Contacts of the helix formed by residues 790 - 817 (chain D) in PDB entry 4UQJ
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 SER 790 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C ILE* 6.0 3.0 - - - +
513D GLY 4.7 18.3 + - - -
514D VAL* 5.1 9.4 - - - +
516D SER* 5.2 2.6 + - - -
791D ASN* 1.3 76.6 + - - +
792D VAL* 3.3 5.4 - - - +
793D ALA* 3.0 28.9 + - - +
794D GLY* 3.4 3.8 + - - -
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Residues in contact with ASN 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611C ILE* 5.7 0.4 - - - +
615C SER* 4.9 9.2 + - - -
513D GLY 5.5 0.2 - - - -
514D VAL* 5.1 5.5 - - - +
516D SER* 4.0 28.6 + - - +
517D PHE* 3.0 40.6 - - - +
616D TYR* 4.8 2.8 + - - -
620D LEU* 4.3 18.8 - - - +
624D LEU* 6.3 0.6 - - - +
790D SER* 1.3 82.5 + - - +
792D VAL* 1.3 68.2 + - + +
793D ALA 3.2 0.9 + - - -
794D GLY* 3.2 13.7 + - - -
795D VAL* 3.9 6.2 + - - +
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Residues in contact with VAL 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C LEU* 6.3 0.4 - - + -
525C ILE* 3.5 44.2 - - + -
611C ILE* 6.2 0.9 - - - -
612C ILE* 4.1 18.6 - - + -
615C SER* 5.1 16.6 - - - +
790D SER 3.3 3.1 - - - +
791D ASN* 1.3 79.3 - - + +
793D ALA* 1.3 61.6 + - - +
795D VAL* 3.2 17.3 + - + +
796D PHE* 3.0 42.2 + - + -
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Residues in contact with ALA 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D VAL* 6.3 0.7 - - + -
790D SER* 3.0 21.9 + - - +
792D VAL* 1.3 80.5 - - - +
794D GLY* 1.3 56.0 - - - +
796D PHE* 2.8 28.0 + - - +
797D TYR* 3.0 33.0 + - + -
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Residues in contact with GLY 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D VAL* 3.5 33.2 - - - +
517D PHE* 5.8 3.5 - - - -
790D SER 3.4 3.6 + - - -
791D ASN 3.2 8.0 + - - -
793D ALA* 1.3 77.9 - - - +
795D VAL* 1.3 61.3 + - - +
797D TYR* 3.7 10.5 + - - +
798D ILE* 3.5 20.1 + - - +
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Residues in contact with VAL 795 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C PHE* 5.1 2.9 - - + -
608C PHE* 3.2 45.1 - - + +
611C ILE* 3.4 39.7 - - + -
612C ILE* 5.5 1.6 - - + -
517D PHE* 3.7 21.5 - - + -
791D ASN 4.0 12.6 - - - +
792D VAL* 3.2 11.9 + - + +
793D ALA 3.0 0.8 - - - -
794D GLY* 1.3 75.9 - - - +
796D PHE* 1.3 61.3 + - - +
797D TYR 3.4 0.2 - - - -
798D ILE* 3.0 25.9 - - + +
799D LEU* 3.4 3.3 + - - +
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Residues in contact with PHE 796 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C ILE* 4.4 4.9 - - + -
528C CYS* 3.3 38.4 - - + -
529C ILE* 3.4 22.9 - - + -
532C ALA* 4.0 11.9 - - + -
608C PHE* 3.3 34.1 - + - -
612C ILE* 4.2 0.9 - - + -
792D VAL* 3.0 46.6 + - + -
793D ALA* 2.8 12.9 + - - +
795D VAL* 1.3 77.9 - - - +
797D TYR* 1.3 63.4 + - + +
799D LEU* 3.2 5.8 + - + +
800D VAL* 3.1 33.0 + - + +
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Residues in contact with TYR 797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D VAL* 6.3 1.3 - - + -
793D ALA* 3.0 42.8 + - + -
794D GLY* 3.7 8.9 + - - +
795D VAL 3.4 0.2 - - - -
796D PHE* 1.3 81.4 - - + +
798D ILE* 1.3 56.9 + - - +
800D VAL* 3.5 6.8 + - + +
801D GLY* 3.0 25.6 + - - -
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Residues in contact with ILE 798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C VAL* 3.9 10.7 - - + +
607C PHE* 4.4 26.0 - - + -
608C PHE* 6.0 1.1 - - + -
517D PHE* 6.3 4.0 - - + -
794D GLY 3.5 7.3 + - - +
795D VAL* 3.0 38.6 - - + +
797D TYR* 1.3 78.4 - - - +
799D LEU* 1.3 58.1 + - - +
801D GLY* 3.9 2.1 - - - +
802D GLY* 3.2 18.0 + - - -
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Residues in contact with LEU 799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C ALA* 3.9 23.8 - - + -
536C VAL* 4.8 2.9 - - + -
604C VAL* 3.6 24.0 - - + +
605C TRP* 3.8 44.9 - - + +
608C PHE* 3.8 20.6 - - + -
795D VAL 3.6 10.5 - - - +
796D PHE* 3.2 10.7 + - + +
797D TYR 3.1 0.6 - - - -
798D ILE* 1.3 79.0 - - - +
800D VAL* 1.3 64.1 + - + +
801D GLY 3.1 1.1 - - - -
802D GLY* 2.9 4.9 + - - -
803D LEU* 2.9 47.4 + - + +
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Residues in contact with VAL 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C ALA* 6.2 2.7 - - + -
796D PHE* 3.1 18.9 + - + +
797D TYR* 4.1 6.1 - - + +
799D LEU* 1.3 79.4 - - + +
801D GLY* 1.3 57.2 + - - +
803D LEU* 3.3 17.9 + - + +
804D GLY* 2.9 26.0 + - - -
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Residues in contact with GLY 801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797D TYR 3.0 18.3 + - - -
798D ILE* 4.0 2.7 - - - -
799D LEU 3.1 0.4 - - - -
800D VAL* 1.3 77.2 - - - +
802D GLY* 1.3 55.3 + - - +
804D GLY* 3.5 1.7 + - - -
805D LEU* 3.0 27.5 + - - +
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Residues in contact with GLY 802 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C ILE* 4.1 6.2 - - - +
601C VAL* 4.9 1.5 - - - +
604C VAL* 4.3 22.2 - - - -
798D ILE 3.2 11.4 + - - -
799D LEU 2.9 8.2 + - - -
801D GLY* 1.3 75.2 - - - +
803D LEU* 1.3 63.7 + - - +
805D LEU* 3.4 10.8 + - - +
806D ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 803 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C ALA* 5.6 2.0 - - + +
535C GLY 4.4 11.4 - - - +
536C VAL* 4.0 27.1 - - + -
539C VAL* 4.6 18.5 - - + +
601C VAL* 3.9 35.3 - - + +
604C VAL* 6.2 0.4 - - + -
799D LEU* 2.9 31.8 + - + +
800D VAL* 3.3 21.7 + - + +
802D GLY* 1.3 77.1 - - - +
804D GLY* 1.3 56.4 + - - +
806D ALA* 3.2 6.7 + - - +
807D MET* 2.9 35.0 + - + +
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Residues in contact with GLY 804 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800D VAL 2.9 15.6 + - - -
801D GLY* 3.9 2.5 - - - -
802D GLY 3.3 0.2 - - - -
803D LEU* 1.3 74.8 - - - +
805D LEU* 1.3 63.1 + - - +
807D MET* 3.2 10.2 + - - +
808D LEU* 3.0 22.9 + - - +
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Residues in contact with LEU 805 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C ILE* 4.2 15.9 - - + -
801D GLY 3.0 17.4 + - - +
802D GLY* 3.6 10.3 - - - +
803D LEU 3.3 0.2 - - - -
804D GLY* 1.3 75.4 - - - +
806D ALA* 1.3 57.0 + - - +
808D LEU* 3.3 19.5 + - + +
809D VAL* 3.0 41.7 + - + +
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Residues in contact with ALA 806 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C VAL* 5.8 0.7 - - + -
597C SER* 3.4 30.5 + - - +
600C ILE* 3.6 13.0 - - + +
601C VAL* 3.6 18.6 - - + -
802D GLY 3.0 13.7 + - - +
803D LEU 3.5 7.6 - - - +
804D GLY 3.2 0.2 - - - -
805D LEU* 1.3 74.0 - - - +
807D MET* 1.3 54.9 + - + +
808D LEU 3.0 4.5 - - - -
809D VAL* 3.1 3.3 + - - +
810D ALA* 2.8 36.2 + - - +
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Residues in contact with MET 807 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C VAL* 3.8 37.0 - - + +
542C LEU* 4.7 18.4 - - + -
543C VAL* 6.4 0.9 - - - -
597C SER* 6.2 0.2 - - - -
803D LEU* 2.9 23.7 + - + +
804D GLY* 3.2 9.8 + - - +
806D ALA* 1.3 74.3 - - - +
808D LEU* 1.3 58.5 + - - +
810D ALA* 4.0 9.2 - - + +
811D LEU* 3.2 36.2 + - + +
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Residues in contact with LEU 808 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804D GLY 3.0 12.1 + - - +
805D LEU* 3.4 22.9 - - + +
806D ALA 3.0 0.4 - - - -
807D MET* 1.3 76.9 - - - +
809D VAL* 1.3 64.9 + - + +
810D ALA 3.2 1.3 - - - -
811D LEU* 3.5 13.7 + - + +
812D ILE* 3.3 38.0 + - + +
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Residues in contact with VAL 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU* 4.2 22.9 - - + -
597C SER* 4.7 6.5 - - - -
600C ILE* 4.8 6.3 - - + -
805D LEU* 3.0 31.9 + - + +
806D ALA* 3.1 7.8 + - - +
808D LEU* 1.3 74.4 - - + +
810D ALA* 1.3 60.6 + - - +
812D ILE* 3.0 34.2 - - + +
813D GLU* 3.1 30.3 - - + +
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Residues in contact with ALA 810 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C VAL* 6.2 1.3 - - + -
597C SER* 3.2 28.9 + - - +
806D ALA 2.8 11.9 + - - +
807D MET* 4.0 13.5 - - + +
808D LEU 3.2 0.2 - - - -
809D VAL* 1.3 76.2 - - - +
811D LEU* 1.3 67.1 + - + +
813D GLU* 3.1 13.4 + - - +
814D PHE* 2.9 33.8 + - + -
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Residues in contact with LEU 811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807D MET* 3.2 24.8 + - + +
808D LEU* 3.5 15.8 + - + +
809D VAL 3.5 0.2 - - - -
810D ALA* 1.3 80.1 - - + +
812D ILE* 1.3 64.3 + - + +
814D PHE* 3.4 11.9 + - + +
815D CYS* 3.2 30.0 + - - -
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Residues in contact with ILE 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808D LEU* 3.3 21.3 - - + +
809D VAL* 3.0 41.7 - - + +
811D LEU* 1.3 77.4 - - + +
813D GLU* 1.3 63.8 + - + +
815D CYS* 3.1 9.5 + - - +
816D TYR* 2.9 54.1 + - + +
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Residues in contact with GLU 813 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595C SER* 5.6 1.7 - - - -
596C LEU* 3.7 22.3 + - - +
597C SER* 3.8 15.7 + - - -
809D VAL* 3.1 37.0 - - + +
810D ALA* 3.1 8.5 + - - +
812D ILE* 1.3 86.7 - - + +
814D PHE* 1.3 65.3 + - + +
816D TYR* 3.4 8.9 + - + +
817D LYS* 3.2 23.9 + - - +
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Residues in contact with PHE 814 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LEU 5.7 3.4 - - - -
543C VAL* 4.8 17.0 - - + -
597C SER* 6.4 0.2 - - - -
810D ALA* 2.9 39.7 + - + -
811D LEU* 3.8 10.5 - - + +
812D ILE 3.3 0.2 - - - -
813D GLU* 1.3 81.7 - - + +
815D CYS* 1.3 62.4 + - - +
817D LYS* 3.7 19.5 + - + +
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Residues in contact with CYS 815 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811D LEU* 3.2 26.0 + - - -
812D ILE* 3.1 13.1 + - - +
814D PHE* 1.3 78.5 - - - +
816D TYR* 1.3 69.2 + - + +
817D LYS 3.4 3.8 + - - +
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Residues in contact with TYR 816 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812D ILE* 2.9 57.4 + - + +
813D GLU* 3.4 9.2 + - + +
815D CYS* 1.3 79.5 - - + +
817D LYS* 1.3 64.1 + - - +
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Residues in contact with LYS 817 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813D GLU 3.2 15.3 + - - +
814D PHE* 4.0 17.3 - - + +
815D CYS 3.2 4.0 - - - +
816D TYR* 1.3 84.6 - - - +
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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