Contacts of the helix formed by residues 672 - 699 (chain A) in PDB entry 6UPX
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 ASP 672 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A ALA* 1.3 81.7 - - - +
673A GLY* 1.3 60.4 + - - +
674A PRO* 4.1 10.7 - - + +
675A THR* 3.3 17.7 - - - +
676A MET* 2.9 28.5 + - - +
736A ASN* 2.5 35.9 + - - +
738A LYS* 5.2 10.8 + - - -
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Residues in contact with GLY 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA 3.9 0.4 + - - -
672A ASP* 1.3 69.4 - - - +
674A PRO* 1.3 68.5 - - - +
676A MET* 3.3 7.1 + - - +
677A ARG* 2.9 29.0 + - - +
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Residues in contact with PRO 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ASP* 4.0 10.1 - - + +
673A GLY* 1.3 87.9 - - - +
675A THR* 1.3 59.0 + - - +
677A ARG* 3.4 8.8 + - + +
678A GLU* 2.9 29.7 + - - +
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Residues in contact with THR 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA* 4.1 8.5 - - + -
672A ASP* 3.3 13.3 + - - +
673A GLY 3.2 0.8 - - - -
674A PRO* 1.3 74.9 - - - +
676A MET* 1.3 60.5 + - - +
678A GLU* 3.4 9.4 + - - +
679A ILE* 2.9 39.4 + - + +
732A LEU* 3.3 35.9 - - + +
736A ASN* 2.3 41.7 + - + -
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Residues in contact with MET 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A THR 5.0 1.3 - - - +
670A ILE* 5.4 1.8 - - + -
671A ALA* 4.6 24.5 - - + +
672A ASP 2.9 20.9 + - - +
673A GLY* 3.3 6.7 + - - +
675A THR* 1.3 75.5 - - - +
677A ARG* 1.3 59.1 + - - +
679A ILE* 3.2 19.5 + - - +
680A THR* 2.9 31.1 + - - +
762A SER* 3.2 29.6 - - - +
763A ALA 5.6 0.4 - - - +
805A LEU* 4.4 19.7 - - + -
806A ARG* 3.8 34.1 + - - +
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Residues in contact with ARG 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A GLY 2.9 16.7 + - - +
674A PRO* 3.7 8.1 - - + +
676A MET* 1.3 78.2 - - - +
678A GLU* 1.3 56.5 + - - +
680A THR* 3.2 13.8 - - + +
681A GLU* 2.9 31.4 + - + +
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Residues in contact with GLU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A PRO 2.9 18.7 + - - +
675A THR* 3.8 9.6 + - - +
676A MET 3.3 0.2 - - - -
677A ARG* 1.3 76.3 - - - +
679A ILE* 1.3 58.0 + - - +
681A GLU* 2.8 34.7 - - - +
682A THR* 2.9 16.2 + - - +
732A LEU* 3.5 35.0 - - + +
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Residues in contact with ILE 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA* 5.4 1.6 - - + -
675A THR* 2.9 27.8 + - + +
676A MET* 3.2 19.0 + - - +
678A GLU* 1.3 76.4 - - - +
680A THR* 1.3 60.8 + - - +
682A THR* 3.2 6.3 + - - -
683A ILE* 3.0 34.5 + - + +
729A ALA* 3.4 41.1 - - + +
732A LEU* 3.8 18.2 - - + -
733A ALA* 4.0 16.6 - - + +
763A ALA* 3.7 30.5 - - + +
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Residues in contact with THR 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A MET 2.9 16.6 + - - +
677A ARG* 3.2 22.9 - - + +
679A ILE* 1.3 75.1 - - - +
681A GLU* 1.3 60.7 + - - +
683A ILE* 3.4 8.8 + - - +
684A ALA* 2.9 28.6 + - - +
801A GLU* 3.8 15.2 + - - +
806A ARG* 5.8 8.3 - - - +
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Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A ARG* 2.9 19.7 + - + +
678A GLU* 2.8 29.6 - - - +
680A THR* 1.3 75.9 - - - +
682A THR* 1.3 68.6 + - - +
684A ALA* 3.3 7.2 + - + +
685A GLU* 2.9 43.4 + - + +
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Residues in contact with THR 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A GLU* 2.9 15.7 + - - +
679A ILE* 3.2 11.4 + - - -
681A GLU* 1.3 83.7 + - - +
683A ILE* 1.3 62.5 + - + +
685A GLU* 3.2 15.7 + - + +
686A ALA* 3.0 22.7 + - + +
725A ALA* 4.2 16.2 - - - +
728A LYS* 3.7 42.9 - - + -
729A ALA* 4.6 3.6 - - - +
732A LEU* 3.5 15.1 - - - +
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Residues in contact with ILE 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A ILE* 3.0 22.3 + - + +
680A THR* 3.7 8.7 - - - +
681A GLU 3.3 0.2 - - - -
682A THR* 1.3 75.7 - - + +
684A ALA* 1.3 58.0 + - - +
686A ALA* 3.3 6.4 + - + +
687A LYS* 2.9 36.7 + - + +
725A ALA* 4.1 32.8 - - + +
729A ALA* 4.3 9.9 - - + -
763A ALA 5.8 0.2 - - - +
764A CYS* 4.4 20.0 - - + -
799A PHE* 4.0 17.7 - - + -
801A GLU* 3.6 41.1 - - + +
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Residues in contact with ALA 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A THR 2.9 18.3 + - - +
681A GLU* 3.6 9.0 - - - +
682A THR 3.2 0.2 - - - -
683A ILE* 1.3 76.6 - - - +
685A GLU* 1.3 57.2 + - - +
687A LYS* 3.1 14.1 + - + +
688A LYS* 2.9 45.8 + - - +
801A GLU* 5.4 0.2 + - - -
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Residues in contact with GLU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A GLU* 2.9 28.8 + - + +
682A THR* 3.2 27.2 + - + +
684A ALA* 1.3 72.8 - - - +
686A ALA* 1.3 60.0 + - - +
688A LYS* 3.4 8.6 + - - +
689A LYS* 3.0 31.8 + - + +
728A LYS* 4.3 19.2 - - - +
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Residues in contact with ALA 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A THR 3.0 14.6 + - - +
683A ILE* 3.5 9.0 - - + +
685A GLU* 1.3 76.1 - - + +
687A LYS* 1.3 58.8 + - - +
689A LYS* 3.3 12.2 + - + +
690A VAL* 2.9 33.4 + - - +
721A PHE* 4.5 9.4 - - + +
722A LEU* 4.7 8.7 - - + -
725A ALA* 3.6 28.3 - - + -
799A PHE* 6.4 0.2 - - + -
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Residues in contact with LYS 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A ILE* 2.9 25.0 + - + +
684A ALA* 3.1 15.7 + - + +
686A ALA* 1.3 77.5 - - + +
688A LYS* 1.3 65.5 + - - +
690A VAL* 3.3 9.4 + - - +
691A LEU* 2.9 29.3 + - - +
722A LEU* 5.8 2.0 - - + -
794A PRO* 4.7 20.1 - - + +
795A GLU* 3.8 35.6 + - - +
799A PHE* 4.9 10.0 - - + -
801A GLU* 3.6 26.7 + - - +
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Residues in contact with LYS 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A ALA* 2.9 38.1 + - - +
685A GLU* 3.7 10.8 - - - +
686A ALA 3.3 0.2 - - - -
687A LYS* 1.3 83.2 - - - +
689A LYS* 1.3 60.5 + - - +
691A LEU* 3.3 15.9 + - + +
692A ASP* 2.9 45.3 + - - +
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Residues in contact with LYS 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A GLU* 3.0 17.7 + - + +
686A ALA* 3.3 13.7 + - - +
688A LYS* 1.3 76.8 - - - +
690A VAL* 1.3 56.2 + - - +
692A ASP* 3.3 6.3 + - - +
693A VAL* 3.0 34.2 + - + +
720A ARG* 5.6 0.6 - - - +
721A PHE* 3.6 41.3 - - + -
724A GLU* 4.4 15.2 + - - -
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Residues in contact with VAL 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ALA 2.9 18.5 + - - +
687A LYS 3.3 7.8 + - - +
689A LYS* 1.3 73.6 - - - +
691A LEU* 1.3 55.1 + - - +
693A VAL* 3.8 3.3 - - - +
694A THR* 2.7 46.0 + - - +
714A PHE* 4.8 0.3 - - - -
718A VAL* 3.8 35.7 - - + -
721A PHE* 4.3 16.4 - - + -
722A LEU* 3.9 19.7 - - + -
792A TYR 5.1 4.5 - - - +
793A SER* 5.3 0.7 - - - -
794A PRO* 3.8 26.7 - - + -
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Residues in contact with LEU 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A LYS 2.9 17.1 + - - +
688A LYS* 3.7 18.4 - - + +
690A VAL* 1.3 77.0 - - - +
692A ASP* 1.3 61.2 + - - +
694A THR* 3.3 12.9 + - + -
695A LYS* 2.9 52.3 + - + +
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Residues in contact with ASP 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LYS* 2.9 28.6 + - - +
689A LYS* 3.8 6.0 - - - +
691A LEU* 1.3 78.1 - - - +
693A VAL* 1.3 63.3 + - + +
695A LYS* 3.4 18.7 + - - +
696A GLU* 2.9 30.4 + - - +
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Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A LYS* 3.0 18.4 + - + +
690A VAL* 4.0 4.0 - - - +
692A ASP* 1.3 75.4 - - + +
694A THR* 1.3 58.6 + - - +
696A GLU* 3.4 13.2 + - - +
697A ALA* 2.9 27.4 + - - +
702A LEU* 5.2 11.2 - - + +
714A PHE* 4.0 21.1 - - + -
717A ASN* 4.5 24.5 - - + +
718A VAL* 4.8 3.6 - - + -
721A PHE* 3.6 26.0 - - + -
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Residues in contact with THR 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A VAL* 2.7 32.6 + - - +
691A LEU* 3.5 15.4 - - + -
692A ASP 3.2 0.2 - - - -
693A VAL* 1.3 76.8 - - - +
695A LYS* 1.3 56.8 + - + +
697A ALA* 3.3 2.9 + - - +
698A GLN* 2.9 50.2 + - + +
714A PHE* 3.2 32.1 - - + -
792A TYR* 5.0 11.9 + - + +
793A SER* 6.1 0.3 - - - -
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Residues in contact with LYS 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A LEU* 2.9 42.7 + - + +
692A ASP* 3.9 19.7 + - - +
694A THR* 1.3 75.1 - - + +
696A GLU* 1.3 60.5 + - - +
698A GLN* 3.1 16.9 + - - +
699A ALA* 2.9 31.0 + - - +
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Residues in contact with GLU 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ASP 2.9 19.0 + - - +
693A VAL* 3.7 12.1 - - - +
695A LYS* 1.3 77.6 - - - +
697A ALA* 1.3 61.9 + - - +
699A ALA* 3.6 5.6 + - - -
701A LEU* 3.3 41.7 + - + +
702A LEU* 3.3 34.1 + - + +
703A THR 5.3 0.3 + - - -
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Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A VAL 2.9 17.4 + - - +
694A THR 3.7 4.3 - - - +
696A GLU* 1.3 76.6 - - - +
698A GLN* 1.3 62.6 + - + +
700A ASN* 3.5 11.1 + - - +
702A LEU* 3.7 31.8 - - + +
714A PHE* 4.1 18.2 - - + -
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Residues in contact with GLN 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A THR* 2.9 36.2 + - + +
695A LYS* 3.1 21.5 + - - +
697A ALA* 1.3 78.5 - - + +
699A ALA* 1.3 57.7 + - - +
700A ASN* 3.2 4.3 + - - +
792A TYR* 6.4 0.2 - - - -
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Residues in contact with ALA 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A LYS 2.9 15.0 + - - +
696A GLU* 4.2 1.1 - - - +
697A ALA 3.4 0.4 - - - -
698A GLN* 1.3 75.1 - - - +
700A ASN* 1.3 68.4 + - - +
701A LEU* 3.1 32.9 + - + +
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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