624J ARG* 3.3 44.2 - - + +
627J LYS* 5.4 6.2 + - - +
631J THR* 4.7 4.0 - - - +
661J SER* 2.9 23.6 + - - +
662J MET* 4.1 1.6 - - - +
664J GLU* 1.3 94.5 - - - +
666J PHE* 1.3 58.3 + - - +
668J LEU* 3.4 25.4 + - - +
669J LEU* 2.9 27.5 + - - +
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Residues in contact with PHE 666 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490J LEU* 4.8 10.3 - - + -
502J VAL* 3.6 29.6 - - + -
504J VAL* 4.6 11.5 - - + +
564J TRP* 4.8 1.2 - + - -
613J LEU* 3.7 40.6 - - + -
616J LEU* 4.2 17.7 - - + -
617J ALA* 4.6 5.4 - - + -
620J LEU* 4.0 21.3 - - + -
662J MET* 3.0 32.1 + - + +
663J VAL* 4.0 5.6 - - - +
665J GLU* 1.3 78.6 - - - +
667J MET* 1.3 70.1 + - + +
669J LEU* 3.3 23.2 + - + +
670J ALA* 3.0 27.5 + - - +
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Residues in contact with MET 667 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488J ASP* 3.3 28.0 - - - +
490J LEU* 3.8 12.3 - - + -
504J VAL* 3.7 36.6 - - + -
506J ILE* 5.7 1.3 - - - -
663J VAL* 3.0 24.8 + - + +
664J GLU 3.8 2.7 - - - +
666J PHE* 1.3 77.7 - - + +
668J LEU* 1.3 60.6 + - - +
670J ALA* 3.4 3.0 + - - +
671J ASN* 2.8 38.8 + - - +
776J THR* 3.7 32.5 - - - +
42R U 3.9 28.5 - - - +
43R U 4.2 6.1 - - - +
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Residues in contact with LEU 668 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664J GLU* 2.9 36.8 + - + +
665J GLU* 3.6 31.2 - - - +
667J MET* 1.3 76.6 - - - +
669J LEU* 1.3 55.7 + - - +
671J ASN* 3.3 6.7 + - - +
672J ILE* 2.9 45.6 + - + +
767J LEU* 4.3 24.5 - - + -
772J TYR* 4.8 11.6 - - + +
41R U 4.2 7.4 - - - +
42R U 3.9 24.2 - - - -
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Residues in contact with LEU 669 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564J TRP* 4.1 24.7 - - + -
572J ILE* 3.8 32.5 - - + -
620J LEU* 5.4 14.4 - - + -
627J LYS* 5.6 9.2 - - - +
665J GLU 2.9 14.7 + - - +
666J PHE* 3.3 26.0 + - + +
668J LEU* 1.3 77.1 - - - +
670J ALA* 1.3 56.7 + - - +
672J ILE* 3.4 11.2 + - + +
673J SER* 2.9 37.5 + - - +
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Residues in contact with ALA 670 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504J VAL* 4.4 13.7 - - + -
506J ILE* 5.7 1.6 - - + -
562J CYS* 5.7 2.9 - - + -
564J TRP* 3.6 24.8 - - + -
666J PHE 3.0 16.1 + - - +
667J MET* 3.7 5.6 - - - +
669J LEU* 1.3 77.3 - - - +
671J ASN* 1.3 59.2 + - - +
673J SER* 3.3 1.7 + - - -
674J VAL* 2.9 37.1 + - + +
775J PHE* 5.7 2.0 - - + -
776J THR* 4.3 15.5 - - + -
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Residues in contact with ASN 671 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667J MET* 2.8 28.8 + - - +
668J LEU 3.8 1.3 - - - +
669J LEU 3.3 0.2 - - - -
670J ALA* 1.3 73.4 - - - +
672J ILE* 1.3 60.5 + - - +
674J VAL* 3.3 6.9 - - - +
675J ALA* 2.9 30.9 + - - +
772J TYR* 3.1 31.7 + - + -
773J THR 3.3 20.6 - - - +
774J HIS* 4.4 1.6 - - - -
775J PHE* 2.9 35.7 + - - +
776J THR* 3.6 15.8 + - - +
42R U 4.1 7.5 + - - -
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Residues in contact with ILE 672 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627J LYS* 4.6 20.0 - - + +
668J LEU* 2.9 33.1 + - + +
669J LEU* 3.8 10.3 - - + +
671J ASN* 1.3 74.2 - - - +
673J SER* 1.3 58.6 + - - +
675J ALA* 3.3 5.5 + - - +
676J LYS* 3.0 55.7 + - + +
769J SER* 4.1 21.5 - - - +
770J PRO* 6.1 1.8 - - + -
771J ILE* 5.0 8.3 - - + +
772J TYR* 4.6 15.5 - - + -
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Residues in contact with SER 673 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564J TRP* 3.3 31.0 + - - -
572J ILE* 5.6 0.2 - - - +
575J THR* 4.8 3.3 + - - +
577J PHE* 4.3 14.7 - - - -
669J LEU* 2.9 23.5 + - - +
670J ALA 3.6 4.9 - - - -
672J ILE* 1.3 79.1 - - - +
674J VAL* 1.3 58.2 + - - +
676J LYS* 3.4 5.6 + - - +
677J LYS* 3.0 27.9 + - - +
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Residues in contact with VAL 674 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562J CYS* 5.9 1.3 - - + -
577J PHE* 3.6 25.4 - - + -
670J ALA* 2.9 21.8 + - + +
671J ASN* 3.3 15.9 - - - +
673J SER* 1.3 75.3 - - - +
675J ALA* 1.3 57.6 + - - +
677J LYS* 3.6 7.5 - - - +
678J ILE* 2.9 37.5 + - + +
773J THR* 4.2 10.1 - - + -
775J PHE* 3.7 49.8 - - + -
787J VAL* 5.3 1.6 - - + -
791J LEU* 4.5 9.2 - - + -
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Residues in contact with ALA 675 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671J ASN 2.9 19.1 + - - +
672J ILE* 3.6 5.2 - - - +
673J SER 3.2 0.2 - - - -
674J VAL* 1.3 75.5 - - - +
676J LYS* 1.3 60.7 + - - +
678J ILE* 3.4 10.7 - - - +
679J HIS* 2.9 31.3 + - - +
688J LEU* 5.2 0.9 - - + -
771J ILE* 4.0 25.3 - - + +
772J TYR* 4.0 7.6 - - - -
773J THR* 4.0 24.5 - - + +
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Residues in contact with LYS 676 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672J ILE* 3.0 39.2 + - + +
673J SER* 3.9 5.6 - - - +
675J ALA* 1.3 75.9 - - - +
677J LYS* 1.3 58.2 + - - +
679J HIS* 3.4 6.6 + - - +
680J GLU* 2.9 29.5 + - - +
770J PRO* 5.0 17.9 - - - +
771J ILE* 4.5 11.2 - - + -
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Residues in contact with LYS 677 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577J PHE* 4.5 24.5 - - + -
673J SER 3.0 17.9 + - - +
674J VAL* 3.6 9.0 - - - +
675J ALA 3.2 0.2 - - - -
676J LYS* 1.3 76.5 - - - +
678J ILE* 1.3 58.1 + - - +
680J GLU* 3.2 8.9 + - + +
681J GLU* 2.9 36.0 + - + +
791J LEU* 4.1 20.6 - - + -
794J ALA* 5.5 3.8 + - + -
795J ILE* 4.1 26.6 - - - +
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Residues in contact with ILE 678 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674J VAL* 2.9 26.3 + - + +
675J ALA* 3.4 7.0 - - - +
677J LYS* 1.3 73.6 - - + +
679J HIS* 1.3 64.1 + - - +
681J GLU* 3.8 5.4 - - - +
682J PHE* 2.8 39.5 + - + +
686J ALA* 3.9 21.2 - - + +
687J LEU 4.1 5.6 - - - +
688J LEU* 3.8 26.2 - - + -
773J THR* 4.1 16.6 - - + -
787J VAL* 5.5 12.1 - - + +
790J LEU* 5.7 6.5 - - + +
791J LEU* 4.4 28.9 - - + +
794J ALA* 5.7 2.9 - - + -
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Residues in contact with HIS 679 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675J ALA 2.9 19.6 + - - +
676J LYS* 3.7 8.3 - - - +
678J ILE* 1.3 80.0 - - - +
680J GLU* 1.3 62.6 + - - +
683J SER* 3.2 42.1 + - - +
688J LEU* 4.9 6.5 - - + -
762J PHE* 5.0 15.0 - + - +
771J ILE* 3.0 33.3 - - + +
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Residues in contact with GLU 680 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676J LYS 2.9 17.8 + - - +
677J LYS* 3.6 9.9 - - + +
679J HIS* 1.3 77.8 - - - +
681J GLU* 1.3 61.8 + - + +
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Residues in contact with GLU 681 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677J LYS* 2.9 26.9 + - - +
678J ILE* 4.4 3.6 - - - +
680J GLU* 1.3 80.5 - - - +
682J PHE* 1.3 85.0 + - + +
683J SER 3.8 1.5 + - - -
684J GLU* 4.4 4.3 - - - +
794J ALA* 4.5 12.8 - - + +
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Residues in contact with PHE 682 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678J ILE* 2.8 19.6 + - + +
681J GLU* 1.3 89.0 - - + +
683J SER* 1.3 56.9 + - - +
684J GLU* 3.1 30.9 + - - -
685J HIS* 3.3 21.5 + - + +
686J ALA* 3.3 24.1 + - + +
790J LEU* 4.8 14.4 - - + -
793J VAL* 4.7 8.3 - - + -
794J ALA* 3.6 37.0 - - + -
800J THR* 6.0 2.0 - - + -
805J THR* 5.3 12.6 - - + -
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Residues in contact with SER 683 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678J ILE 3.4 3.6 + - - -
679J HIS* 3.2 44.6 + - - +
681J GLU 3.8 1.4 - - - -
682J PHE* 1.3 73.9 - - - +
684J GLU* 1.3 63.2 + - - +
686J ALA* 5.3 1.3 - - - -
688J LEU* 6.1 2.5 - - - -
756J SER* 2.8 22.6 + - - +
762J PHE* 4.4 7.2 - - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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