Contacts of the helix formed by residues 720 - 745 (chain A) in PDB entry 4NGM
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 720 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A LYS* 4.5 2.7 - - - +
719A VAL* 1.3 85.5 - - + +
721A PRO* 1.3 63.6 - - - +
722A SER* 3.3 12.0 + - - -
723A LYS* 3.0 44.9 + - + +
724A ALA* 3.1 13.1 + - - +
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Residues in contact with PRO 721 (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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621A GLU* 5.6 3.4 - - + -
625A TYR* 3.7 17.5 - - + +
715A ILE* 5.8 2.7 - - + +
718A LYS* 4.2 8.9 - - + +
719A VAL 3.1 13.9 - - - +
720A ASP* 1.3 85.1 - - - +
722A SER* 1.3 57.4 + - - +
724A ALA* 4.3 7.4 - - + -
725A TRP* 2.8 48.7 + - + +
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Residues in contact with SER 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A TYR* 3.6 32.2 + - - -
720A ASP* 3.2 10.2 + - - -
721A PRO* 1.3 80.0 - - - +
723A LYS* 1.3 58.5 + - - +
725A TRP* 4.0 0.9 - - - +
726A GLY* 3.0 25.3 + - - -
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Residues in contact with LYS 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A ASP* 3.0 32.9 + - + +
722A SER* 1.3 80.8 - - - +
724A ALA* 1.3 62.0 + - - +
726A GLY* 3.3 2.5 + - - -
727A GLU* 3.2 22.4 + - + +
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Residues in contact with ALA 724 (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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711A ALA 4.6 3.6 - - - +
715A ILE* 3.7 27.9 - - + +
718A LYS* 4.0 24.5 - - + +
720A ASP 3.1 11.7 + - - +
721A PRO* 3.3 7.6 + - + +
723A LYS* 1.3 77.6 - - - +
725A TRP* 1.4 56.1 + - - +
727A GLU* 3.2 8.9 + - - +
728A VAL* 3.1 27.9 + - - +
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Residues in contact with TRP 725 (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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615A SER* 3.6 21.8 - - - -
618A HIS* 3.5 39.5 - + + -
621A GLU* 3.5 20.9 - - + +
622A MET* 4.2 10.5 - - + -
625A TYR* 3.7 38.6 - + + -
627A VAL* 3.7 18.4 - - + -
712A LEU* 3.6 24.7 - - + -
715A ILE* 3.4 27.4 + - + +
721A PRO* 2.8 37.6 + - + +
724A ALA* 1.4 69.1 - - - +
726A GLY* 1.3 66.1 + - - +
728A VAL* 3.2 17.3 + - + +
729A LYS* 2.9 28.5 + - - +
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Residues in contact with GLY 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A TYR* 5.6 0.8 - - - +
722A SER 3.0 15.6 + - - -
723A LYS* 3.7 4.7 - - - -
724A ALA 3.3 0.2 - - - -
725A TRP* 1.3 77.7 - - - +
727A GLU* 1.3 56.2 + - - +
729A LYS* 3.3 12.3 + - - +
730A ARG* 2.9 26.7 + - - +
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Residues in contact with GLU 727 (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 PRO* 4.2 7.6 - - - +
711A ALA* 4.2 14.1 - - + -
723A LYS* 3.2 13.3 + - + +
724A ALA* 3.2 9.6 + - - +
725A TRP 3.2 0.2 - - - -
726A GLY* 1.3 73.8 - - - +
728A VAL* 1.3 64.8 + - - +
730A ARG* 3.1 31.9 + - - +
731A GLN* 3.0 50.1 + - - +
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Residues in contact with VAL 728 (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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627A VAL* 4.2 4.0 - - + -
629A PHE* 5.0 1.8 - - + -
708A ILE* 4.5 7.1 - - + +
711A ALA* 3.7 34.7 - - + +
712A LEU* 4.0 24.5 - - + -
715A ILE* 3.7 14.8 - - + -
724A ALA 3.1 14.9 + - - +
725A TRP* 3.2 21.7 + - + +
727A GLU* 1.3 76.3 - - - +
729A LYS* 1.3 63.4 + - - +
731A GLN* 3.2 4.2 + - - +
732A ILE* 2.9 37.8 + - + +
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Residues in contact with LYS 729 (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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625A TYR* 2.9 30.1 + - + +
626A SER* 3.2 21.8 + - - +
627A VAL* 4.1 23.8 - - + -
628A SER 5.2 1.6 - - - +
725A TRP 2.9 20.3 + - - +
726A GLY* 3.5 11.2 - - - +
728A VAL* 1.3 76.1 - - - +
730A ARG* 1.3 63.0 + - - +
732A ILE* 3.2 11.0 + - + +
733A TYR* 3.1 22.3 + - - +
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Residues in contact with ARG 730 (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 PRO* 4.1 9.9 - - - +
726A GLY 2.9 15.0 + - - +
727A GLU* 3.1 44.4 + - - +
729A LYS* 1.3 75.5 - - - +
731A GLN* 1.3 73.2 + - - +
733A TYR* 3.2 17.6 + - + +
734A VAL* 2.9 44.5 + - + +
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Residues in contact with GLN 731 (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 LEU* 4.8 4.3 - - - +
682A PRO* 3.6 16.6 - - - +
707A GLY* 3.3 34.5 - - - +
708A ILE* 3.7 22.0 - - - +
711A ALA* 4.2 4.7 - - + -
727A GLU* 3.0 39.9 + - - +
728A VAL* 3.7 5.2 - - - +
730A ARG* 1.3 94.4 - - - +
732A ILE* 1.4 65.5 + - - +
734A VAL* 3.8 15.6 - - - +
735A ALA* 2.9 25.6 + - - +
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Residues in contact with ILE 732 (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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627A VAL* 3.9 16.6 - - + -
628A SER 3.7 21.8 - - - +
629A PHE* 3.7 49.6 - - + -
631A SER* 3.7 19.7 - - - +
632A LEU* 4.5 10.8 - - + +
708A ILE* 4.0 13.9 - - + -
728A VAL* 2.9 23.0 + - + +
729A LYS* 3.5 12.3 - - + +
731A GLN* 1.4 77.0 - - - +
733A TYR* 1.3 57.6 + - - +
735A ALA* 3.3 2.1 + - - +
736A ALA* 2.9 27.5 + - - +
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Residues in contact with TYR 733 (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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631A SER* 4.9 3.6 - - - -
729A LYS 3.1 11.7 + - - +
730A ARG* 3.3 20.9 - - + +
732A ILE* 1.3 76.0 - - - +
734A VAL* 1.3 68.2 + - + +
736A ALA* 3.9 4.1 - - - +
737A PHE* 2.9 46.5 + + + +
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Residues in contact with VAL 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A ASP* 3.7 23.6 - - - +
681A LEU* 6.4 2.0 - - + -
690A VAL* 4.7 10.3 - - + -
730A ARG* 2.9 41.8 + - + +
731A GLN* 3.8 17.3 - - - +
733A TYR* 1.3 89.6 - - + +
735A ALA* 1.3 57.6 + - - +
737A PHE* 3.7 6.9 - - + +
738A THR* 2.8 39.0 + - - +
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Residues in contact with ALA 735 (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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632A LEU* 4.1 5.6 - - + -
690A VAL* 4.0 14.5 - - + +
705A PHE* 3.9 22.4 - - + -
708A ILE* 3.9 20.0 - - + -
731A GLN 2.9 17.5 + - - +
732A ILE 3.7 3.1 - - - +
734A VAL* 1.3 75.9 - - - +
736A ALA* 1.3 61.2 + - - +
738A THR* 3.3 1.6 + - - -
739A VAL* 2.9 35.0 + - - +
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Residues in contact with ALA 736 (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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631A SER* 3.6 43.5 - - - +
632A LEU* 3.6 12.1 - - - +
635A ALA* 3.3 11.9 - - + +
732A ILE 2.9 18.3 + - - +
733A TYR* 3.9 3.4 - - - +
735A ALA* 1.3 73.1 - - - +
737A PHE* 1.3 66.5 + - - +
739A VAL 3.4 0.3 + - - -
740A GLN* 2.9 23.1 + - - +
1G NAG 4.8 4.5 - - + -
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Residues in contact with PHE 737 (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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733A TYR* 2.9 31.8 + + + +
734A VAL* 3.7 5.8 - - + +
736A ALA* 1.3 78.1 - - - +
738A THR* 1.3 68.5 + - + +
740A GLN* 3.3 6.2 + - + +
741A ALA* 2.8 47.7 + - + +
1G NAG 6.1 0.4 - - - -
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Residues in contact with THR 738 (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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674A ALA 3.7 20.0 - - - +
675A PHE* 3.8 25.8 - - + +
676A ILE 5.0 2.9 - - - +
677A ASP* 4.8 3.9 + - + +
690A VAL* 3.7 26.4 - - + +
691A ILE* 5.9 0.2 - - - -
734A VAL* 2.8 25.8 + - - +
735A ALA 3.9 2.9 - - - -
736A ALA 3.3 0.2 - - - -
737A PHE* 1.3 89.9 - - - +
739A VAL* 1.3 56.2 + - - +
741A ALA* 3.3 4.8 + - + +
742A ALA* 2.9 29.0 + - - +
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Residues in contact with VAL 739 (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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604A LEU* 4.2 14.6 - - + -
632A LEU* 4.5 3.1 - - + -
635A ALA* 3.6 31.4 - - + +
636A VAL* 3.9 13.5 - - + +
639A PHE* 3.7 10.5 - - + -
675A PHE* 4.5 3.1 - - + -
691A ILE* 3.9 27.4 - - + -
705A PHE* 4.3 12.3 - - + -
735A ALA 2.9 21.2 + - - +
736A ALA* 3.9 2.9 - - - +
738A THR* 1.3 71.8 - - - +
740A GLN* 1.4 61.7 - - - +
742A ALA* 3.2 7.2 + - - +
743A ALA* 2.9 28.6 + - - +
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Residues in contact with GLN 740 (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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635A ALA* 3.7 8.4 - - + +
638A ASN* 2.7 42.5 + - - +
642A ILE* 4.6 7.7 - - - +
736A ALA 2.9 16.9 + - - +
737A PHE* 3.7 7.4 - - + +
739A VAL* 1.4 76.7 - - - +
741A ALA* 1.3 61.7 + - - +
743A ALA* 3.3 6.1 + - - +
744A GLU* 3.0 56.2 + - - +
1G NAG 3.2 30.7 + - + +
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Residues in contact with ALA 741 (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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674A ALA* 5.0 4.9 - - - +
737A PHE* 2.8 44.5 + - + +
738A THR* 3.6 7.0 - - + +
739A VAL 3.3 0.2 - - - -
740A GLN* 1.3 71.9 - - - +
742A ALA* 1.3 63.3 + - - +
744A GLU* 3.3 13.3 + - - +
745A THR* 3.3 24.3 + - - +
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Residues in contact with ALA 742 (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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639A PHE* 4.0 6.3 - - + -
671A LEU* 3.8 7.9 - - + +
674A ALA* 3.6 27.0 + - + +
675A PHE* 3.5 31.6 - - + -
738A THR 2.9 17.8 + - - +
739A VAL 3.5 4.5 - - - +
741A ALA* 1.3 75.7 - - - +
743A ALA* 1.3 61.9 + - - +
745A THR* 2.8 24.4 + - - -
746A LEU* 3.9 0.9 + - - +
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Residues in contact with ALA 743 (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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638A ASN 4.5 0.2 - - - -
639A PHE* 3.6 40.5 - - + +
642A ILE* 3.3 27.1 - - + +
739A VAL 2.9 13.3 + - - +
740A GLN* 3.5 13.5 - - - +
742A ALA* 1.3 76.9 - - - +
744A GLU* 1.4 56.7 + - - +
746A LEU* 2.8 31.3 + - - +
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Residues in contact with GLU 744 (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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642A ILE* 4.8 2.9 - - + -
740A GLN* 3.0 52.0 + - - +
741A ALA* 3.7 10.4 - - - +
742A ALA 3.3 0.6 - - - -
743A ALA* 1.4 74.4 - - - +
745A THR* 1.4 60.4 + - - +
746A LEU 3.1 0.2 - - - -
747A SER* 3.2 29.3 + - - +
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Residues in contact with THR 745 (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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667A GLN* 2.9 31.1 + - - +
670A PHE* 5.3 7.0 - - + +
671A LEU* 4.0 16.8 - - - +
674A ALA* 4.0 18.2 - - + +
741A ALA 3.3 16.5 + - - +
742A ALA* 2.8 17.0 + - - +
744A GLU* 1.4 75.1 - - - +
746A LEU* 1.3 61.2 + - - +
747A SER 3.4 1.0 - - - +
749A VAL* 5.4 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