Contacts of the helix formed by residues 710 - 737 (chain D) in PDB entry 1P93
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 GLN 710 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708D SER 3.1 19.0 + - - -
709D SER* 1.3 84.1 + - - +
711D ASN* 1.3 55.4 + - - +
712D TRP* 2.5 23.2 + - + +
713D GLN* 2.8 38.6 + - + +
714D ARG* 4.4 7.1 + - - +
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Residues in contact with ASN 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D ILE* 3.3 18.1 + - + +
702D VAL* 3.2 39.4 - - + +
704D ARG 4.6 2.1 + - - +
708D SER* 2.7 44.0 - - - -
709D SER 2.8 11.8 + - - +
710D GLN* 1.3 73.0 + - - +
712D TRP* 1.3 56.6 + - + +
713D GLN 3.3 0.4 - - - -
714D ARG* 3.4 10.1 + - - +
715D PHE* 3.1 24.9 + - - +
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Residues in contact with TRP 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709D SER 6.1 0.4 - - - -
710D GLN* 2.5 13.4 + - - +
711D ASN* 1.3 71.9 - - + +
713D GLN* 1.3 58.4 + - - +
715D PHE* 3.3 34.9 - + + +
716D TYR* 3.2 21.3 + - - +
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Residues in contact with GLN 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710D GLN* 2.8 36.3 + - + +
712D TRP* 1.3 71.3 - - - +
714D ARG* 1.3 66.7 + - - +
715D PHE 3.2 0.2 - - - -
716D TYR* 3.0 17.9 + - + +
717D GLN* 3.0 34.9 + - + +
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Residues in contact with ARG 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D LEU* 2.8 33.9 + - - +
657D GLN* 5.0 0.6 - - - +
658D VAL* 3.5 9.5 - - - +
662D GLU* 2.6 32.1 + - - -
701D ILE* 3.1 31.2 - - + -
704D ARG* 2.8 31.4 - - - +
710D GLN* 3.9 5.9 + - - +
711D ASN* 3.4 16.2 + - - +
713D GLN* 1.3 74.5 - - - +
715D PHE* 1.3 68.1 + - - +
716D TYR 3.0 0.7 + - - -
717D GLN* 3.2 18.7 + - - +
718D LEU* 3.1 43.4 + - + +
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Residues in contact with PHE 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D ILE* 4.2 35.7 - - + -
697D LEU* 5.1 9.4 - - + -
698D GLY* 5.1 9.2 - - - -
701D ILE* 3.9 21.1 - - + +
711D ASN 3.1 10.0 + - - +
712D TRP* 3.3 39.3 - + + +
714D ARG* 1.3 82.3 - - - +
716D TYR* 1.3 63.3 + - - +
718D LEU* 4.1 1.5 - - - +
719D THR* 2.8 48.7 + - + -
774D PHE* 6.0 3.4 - + - -
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Residues in contact with TYR 716 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712D TRP 3.2 9.3 + - - +
713D GLN* 3.0 15.7 + - + +
715D PHE* 1.3 82.6 - - - +
717D GLN* 1.3 75.9 + - + +
719D THR* 3.2 6.0 + - - -
720D LYS* 3.1 49.2 + - + +
775D HIS* 3.8 30.1 - + - -
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Residues in contact with GLN 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655D ARG* 5.0 11.1 + - - +
656D LEU* 3.7 34.6 - - + +
713D GLN* 3.0 34.7 + - + +
714D ARG* 3.8 18.4 + - - +
716D TYR* 1.3 89.2 - - + +
718D LEU* 1.3 63.7 + - + +
720D LYS* 3.9 3.5 + - - +
721D LEU* 3.8 15.9 + - - +
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Residues in contact with LEU 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D LEU* 4.8 8.1 - - + -
658D VAL* 4.1 15.5 - - + -
662D GLU* 3.9 15.5 - - + +
666D MET* 4.2 16.1 - - + +
697D LEU* 4.2 21.3 - - + -
701D ILE* 3.2 38.8 - - + -
714D ARG* 3.1 45.6 + - - +
715D PHE* 4.1 2.5 - - - +
717D GLN* 1.3 79.7 - - + +
719D THR* 1.3 64.0 + - - +
721D LEU* 3.1 23.6 - - + +
722D LEU* 3.5 10.7 + - - +
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Residues in contact with THR 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697D LEU* 5.5 4.7 - - - +
715D PHE* 2.8 44.5 + - + -
716D TYR* 3.2 4.8 + - - -
718D LEU* 1.3 74.7 - - - +
720D LYS* 1.3 51.3 + - - +
721D LEU 2.8 10.5 + - - -
722D LEU* 2.9 18.7 + - - +
723D ASP* 2.5 20.8 + - - +
774D PHE* 2.9 47.3 - - + -
775D HIS* 3.2 14.1 - - + +
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Residues in contact with LYS 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716D TYR* 3.1 41.0 + - + +
717D GLN* 4.4 4.0 - - - +
718D LEU 3.5 0.2 - - - -
719D THR* 1.3 77.2 - - - +
721D LEU* 1.3 59.3 + - - +
723D ASP* 3.2 33.2 - - - +
724D SER* 3.5 16.3 + - - +
775D HIS* 3.1 46.4 + - + +
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Residues in contact with LEU 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D PHE* 4.5 12.8 - - + -
648D TYR* 3.9 22.4 - - + +
649D VAL* 6.1 4.0 - - + -
652D GLU* 4.0 26.5 - - + +
653D LEU* 5.2 8.7 - - + -
656D LEU* 5.8 6.1 - - + -
658D VAL* 5.7 4.5 - - + -
666D MET* 3.7 25.6 - - + -
717D GLN 3.8 10.3 + - - +
718D LEU* 3.1 12.3 + - + +
719D THR 2.8 1.2 + - - -
720D LYS* 1.3 76.3 - - - +
722D LEU* 1.3 60.9 + - + +
723D ASP 3.0 1.8 - - - -
724D SER* 2.7 32.6 + - - +
725D MET* 3.3 16.1 + - - +
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Residues in contact with LEU 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D PHE* 4.8 3.8 - - + -
666D MET* 3.4 38.6 - - + +
669D LEU* 3.6 43.5 - - + -
670D LEU* 3.8 21.8 - - + -
673D SER* 4.1 5.3 + - - +
697D LEU* 5.2 2.0 - - + -
718D LEU 3.5 9.2 + - - +
719D THR* 2.9 11.7 + - - +
721D LEU* 1.3 79.8 - - + +
723D ASP* 1.3 60.8 + - - +
725D MET* 3.4 21.3 - - + +
726D HIS* 3.9 10.6 + - - -
774D PHE* 3.6 23.8 - - + -
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Residues in contact with ASP 723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719D THR 2.5 27.9 - - - +
720D LYS* 3.2 32.6 - - - +
721D LEU 3.0 0.4 - - - -
722D LEU* 1.3 73.2 - - - +
724D SER* 1.3 67.2 - - - +
725D MET 3.0 3.2 + - - -
726D HIS* 3.3 22.0 + - - +
727D GLU* 4.0 6.6 + - - +
773D LEU* 3.1 27.9 - - + +
774D PHE* 2.4 43.4 + - - -
775D HIS* 3.5 4.7 + - - -
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Residues in contact with SER 724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D TYR* 2.5 39.0 + - - -
720D LYS* 3.5 8.7 + - - +
721D LEU* 2.7 22.7 + - - -
723D ASP* 1.3 80.3 - - - +
725D MET* 1.3 53.1 + - - -
727D GLU* 2.9 25.5 + - - +
728D VAL* 2.9 23.6 + - - +
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Residues in contact with MET 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D SER* 3.8 36.1 - - - +
605D ALA* 4.3 15.9 - - + -
606D PHE* 4.0 17.7 - - + +
648D TYR* 5.5 0.2 - - - -
649D VAL* 4.6 13.5 - - + -
670D LEU* 3.7 26.0 - - + -
721D LEU* 3.3 21.3 + - - +
722D LEU* 3.4 20.4 - - + +
723D ASP 3.0 0.2 - - - -
724D SER* 1.3 72.6 - - - +
726D HIS* 1.3 60.8 + - + +
727D GLU 2.7 5.4 + - - -
728D VAL* 2.8 16.8 + - + -
729D VAL* 2.6 37.6 + - + +
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Residues in contact with HIS 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598D TYR* 2.9 33.9 + + - -
602D SER* 5.2 0.7 - - - -
673D SER* 3.1 45.1 + - - -
674D SER* 3.5 4.9 - - - -
722D LEU 3.9 8.8 + - - -
723D ASP* 3.3 16.5 + - - +
725D MET* 1.3 76.3 - - + +
727D GLU* 1.3 57.3 + - + +
729D VAL* 4.5 0.4 - - - -
730D GLU* 3.0 26.7 + - - +
771D LYS* 3.3 46.3 + - + +
772D LEU 3.0 28.1 + - - -
773D LEU* 4.3 4.3 - - + +
774D PHE* 6.0 0.7 - + - -
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Residues in contact with GLU 727 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723D ASP 4.3 5.5 - - - +
724D SER* 2.9 24.3 + - - +
725D MET 2.7 0.6 + - - -
726D HIS* 1.3 77.3 - - + +
728D VAL* 1.3 62.4 + - + +
730D GLU* 2.8 25.8 + - - +
731D ASN* 2.7 25.0 - - - +
771D LYS* 5.3 3.6 - - - +
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Residues in contact with VAL 728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D ALA* 4.9 2.9 - - + -
645D HIS* 3.5 28.5 - - + +
648D TYR* 3.3 33.0 - - + -
649D VAL* 4.2 12.8 - - + -
724D SER* 2.9 24.2 + - - +
725D MET* 2.8 23.5 + - + +
727D GLU* 1.3 74.7 - - + +
729D VAL* 1.3 64.4 + - - +
731D ASN* 3.2 15.8 + - - +
732D LEU* 3.4 24.3 + - + +
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Residues in contact with VAL 729 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598D TYR* 4.3 19.1 - - + +
601D MET* 3.9 18.4 - - + -
602D SER* 3.3 41.3 - - - +
605D ALA* 5.2 3.1 - - + -
725D MET* 2.6 29.0 + - + +
726D HIS 4.3 2.5 - - - +
728D VAL* 1.3 73.1 - - + +
730D GLU* 1.3 64.4 + - - +
732D LEU* 3.1 19.3 + - - +
733D LEU* 3.1 34.3 + - + +
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Residues in contact with GLU 730 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726D HIS 3.0 12.1 + - - +
727D GLU* 2.8 23.7 + - - +
729D VAL* 1.3 81.2 - - - +
731D ASN* 1.3 62.2 + - - +
733D LEU* 3.5 6.5 + - - +
734D ASN* 3.3 38.8 + - - +
764D TYR* 5.0 4.7 + - - +
771D LYS* 3.9 20.2 + - - +
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Residues in contact with ASN 731 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645D HIS* 4.1 37.7 + - + +
727D GLU 2.7 29.5 - - - +
728D VAL* 3.2 7.2 + - - +
730D GLU* 1.3 72.9 - - - +
732D LEU* 1.3 65.0 + - - +
733D LEU 2.9 6.3 + - - -
734D ASN* 3.1 12.0 + - - +
735D TYR* 3.0 25.7 + - + +
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Residues in contact with LEU 732 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D MET* 4.2 16.6 - - + -
605D ALA* 4.1 26.2 - - + -
642D GLN* 3.9 13.2 - - + +
645D HIS* 3.9 26.2 - - + +
646D MET* 4.2 15.0 - - + -
728D VAL* 3.7 20.0 - - + +
729D VAL* 3.1 9.9 + - - +
731D ASN* 1.3 77.8 - - - +
733D LEU* 1.3 52.6 - - - +
735D TYR* 3.7 5.9 - - + +
736D CYS* 2.7 34.5 + - - +
4999D DEX 3.7 36.4 - - + +
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Residues in contact with LEU 733 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598D TYR* 5.5 6.1 - - + +
600D TRP* 4.6 11.2 - - + +
601D MET* 3.5 31.9 - - + -
729D VAL* 3.1 36.8 + - + +
730D GLU* 3.8 5.8 - - - +
731D ASN 2.9 1.2 + - - -
732D LEU* 1.3 76.4 - - - +
734D ASN* 1.3 53.9 + - - +
735D TYR 2.7 8.0 + - - -
736D CYS* 3.4 5.4 - - + +
737D PHE* 2.5 38.0 + - - +
757D ILE* 6.2 0.2 - - + -
760D GLN* 5.2 3.8 - - - +
761D ILE* 3.9 26.5 - - + -
764D TYR* 4.1 27.8 - - + +
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Residues in contact with ASN 734 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730D GLU* 3.3 30.7 + - - +
731D ASN* 3.1 11.5 + - - +
733D LEU* 1.3 76.7 - - - +
735D TYR* 1.3 56.4 + - - +
737D PHE* 4.3 4.2 - - - +
738D GLN* 2.9 31.7 + - - +
761D ILE* 5.9 2.3 - - - +
764D TYR* 4.3 10.7 + - - -
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Residues in contact with TYR 735 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D ASP* 3.9 19.9 + - - +
641D ASP* 3.7 42.0 - - + +
642D GLN* 3.6 41.1 - - + -
645D HIS* 5.5 6.1 - + + -
731D ASN* 3.0 16.2 + - + +
732D LEU* 3.7 8.5 - - + +
733D LEU 2.7 0.6 - - - -
734D ASN* 1.3 80.9 - - - +
736D CYS* 1.3 60.9 + - - +
737D PHE 3.2 1.3 - - - -
738D GLN* 3.4 14.5 + - - +
739D THR* 3.0 37.1 + - + +
4999D DEX 4.3 4.0 - - + -
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Residues in contact with CYS 736 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D TRP* 4.9 2.9 - - - -
601D MET* 3.7 20.0 - - + -
732D LEU 2.7 24.1 + - - +
733D LEU* 3.0 9.4 + - - +
735D TYR* 1.3 71.7 - - - +
737D PHE* 1.3 66.0 + - - +
739D THR* 3.2 8.7 + - - -
740D PHE* 3.1 14.9 - - - +
749D PHE* 3.7 1.9 - - - -
757D ILE* 3.6 28.7 - - - -
761D ILE* 5.0 0.7 - - - -
4999D DEX 3.3 35.2 - - + +
----------------------------------------------------------
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Residues in contact with PHE 737 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733D LEU 2.5 22.1 + - - +
734D ASN* 4.7 4.0 - - - +
736D CYS* 1.3 74.9 - - - +
738D GLN* 1.3 61.3 + - + +
740D PHE* 2.9 23.0 + + - +
741D LEU* 2.8 50.6 - - + +
757D ILE* 3.2 29.2 - - + -
761D ILE* 3.0 47.3 - - + -
762D PRO* 3.6 27.1 - - + -
765D SER* 5.7 1.6 - - - -
----------------------------------------------------------
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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