Contacts of the helix formed by residues 709 - 737 (chain A) in PDB entry 4V1M
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 THR 709 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ALA* 4.1 0.2 - - - -
708A MET* 1.4 75.9 - - - +
710A LEU* 1.3 68.3 + - - +
711A ARG* 3.5 17.3 - - + +
712A GLU* 2.9 35.2 + - + +
713A SER* 3.0 21.3 + - - -
1281A ARG* 5.0 2.0 + - - +
93I LYS* 3.2 36.6 + - - +
94I ASP* 3.3 19.6 + - - +
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Residues in contact with LEU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ALA* 5.5 2.7 - - - +
700A ASN* 3.9 15.9 - - - +
702A LEU* 3.4 44.0 - - + +
703A THR* 4.3 0.7 - - - -
704A ALA* 3.4 30.4 - - + +
708A MET 3.9 1.0 + - - -
709A THR* 1.3 74.4 - - - +
711A ARG* 1.4 56.8 + - + +
713A SER* 3.4 4.4 - - - -
714A PHE* 3.1 26.3 + - - +
94I ASP 4.2 11.5 + - - +
95I THR 4.9 2.2 - - - +
96I SER* 3.8 29.4 - - - -
97I MET* 4.2 8.5 - - + +
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Residues in contact with ARG 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A THR* 3.5 8.0 - - + +
710A LEU* 1.4 72.9 - - + +
712A GLU* 1.4 65.0 + - - +
714A PHE* 3.0 4.8 + - + +
715A GLU* 2.9 30.1 + - + +
792A TYR* 4.0 11.0 + - - -
87I GLN* 2.9 43.0 + - - +
88I SER 5.1 3.2 + - - -
90I GLN 5.5 0.2 + - - -
92I ARG 4.1 7.5 + - - -
93I LYS 3.9 9.2 - - - -
95I THR* 3.2 51.0 + - - +
96I SER 3.9 9.8 + - - -
97I MET* 3.6 31.6 - - + +
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Residues in contact with GLU 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A MET* 3.3 20.7 - - + +
709A THR* 2.9 46.1 + - - +
711A ARG* 1.4 76.1 - - - +
713A SER* 1.4 62.4 + - - +
715A GLU* 3.5 5.9 + - - +
716A ASP* 3.1 24.1 + - - +
1281A ARG* 3.2 29.0 + - - -
93I LYS* 5.4 8.5 + - - -
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Residues in contact with SER 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A LEU* 5.0 4.5 - - - -
704A ALA* 3.6 11.2 - - - -
705A LYS* 3.1 36.1 + - - +
708A MET* 3.5 19.8 - - - +
709A THR 3.0 18.9 + - - -
710A LEU 3.4 5.8 - - - -
712A GLU* 1.4 76.3 - - - +
714A PHE* 1.4 59.2 + - - +
716A ASP* 3.4 5.5 - - - +
717A ASN* 3.0 28.8 + - - -
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Residues in contact with PHE 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A VAL* 3.7 22.4 - - + -
694A THR* 3.4 41.7 - - + -
697A ALA* 4.1 8.1 - - + -
702A LEU* 3.8 8.4 - - + +
710A LEU 3.1 7.6 + - - +
711A ARG* 3.0 10.6 + - - +
713A SER* 1.4 72.8 - - - +
715A GLU* 1.4 99.5 + - + +
717A ASN* 2.9 22.0 + - - +
718A VAL* 3.0 33.9 + - + +
774A ARG* 4.9 0.2 - - - -
792A TYR* 4.2 25.4 - + + -
97I MET* 3.6 35.0 - - + -
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Residues in contact with GLU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A ARG* 2.9 22.3 + - + +
712A GLU* 3.9 6.1 - - - +
714A PHE* 1.4 90.5 - - + +
716A ASP* 1.4 63.7 + - - +
718A VAL* 3.4 3.2 + - - +
719A VAL* 3.0 31.6 + - + +
773A LYS* 5.6 2.3 - - - +
774A ARG* 2.7 54.9 + - - +
792A TYR* 4.0 12.6 - - + -
797A LYS* 3.9 13.5 + - - +
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Residues in contact with ASP 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LYS* 2.9 23.7 + - - +
708A MET* 4.9 9.9 - - - -
712A GLU 3.1 14.0 + - - +
713A SER* 3.4 11.9 - - - +
715A GLU* 1.4 75.1 - - - +
717A ASN* 1.4 55.2 + - - +
719A VAL* 3.6 8.5 + - - +
720A ARG* 3.0 51.3 + - - +
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Residues in contact with ASN 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A VAL* 4.3 16.5 - - + +
702A LEU* 5.0 6.5 - - - +
705A LYS* 2.8 25.4 + - - +
713A SER* 3.0 23.1 + - - -
714A PHE* 2.9 11.4 + - - +
716A ASP* 1.4 72.0 - - - +
718A VAL* 1.3 52.6 + - - +
720A ARG* 3.0 34.9 + - - +
721A PHE* 2.9 51.9 + - + -
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Residues in contact with VAL 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A VAL* 3.7 36.3 - - + +
693A VAL* 5.1 3.6 - - + -
714A PHE* 3.0 53.3 + - + +
715A GLU* 3.7 2.7 - - - +
717A ASN* 1.3 73.0 - - + +
719A VAL* 1.4 55.5 + - - +
721A PHE* 3.1 6.7 + - - +
722A LEU* 3.0 44.4 + - + +
774A ARG* 3.5 27.4 - - - +
792A TYR 4.8 2.0 - - - +
794A PRO* 5.5 0.7 - - + -
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Residues in contact with VAL 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A GLU* 3.0 21.5 + - + +
716A ASP* 3.7 8.3 - - - +
718A VAL* 1.4 74.3 - - - +
720A ARG* 1.3 62.1 + - - +
722A LEU* 3.7 7.3 + - - +
723A ASN* 3.0 45.7 + - - +
767A GLN* 4.9 7.9 - - + -
773A LYS* 6.2 0.9 - - - -
774A ARG* 3.6 36.3 - - + +
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Residues in contact with ARG 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LYS* 4.1 1.8 - - - +
716A ASP* 3.0 41.1 + - - +
717A ASN* 3.0 40.3 + - - +
719A VAL* 1.3 76.6 - - + +
721A PHE* 1.4 87.5 + - - +
723A ASN* 3.4 5.4 + - - +
724A GLU* 3.0 51.5 + - + +
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Residues in contact with PHE 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ALA* 4.4 9.6 - - + +
689A LYS* 3.7 43.7 - - + -
690A VAL* 3.7 26.0 - - + -
693A VAL* 3.5 34.3 - - + -
717A ASN* 2.9 27.7 + - + -
718A VAL* 3.1 4.2 + - - +
720A ARG* 1.4 99.3 - - - +
722A LEU* 1.3 58.3 + - - +
724A GLU* 3.3 24.0 - - - +
725A ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ALA* 5.5 7.4 - - + +
687A LYS* 5.7 4.5 - - + -
690A VAL* 4.3 10.8 - - + -
718A VAL* 3.0 35.9 + - + +
719A VAL* 3.9 7.9 - - - +
721A PHE* 1.3 79.1 - - - +
723A ASN* 1.3 61.1 + - - +
725A ALA* 3.3 7.4 - - + +
726A ARG* 3.1 21.8 + - - +
767A GLN* 3.5 26.5 - - + +
774A ARG* 4.7 2.5 - - - +
794A PRO* 3.7 32.3 - - + -
799A PHE* 3.7 39.2 - - + -
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Residues in contact with ASN 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A VAL* 3.0 33.0 + - - +
720A ARG* 3.4 5.6 + - - +
721A PHE 3.2 0.2 - - - -
722A LEU* 1.3 74.6 - - - +
724A GLU* 1.4 65.8 + - - +
725A ALA 3.0 2.2 + - - -
726A ARG* 3.0 33.3 + - - +
727A ASP* 3.0 32.9 + - - +
767A GLN* 3.8 21.6 + - - +
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Residues in contact with GLU 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A LYS* 3.4 25.6 + - - +
720A ARG* 3.0 39.7 + - + +
721A PHE* 3.3 21.9 - - - +
723A ASN* 1.4 73.2 - - - +
725A ALA* 1.4 55.8 + - - +
727A ASP* 3.8 8.2 + - - +
728A LYS* 3.0 29.6 + - - +
731A ARG* 4.2 4.0 + - - -
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Residues in contact with ALA 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A THR* 4.2 10.2 - - + +
683A ILE* 5.1 7.9 - - + -
686A ALA* 3.7 24.5 - - + -
721A PHE 3.0 14.1 + - - +
722A LEU* 3.3 13.0 - - + +
724A GLU* 1.4 72.1 - - - +
726A ARG* 1.4 67.7 + - - +
727A ASP 3.1 0.9 - - - -
728A LYS* 3.0 9.6 + - - +
729A ALA* 3.0 25.7 + - - +
799A PHE* 5.1 6.7 - - + -
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Residues in contact with ARG 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A LEU 3.1 9.8 + - - +
723A ASN* 3.0 41.1 + - - +
725A ALA* 1.4 77.2 - - - +
727A ASP* 1.3 82.6 + - - +
729A ALA* 3.6 4.3 - - - +
730A GLY* 3.0 24.4 + - - -
755A PHE* 5.7 0.6 - - - -
756A ILE* 3.4 28.2 - - - +
759A ALA* 4.7 7.6 - - + +
760A GLN* 4.7 6.1 - - - +
764A CYS* 3.8 28.5 - - - +
765A VAL 3.2 25.4 - - - -
766A GLY* 3.5 15.7 - - - -
767A GLN 4.6 4.0 + - - +
799A PHE* 5.2 0.6 - - - -
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Residues in contact with ASP 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A ASN* 3.0 23.9 + - - +
724A GLU* 3.9 7.0 + - - +
726A ARG* 1.3 104.9 + - - +
728A LYS* 1.3 55.0 + - - +
730A GLY* 3.1 1.0 + - - -
731A ARG* 2.8 51.9 + - - +
755A PHE* 3.6 20.0 - - + -
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Residues in contact with LYS 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A THR* 3.7 21.5 - - + +
685A GLU* 3.6 30.0 + - - -
724A GLU 3.0 19.0 + - - +
725A ALA* 3.0 7.2 + - - +
727A ASP* 1.3 74.9 - - - +
729A ALA* 1.4 52.4 + - - +
731A ARG* 3.2 28.6 + - - +
732A LEU* 2.9 44.7 + - + +
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Residues in contact with ALA 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ILE* 3.4 25.7 - - + +
682A THR* 4.2 7.5 - - + +
683A ILE* 4.9 5.6 - - + -
725A ALA 3.0 16.5 + - - +
726A ARG 3.6 5.6 - - - +
728A LYS* 1.4 74.1 - - - +
730A GLY* 1.3 62.9 + - - +
732A LEU* 3.4 26.3 - - - +
733A ALA 3.4 1.9 + - - -
763A ALA* 3.3 20.5 - - + +
764A CYS* 4.4 10.8 - - + -
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Residues in contact with GLY 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A ARG 3.0 11.4 + - - -
727A ASP 3.1 3.6 + - - -
729A ALA* 1.3 72.0 - - - +
731A ARG* 1.4 55.7 + - - +
732A LEU 3.0 3.4 - - - -
733A ALA* 2.9 22.7 + - - +
734A GLU* 3.0 12.6 + - - +
755A PHE* 3.6 7.6 - - - -
758A ILE* 5.0 0.5 - - - +
759A ALA* 3.6 34.9 - - - -
763A ALA* 4.0 3.7 - - - +
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Residues in contact with ARG 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A GLU 4.2 4.9 + - - -
727A ASP* 2.8 25.9 + - - +
728A LYS* 3.2 45.8 + - - +
730A GLY* 1.4 68.9 - - - +
732A LEU* 1.3 60.4 + - - +
734A GLU* 3.6 17.7 - - - +
735A VAL* 3.3 29.1 + - + +
755A PHE* 3.4 18.9 - - + -
----------------------------------------------------------
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Residues in contact with LEU 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A THR* 3.9 8.2 - - + +
678A GLU* 3.4 39.9 - - + +
679A ILE* 3.7 25.4 - - + -
682A THR* 3.6 24.7 - - + +
728A LYS* 2.9 25.4 + - + +
729A ALA* 3.4 11.0 - - - +
730A GLY 3.0 0.4 + - - -
731A ARG* 1.3 74.3 - - - +
733A ALA* 1.4 62.5 + - - +
735A VAL* 3.4 7.4 + - - +
736A ASN* 3.1 22.0 + - - +
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Residues in contact with ALA 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA* 4.4 8.5 - - + -
675A THR* 4.1 10.5 - - - +
679A ILE* 4.3 10.7 - - + +
729A ALA 3.4 6.4 + - - +
730A GLY* 2.9 8.6 + - - +
732A LEU* 1.4 74.7 - - - +
734A GLU* 1.4 55.0 + - - +
736A ASN* 2.9 23.2 + - - +
737A LEU* 2.9 23.8 + - + +
758A ILE* 4.6 4.5 - - + +
762A SER* 4.0 27.1 - - - -
763A ALA* 4.4 4.0 - - + -
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Residues in contact with GLU 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A GLY 3.0 13.2 + - - +
731A ARG* 3.6 19.0 - - - +
733A ALA* 1.4 74.9 - - - +
735A VAL* 1.3 65.3 + - + +
737A LEU* 3.8 6.4 + - - +
744A LYS* 3.4 32.2 + - + +
755A PHE* 3.3 42.2 - - + +
758A ILE* 4.2 27.2 - - + +
----------------------------------------------------------
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Residues in contact with VAL 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A ARG* 3.3 19.0 + - + +
732A LEU* 3.4 6.2 + - - +
733A ALA 3.1 0.4 - - - -
734A GLU* 1.3 84.5 - - + +
736A ASN* 1.3 62.7 + - - +
737A LEU 3.3 8.8 + - - +
744A LYS* 4.2 2.3 + - - +
19H ARG* 4.2 12.6 + - - -
----------------------------------------------------------
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Residues in contact with ASN 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA* 3.7 12.3 - - - +
672A ASP* 3.0 52.6 + - - +
675A THR* 3.1 24.5 + - + +
732A LEU 3.1 13.0 + - - +
733A ALA 2.9 6.7 + - - +
735A VAL* 1.3 73.4 - - - +
737A LEU* 1.3 65.3 + - - +
738A LYS* 3.5 12.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASP 4.2 7.6 - - - +
670A ILE 3.5 23.6 - - - +
671A ALA* 4.4 12.3 - - + -
733A ALA 2.9 18.9 + - - +
734A GLU* 4.2 3.1 - - - +
735A VAL 3.3 4.3 - - - +
736A ASN* 1.3 80.0 - - - +
738A LYS* 1.3 58.8 + - - +
741A ASN* 3.5 38.6 - - + +
743A VAL* 5.9 0.4 - - + -
744A LYS* 2.8 40.9 + - + +
758A ILE* 3.7 35.7 - - + -
762A SER* 4.4 6.7 - - - +
19H ARG* 4.3 0.9 + - - -
----------------------------------------------------------
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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