Contacts of the helix formed by residues 697 - 729 (chain D) in PDB entry 6UZA
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 HIS 697 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C ARG* 3.2 29.2 + - + -
584C ILE 5.0 2.7 + - - -
586C TRP* 3.9 22.9 + + + +
587C ASP 4.1 8.5 - - - -
588C PRO* 4.1 7.2 - - + -
593C ILE* 3.8 33.1 - - + +
659D TYR* 3.1 35.1 + + - +
693D ILE* 3.4 22.8 - - + +
695D TYR* 3.3 24.7 - + + +
696D ASN* 1.3 79.8 + - + +
698D LYS* 1.3 64.1 + - - +
699D PHE 3.2 4.5 + - - +
700D ILE* 3.5 5.0 + - + +
701D GLU* 3.5 8.5 + - - +
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Residues in contact with LYS 698 (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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588C PRO* 5.6 0.6 - - - +
692D VAL* 5.3 1.2 - - - +
693D ILE* 3.7 10.5 + - - +
694D ASN 5.2 0.2 - - - -
695D TYR 3.2 26.2 + - - -
696D ASN* 3.2 21.8 + - - +
697D HIS* 1.3 72.2 - - - +
699D PHE* 1.3 59.2 + - - +
700D ILE 3.4 0.2 - - - -
701D GLU* 2.7 38.4 + - - +
702D ASN* 2.9 38.5 + - - +
1001D Y01 3.7 29.2 + - + +
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Residues in contact with PHE 699 (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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588C PRO 4.8 13.0 + - - +
593C ILE* 3.3 33.0 - - + +
594C ILE* 3.8 44.9 - - + -
597C GLY* 3.9 14.1 - - - -
598C LEU* 4.6 9.0 - - + -
697D HIS* 3.2 0.4 - - - +
698D LYS* 1.3 76.1 - - - +
700D ILE* 1.3 58.9 + - - +
702D ASN* 3.2 4.2 + - - +
703D ILE* 3.0 37.9 + - + +
1001D Y01 3.5 66.7 + - + +
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Residues in contact with ILE 700 (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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593C ILE* 4.0 33.2 - - + +
596C GLU* 4.6 13.5 - - + +
597C GLY* 4.7 1.8 - - - -
655D LEU* 3.8 32.8 - - + +
656D TYR* 3.7 18.9 + - + -
659D TYR* 3.4 42.0 - - + +
693D ILE* 4.5 5.8 - - + -
697D HIS* 3.5 11.0 + - + +
699D PHE* 1.3 77.1 - - + +
701D GLU* 1.3 57.3 + - - +
703D ILE* 3.3 8.6 + - - +
704D GLY* 2.9 23.0 + - - -
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Residues in contact with GLU 701 (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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676C LYS* 5.7 0.5 + - - -
656D TYR* 3.8 9.3 + - - -
691D VAL 3.6 14.5 - - - +
692D VAL* 4.2 19.3 - - - +
693D ILE* 3.8 18.9 + - + +
697D HIS 3.5 10.4 + - - +
698D LYS* 2.7 46.0 + - - +
699D PHE 3.3 0.4 - - - -
700D ILE* 1.3 79.8 - - - +
702D ASN* 1.3 60.3 + - - +
704D GLY* 3.3 1.7 + - - -
705D TYR* 2.9 55.3 + - + -
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Residues in contact with ASN 702 (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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672C GLU* 5.0 2.5 + - - +
676C LYS* 5.4 1.6 + - - -
1004C SBJ 3.4 36.3 + - - +
698D LYS* 2.9 24.8 + - - +
699D PHE 3.7 3.1 - - - +
701D GLU* 1.3 77.8 - - - +
703D ILE* 1.3 66.5 + - - +
705D TYR* 3.4 11.2 + - - +
706D VAL* 3.0 30.4 + - - +
1001D Y01 2.6 48.0 + - + +
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Residues in contact with ILE 703 (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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597C GLY* 3.7 22.7 - - - +
600C ALA* 4.8 1.1 - - + -
601C ILE* 3.7 31.2 - - + -
655D LEU* 3.8 18.8 - - + -
699D PHE* 3.0 32.9 + - + +
700D ILE* 3.6 9.9 - - - +
701D GLU 3.3 0.2 - - - -
702D ASN* 1.3 75.3 - - - +
704D GLY* 1.3 56.5 + - - +
706D VAL* 3.4 4.6 + - - +
707D LEU* 2.9 36.5 + - + +
1001D Y01 3.6 39.5 - - + -
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Residues in contact with GLY 704 (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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652D MET* 4.3 3.1 - - - +
655D LEU* 3.7 12.3 - - - +
656D TYR* 3.6 23.3 - - - -
691D VAL* 4.0 9.3 - - - +
700D ILE 2.9 12.1 + - - -
701D GLU 3.3 0.4 + - - -
702D ASN 3.3 0.2 - - - -
703D ILE* 1.3 77.5 - - - +
705D TYR* 1.3 55.7 + - - +
707D LEU* 3.9 4.0 - - - +
708D TYR* 3.0 31.5 + - - +
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Residues in contact with TYR 705 (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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676C LYS* 4.4 26.6 + - + +
680C TRP* 4.0 14.1 - + - -
1004C SBJ 3.7 43.4 - - + +
688D VAL* 3.6 28.6 + - + +
691D VAL* 3.8 19.4 - - + +
692D VAL* 3.6 17.3 - - + +
701D GLU* 2.9 52.9 + - + +
702D ASN* 3.6 14.6 - - - +
703D ILE 3.3 0.2 - - - -
704D GLY* 1.3 76.3 - - - +
706D VAL* 1.3 57.1 + - - +
708D TYR* 3.5 3.1 + - - +
709D GLY 3.0 24.1 + - - -
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Residues in contact with VAL 706 (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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601C ILE* 6.4 1.1 - - + -
1004C SBJ 4.2 56.7 - - + +
702D ASN 3.0 20.2 + - - +
703D ILE* 3.9 3.4 - - - +
705D TYR* 1.3 76.7 - - - +
707D LEU* 1.3 64.2 + - + +
709D GLY* 3.4 1.2 + - - -
710D VAL* 3.0 40.0 + - + +
1001D Y01 3.8 40.6 - - + -
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Residues in contact with LEU 707 (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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600C ALA* 4.3 23.3 - - + +
601C ILE* 4.7 18.4 - - + -
604C VAL* 4.3 31.0 - - + -
648D PHE* 3.6 15.2 - - + -
651D GLY 4.4 1.6 - - - +
652D MET* 3.9 31.2 - - + -
655D LEU* 4.6 4.0 - - + -
703D ILE* 2.9 29.1 + - + +
704D GLY 4.0 2.7 - - - +
706D VAL* 1.3 81.3 - - + +
708D TYR* 1.3 58.0 + - - +
710D VAL* 3.5 5.7 + - + -
711D TYR* 2.9 29.1 + - - +
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Residues in contact with TYR 708 (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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680C TRP* 3.5 25.6 - + + -
685C LEU* 4.8 4.5 - - + +
652D MET* 3.9 18.7 - - + +
668D PHE* 4.5 7.9 - + - -
677D THR* 4.1 2.7 + - + +
678D LEU* 4.1 18.6 - - + -
681D ALA* 3.4 14.9 - - + +
686D SER* 3.3 35.7 + - - -
687D GLU 4.0 16.0 + - - -
688D VAL* 4.7 8.7 - - + -
690D SER* 4.5 7.4 + - - -
691D VAL* 4.1 18.4 - - + -
704D GLY 3.0 18.6 + - - +
705D TYR* 3.9 3.6 - - - +
707D LEU* 1.3 77.3 - - - +
709D GLY* 1.3 54.2 + - - +
711D TYR* 3.3 5.4 + + - +
712D ASN* 2.6 50.3 + - - -
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Residues in contact with GLY 709 (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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679C PHE* 3.9 15.6 - - - -
680C TRP* 3.6 16.9 - - - -
1004C SBJ 4.3 7.9 - - - -
705D TYR 3.0 13.5 + - - -
706D VAL 3.8 2.2 - - - -
708D TYR* 1.3 77.1 - - - +
710D VAL* 1.3 58.3 + - - +
712D ASN* 3.3 2.7 + - - +
713D VAL* 3.0 36.0 + - - +
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Residues in contact with VAL 710 (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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604C VAL* 6.1 0.2 - - + -
1003C S9Y 5.5 6.3 - - + -
1004C SBJ 4.0 53.4 - - + +
648D PHE* 3.7 21.1 - - + -
706D VAL* 3.0 31.3 + - + +
707D LEU* 3.9 7.9 - - + +
709D GLY* 1.3 74.0 - - - +
711D TYR* 1.3 54.6 + - - +
713D VAL* 3.9 5.1 - - - +
714D THR* 2.5 44.0 + - - +
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Residues in contact with TYR 711 (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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644D VAL* 4.9 0.4 - - + -
645D PHE* 3.4 17.5 - + - -
648D PHE* 3.8 39.9 - + + -
652D MET* 4.6 1.8 - - + -
678D LEU* 2.5 61.8 + - + -
681D ALA* 4.1 15.3 - - + -
682D ILE* 3.9 9.1 - - + +
707D LEU 2.9 18.8 + - - +
708D TYR* 3.5 8.3 - + - +
710D VAL* 1.3 77.0 - - - +
712D ASN* 1.3 72.2 + - - +
714D THR* 3.4 1.4 + - - -
715D MET* 3.0 63.3 + - + +
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Residues in contact with ASN 712 (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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680C TRP* 3.7 18.4 - - - -
683C PHE* 3.8 33.2 - - + +
685C LEU* 5.0 5.0 - - - +
681D ALA* 4.0 20.4 - - - +
708D TYR* 2.6 52.6 + - - +
709D GLY* 3.3 4.9 + - - +
711D TYR* 1.3 82.8 - - - +
713D VAL* 1.3 62.8 + - - +
715D MET* 3.4 5.0 + - - +
716D VAL* 3.0 28.6 + - - +
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Residues in contact with VAL 713 (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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638C MET* 5.0 9.0 - - + -
679C PHE* 4.1 15.7 - - + -
683C PHE* 4.0 17.7 - - + -
1004C SBJ 3.8 33.2 - - + -
709D GLY 3.0 17.9 + - - +
710D VAL 4.0 3.1 - - - +
712D ASN* 1.3 74.8 - - - +
714D THR* 1.3 58.0 + - - +
716D VAL* 3.3 7.3 + - + +
717D ILE* 3.0 45.7 + - + +
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Residues in contact with THR 714 (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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1003C S9Y 5.1 7.7 - - + +
1004C SBJ 3.7 31.6 - - + +
644D VAL* 3.8 33.4 - - + -
648D PHE* 4.5 4.2 - - + -
710D VAL* 2.5 32.1 + - - +
711D TYR* 3.8 4.0 - - - -
713D VAL* 1.3 77.2 - - - +
715D MET* 1.3 57.5 + - - +
717D ILE* 3.3 9.6 + - - +
718D VAL* 3.0 33.3 + - + +
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Residues in contact with MET 715 (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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641D PHE* 3.5 63.9 - - + +
644D VAL* 3.7 22.7 - - + -
645D PHE* 3.9 6.7 - - + +
682D ILE* 5.4 7.2 - - + -
711D TYR* 3.0 57.7 + - + +
712D ASN* 4.0 5.2 - - - +
713D VAL 3.3 0.2 - - - -
714D THR* 1.3 72.4 - - - +
716D VAL* 1.3 61.3 + - + +
718D VAL* 3.4 5.6 + - - +
719D LEU* 3.0 40.2 + - + +
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Residues in contact with VAL 716 (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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683C PHE* 3.9 23.8 - - + -
722C MET* 6.3 2.2 - - + -
712D ASN 3.0 20.6 + - - +
713D VAL* 3.3 7.6 + - + +
715D MET* 1.3 77.2 - - + +
717D ILE* 1.3 59.6 + - + +
719D LEU* 3.9 5.5 - - + +
720D LEU* 3.0 38.4 + - + +
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Residues in contact with ILE 717 (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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627C LEU* 5.1 9.0 - - + -
630C THR* 4.9 9.8 + - - +
631C VAL* 4.6 20.2 - - + -
634C ILE* 3.7 29.4 - - + -
638C MET* 5.1 1.6 - - + -
1004C SBJ 3.8 35.2 - - + -
713D VAL* 3.0 36.5 + - + +
714D THR* 3.6 4.7 - - - +
716D VAL* 1.3 80.4 - - + +
718D VAL* 1.3 59.6 + - + +
720D LEU* 3.4 10.6 + - + +
721D ASN* 2.9 28.7 + - + +
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Residues in contact with VAL 718 (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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627C LEU* 4.7 23.1 - - + -
1004C SBJ 6.3 0.4 - - + -
637D PHE* 5.1 10.7 - - + +
640D ILE* 4.9 8.1 - - + -
641D PHE* 4.0 35.0 - - + +
644D VAL* 4.9 12.1 - - + -
714D THR* 3.0 30.7 + - + +
715D MET* 3.9 8.5 - - - +
717D ILE* 1.3 79.1 - - + +
719D LEU* 1.3 59.1 + - + +
721D ASN* 3.4 9.0 + - - +
722D MET* 3.0 29.4 + - + +
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Residues in contact with LEU 719 (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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641D PHE* 3.6 28.7 - - + -
682D ILE* 4.2 25.1 - - + +
715D MET* 3.0 23.5 + - + +
716D VAL* 4.1 4.9 - - + +
718D VAL* 1.3 77.0 - - + +
720D LEU* 1.3 57.5 + - - +
722D MET* 3.3 31.8 + - + +
723D LEU* 3.0 28.9 + - - +
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Residues in contact with LEU 720 (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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630C THR* 5.5 2.5 - - - +
634C ILE* 5.0 6.5 - - + -
722C MET* 4.0 22.7 - - + -
723C LEU* 4.2 25.1 - - + -
726C MET* 3.7 33.9 - - + -
716D VAL* 3.0 26.4 + - + +
717D ILE* 3.9 8.5 - - + +
719D LEU* 1.3 73.8 - - - +
721D ASN* 1.3 63.8 + - + +
723D LEU* 3.4 8.7 + - + +
724D ILE* 3.0 41.6 + - + +
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Residues in contact with ASN 721 (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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623C LEU 4.8 0.4 + - - -
626C SER* 3.3 26.9 + - - +
627C LEU* 3.5 37.6 - - + +
630C THR* 3.9 22.4 - - - +
637D PHE* 3.9 18.7 - - - -
717D ILE* 2.9 19.0 + - + +
718D VAL* 3.7 5.9 + - - +
720D LEU* 1.3 80.3 - - - +
722D MET* 1.3 55.6 + - - +
724D ILE* 3.9 5.9 - - - +
725D ALA* 2.9 30.1 + - - +
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Residues in contact with MET 722 (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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716A VAL* 6.3 2.5 - - + -
720A LEU* 4.0 26.9 - - + -
634D ILE* 4.2 24.5 - - + +
637D PHE* 3.9 43.3 - - + -
641D PHE* 6.4 0.9 - - - -
718D VAL* 3.0 18.1 + - + +
719D LEU* 3.6 32.3 - - + +
721D ASN* 1.3 78.1 - - - +
723D LEU* 1.3 56.3 + - - +
725D ALA* 3.4 1.7 + - - +
726D MET* 2.9 47.1 + - - +
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Residues in contact with LEU 723 (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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720A LEU* 4.2 26.0 - - + -
723A LEU* 4.1 24.9 - - + -
724A ILE* 4.4 9.4 - - + -
723C LEU* 4.1 30.7 - - + -
727C ILE* 5.6 0.2 - - + -
719D LEU 3.0 16.5 + - - +
720D LEU* 3.8 6.7 - - + +
721D ASN 3.4 0.2 - - - -
722D MET* 1.3 77.0 - - - +
724D ILE* 1.3 58.2 + - - +
726D MET* 3.4 5.0 + - - +
727D ILE* 2.9 51.3 + - + +
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Residues in contact with ILE 724 (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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630C THR* 5.5 7.9 - - + -
723C LEU* 4.4 11.9 - - + -
726C MET* 3.8 48.0 - - + +
727C ILE* 3.9 20.6 - - + +
730C SER* 3.8 25.4 - - - +
720D LEU* 3.0 31.6 + - + +
721D ASN* 4.0 6.7 - - - +
723D LEU* 1.3 76.8 - - + +
725D ALA* 1.3 59.0 + - - +
727D ILE* 3.3 7.7 + - - +
728D ASN* 2.9 28.0 + - + +
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Residues in contact with ALA 725 (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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626C SER* 5.4 6.3 - - - +
637D PHE* 3.8 27.1 - - + -
721D ASN* 2.9 23.2 + - - +
722D MET 3.8 0.9 - - - +
723D LEU 3.3 0.2 - - - -
724D ILE* 1.3 77.4 - - - +
726D MET* 1.3 58.2 + - - +
728D ASN* 3.7 5.8 - - - +
729D SER* 2.9 30.5 + - - -
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Residues in contact with MET 726 (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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720A LEU* 3.7 29.4 - - + -
724A ILE* 3.8 19.3 - - + +
630D THR* 3.7 34.8 - - + +
633D ASP* 4.2 25.0 - - + +
634D ILE* 3.6 22.9 - - + -
637D PHE* 5.0 4.5 - - + -
722D MET* 2.9 32.5 + - + +
723D LEU* 4.0 1.6 - - - +
725D ALA* 1.3 75.5 - - - +
727D ILE* 1.3 64.8 + - - +
729D SER* 3.6 13.1 + - - +
730D SER* 3.2 19.4 + - - -
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Residues in contact with ILE 727 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A LEU* 5.6 0.2 - - + -
724A ILE* 3.9 23.3 - - + -
727A ILE* 3.8 32.5 - - + -
727C ILE* 3.8 41.1 - - + -
731C PHE* 4.5 8.3 - - + -
723D LEU* 2.9 37.6 + - + +
724D ILE* 3.3 5.4 + - + +
726D MET* 1.3 77.8 - - - +
728D ASN* 1.3 62.1 + - - +
730D SER* 3.5 8.2 + - - -
731D PHE* 3.4 32.2 - - + -
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Residues in contact with ASN 728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730C SER* 4.0 28.4 + - - +
731C PHE* 3.4 35.6 - - + +
724D ILE* 2.9 17.3 + - + +
725D ALA* 3.7 7.2 - - - +
727D ILE* 1.3 79.5 - - - +
729D SER* 1.3 57.2 + - - +
730D SER 3.1 4.7 + - - -
731D PHE* 3.6 4.9 + - - +
732D GLN* 3.4 28.9 + - - +
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Residues in contact with SER 729 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D ASP* 3.9 19.2 + - - +
725D ALA 2.9 19.5 + - - -
726D MET* 3.6 11.5 + - - +
727D ILE 3.4 0.4 - - - -
728D ASN* 1.3 74.2 - - - +
730D SER* 1.3 62.7 + - - +
731D PHE 3.9 0.2 - - - -
732D GLN* 4.3 13.2 - - - -
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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) + - + + + + + -
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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