Contacts of the helix formed by residues 633 - 662 (chain A) in PDB entry 5M7R
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 ASN 633 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLU* 6.0 0.2 - - - -
390A GLU* 2.8 30.7 + - - +
391A PHE* 3.1 12.7 + - - +
393A VAL* 3.2 18.1 + - - +
394A PRO* 4.3 6.6 + - - -
395A HIS* 4.3 10.4 + - - +
631A CYS* 3.4 12.0 - - - -
632A ALA* 1.3 72.5 - - - +
634A ARG* 1.3 62.3 + - - +
635A THR* 3.3 11.6 + - - -
636A ILE* 3.1 37.8 + - + +
637A LEU 3.2 15.4 + - - -
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Residues in contact with ARG 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A HIS* 5.3 3.2 - - + +
629A SER 2.8 30.3 + - - -
630A ASN* 3.9 4.2 - - - +
631A CYS 3.2 23.2 + - - -
632A ALA* 3.3 14.0 + - - +
633A ASN* 1.3 70.4 + - - +
635A THR* 1.3 61.6 + - - +
637A LEU* 3.2 27.3 + - - +
638A TYR* 2.8 60.4 + - + +
99B ASP* 2.8 33.9 + - - +
101B TYR* 3.8 44.1 - - + +
105B MET* 5.1 4.4 - - - +
106B PHE* 5.2 1.8 - - - -
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Residues in contact with THR 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 6.0 3.6 - - - +
319A GLU* 3.9 24.4 - - + +
395A HIS* 3.3 39.3 - - + +
633A ASN* 3.5 7.6 - - - -
634A ARG* 1.3 76.1 - - - +
636A ILE* 1.3 65.6 + - - +
638A TYR* 3.5 8.6 + - - +
639A ASP* 3.3 24.5 + - - +
71B ARG* 4.9 4.6 + - - +
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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
----------------------------------------------------------
319A GLU* 3.6 32.3 - - + +
387A TRP* 4.0 25.1 - - + +
390A GLU* 3.8 25.4 - - + +
391A PHE* 3.6 34.3 - - + -
633A ASN* 3.1 37.4 + - + +
635A THR* 1.3 78.3 - - - +
637A LEU* 1.3 66.1 + - - +
639A ASP* 3.2 12.5 + - - +
640A MET* 3.3 17.8 + - - +
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE* 6.2 0.7 - - - -
625A PHE* 6.3 0.7 - - + -
628A LEU* 3.7 30.5 - - + +
629A SER* 3.8 15.3 - - - +
631A CYS* 4.2 9.2 - - - -
633A ASN 3.2 11.6 + - - +
634A ARG* 3.2 48.2 + - - +
636A ILE* 1.3 79.4 - - - +
638A TYR* 1.3 68.0 + - + +
640A MET* 3.1 6.6 + - + -
641A TYR* 2.9 52.2 + - + -
644A VAL* 6.0 3.8 - - + -
99B ASP* 5.2 2.7 - - + +
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Residues in contact with TYR 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG* 2.8 52.0 + - + +
635A THR* 4.1 4.0 - - - +
636A ILE 3.3 0.2 - - - -
637A LEU* 1.3 81.8 - - + +
639A ASP* 1.3 65.2 + - - +
640A MET 3.2 0.5 + - - -
641A TYR* 3.5 14.6 + + + +
642A SER 5.1 0.5 + - - -
70B GLY 4.3 4.7 - - - -
71B ARG* 3.4 61.7 + - + +
72B PRO* 3.3 31.5 - - + +
99B ASP* 3.4 26.5 + - + -
100B ASP* 4.0 9.0 + - - -
101B TYR* 5.9 0.2 - - - -
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Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN* 4.7 6.4 + - - -
317A GLU* 3.4 44.8 - - + +
318A PHE* 3.3 9.2 + - - +
319A GLU* 2.9 40.9 + - + +
635A THR* 3.3 10.8 + - - +
636A ILE 3.2 10.3 + - - +
638A TYR* 1.3 79.6 - - - +
640A MET* 1.3 64.2 + - + +
641A TYR 3.9 0.2 + - - -
642A SER* 5.3 0.5 + - - -
643A TYR* 4.1 6.9 - - - -
71B ARG* 3.1 18.0 + - - +
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Residues in contact with MET 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 3.5 20.2 - - + -
293A LEU* 3.4 36.8 - - + -
320A ALA* 4.6 12.8 - - + +
387A TRP* 3.9 23.8 - - + -
391A PHE* 5.4 2.2 - - - -
561A LEU* 3.8 21.1 - - + -
628A LEU* 6.2 1.8 - - + -
636A ILE* 3.3 21.7 + - + +
637A LEU* 3.1 5.1 + - + +
639A ASP* 1.3 87.1 - - + +
641A TYR* 1.3 64.7 + - - +
642A SER 3.4 2.0 - - - -
643A TYR* 3.1 21.9 + - - +
644A VAL* 3.2 19.9 + - + +
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Residues in contact with TYR 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A PHE* 3.7 16.4 - + - -
629A SER* 4.0 13.4 + - - -
637A LEU* 2.9 37.4 + - + +
638A TYR* 3.5 15.8 + + - +
640A MET* 1.3 76.1 - - - +
642A SER* 1.3 65.8 + - - +
643A TYR 3.1 0.2 + - - -
644A VAL* 3.2 5.6 + - + +
645A TRP* 2.8 56.6 + + + -
69B TYR* 3.3 23.9 - - + +
70B GLY* 3.5 31.0 - - - -
71B ARG 5.0 1.8 - - - +
99B ASP* 3.0 33.4 + - + -
104B ARG* 5.4 0.2 + - - -
285B ASP* 6.0 1.1 - - + -
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Residues in contact with SER 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR 5.1 0.6 + - - -
639A ASP 5.3 0.9 + - - -
641A TYR* 1.3 87.0 - - - +
643A TYR* 1.3 67.0 + - - +
645A TRP* 3.9 4.9 - - - +
646A ASP* 3.2 27.7 + - - +
288B GLN* 3.3 29.9 + - - +
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Residues in contact with TYR 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASN* 3.5 7.0 + - - -
288A GLN 3.7 15.1 + - - -
289A LYS 3.6 13.7 - - - -
290A ARG 3.2 23.4 + - - -
291A LEU* 3.9 29.6 - - + -
317A GLU* 2.8 41.0 + - + -
565A PHE* 3.3 28.6 - + + -
639A ASP 4.1 11.9 - - - -
640A MET 3.1 11.2 + - - +
641A TYR 3.1 0.6 - - - -
642A SER* 1.3 81.2 - - - +
644A VAL* 1.3 66.4 + - + +
646A ASP* 3.2 3.9 + - - +
647A ILE 3.1 18.9 + - - -
288B GLN* 3.2 24.9 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
561A LEU* 3.7 23.6 - - + -
565A PHE* 4.7 0.9 - - - -
624A MET* 4.2 11.4 - - + -
625A PHE* 3.6 37.0 - - + -
628A LEU* 3.7 22.0 - - + -
637A LEU* 6.0 4.0 - - + -
640A MET* 3.2 24.2 + - + +
641A TYR* 3.9 6.7 - - - +
643A TYR* 1.3 76.4 - - + +
645A TRP* 1.3 62.2 + - - +
647A ILE* 3.4 8.0 - - + +
648A LYS* 3.2 21.5 + - - +
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Residues in contact with TRP 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A PHE* 4.0 8.6 - + - -
641A TYR* 2.8 53.6 + + + +
642A SER* 3.9 6.1 - - - +
644A VAL* 1.3 76.4 - - - +
646A ASP* 1.3 65.2 + - + +
648A LYS* 3.2 34.4 - - - +
649A SER* 2.9 53.2 + - - -
682A ARG* 4.0 3.8 - - - -
714A VAL 3.7 23.3 - - - -
715A TYR* 4.1 17.9 + + - +
69B TYR* 4.7 13.4 - - + +
285B ASP 3.8 15.0 - - - +
286B TYR* 3.3 42.2 - - + -
287B ASP* 5.1 0.4 - - - -
288B GLN 6.1 0.9 - - - -
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Residues in contact with ASP 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 2.6 29.1 + - - +
565A PHE* 5.7 2.3 - - + -
642A SER 3.2 17.5 + - - +
643A TYR* 3.2 5.1 + - - +
645A TRP* 1.3 89.2 - - + +
647A ILE* 1.3 56.8 + - - +
649A SER* 3.3 2.0 + - - -
650A ILE* 3.0 30.7 + - - +
682A ARG* 3.0 31.9 + - - -
288B GLN* 3.7 20.5 + - + +
686B ALA* 3.4 20.3 - - - +
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Residues in contact with ILE 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A LEU* 4.0 26.2 - - + -
565A PHE* 4.0 22.4 - - + -
621A VAL* 4.1 13.9 - - + -
624A MET* 4.5 5.8 - - + -
643A TYR 3.1 11.4 + - - +
644A VAL* 3.4 14.1 - - + +
646A ASP* 1.3 78.3 + - - +
648A LYS* 1.3 62.4 + - + +
650A ILE* 3.4 4.4 + - + +
651A MET* 2.8 51.0 + - + +
685B LEU* 4.6 12.8 - - + -
686B ALA* 3.9 32.5 - - + +
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Residues in contact with LYS 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A VAL* 3.9 8.7 - - + -
622A MET* 3.2 34.2 - - + +
625A PHE* 3.2 57.7 - - + -
644A VAL 3.2 12.8 + - - +
645A TRP* 3.2 41.4 + - - +
647A ILE* 1.3 81.1 - - + +
649A SER* 1.3 63.5 + - - +
652A SER* 3.0 27.4 + - - -
715A TYR 4.1 15.4 + - - -
----------------------------------------------------------
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Residues in contact with SER 649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A TRP* 2.9 53.2 + - - -
646A ASP 3.8 2.9 - - - -
648A LYS* 1.3 84.6 - - - +
650A ILE* 1.3 61.5 + - - +
652A SER* 3.6 6.6 + - - -
653A MET* 3.3 21.1 + - - +
679A TRP* 5.1 6.6 + - - -
682A ARG* 3.9 11.2 + - - -
714A VAL 5.0 3.4 + - - -
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Residues in contact with ILE 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A ASP* 3.0 34.6 + - - +
647A ILE* 3.9 5.2 - - + +
649A SER* 1.3 74.8 - - - +
651A MET* 1.3 69.1 + - - +
652A SER 3.1 0.2 - - - -
653A MET* 3.1 6.0 + - - +
654A VAL* 2.9 23.2 + - + +
679A TRP* 4.1 20.9 - - + -
682A ARG* 3.2 31.6 - - - +
686B ALA* 3.8 21.5 - - + +
689B PHE* 3.9 29.6 - - + -
690B GLN* 3.9 16.2 - - + +
693B LEU* 5.5 0.7 - - + -
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Residues in contact with MET 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A LEU* 4.6 9.2 - - + -
578A MET* 4.0 20.9 - - - +
614A PHE* 5.2 0.4 - - - -
618A CYS* 3.9 16.0 - - + +
621A VAL* 4.0 20.2 - - + -
622A MET* 3.9 16.8 - - + -
647A ILE* 2.8 40.9 + - + +
650A ILE* 1.3 73.9 - - - +
652A SER* 1.3 62.0 + - - +
654A VAL* 3.8 7.4 - - - +
655A LYS* 2.9 25.8 + - - +
685B LEU* 4.8 0.2 - - + -
689B PHE* 3.4 52.3 - - + -
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Residues in contact with SER 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A MET* 3.8 18.6 - - - +
648A LYS* 3.0 20.0 + - - -
649A SER* 3.6 9.2 - - - -
650A ILE 3.1 0.4 - - - -
651A MET* 1.3 78.8 - - - +
653A MET* 1.3 56.5 + - - +
655A LYS* 3.7 8.7 - - - +
656A SER* 3.2 25.6 + - - -
710A PRO* 5.8 0.2 - - - +
713A LYS* 5.8 4.7 + - - -
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Residues in contact with MET 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A SER 3.3 13.9 + - - +
650A ILE 3.1 4.6 + - - +
652A SER* 1.3 78.2 + - - +
654A VAL* 1.3 63.2 + - - +
656A SER* 3.4 6.4 - - - -
657A PHE* 3.2 22.2 + - - +
671A PHE* 3.6 33.4 - - - -
672A LEU* 4.9 6.5 - - + -
679A TRP* 3.7 49.6 - - + +
710A PRO* 3.5 40.4 - - + +
711A THR* 3.7 4.9 - - - +
693B LEU* 3.9 14.9 - - + +
----------------------------------------------------------
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Residues in contact with VAL 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A PHE* 3.7 23.1 - - + -
614A PHE* 3.5 31.4 - - + -
650A ILE* 2.9 22.4 + - + +
651A MET* 3.3 8.3 + - - +
653A MET* 1.3 76.6 - - - +
655A LYS* 1.3 61.1 + - - +
657A PHE* 3.1 9.2 + - - +
658A VAL* 3.0 20.8 + - - +
689B PHE* 3.7 34.1 - - + -
693B LEU* 4.2 17.3 - - + -
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Residues in contact with LYS 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A PHE* 4.6 1.6 - - - -
615A GLU* 3.7 34.9 - - + +
618A CYS* 3.8 25.3 - - + -
619A GLY* 5.0 6.7 - - - +
622A MET* 6.0 3.8 - - - -
651A MET 2.9 17.3 + - - +
652A SER* 3.7 9.2 - - - +
654A VAL* 1.3 76.1 - - - +
656A SER* 1.3 57.7 + - - +
658A VAL* 3.3 8.5 + - - +
659A GLN* 2.9 56.8 + - - +
----------------------------------------------------------
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Residues in contact with SER 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A SER 3.2 12.1 + - - -
653A MET 3.4 11.9 - - - -
655A LYS* 1.3 80.0 - - - +
657A PHE* 1.3 57.8 + - - +
659A GLN* 3.5 17.4 + - - +
660A TRP* 3.0 26.5 + - - +
671A PHE* 3.7 5.1 - - - -
710A PRO* 3.3 34.7 - - - +
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Residues in contact with PHE 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A PHE* 3.7 26.2 - + - -
586A ARG* 4.3 19.1 - - + -
653A MET 3.2 5.3 + - - +
654A VAL 3.1 7.9 + - - +
656A SER* 1.3 77.0 - - - +
658A VAL* 1.3 59.9 + - - +
660A TRP* 3.2 29.7 + + - +
661A LEU* 2.9 55.7 + - + +
671A PHE* 3.5 32.5 - + + -
692B LEU 5.0 1.1 - - - -
693B LEU* 3.6 20.9 - - + -
694B PRO* 3.7 26.0 - - + -
----------------------------------------------------------
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Residues in contact with VAL 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A PHE* 3.7 34.5 - - + -
585A LEU* 4.3 12.6 - - + -
607A TRP* 3.7 8.7 - - + -
611A ALA* 4.0 24.9 - - + +
614A PHE* 3.8 18.4 - - + -
615A GLU* 4.0 18.3 - - + +
654A VAL 3.0 11.5 + - - +
655A LYS* 3.3 7.8 + - - +
657A PHE* 1.3 73.2 - - - +
659A GLN* 1.3 65.0 + - - +
661A LEU* 3.4 21.6 + - + +
662A GLY* 3.4 9.0 + - - -
----------------------------------------------------------
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Residues in contact with GLN 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A GLU* 3.7 30.5 + - - +
655A LYS* 2.9 42.7 + - - +
656A SER* 3.5 23.4 + - - +
658A VAL* 1.3 75.3 - - - +
660A TRP* 1.3 62.4 + - - +
662A GLY* 3.3 11.0 + - - -
663A CYS* 3.5 19.4 + - - -
----------------------------------------------------------
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Residues in contact with TRP 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A SER 3.0 17.3 + - - +
657A PHE* 3.2 29.6 + + - +
659A GLN* 1.3 73.9 - - - +
661A LEU* 1.3 85.8 + - + +
663A CYS* 3.2 18.1 + - + +
664A ARG* 3.3 42.5 + - + +
667A SER* 5.4 3.9 + - - -
669A ALA* 3.0 38.0 + - + -
670A GLN* 3.8 9.7 - - - -
671A PHE* 3.8 39.0 - + + -
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Residues in contact with LEU 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A PHE* 5.2 0.7 - - + -
585A LEU* 4.1 20.4 - - + +
586A ARG* 4.4 8.1 - - + -
589A SER* 3.4 27.6 - - - +
592A VAL* 4.4 11.4 - - - +
607A TRP* 3.8 15.0 - - + -
657A PHE* 2.9 46.4 + - + +
658A VAL* 3.4 18.6 + - + +
660A TRP* 1.3 99.8 - - + +
662A GLY* 1.3 56.2 + - - +
663A CYS 3.3 1.8 + - - -
664A ARG* 3.6 25.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A VAL* 4.0 7.0 - - - +
607A TRP* 3.7 13.4 - - - -
608A ARG* 2.9 36.2 + - - -
658A VAL 3.4 4.8 + - - -
659A GLN* 3.3 7.6 + - - -
660A TRP 3.2 0.8 - - - -
661A LEU* 1.3 77.0 - - - +
663A CYS* 1.3 63.7 + - - +
664A ARG 3.6 0.4 - - - -
665A SER* 5.7 0.7 + - - -
666A HIS* 4.4 5.9 - - - -
----------------------------------------------------------
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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