Contacts of the helix formed by residues 789 - 825 (chain A) in PDB entry 5VOT
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 LEU 789 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A LEU 4.5 5.2 - - - +
788A SER* 1.3 82.6 + - - +
790A SER* 1.3 61.7 + - - +
791A ASN 3.7 0.9 - - - -
792A VAL* 3.9 24.2 - - + +
793A ALA* 4.2 5.5 + - - +
522D ALA* 5.6 7.4 - - + -
523D TYR 6.0 1.6 - - - +
525D ILE* 3.6 33.7 - - + +
528D CYS* 6.1 1.8 - - - -
157E ILE* 5.2 10.5 - - + +
158E SER* 5.2 18.6 - - - +
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Residues in contact with SER 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LYS* 6.2 2.5 - - - -
512A PRO 2.9 26.5 + - - -
513A GLY* 3.7 9.1 + - - +
516A SER* 3.4 10.5 + - - -
788A SER* 2.8 18.5 + - - -
789A LEU* 1.3 76.6 - - - +
791A ASN* 1.3 69.7 + - - +
792A VAL 3.2 0.5 + - - -
793A ALA* 3.4 6.2 + - - +
794A GLY* 2.9 17.3 + - - -
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Residues in contact with ASN 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLY 5.2 0.2 - - - -
516A SER* 3.3 38.6 + - - +
517A PHE* 3.6 9.0 + - + +
620A LEU* 6.4 0.4 - - - +
624A LEU* 4.5 20.0 - - - +
787A LEU* 6.3 1.6 - - - +
788A SER* 4.9 9.1 + - - +
790A SER* 1.3 80.3 - - - +
792A VAL* 1.3 65.7 + - + +
794A GLY* 2.8 14.6 + - - +
795A VAL* 3.0 19.0 + - - +
611D ILE* 5.1 19.4 - - + +
612D ILE* 6.0 3.1 - - + -
615D SER* 5.2 5.3 + - - -
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Residues in contact with VAL 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A SER 4.2 6.7 - - - +
789A LEU* 3.9 37.2 - - + +
790A SER 3.1 0.2 - - - -
791A ASN* 1.3 76.4 - - + +
793A ALA* 1.3 52.1 + - + +
795A VAL* 4.1 3.6 - - - +
796A PHE* 2.4 47.1 + - + +
521D LEU* 6.0 5.2 - - + +
525D ILE* 4.1 18.6 - - + +
528D CYS* 4.9 16.8 - - + -
529D ILE* 6.4 1.1 - - + -
608D PHE* 4.8 5.0 - - + -
612D ILE* 5.4 12.3 - - + +
154E ILE* 6.0 4.3 - - + -
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Residues in contact with ALA 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A LEU 4.2 4.6 + - - +
790A SER 3.4 5.8 + - - +
791A ASN 3.2 0.2 - - - -
792A VAL* 1.3 76.7 - - + +
794A GLY* 1.3 65.9 + - - +
795A VAL 2.9 4.7 + - - -
796A PHE* 3.6 9.0 - - + -
797A TYR* 2.9 65.1 + - + +
154E ILE* 6.0 3.4 - - + +
158E SER* 5.2 10.1 - - - -
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Residues in contact with GLY 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLY 4.1 4.5 - - - -
514A VAL* 3.2 54.5 - - - +
517A PHE* 4.4 7.3 - - - +
790A SER 2.9 12.7 + - - -
791A ASN* 2.8 10.7 + - - -
793A ALA* 1.3 76.9 - - - +
795A VAL* 1.3 56.7 + - - +
797A TYR* 5.5 0.2 - - - +
798A ILE* 4.5 5.2 - - - +
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Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 4.6 11.9 - - + +
791A ASN 3.0 16.1 + - - +
792A VAL 4.1 2.2 - - - +
794A GLY* 1.3 74.2 - - - +
796A PHE* 1.3 63.7 + - - +
797A TYR 3.2 2.5 - - - -
798A ILE* 2.8 31.1 + - + +
799A LEU* 3.0 10.3 + - + +
604D VAL* 6.4 1.1 - - + -
607D PHE* 4.1 32.8 - - + +
608D PHE* 3.9 22.4 - - + -
611D ILE* 3.7 33.2 - - + -
612D ILE* 5.0 2.5 - - + -
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Residues in contact with PHE 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A VAL* 2.4 41.8 + - + +
793A ALA* 3.0 3.3 + - - -
795A VAL* 1.3 79.4 - - - +
797A TYR* 1.3 70.5 + + - +
799A LEU* 2.9 33.2 + - + +
800A VAL* 2.9 37.1 + - + +
803A LEU* 6.2 0.4 - - + -
528D CYS* 4.9 9.9 - - + -
531D PHE* 6.1 1.3 - - + -
532D ALA* 3.4 33.4 - - + -
608D PHE* 4.3 13.2 - + + -
150E ILE* 5.3 6.3 - - + -
151E ILE* 4.4 11.0 - - + -
154E ILE* 3.9 29.4 - - + -
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Residues in contact with TYR 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A VAL* 4.4 19.1 - - + -
793A ALA* 2.9 42.3 + - + +
796A PHE* 1.3 85.6 - + - +
798A ILE* 1.3 64.5 + - + +
799A LEU 3.2 0.2 + - - -
800A VAL* 3.3 5.5 + - + +
801A GLY* 2.9 21.8 + - - -
154E ILE* 5.9 3.6 - - + -
155E VAL* 4.6 23.8 - - + +
158E SER* 4.4 12.5 + - - -
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Residues in contact with ILE 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A VAL* 4.8 11.0 - - + -
517A PHE* 5.7 5.6 - - + -
794A GLY 4.5 13.9 - - - +
795A VAL* 2.8 21.7 + - + +
797A TYR* 1.3 77.4 - - + +
799A LEU* 1.3 61.6 + - - +
801A GLY* 4.6 1.3 - - - +
802A GLY* 2.9 21.5 + - - -
604D VAL* 3.8 12.7 - - + +
607D PHE* 4.8 20.4 - - + -
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Residues in contact with LEU 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A VAL* 3.0 6.7 + - + +
796A PHE* 2.9 46.7 + - + +
798A ILE* 1.3 76.0 - - - +
800A VAL* 1.3 63.9 + - - +
802A GLY* 3.0 4.7 + - - -
803A LEU* 2.9 32.2 + - + +
532D ALA* 3.7 16.8 - - + -
536D VAL* 4.2 21.8 - - + -
604D VAL* 3.6 38.6 - - + +
605D TRP* 4.5 14.1 - - + -
608D PHE* 4.6 12.8 - - + -
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Residues in contact with VAL 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 2.9 43.0 + - + +
797A TYR* 4.0 5.4 - - + +
799A LEU* 1.3 73.5 - - - +
801A GLY* 1.3 59.8 + - - +
803A LEU* 2.8 37.6 + - + +
804A GLY* 3.0 12.2 + - - +
147E LEU* 5.2 9.4 - - + +
148E SER* 5.7 2.0 - - - -
151E ILE* 4.0 25.1 - - + +
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Residues in contact with GLY 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A TYR 2.9 15.9 + - - -
798A ILE* 3.9 2.0 - - - -
800A VAL* 1.3 77.5 - - - +
802A GLY* 1.3 55.6 + - - +
804A GLY* 3.5 1.5 + - - -
805A LEU* 2.9 29.0 + - - +
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Residues in contact with GLY 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A ILE 2.9 15.9 + - - -
799A LEU 3.0 3.8 + - - -
801A GLY* 1.3 75.3 - - - +
803A LEU* 1.3 63.0 + - - +
805A LEU* 3.2 14.4 - - - +
806A ALA* 2.9 24.9 + - - +
600D ILE* 4.4 8.1 - - - +
601D VAL* 5.6 0.8 - - - +
604D VAL* 4.8 14.6 - - - -
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Residues in contact with LEU 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 6.2 0.2 - - + -
799A LEU* 2.9 27.1 + - + +
800A VAL* 2.8 33.2 + - + +
802A GLY* 1.3 78.5 - - - +
804A GLY* 1.3 63.3 + - - +
806A ALA* 3.1 5.4 + - - +
807A MET* 2.9 26.2 + - + +
532D ALA* 6.5 0.9 - - - -
535D GLY* 5.8 1.8 - - - -
536D VAL* 3.9 37.9 - - + +
539D VAL* 4.8 21.6 - - + +
601D VAL* 5.3 9.2 - - + -
604D VAL* 5.3 3.6 - - + -
147E LEU* 4.8 17.5 - - + -
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Residues in contact with GLY 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A VAL* 3.0 11.8 + - - +
801A GLY* 4.0 1.8 - - - -
803A LEU* 1.3 75.7 - - - +
805A LEU* 1.3 62.5 + - - +
807A MET* 3.2 11.7 + - - +
808A LEU* 2.9 23.7 + - - +
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Residues in contact with LEU 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A GLY 2.9 16.1 + - - +
802A GLY* 3.2 12.6 - - - +
804A GLY* 1.3 77.1 - - - +
806A ALA* 1.3 64.2 + - - +
808A LEU* 3.1 9.4 + - + +
809A VAL* 2.9 36.2 + - + +
600D ILE* 4.2 26.7 - - + -
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Residues in contact with ALA 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A GLY 2.9 18.8 + - - +
803A LEU* 3.7 3.8 - - - +
805A LEU* 1.3 74.7 - - - +
807A MET* 1.3 63.5 + - - +
809A VAL* 3.1 9.9 + - - +
810A ALA* 2.9 26.2 + - - +
539D VAL* 5.6 1.3 - - + -
543D VAL* 4.8 8.6 - - + +
597D SER* 4.5 14.4 - - - +
600D ILE* 4.5 8.3 - - + -
601D VAL* 3.8 28.9 - - + -
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Residues in contact with MET 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LEU* 2.9 19.5 + - + +
804A GLY* 3.2 15.0 - - - +
806A ALA* 1.3 77.2 - - - +
808A LEU* 1.3 64.3 + - - +
810A ALA* 3.3 3.1 + - - +
811A LEU* 2.9 40.3 + - + +
539D VAL* 3.6 31.0 - - + -
542D LEU* 5.2 12.3 - - + -
543D VAL* 4.7 9.0 - - - -
140E ILE* 4.1 29.2 - - + +
143E VAL* 6.3 1.3 - - + -
144E SER* 4.2 25.6 - - - +
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Residues in contact with LEU 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A GLY 2.9 11.8 + - - +
805A LEU* 3.6 13.2 - - + +
807A MET* 1.3 75.8 - - - +
809A VAL* 1.3 69.0 + - + +
811A LEU* 4.3 9.4 - - - +
812A ILE* 2.9 49.7 + - + +
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Residues in contact with VAL 809 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A LEU* 2.9 33.3 + - + +
806A ALA* 3.1 12.3 + - - +
808A LEU* 1.3 82.1 - - + +
810A ALA* 1.3 65.3 + - - +
812A ILE* 4.3 0.8 - - - +
813A GLU* 2.9 34.2 + - + +
596D LEU* 4.8 8.5 - - + +
597D SER* 3.6 25.8 - - - -
600D ILE* 4.3 16.8 - - + -
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Residues in contact with ALA 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ALA 2.9 17.0 + - - +
807A MET* 4.0 2.5 - - - +
809A VAL* 1.3 74.7 - - - +
811A LEU* 1.3 66.4 + - + +
814A PHE* 2.9 49.9 + - + +
542D LEU* 6.3 1.3 - - + -
543D VAL* 3.9 33.7 - - + +
597D SER* 4.3 1.8 - - - +
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Residues in contact with LEU 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A MET* 2.9 42.1 + - + +
808A LEU* 3.7 7.9 - - - +
810A ALA* 1.3 75.9 - - + +
812A ILE* 1.3 64.7 + - + +
815A CYS* 2.9 39.6 + - + +
542D LEU* 6.1 4.5 - - + -
140E ILE* 4.5 20.2 - - + -
141E PHE* 6.0 5.2 - - + -
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Residues in contact with ILE 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A LEU* 2.9 43.8 + - + +
809A VAL* 4.3 0.9 - - - +
811A LEU* 1.3 78.2 - - + +
813A GLU* 1.3 54.0 + - - +
815A CYS* 5.0 1.6 - - + -
816A TYR* 2.6 46.8 + - + +
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Residues in contact with GLU 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A VAL* 2.9 24.4 + - + +
810A ALA 4.2 1.1 - - - +
812A ILE* 1.3 78.8 - - - +
814A PHE* 1.3 70.1 + - + +
816A TYR* 3.2 18.1 - - - +
817A LYS* 2.9 26.4 + - + +
596D LEU* 4.5 23.3 - - + +
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Residues in contact with PHE 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A ALA* 2.9 43.6 + - + +
813A GLU* 1.3 88.8 - - + +
815A CYS* 1.3 62.4 + - - +
816A TYR 3.1 0.7 - - - -
817A LYS* 3.1 8.4 + - + +
818A SER* 2.9 32.6 + - - -
543D VAL 5.4 6.1 - - - -
546D PHE 5.2 4.5 - - - +
547D SER* 3.9 38.9 - - - +
595D SER* 4.1 20.9 - - - -
596D LEU* 5.4 5.4 - - + -
597D SER* 4.3 13.0 - - - -
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Residues in contact with CYS 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A LEU* 2.9 22.1 + - + +
812A ILE* 4.6 1.3 - - - +
814A PHE* 1.3 75.4 - - - +
816A TYR* 1.3 58.9 + - - +
818A SER* 5.1 2.5 - - - -
819A ARG* 2.8 43.8 + - - +
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Residues in contact with TYR 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A ILE* 2.6 30.7 + - + +
813A GLU* 3.2 18.8 - - - +
815A CYS* 1.3 75.8 - - - +
817A LYS* 1.3 62.2 + - + +
819A ARG* 4.1 2.1 - - - +
820A ALA* 2.9 45.2 + - + +
----------------------------------------------------------
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Residues in contact with LYS 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A GLU* 2.9 17.5 + - + +
814A PHE* 3.1 12.7 + - + +
816A TYR* 1.3 82.5 - - + +
818A SER* 1.3 64.3 + - - +
820A ALA* 3.1 3.5 + - - +
821A GLU* 2.9 30.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 818 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A PHE 2.9 18.2 + - - -
815A CYS* 4.6 2.2 - - - -
817A LYS* 1.3 73.8 - - - +
819A ARG* 1.3 58.2 + - - +
821A GLU* 5.3 1.6 - - - -
822A ALA* 2.8 43.2 + - - +
547D SER 5.0 11.0 - - - -
548D PRO 5.9 2.1 - - - -
----------------------------------------------------------
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Residues in contact with ARG 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A CYS* 2.8 31.5 + - - +
816A TYR* 4.1 1.8 - - - +
818A SER* 1.3 78.1 + - - +
820A ALA* 1.3 53.0 + - - +
822A ALA* 4.9 0.4 - - - -
823A LYS* 2.6 41.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A TYR* 2.9 35.8 + - + +
817A LYS* 3.6 3.4 - - - +
819A ARG* 1.3 73.8 - - - +
821A GLU* 1.3 59.8 + - - +
823A LYS* 4.0 1.6 - - - +
824A ARG* 2.9 33.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A LYS 2.9 17.3 + - - +
818A SER* 4.7 1.3 - - - +
820A ALA* 1.3 74.9 - - - +
822A ALA* 1.3 54.6 + - - +
824A ARG* 4.7 2.5 - - - -
825A MET* 2.7 76.0 + - + +
----------------------------------------------------------
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Residues in contact with ALA 822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A SER* 2.8 29.1 + - - +
819A ARG* 4.9 0.9 - - - -
821A GLU* 1.3 79.1 - - - +
823A LYS* 1.3 57.1 + - - +
825A MET* 2.7 26.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 823 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A ARG* 2.6 25.4 + - + +
820A ALA* 4.0 2.0 - - - +
822A ALA* 1.3 79.0 - - - +
824A ARG* 1.3 63.6 + - - +
825A MET 3.3 5.7 - - - +
----------------------------------------------------------
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Residues in contact with ARG 824 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A ALA 2.9 18.5 + - - +
821A GLU* 3.8 3.8 - - - +
823A LYS* 1.3 79.5 - - - +
825A MET* 1.3 64.6 + - + +
----------------------------------------------------------
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Residues in contact with MET 825 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A GLU* 2.7 56.0 + - + +
822A ALA* 2.7 20.8 - - - +
823A LYS 3.3 4.7 - - - +
824A ARG* 1.3 79.9 - - + +
----------------------------------------------------------
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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