Contacts of the helix formed by residues 679 - 705 (chain A) in PDB entry 6S1M
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 679 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A GLU* 3.9 6.1 + - - +
678A THR* 1.3 81.2 + - - +
680A PRO* 1.3 74.0 - - - +
681A LEU* 5.0 2.0 - - - -
682A ARG* 3.7 34.7 + - + +
683A ARG* 3.0 30.0 + - - +
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Residues in contact with PRO 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A THR 4.0 4.9 - - - +
679A ASP* 1.3 93.4 - - - +
681A LEU* 1.3 62.1 + - + +
683A ARG* 3.1 10.9 + - + +
684A GLN* 3.0 28.2 + - - +
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Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A PHE* 4.0 29.8 - - + +
525A ARG* 4.5 16.2 - - + +
526A LEU* 5.3 5.2 - - + -
679A ASP* 3.6 2.6 - - - +
680A PRO* 1.3 81.7 - - + +
682A ARG* 1.3 89.5 + - + +
684A GLN* 3.2 28.9 - - + +
685A VAL* 3.0 37.7 + - + +
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Residues in contact with ARG 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ARG* 2.3 57.3 + - - +
527A MET* 4.9 8.7 - - - +
677A GLU* 3.3 29.4 - - + +
679A ASP* 3.7 27.5 + - + +
680A PRO 3.2 0.6 - - - -
681A LEU* 1.3 100.4 - - + +
683A ARG* 1.3 62.4 + - - +
685A VAL* 3.2 14.4 + - + +
686A LEU* 3.0 32.8 + - + +
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Residues in contact with ARG 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU* 3.3 36.4 + - + +
675A ALA* 5.2 8.3 + - - +
677A GLU* 3.0 39.9 + - + +
678A THR* 4.6 4.9 - - - +
679A ASP 3.0 23.7 + - - +
680A PRO* 3.1 8.9 + - + +
682A ARG* 1.3 76.2 - - - +
684A GLN* 1.3 56.8 + - - +
686A LEU* 4.7 0.2 - - - -
687A ASP* 3.0 24.3 + - - +
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Residues in contact with GLN 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TYR* 4.7 11.7 + - - -
481A PHE* 4.9 14.5 - - - -
526A LEU* 4.9 2.2 - - - +
680A PRO 3.0 16.2 + - - +
681A LEU* 3.2 30.9 - - + +
683A ARG* 1.3 76.1 - - - +
685A VAL* 1.3 80.1 + - - +
687A ASP* 3.3 11.0 + - + +
688A GLY* 2.9 22.2 + - - -
691A LEU* 5.2 0.2 - - - +
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TYR* 5.1 3.8 - - - +
525A ARG 4.8 0.2 - - - +
526A LEU* 4.2 31.0 - - + +
527A MET* 3.7 30.1 - - + +
531A ASN* 4.6 6.2 + - - +
681A LEU* 3.0 32.0 + - + +
682A ARG* 3.2 26.4 + - - +
684A GLN* 1.3 93.6 - - - +
686A LEU* 1.3 63.1 + - - +
688A GLY* 3.2 4.0 + - - +
689A ARG* 3.0 24.4 + - - +
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Residues in contact with LEU 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A MET* 3.8 33.0 - - + -
670A ALA* 5.3 2.9 - - - +
673A GLU* 3.3 37.2 - - - +
674A LEU* 3.7 39.6 - - + +
677A GLU* 4.0 22.9 - - + +
682A ARG* 3.0 17.7 + - + +
685A VAL* 1.3 73.3 - - - +
687A ASP* 1.3 64.8 + - - +
689A ARG* 3.3 13.6 + - + +
690A GLN* 3.1 24.1 + - - +
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Residues in contact with ASP 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU* 4.0 8.6 - - + +
683A ARG 3.0 15.4 + - - +
684A GLN* 3.4 15.2 - - + +
685A VAL 3.3 0.2 - - - -
686A LEU* 1.3 77.2 - - - +
688A GLY* 1.3 55.9 + - - +
690A GLN* 2.5 38.5 + - - +
691A LEU* 2.9 32.8 + - - +
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Residues in contact with GLY 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 4.9 2.4 - - - +
467A TYR* 5.8 3.4 - - - -
531A ASN* 5.5 1.1 - - - -
684A GLN 2.9 15.2 + - - -
685A VAL* 3.2 6.0 + - - -
687A ASP* 1.3 71.5 - - - +
689A ARG* 1.3 59.2 + - - +
691A LEU* 2.4 51.6 - - - +
692A ALA* 3.0 7.3 + - - +
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Residues in contact with ARG 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A MET* 4.9 9.3 - - + +
530A VAL* 6.3 0.6 - - - +
531A ASN* 3.3 34.8 - - + +
534A GLU* 2.4 41.2 + - - +
666A ALA 5.6 0.8 + - - -
669A ARG* 5.4 6.7 - - - +
670A ALA* 3.7 31.8 + - + +
673A GLU* 3.4 28.1 + - - +
685A VAL 3.0 12.9 + - - +
686A LEU* 3.3 15.3 + - - +
688A GLY* 1.3 74.9 - - - +
690A GLN* 1.3 62.4 + - - +
692A ALA* 3.3 8.8 + - - +
693A LEU* 3.2 27.1 + - + +
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Residues in contact with GLN 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A ARG* 2.8 57.9 + - + +
670A ALA* 4.3 13.2 - - + -
671A LYS* 4.2 20.5 + - + +
674A LEU* 4.1 13.2 - - + +
686A LEU 3.1 16.6 + - - +
687A ASP* 2.5 36.9 + - - +
689A ARG* 1.3 75.8 - - - +
691A LEU* 1.3 63.7 + - - +
693A LEU* 3.3 1.6 + - - +
694A LYS* 3.0 22.2 + - - +
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Residues in contact with LEU 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 3.3 24.7 - - - +
687A ASP* 2.9 18.5 + - - +
688A GLY* 2.4 56.1 - - - +
690A GLN* 1.3 84.0 - - - +
692A ALA* 1.3 71.4 + - + +
694A LYS* 3.3 10.4 + - - +
695A VAL* 2.9 37.6 + - + +
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Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 5.8 0.4 - - + +
535A MET* 5.0 13.0 - - - -
688A GLY 3.0 12.6 + - - +
689A ARG* 3.5 11.9 - - - +
690A GLN 3.3 0.2 - - - -
691A LEU* 1.3 84.7 - - + +
693A LEU* 1.3 58.7 + - + +
695A VAL* 3.4 8.5 + - - +
696A SER* 3.0 31.7 + - - -
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A GLU* 3.8 24.2 - - - +
535A MET* 4.2 25.6 - - + -
538A VAL* 4.8 7.6 - - + -
663A LEU* 4.4 21.4 - - + +
666A ALA* 4.0 18.8 - - + +
667A ARG* 3.9 33.7 - - + +
670A ALA* 4.2 11.2 - - + -
689A ARG* 3.2 19.4 + - + +
690A GLN* 3.3 5.4 + - - +
691A LEU 3.3 0.2 - - - -
692A ALA* 1.3 76.9 - - + +
694A LYS* 1.3 62.0 + - - +
696A SER* 3.4 4.9 + - - -
697A ALA* 3.1 22.3 + - - +
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Residues in contact with LYS 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A SER* 6.0 0.2 - - - +
667A ARG* 3.5 44.3 - - - +
690A GLN 3.0 11.1 + - - +
691A LEU* 3.3 8.5 + - + +
693A LEU* 1.3 75.6 - - - +
695A VAL* 1.3 64.2 + - - +
697A ALA* 3.3 6.2 + - - +
698A ASN* 3.0 42.4 + - - +
101T TTP 3.2 67.6 + - - +
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Residues in contact with VAL 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLN* 4.5 16.6 - - - +
691A LEU* 2.9 26.2 + - + +
692A ALA* 3.7 8.1 - - - +
693A LEU 3.3 0.4 - - - -
694A LYS* 1.3 82.6 - - - +
696A SER* 1.3 57.4 + - - +
698A ASN* 3.4 5.4 + - - +
699A SER* 2.9 29.4 + - - -
0T A 4.6 21.8 + - + +
101T TTP 5.4 6.3 - - + +
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Residues in contact with SER 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A MET* 3.4 23.2 - - - +
539A THR* 5.9 1.3 - - - -
551A GLN* 4.8 5.4 + - - -
554A LYS* 4.0 11.6 + - - -
663A LEU* 4.1 20.9 - - - -
692A ALA 3.0 15.3 + - - -
693A LEU 3.6 8.5 - - - -
694A LYS 3.3 0.2 - - - -
695A VAL* 1.3 77.4 - - - +
697A ALA* 1.3 62.8 + - - +
699A SER* 3.3 6.5 + - - -
700A VAL* 3.1 25.3 + - - +
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Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A PRO* 4.1 15.9 - - + +
660A LEU* 3.5 21.8 - - + +
663A LEU* 4.0 23.3 - - + +
664A LEU* 5.6 2.5 - - + +
693A LEU 3.1 15.4 + - - +
694A LYS* 3.3 7.2 + - - +
696A SER* 1.3 75.7 - - - +
698A ASN* 1.3 62.8 + - - +
700A VAL* 3.4 16.2 - - - +
701A TYR* 3.9 3.1 + - - +
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Residues in contact with ASN 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A TYR* 4.7 1.2 - - - +
608A PRO* 3.5 25.6 - - - +
694A LYS* 3.0 34.3 + - - +
695A VAL* 4.0 5.1 - - - +
697A ALA* 1.3 74.4 - - - +
699A SER* 1.3 62.2 + - - +
700A VAL 3.2 0.7 - - - -
701A TYR* 3.2 14.2 + - + +
702A GLY 3.0 20.3 + - - -
0T A 3.8 6.5 - - - +
101T TTP 3.6 68.8 + - + +
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Residues in contact with SER 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLN* 3.5 33.4 + - - +
555A VAL* 5.4 2.8 - - - +
695A VAL* 2.9 18.8 + - - -
696A SER* 3.8 7.0 - - - -
698A ASN* 1.3 72.7 - - - +
700A VAL* 1.3 60.8 + - - +
702A GLY 3.7 0.7 - - - -
703A PHE* 3.0 27.4 + - - +
0T A 3.8 36.3 + - - -
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Residues in contact with VAL 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A VAL* 4.2 29.3 - - + +
558A GLN* 4.8 5.4 - - - +
611A MET* 5.6 2.2 - - - +
656A LEU* 4.9 21.5 - - + +
659A ILE* 5.0 8.1 - - + -
660A LEU* 3.8 24.9 - - + -
663A LEU* 4.1 20.2 - - + -
696A SER 3.1 15.8 + - - +
697A ALA 3.4 10.5 - - - +
698A ASN 3.2 0.4 - - - -
699A SER* 1.3 75.7 - - - +
701A TYR* 1.3 62.0 + - - +
703A PHE* 3.4 16.5 - - - +
704A THR* 4.1 5.9 + - - -
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Residues in contact with TYR 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A TYR* 3.3 19.7 + - - -
607A TYR* 3.5 42.3 - + + -
608A PRO* 5.8 2.0 - - + -
611A MET* 4.3 22.7 - - + -
660A LEU* 5.5 1.3 - - + +
697A ALA 3.9 3.2 + - - +
698A ASN* 3.2 15.8 + - - +
700A VAL* 1.3 78.6 - - - +
702A GLY* 1.3 73.2 + - - +
704A THR* 3.2 21.1 + - - -
705A GLY 4.1 2.1 + - - -
716A ILE* 5.9 0.9 - - + -
717A SER* 4.4 14.3 + - - -
720A VAL* 3.7 38.1 - - + -
721A THR* 3.7 10.7 - - - +
0T A 5.2 0.7 - + - -
1T G 5.0 13.9 + - - +
101T TTP 3.8 16.2 - - + -
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Residues in contact with GLY 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A ASN 3.0 11.3 + - - -
699A SER 3.4 1.3 + - - -
700A VAL 3.4 0.4 - - - -
701A TYR* 1.3 82.9 - - - +
703A PHE* 1.3 64.4 + - - +
704A THR 3.2 0.4 - - - -
705A GLY* 3.7 8.7 + - - -
706A ALA* 3.8 8.0 + - - +
0T A 3.5 41.2 - - - +
1T G 4.2 10.0 - - - +
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Residues in contact with PHE 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLN 5.6 0.4 - - - -
552A GLN* 4.0 31.9 - - + -
555A VAL* 3.9 34.1 - - + -
556A VAL* 4.4 19.1 - - + -
559A LEU* 5.4 8.1 - - + -
618A TYR* 3.9 26.0 - + - -
699A SER 3.0 12.9 + - - +
700A VAL* 3.4 14.6 - - - +
701A TYR 3.1 0.4 - - - -
702A GLY* 1.3 77.7 - - - +
704A THR* 1.3 62.9 + - - +
705A GLY 3.5 0.2 + - - -
706A ALA* 3.6 15.6 + - + +
709A GLY* 5.7 0.4 - - - -
710A LYS* 4.5 13.2 - - + -
711A LEU* 4.1 30.9 - - + +
712A PRO* 4.8 0.5 - - - +
0T A 5.1 4.5 - - - -
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Residues in contact with THR 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A MET* 5.5 1.8 - - - +
618A TYR* 4.2 19.4 + - - -
656A LEU* 4.7 11.4 - - - +
700A VAL 4.3 5.7 + - - -
701A TYR* 3.2 15.0 + - - -
703A PHE* 1.3 79.8 - - - +
705A GLY* 1.3 57.6 + - - +
712A PRO* 3.3 10.4 - - - +
713A CYS* 3.0 55.6 + - + +
714A LEU 4.2 0.2 + - - -
716A ILE* 3.7 24.7 - - + +
717A SER* 3.3 13.0 - - - +
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Residues in contact with GLY 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A TYR* 5.0 8.3 - - - -
701A TYR 4.1 2.4 + - - -
702A GLY* 3.7 6.9 + - - -
703A PHE 3.4 0.4 - - - -
704A THR* 1.3 78.2 - - - +
706A ALA* 1.3 58.0 + - - +
707A GLN* 3.2 10.7 + - - +
712A PRO* 5.0 0.2 - - - -
714A LEU* 3.5 23.9 - - - +
717A SER* 3.5 18.1 + - - -
1T G 4.6 15.2 - - - +
2T C 5.5 1.0 + - - -
----------------------------------------------------------
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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