Contacts of the helix formed by residues 616 - 648 (chain A) in PDB entry 4BEJ
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 616 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A ASP* 1.3 73.1 + - - +
618A CYS* 4.7 5.6 - - - +
619A GLU* 3.2 48.5 - - + +
620A VAL* 3.8 13.4 + - - +
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Residues in contact with ASP 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 6.0 2.2 - - + -
396A ILE* 4.1 22.7 - - + -
409A PRO* 5.9 0.3 - - - +
616A ARG* 1.3 79.5 + - - +
618A CYS* 1.3 63.0 + - - +
619A GLU 3.1 0.2 - - - -
620A VAL* 3.2 24.0 - - - +
621A ILE* 3.7 8.0 + - - +
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Residues in contact with CYS 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A THR* 3.9 23.8 - - + -
392A ILE* 3.5 34.5 - - + +
393A LEU* 4.0 15.2 - - + +
396A ILE* 4.5 1.3 - - + +
616A ARG* 5.2 6.1 - - - -
617A ASP* 1.3 77.4 - - - +
619A GLU* 1.3 72.1 + - - +
620A VAL 3.3 0.2 - - - -
621A ILE* 3.9 4.3 - - - -
622A GLU* 3.1 33.2 + - - +
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Residues in contact with GLU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ARG* 3.2 47.3 - - + +
617A ASP 3.1 0.2 - - - -
618A CYS* 1.3 87.3 - - - +
620A VAL* 1.3 64.2 + - + +
622A GLU* 3.7 14.2 - - - +
623A ARG* 3.8 7.4 + - - +
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Residues in contact with VAL 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PRO* 5.4 9.2 - - + -
616A ARG 4.0 11.9 - - - +
617A ASP* 3.2 15.9 - - - +
619A GLU* 1.3 79.8 - - + +
621A ILE* 1.3 81.3 + - + +
622A GLU 3.1 1.8 - - - -
623A ARG* 2.8 42.7 + - - +
624A LEU* 2.9 21.6 + - + +
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Residues in contact with ILE 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ILE* 4.4 8.1 - - + -
396A ILE* 4.1 23.6 - - + -
409A PRO* 4.0 20.9 - - + +
412A SER* 3.7 28.3 - - - -
413A PHE* 4.7 8.5 - - + +
416A LEU* 3.7 13.9 - - + -
617A ASP 3.7 10.3 + - - +
618A CYS* 3.5 8.2 + - - +
620A VAL* 1.3 85.4 - - + +
622A GLU* 1.3 57.8 + - - +
624A LEU* 3.0 17.5 + - + +
625A ILE* 2.9 49.5 + - + +
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Residues in contact with GLU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A LEU* 3.5 28.9 - - + +
389A THR* 4.6 10.4 + - - -
392A ILE* 4.5 14.0 - - + +
618A CYS* 3.1 23.9 + - - +
619A GLU* 3.7 8.1 - - - +
621A ILE* 1.3 79.8 - - - +
623A ARG* 1.3 61.0 + - - +
625A ILE* 3.6 2.9 + - - +
626A LYS* 3.2 44.1 + - - +
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Residues in contact with ARG 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A CYS* 2.4 56.0 + - - +
506A GLY* 4.3 9.2 - - - -
507A LEU 3.6 22.8 + - - -
619A GLU 3.8 6.7 + - - +
620A VAL* 2.8 34.6 + - - +
622A GLU* 1.3 73.2 - - - +
624A LEU* 1.3 81.8 - - - +
626A LYS* 3.5 16.3 + - - +
627A SER* 3.0 21.8 + - - -
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A PRO* 5.7 6.7 - - + -
410A GLU* 6.0 3.8 - - + -
413A PHE* 3.2 36.5 - - + -
501A PHE* 4.3 7.5 - - + -
505A CYS* 3.9 22.9 - - - -
620A VAL* 2.9 24.0 + - + +
621A ILE* 3.0 19.7 + - + +
623A ARG* 1.3 91.8 - - - +
625A ILE* 1.3 65.0 + - - +
627A SER* 2.9 9.8 + - - -
628A TYR* 2.8 23.7 + - - +
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Residues in contact with ILE 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A LEU* 4.4 11.7 - - + +
387A LEU* 3.6 15.3 - - + -
392A ILE* 4.5 2.0 - - + -
413A PHE* 3.7 13.9 - - + -
416A LEU* 3.6 38.1 - - + -
417A VAL* 3.6 28.9 - - + +
420A GLN* 4.3 29.6 - - + +
621A ILE* 2.9 25.4 + - + +
622A GLU 3.9 3.4 - - - +
624A LEU* 1.3 74.4 - - - +
626A LYS* 1.3 64.6 + - - +
629A PHE* 3.0 30.0 + - + +
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Residues in contact with LYS 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A PRO* 3.8 29.2 - - + +
384A LEU* 3.5 37.1 - - + +
622A GLU* 3.2 38.5 + - - +
623A ARG* 3.7 11.8 - - - +
624A LEU 3.2 0.6 - - - -
625A ILE* 1.3 78.0 - - - +
627A SER* 1.3 63.8 + - - +
629A PHE* 4.1 1.0 - - - +
630A LEU* 3.1 24.9 + - - +
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Residues in contact with SER 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A PHE* 3.6 17.2 + - - -
504A ALA* 3.0 40.4 + - - +
505A CYS* 3.1 13.6 + - - -
623A ARG 3.0 14.8 + - - -
624A LEU* 2.9 10.9 + - - -
626A LYS* 1.3 76.6 - - - +
628A TYR* 1.3 62.1 + - - +
630A LEU* 3.2 20.4 - - - +
631A ILE* 3.5 11.1 + - - +
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Residues in contact with TYR 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A PHE* 3.8 15.9 - + + -
417A VAL* 3.6 23.8 - - + -
421A ILE* 4.9 2.5 - - + -
490A GLU* 5.6 1.3 - - + -
494A ILE* 3.2 32.4 - - + -
495A ASN* 3.4 25.6 + - - -
498A HIS* 5.2 2.9 - + + -
501A PHE* 3.5 29.8 - + + -
624A LEU 2.8 10.5 + - - +
625A ILE 4.2 1.1 - - - +
627A SER* 1.3 69.3 + - - +
629A PHE* 1.3 66.3 + - - +
630A LEU 3.0 2.0 - - - -
631A ILE* 2.9 40.0 + - + +
632A VAL* 3.0 30.2 + - + +
642B LYS* 3.2 34.3 + - - -
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Residues in contact with PHE 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A VAL* 3.7 39.7 - - + -
383A PRO* 3.9 27.8 - - + -
417A VAL* 4.7 2.1 - - + +
420A GLN* 3.4 42.8 - - + -
421A ILE* 3.7 26.5 - - + -
423A ARG* 4.3 9.9 - - + -
424A LEU* 3.7 25.6 - - + -
625A ILE* 3.0 21.2 + - + +
626A LYS 4.1 1.6 - - - +
628A TYR* 1.3 77.4 - - - +
630A LEU* 1.3 59.7 + - - +
632A VAL* 3.3 1.2 + - - +
633A ARG* 2.8 37.7 + - + +
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Residues in contact with LEU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A PRO* 6.3 1.3 - - + -
504A ALA* 3.9 27.6 - - + +
626A LYS 3.1 15.7 + - - +
627A SER* 3.2 10.3 - - - +
628A TYR 3.0 0.2 - - - -
629A PHE* 1.3 81.3 - - - +
631A ILE* 1.3 63.6 + - + +
633A ARG* 3.5 29.0 - - - +
634A LYS* 3.1 51.8 + - - +
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Residues in contact with ILE 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A HIS* 3.9 35.7 - - + +
500A ASP* 3.6 35.0 - - + +
501A PHE* 5.1 3.1 - - + -
504A ALA* 4.7 6.5 - - + -
627A SER 3.6 13.0 - - - +
628A TYR* 2.9 42.0 + - + +
630A LEU* 1.3 74.9 - - + +
632A VAL* 1.3 75.9 + - + +
634A LYS* 3.1 16.5 + - + +
635A ASN* 3.0 36.2 + - - +
638B ASP* 5.3 1.8 - - - +
642B LYS* 6.2 0.4 - - - -
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Residues in contact with VAL 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A ILE* 3.6 42.4 - - + -
424A LEU* 4.2 5.7 - - + +
490A GLU* 3.6 24.7 - - + +
628A TYR* 3.0 52.4 + - + +
629A PHE 3.7 3.6 - - - +
631A ILE* 1.3 80.8 - - + +
633A ARG* 1.3 60.7 + - - +
635A ASN* 3.2 19.8 - - - +
636A ILE* 3.3 11.6 + - + +
642B LYS* 5.5 0.4 - - - +
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Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A LEU* 3.1 29.0 + - + +
379A GLU* 3.9 31.7 + - - +
381A VAL* 4.4 6.2 + - + -
424A LEU* 3.8 32.3 - - + +
629A PHE* 2.8 25.5 + - + +
630A LEU* 3.5 28.0 - - - +
632A VAL* 1.3 73.7 - - - +
634A LYS* 1.3 81.4 + - - +
635A ASN 3.0 2.2 + - - -
636A ILE* 3.2 3.5 + - - +
637A GLN* 3.1 50.7 + - - +
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Residues in contact with LYS 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ASP* 5.6 10.1 + - + +
504A ALA* 6.0 1.6 - - - +
630A LEU* 3.1 42.6 + - - +
631A ILE* 3.3 17.0 - - + +
633A ARG* 1.3 94.0 - - - +
635A ASN* 1.3 65.5 + - - +
637A GLN* 3.5 22.0 - - - +
638A ASP* 3.8 10.2 - - - +
498B HIS* 5.5 2.4 + - - -
499B PRO* 5.5 13.0 - - + -
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Residues in contact with ASN 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A GLU* 3.2 23.7 + - - +
498A HIS* 5.0 5.5 + - - -
631A ILE* 3.0 32.7 + - - +
632A VAL* 3.2 10.7 - - - +
633A ARG 3.0 0.2 - - - -
634A LYS* 1.3 79.4 - - - +
636A ILE* 1.3 60.3 + - + +
638A ASP* 3.1 7.5 + - - +
639A SER* 2.8 37.6 + - - +
635B ASN* 5.4 6.1 - - - +
638B ASP* 3.4 21.2 + - - -
639B SER* 5.0 4.6 + - - -
642B LYS* 5.8 0.6 - - - +
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Residues in contact with ILE 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A PHE* 3.9 0.7 - - + -
378A LEU* 3.5 17.7 - - + -
421A ILE* 5.8 0.4 - - + -
424A LEU* 4.6 13.9 - - + +
428A SER* 3.3 24.5 - - - +
486A LEU* 4.3 11.4 - - + +
487A VAL* 4.1 22.7 - - + +
490A GLU* 3.8 32.3 - - + +
632A VAL* 3.3 17.7 + - + +
633A ARG 3.2 6.7 + - - +
635A ASN* 1.3 74.8 - - + +
637A GLN* 1.3 58.1 + - - +
638A ASP 2.8 10.8 + - - -
639A SER* 4.2 7.4 - - - +
640A VAL* 2.8 36.8 + - + +
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Residues in contact with GLN 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PHE 5.1 1.7 - - - +
371A HIS* 5.0 16.5 + - - -
374A PHE* 3.4 19.8 - - + +
375A GLY* 4.5 14.1 - - - -
378A LEU* 3.4 20.4 - - + -
379A GLU* 4.0 19.7 + - - +
633A ARG* 3.1 42.4 + - - +
634A LYS* 3.5 21.5 - - - +
636A ILE* 1.3 76.5 - - - +
638A ASP* 1.3 57.0 + - + +
641A PRO* 3.5 18.2 - - - +
499B PRO* 6.0 7.3 - - - +
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Residues in contact with ASP 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A HIS* 5.9 1.1 - - + -
634A LYS 3.8 9.9 - - - +
635A ASN* 3.1 7.6 + - - +
636A ILE 2.9 0.6 - - - -
637A GLN* 1.3 80.9 - - + +
639A SER* 1.3 67.8 + - - +
640A VAL 3.5 0.7 - - - -
641A PRO* 3.3 10.4 - - - +
642A LYS* 3.1 35.5 + - - +
493B TYR* 5.6 0.3 - - - -
495B ASN* 3.0 39.5 + - - +
498B HIS* 3.5 20.5 + - + +
499B PRO* 6.1 1.3 - - + -
628B TYR* 5.0 0.2 + - - -
631B ILE* 5.3 0.6 - - - +
635B ASN* 3.5 24.4 + - - -
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Residues in contact with SER 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A LEU* 3.9 26.5 - - - +
635A ASN* 2.8 25.3 + - - +
636A ILE* 4.0 5.8 - - - -
638A ASP* 1.3 80.9 + - - +
640A VAL* 1.3 54.0 + - - +
642A LYS* 3.2 13.4 - - - +
643A ALA* 2.7 33.4 + - - +
489B ILE* 4.6 7.7 - - - +
490B GLU* 5.9 0.4 - - - -
635B ASN* 5.0 5.4 + - - -
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Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A PHE* 3.8 10.3 - - + -
428A SER* 3.5 36.6 - - - +
431A CYS* 4.4 5.2 - - + -
483A VAL* 4.3 17.7 - - + -
486A LEU* 4.7 9.0 - - + -
487A VAL* 5.7 0.9 - - + -
636A ILE* 2.8 46.8 + - + +
639A SER* 1.3 69.3 - - - +
641A PRO* 1.3 72.4 - - + +
643A ALA* 2.9 8.8 + - - +
644A VAL* 2.8 29.4 + - + +
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Residues in contact with PRO 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PHE* 3.4 48.6 - - + +
371A HIS* 5.9 3.6 - - + +
374A PHE* 3.9 14.4 - - + -
637A GLN 3.5 24.2 - - - +
638A ASP* 3.3 13.9 - - - +
640A VAL* 1.3 94.3 - - + +
642A LYS* 1.3 61.3 + - - +
644A VAL* 3.2 2.9 + - - +
645A MET* 2.8 30.0 + - - +
493B TYR* 4.7 10.8 - - + -
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Residues in contact with LYS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A ASP* 3.1 40.4 + - - +
639A SER* 3.2 11.4 + - - +
641A PRO* 1.3 79.0 - - - +
643A ALA* 1.3 64.9 + - - +
645A MET* 3.3 3.5 + - - +
646A HIS* 3.1 19.2 + - - +
489B ILE* 4.0 22.1 + - + +
490B GLU* 3.1 60.9 + - - +
493B TYR* 3.9 24.0 - - + +
494B ILE 4.0 5.1 - - - +
495B ASN* 4.2 2.5 - - - -
628B TYR* 3.6 26.8 + - - -
631B ILE* 6.1 1.1 - - - -
632B VAL* 5.2 1.3 - - - +
635B ASN* 5.1 1.6 - - - +
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Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A THR* 4.9 2.0 - - - +
482A MET* 4.2 11.9 - - + -
483A VAL* 4.6 9.6 - - + -
486A LEU* 3.6 25.6 - - + -
639A SER 2.7 14.5 + - - +
640A VAL* 2.9 10.5 + - - +
642A LYS* 1.3 74.3 - - - +
644A VAL* 1.3 65.6 + - - +
646A HIS* 2.9 15.4 + - - +
647A PHE* 3.2 16.6 + - - -
489B ILE* 3.9 13.6 - - + +
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Residues in contact with VAL 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PHE* 3.5 32.1 - - + -
431A CYS* 4.8 0.2 - - - -
432A VAL* 3.4 32.5 - - + +
435A VAL* 3.7 26.2 - - + -
479A THR* 4.1 8.7 + - - -
640A VAL* 2.8 29.1 + - + +
641A PRO 3.5 0.2 - - - +
643A ALA* 1.3 71.9 - - + +
645A MET* 1.3 59.8 + - - +
646A HIS 3.1 0.2 + - - -
648A LEU* 2.7 45.0 + - + -
649A VAL* 3.3 7.6 + - + -
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Residues in contact with MET 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ILE* 3.5 19.7 - - + -
367A CYS* 6.2 0.4 - - - -
370A PHE* 3.2 26.5 - - + -
641A PRO 2.8 18.8 + - - +
642A LYS 3.4 9.2 - - - +
644A VAL* 1.3 73.6 - - - +
646A HIS* 1.3 57.1 + - - +
649A VAL* 3.5 39.9 - - + -
650A ASN* 2.9 50.0 + - - +
492B ALA* 4.1 2.0 - - - +
493B TYR* 3.3 44.0 - - + -
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Residues in contact with HIS 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ARG* 4.9 0.7 + - - -
642A LYS 3.1 7.4 + - - +
643A ALA 2.9 11.1 + - - +
645A MET* 1.3 80.4 - - - +
647A PHE* 1.3 104.1 + + + +
650A ASN* 4.3 2.8 - - + +
651A HIS* 3.5 18.0 + - - +
484B HIS* 5.9 2.9 + - - -
485B ASN* 4.8 7.6 + - - -
488B ALA* 4.2 31.4 - - + +
489B ILE* 4.4 12.2 - - + +
492B ALA* 3.7 19.0 - - + +
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Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A ARG* 3.0 51.2 + - - +
478A VAL* 3.6 18.2 - - + -
479A THR* 3.7 27.4 - - - +
482A MET* 3.4 40.2 - - + -
643A ALA 3.2 15.1 + - - +
646A HIS* 1.3 114.9 - + + +
648A LEU* 1.3 60.1 + - - +
651A HIS* 3.3 6.3 - - - +
485B ASN* 4.0 23.8 - - - -
489B ILE* 4.6 4.5 - - + -
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 4.0 15.7 - - + +
435A VAL* 3.7 32.5 - - + -
436A HIS* 4.2 13.0 - - + +
439A MET* 4.0 7.6 - - - +
472A LEU* 4.4 36.8 - - + +
475A ARG* 4.4 10.8 - - + -
476A LEU* 5.0 9.9 - - + +
479A THR* 4.4 11.9 - - + -
644A VAL* 2.7 26.5 + - + +
647A PHE* 1.3 75.3 - - - +
649A VAL* 1.3 64.8 + - - +
650A ASN 3.6 0.2 - - - -
651A HIS 4.4 0.2 - - - -
652A VAL* 3.0 30.2 + - + +
----------------------------------------------------------
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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