Contacts of the helix formed by residues 653 - 684 (chain C) in PDB entry 5VEY
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 653 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650C GLY* 2.5 37.7 + - - +
651C HIS 3.4 3.3 - - - +
652C MET* 1.3 78.6 - - - +
654C PRO* 1.3 68.0 - - - +
655C VAL* 3.1 11.2 + - - +
656C LEU* 3.5 41.5 + - + +
657C ARG* 4.3 4.3 + - - +
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Residues in contact with PRO 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C MET* 3.2 24.2 - - + +
653C ASP* 1.3 88.0 - - - +
655C VAL* 1.3 71.3 + - + +
656C LEU 3.2 0.2 - - - -
657C ARG* 3.3 14.3 + - + +
658C GLU* 3.0 38.1 + - + +
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Residues in contact with VAL 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C ASP* 3.1 4.4 - - - -
654C PRO* 1.3 87.6 - - + +
656C LEU* 1.3 53.6 + - + +
658C GLU* 3.2 14.7 + - + +
659C MET* 2.8 64.3 + - + +
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Residues in contact with LEU 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C ASP* 3.5 38.5 + - + +
654C PRO 3.2 0.4 - - - -
655C VAL* 1.3 77.7 - - + +
657C ARG* 1.3 63.7 + - + +
659C MET* 3.4 22.4 + - + +
660C GLU* 3.1 36.9 + - + +
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Residues in contact with ARG 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C MET 5.6 3.2 + - - -
653C ASP 4.9 5.4 - - - +
654C PRO* 3.3 15.7 + - + +
656C LEU* 1.3 77.6 - - + +
658C GLU* 1.3 63.0 + - + +
660C GLU* 3.4 15.5 + - - +
661C GLN* 3.3 34.8 + - - +
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Residues in contact with GLU 658 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654C PRO* 3.0 27.3 + - + +
655C VAL* 3.6 15.2 - - + +
657C ARG* 1.3 76.3 - - + +
659C MET* 1.3 60.6 + - + +
661C GLN* 3.4 10.2 + - - +
662C LYS* 2.9 61.9 + - + +
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Residues in contact with MET 659 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655C VAL* 2.8 47.0 + - + +
656C LEU* 3.5 33.0 - - + +
657C ARG 3.3 0.2 - - - -
658C GLU* 1.3 75.8 - - + +
660C GLU* 1.3 54.1 + - + +
662C LYS* 3.9 7.4 - - + +
663C LEU* 2.8 51.8 + - + +
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Residues in contact with GLU 660 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C LEU* 3.1 25.1 + - + +
657C ARG* 3.7 16.0 + - - +
658C GLU 3.3 0.2 - - - -
659C MET* 1.3 77.6 - - + +
661C GLN* 1.3 63.2 + - + +
663C LEU* 3.7 9.8 - - + +
664C GLN* 3.2 29.0 + - - +
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Residues in contact with GLN 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ARG* 3.3 21.5 + - - +
658C GLU* 3.8 10.9 - - - +
660C GLU* 1.3 73.9 - - + +
662C LYS* 1.3 67.4 + - + +
664C GLN* 3.3 9.3 + - - +
665C GLN* 3.3 30.7 + - - +
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Residues in contact with LYS 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658C GLU* 2.9 48.2 + - - +
659C MET* 3.9 7.0 - - + +
661C GLN* 1.3 74.8 - - + +
663C LEU* 1.3 56.1 + - + +
665C GLN* 3.3 13.4 + - - +
666C GLU* 2.7 37.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659C MET* 2.8 41.4 + - + +
660C GLU* 3.7 10.5 - - + +
661C GLN 3.3 0.2 - - - -
662C LYS* 1.3 74.4 - - + +
664C GLN* 1.3 60.9 + - + +
666C GLU* 3.6 21.7 - - - +
667C GLU* 2.8 45.9 + - - +
670C ARG* 4.2 11.0 - - - +
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Residues in contact with GLN 664 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660C GLU 3.2 16.8 + - - +
661C GLN* 3.6 10.3 - - - +
662C LYS 3.3 0.2 - - - -
663C LEU* 1.3 79.5 - - - +
665C GLN* 1.3 63.7 + - + +
667C GLU* 4.0 17.1 + - - +
668C GLU* 3.2 22.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN 665 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661C GLN* 3.3 21.5 + - - +
662C LYS* 3.3 12.9 + - - +
663C LEU 3.3 0.2 - - - -
664C GLN* 1.3 76.3 - - + +
666C GLU* 1.3 66.2 + - - +
668C GLU* 3.3 17.1 + - - +
669C ASP* 3.2 28.1 + - - +
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Residues in contact with GLU 666 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 2.7 43.7 + - - +
66B THR* 5.2 6.1 - - + +
68B HIS* 3.4 27.6 + - + +
662C LYS* 2.7 23.7 + - - +
663C LEU* 3.6 18.9 - - - +
665C GLN* 1.3 73.2 - - - +
667C GLU* 1.3 57.4 + - - +
669C ASP* 3.2 2.3 + - - -
670C ARG* 2.9 47.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 667 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C LEU* 2.8 29.7 + - - +
664C GLN* 4.0 18.0 + - - +
666C GLU* 1.3 73.4 - - - +
668C GLU* 1.3 60.2 - - - +
670C ARG* 3.2 31.9 + - - +
671C GLN* 2.8 49.0 + - + +
----------------------------------------------------------
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Residues in contact with GLU 668 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 4.5 10.6 - - - +
47B GLY* 5.0 2.0 - - - -
664C GLN 3.2 14.1 + - - +
665C GLN* 3.3 21.5 - - - +
666C GLU 3.2 0.2 - - - -
667C GLU* 1.3 77.4 - - - +
669C ASP* 1.3 67.2 + - - +
671C GLN* 3.8 12.3 + - - +
672C LEU* 3.2 22.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 669 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 4.9 4.1 - - + +
46B ALA* 2.9 20.7 + - - +
47B GLY* 2.6 37.5 + - - +
66B THR* 4.6 7.8 - - - +
68B HIS* 3.4 34.9 + - + +
665C GLN* 3.2 14.3 + - - +
666C GLU* 3.7 4.2 - - - +
668C GLU* 1.3 77.8 - - - +
670C ARG* 1.3 56.0 + - - +
672C LEU* 3.4 2.8 + - - +
673C ALA* 2.8 36.8 + - - +
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Residues in contact with ARG 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 3.3 28.0 - - - +
7B THR 5.4 3.1 - - - -
8B LEU* 3.9 18.5 - - + +
10B GLY* 5.8 2.0 - - - -
68B HIS* 3.1 29.6 - - + +
663C LEU* 4.2 9.5 - - - +
666C GLU* 2.9 35.4 + - - +
667C GLU* 3.2 36.3 + - - +
669C ASP* 1.3 74.5 - - - +
671C GLN* 1.3 56.4 + - + +
673C ALA* 3.3 6.8 + - - +
674C LEU* 2.7 35.2 + - - +
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Residues in contact with GLN 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667C GLU* 2.8 39.2 + - + +
668C GLU* 3.8 12.7 - - - +
670C ARG* 1.3 71.5 - - + +
672C LEU* 1.3 63.8 + - - +
674C LEU* 3.3 12.0 + - + +
675C GLN* 3.2 27.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 672 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.9 9.6 - - + -
47B GLY* 3.2 32.8 - - - +
48B LYS* 5.3 0.9 - - - -
49B GLN 5.3 1.1 - - - +
668C GLU* 3.2 15.1 + - + +
669C ASP 3.8 3.6 - - - +
671C GLN* 1.3 78.8 - - - +
673C ALA* 1.3 64.1 + - - +
675C GLN* 3.1 33.7 + - + +
676C LEU* 3.2 37.2 + - + +
679C MET* 6.1 0.7 - - + -
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Residues in contact with ALA 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.8 16.6 - - + -
44B ILE* 3.8 10.8 - - + -
68B HIS* 4.8 6.7 - - + -
70B VAL* 3.3 39.0 - - + +
669C ASP 2.8 19.5 + - - +
670C ARG* 3.5 5.8 - - - +
672C LEU* 1.3 77.2 - - - +
674C LEU* 1.3 56.7 + - - +
676C LEU* 3.2 2.6 + - - +
677C GLN* 3.0 24.3 + - - +
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Residues in contact with LEU 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.5 12.8 - - + +
670C ARG 2.7 21.9 + - - +
671C GLN* 3.4 11.4 - - + +
673C ALA* 1.3 73.3 - - - +
675C GLN* 1.3 58.2 + - + +
677C GLN* 3.2 12.4 + - + +
678C ARG* 2.8 73.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN 675 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C GLN* 3.2 11.8 + - - +
672C LEU* 3.1 35.9 + - + +
674C LEU* 1.3 77.8 - - + +
676C LEU* 1.3 57.6 + - - +
678C ARG* 3.2 11.0 + - - +
679C MET* 2.8 45.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 676 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.0 33.7 - - - +
44B ILE* 3.5 32.3 - - + -
49B GLN* 3.7 14.8 - - + +
70B VAL* 4.1 8.1 - - + -
672C LEU* 3.2 23.8 + - + +
673C ALA 3.2 7.0 + - - +
675C GLN* 1.3 76.2 - - - +
677C GLN* 1.3 57.8 + - - +
679C MET* 3.3 25.2 + - + +
680C PHE* 2.9 37.9 + - + -
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Residues in contact with GLN 677 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.3 13.6 - - + +
70B VAL* 3.3 5.8 - - + +
71B LEU* 2.9 58.1 + - - +
73B LEU* 4.0 9.1 - - - +
673C ALA 3.0 13.2 + - - +
674C LEU* 3.5 16.8 - - + +
676C LEU* 1.3 77.9 - - - +
678C ARG* 1.3 61.2 + - + +
680C PHE* 3.6 2.7 + - - +
681C ASP* 2.9 49.3 + - - +
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Residues in contact with ARG 678 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674C LEU* 2.8 55.4 + - + +
675C GLN* 3.2 9.8 + - - +
677C GLN* 1.3 75.5 - - + +
679C MET* 1.3 60.7 + - + +
681C ASP* 3.3 8.1 + - - +
682C ASN* 3.0 38.9 + - - +
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Residues in contact with MET 679 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C LEU* 6.1 0.7 - - + -
675C GLN* 2.8 34.1 + - + +
676C LEU* 3.3 37.4 + - + +
678C ARG* 1.3 70.7 - - + +
680C PHE* 1.3 67.0 + - + +
682C ASN* 3.1 22.9 + - - +
683C GLU* 3.2 19.2 + - - +
----------------------------------------------------------
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Residues in contact with PHE 680 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.0 61.5 - - - -
70B VAL* 5.1 0.4 - - + -
71B LEU 3.7 14.8 - - - +
72B ARG* 4.2 15.9 - - + -
73B LEU* 3.5 55.1 - - + +
74B ARG* 4.8 10.1 - - + -
676C LEU* 2.9 29.2 + - + +
677C GLN 3.8 2.9 - - - +
679C MET* 1.3 77.6 - - + +
681C ASP* 1.3 62.5 + - - +
683C GLU* 3.3 25.1 + - + +
684C ARG* 3.8 4.0 + - - +
----------------------------------------------------------
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Residues in contact with ASP 681 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.1 19.4 - - - +
677C GLN* 2.9 31.6 + - - +
678C ARG* 3.6 11.4 - - - +
679C MET 3.2 0.2 - - - -
680C PHE* 1.3 76.2 - - - +
682C ASN* 1.3 66.3 + - - +
684C ARG* 3.1 32.7 + - - +
686C THR 3.7 14.6 - - - +
----------------------------------------------------------
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Residues in contact with ASN 682 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C ARG* 3.0 29.5 + - - +
679C MET* 3.1 17.1 + - - +
681C ASP* 1.3 75.0 - - - +
683C GLU* 1.3 59.0 + - + +
685C ARG* 2.8 29.3 + - - +
686C THR 5.2 2.0 - - - -
687C VAL* 4.2 23.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU 683 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU 5.3 5.4 - - - +
679C MET 3.2 14.8 + - - +
680C PHE* 3.3 20.2 - - + +
681C ASP 3.2 0.2 - - - -
682C ASN* 1.3 78.0 - - - +
684C ARG* 1.3 63.0 + - + +
685C ARG* 3.0 14.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 684 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 4.8 11.3 - - - +
102A SER* 4.5 31.1 + - - +
73B LEU* 3.7 32.7 - - + +
74B ARG 5.3 1.4 - - - +
680C PHE 3.9 7.4 - - - +
681C ASP* 3.1 38.5 + - - +
682C ASN 3.1 0.4 - - - -
683C GLU* 1.3 75.4 - - + +
685C ARG* 1.4 67.9 + - - +
686C THR* 3.1 22.5 + - - +
----------------------------------------------------------
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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