Contacts of the helix formed by residues 681 - 706 (chain A) in PDB entry 4MS0
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 681 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A HIS* 5.1 16.7 + - + +
680A LYS* 1.3 75.0 - - - +
682A TRP* 1.3 69.1 + - - +
683A PRO* 3.4 2.9 - - + -
684A VAL* 2.8 20.3 + - + +
685A THR* 3.0 9.6 + - - -
727B LEU* 3.7 33.2 - - + -
763B GLU* 4.2 28.7 - - + +
766B ILE* 4.3 24.0 - - + -
767B ARG* 4.1 26.2 - - + -
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Residues in contact with TRP 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LYS 3.6 2.2 + - - -
681A LEU* 1.3 70.0 - - - +
683A PRO* 1.3 68.9 - - + +
685A THR* 3.1 12.1 + - + -
686A LYS* 2.7 51.7 + - + +
758A ASN* 3.3 35.5 + - - +
761A GLN* 3.5 40.8 + - + +
762A TRP* 3.5 57.0 - + - -
765A VAL* 4.1 17.3 - - + -
770A GLU* 5.1 4.1 + - + +
721B GLU* 5.2 2.8 + - - -
724B GLN* 3.4 35.2 + - + +
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Residues in contact with PRO 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 3.4 12.1 - - + -
682A TRP* 1.3 99.6 - - + +
684A VAL* 1.3 56.2 + - + +
686A LYS* 3.8 6.4 - - + +
687A LEU* 3.0 36.7 + - - +
724B GLN* 3.2 39.7 - - + +
727B LEU* 4.0 16.4 - - + -
728B GLY* 3.7 25.8 - - - +
766B ILE* 5.3 0.9 - - + -
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Residues in contact with VAL 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ASP* 3.5 44.0 - - + +
680A LYS* 3.6 24.9 - - + -
681A LEU* 2.8 19.3 + - + +
683A PRO* 1.3 69.1 - - - +
685A THR* 1.3 66.3 + - - +
687A LEU* 3.4 8.0 + - - +
688A THR* 3.1 33.4 + - - +
727B LEU* 4.4 14.4 - - + -
731B ASN* 4.0 16.4 - - - +
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Residues in contact with THR 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A SER* 2.8 28.6 + - - +
678A VAL* 4.3 1.8 - - + -
680A LYS 3.2 10.6 + - - -
681A LEU 3.0 3.4 + - - -
682A TRP* 3.4 17.9 - - + -
684A VAL* 1.3 74.9 - - - +
686A LYS* 1.3 65.4 + - - +
688A THR* 3.5 4.5 + - - -
689A ALA* 3.1 22.5 + - + +
730A TYR* 3.5 25.1 - - - +
758A ASN* 2.8 32.8 + - - +
762A TRP* 4.6 2.9 - - + +
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Residues in contact with LYS 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A TRP* 2.7 42.7 + - + +
683A PRO* 3.8 7.2 - - + +
685A THR* 1.3 73.6 - - - +
687A LEU* 1.3 65.0 + - + +
689A ALA* 3.3 14.9 + - + +
690A ASN* 3.3 33.0 + - - +
762A TRP* 3.8 33.2 - - + -
765A VAL* 5.4 1.3 - - - -
770A GLU* 3.8 21.5 + - - -
773A THR* 5.0 16.2 - - - -
774A TRP 6.1 1.1 - - - +
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Residues in contact with LEU 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A PRO 3.0 25.3 + - - +
684A VAL* 3.7 6.3 - - - +
685A THR 3.3 0.2 - - - -
686A LYS* 1.3 79.5 - - + +
688A THR* 1.3 62.1 + - - +
690A ASN* 3.2 24.0 + - - +
691A ASP* 3.6 9.6 + - - +
774A TRP 3.6 7.4 - - - +
775A ILE* 3.5 37.7 - - + -
728B GLY* 4.0 17.3 - - - +
731B ASN* 3.8 29.8 - - + -
732B ALA* 4.1 9.6 - - + +
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Residues in contact with THR 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A TYR* 3.5 29.6 - - + -
528A LYS* 5.3 8.4 + - - +
677A SER* 3.6 28.0 - - - +
684A VAL* 3.1 24.1 + - - +
685A THR 3.9 4.0 - - - -
687A LEU* 1.3 74.7 - - - +
689A ALA* 1.3 63.3 + - - +
691A ASP* 2.9 21.7 + - + +
692A ILE* 3.0 12.9 + - + +
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Residues in contact with ALA 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A SER* 5.7 0.2 + - - -
685A THR* 3.1 14.7 + - + +
686A LYS* 3.5 10.8 - - + +
687A LEU 3.3 0.4 - - - -
688A THR* 1.3 77.8 - - - +
690A ASN* 1.3 61.5 + - - +
692A ILE* 3.3 13.7 + - + +
693A TYR* 3.0 38.3 + - + -
722A VAL* 6.2 0.2 - - + -
726A GLN* 4.8 7.9 - - - +
762A TRP* 4.2 26.0 - - + -
900A 2ZX 5.8 0.7 - - - +
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Residues in contact with ASN 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A LYS* 3.3 34.1 + - - +
687A LEU* 3.2 20.3 + - - +
689A ALA* 1.3 75.8 - - - +
691A ASP* 1.3 61.0 + - - +
693A TYR* 3.8 4.4 - - - +
694A ALA* 2.8 29.9 + - - +
697A TRP* 5.3 3.7 - - - -
775A ILE* 3.2 32.9 - - - +
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Residues in contact with ASP 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PRO* 3.3 27.5 - - - +
524A TYR* 3.7 18.3 - - + +
526A ASN* 5.7 0.2 + - - -
528A LYS* 5.0 12.3 + - - +
687A LEU 3.6 12.4 + - - +
688A THR* 2.9 14.2 + - + +
690A ASN* 1.3 77.8 - - - +
692A ILE* 1.3 64.9 + - - +
694A ALA* 3.3 8.2 + - - +
695A GLU* 3.1 19.1 + - - +
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Residues in contact with ILE 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A TYR* 3.5 44.4 - - + +
677A SER* 4.3 8.3 - - - +
688A THR* 3.0 18.7 + - + +
689A ALA* 3.5 16.4 - - + +
691A ASP* 1.3 76.2 - - - +
693A TYR* 1.3 64.3 + - + +
695A GLU* 3.4 4.0 + - - +
696A PHE* 3.1 54.5 + - + -
726A GLN* 5.9 0.2 - - - +
900A 2ZX 3.5 47.6 - - + +
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Residues in contact with TYR 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ALA* 3.0 32.2 + - + +
690A ASN* 4.1 3.6 - - - +
692A ILE* 1.3 81.9 - - + +
694A ALA* 1.3 66.7 + - - +
696A PHE* 3.1 7.6 + + - +
697A TRP* 2.8 57.8 + + + -
713A MET* 3.6 48.4 - - + +
722A VAL* 3.5 44.5 + - + +
725A GLY* 4.3 4.5 - - - -
726A GLN* 3.1 43.9 + - + +
900A 2ZX 5.0 0.7 - - + -
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Residues in contact with ALA 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PRO* 4.0 18.0 - - + +
690A ASN 2.8 19.9 + - - +
691A ASP* 3.3 7.8 + - - +
693A TYR* 1.3 75.5 - - - +
695A GLU* 1.3 60.8 + - - +
697A TRP* 3.6 15.0 + - + +
698A ALA* 3.3 22.2 + - - +
716A ARG* 4.9 2.3 + - - +
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Residues in contact with GLU 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A VAL* 3.7 7.1 - - - +
523A PRO* 4.1 16.5 - - + +
524A TYR* 3.2 10.3 + - + +
525A HIS* 2.6 56.6 + - - -
567A HIS* 3.5 3.3 - - - -
569A GLY* 3.2 38.6 - - - +
691A ASP 3.1 12.4 + - - +
692A ILE 3.7 7.9 - - - +
694A ALA* 1.3 74.9 - - - +
696A PHE* 1.3 69.1 + - + +
698A ALA* 3.4 7.1 + - - +
699A GLU* 3.3 18.5 + - - +
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Residues in contact with PHE 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A HIS* 5.6 11.0 - + - -
571A SER* 5.7 4.7 - - - -
692A ILE* 3.1 46.0 + - + -
693A TYR* 3.1 13.7 + + - +
695A GLU* 1.3 80.2 - - + +
697A TRP* 1.3 58.2 + - - +
699A GLU* 2.9 25.2 + - - +
700A GLY 2.9 10.9 + - - -
713A MET* 3.7 47.6 - - + +
714A MET* 3.6 35.8 - - + +
900A 2ZX 3.7 17.0 - + + -
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Residues in contact with TRP 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ASN* 5.3 3.6 - - - -
693A TYR* 2.8 48.2 + + + +
694A ALA* 4.0 14.6 - - + +
696A PHE* 1.3 72.1 - - - +
698A ALA* 1.3 57.3 + - - +
700A GLY* 3.3 1.2 + - - -
701A ASP* 3.0 33.8 + - - +
712A PRO 5.2 0.2 + - - -
713A MET 3.7 13.4 + - - -
714A MET 3.4 13.0 - - - +
715A ASP 3.7 12.6 + - - -
716A ARG* 3.5 57.2 - - + +
719A LYS* 3.6 44.8 - - + +
722A VAL* 4.4 10.5 - - + +
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Residues in contact with ALA 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PRO* 6.2 1.8 - - + -
569A GLY 6.1 0.2 - - - +
570A PHE* 5.6 0.9 - - - -
694A ALA 3.3 15.7 + - - +
695A GLU* 3.7 7.0 - - - +
696A PHE 3.2 0.4 - - - -
697A TRP* 1.3 75.3 - - - +
699A GLU* 1.3 66.0 + - - +
701A ASP* 3.4 7.0 + - - +
702A GLU* 3.3 26.0 + - - +
716A ARG* 3.7 9.8 - - - +
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Residues in contact with GLU 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A GLY 3.9 9.4 + - - +
570A PHE* 3.6 14.9 - - + -
571A SER* 2.5 50.3 + - - -
573A SER* 4.8 0.9 - - - -
574A TYR* 3.3 28.6 + - + +
695A GLU 3.3 10.4 + - - +
696A PHE* 2.9 14.9 + - - +
698A ALA* 1.3 75.2 - - - +
700A GLY* 1.3 66.3 + - - +
702A GLU* 2.9 15.6 + - - +
703A MET* 3.0 16.8 + - + +
714A MET* 3.3 24.4 - - - +
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Residues in contact with GLY 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A PHE 2.9 9.9 + - - -
697A TRP 3.3 0.6 + - - -
699A GLU* 1.3 75.9 - - - +
701A ASP* 1.3 62.9 + - - +
703A MET* 3.2 7.2 + - - +
704A LYS* 3.1 30.3 + - - +
710A PRO* 3.8 18.1 - - - +
714A MET* 3.3 24.1 - - - +
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Residues in contact with ASP 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A TRP 3.0 21.7 + - - +
698A ALA* 3.5 10.9 - - - +
699A GLU 3.1 0.4 - - - -
700A GLY* 1.3 76.3 - - - +
702A GLU* 1.3 63.3 - - + +
704A LYS* 3.4 24.6 + - - +
705A LYS* 3.5 27.7 + - - +
714A MET 5.2 0.2 - - - +
716A ARG* 2.7 45.9 + - - +
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Residues in contact with GLU 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A PHE* 4.0 21.5 - - + -
574A TYR* 3.8 22.4 + - + +
698A ALA 3.5 13.5 - - - +
699A GLU 2.9 9.0 + - - +
701A ASP* 1.3 76.1 - - - +
703A MET* 1.3 65.5 + - - +
704A LYS 3.3 0.5 + - - -
705A LYS* 3.3 43.3 + - - +
706A LEU* 3.5 18.8 + - - +
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Residues in contact with MET 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TYR* 4.0 20.2 - - + -
577A LYS* 5.4 6.1 - - + -
578A PHE* 4.2 17.7 - - + -
699A GLU* 3.0 22.1 + - - +
700A GLY* 3.2 6.9 + - - +
702A GLU* 1.3 77.0 - - - +
704A LYS* 1.3 60.2 + - - +
706A LEU* 3.1 9.7 + - - +
707A GLY 3.3 0.2 + - - -
708A ILE* 2.9 58.0 + - + +
709A GLN 4.4 0.2 - - - +
710A PRO* 3.9 28.7 - - + -
711A ILE* 5.1 2.5 - - + +
714A MET* 4.4 19.5 - - - +
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Residues in contact with LYS 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A GLY 3.1 19.1 + - - +
701A ASP* 3.6 18.7 + - - +
702A GLU 3.2 0.4 - - - -
703A MET* 1.3 75.6 - - - +
705A LYS* 1.3 61.8 + - + +
707A GLY* 3.3 12.3 + - - -
708A ILE 3.4 6.3 - - - +
709A GLN* 4.6 11.7 - - - +
710A PRO* 3.7 27.1 - - + -
715A ASP* 2.8 31.3 + - - +
716A ARG* 4.9 4.0 - - - +
717A ASP* 3.3 22.0 + - - +
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Residues in contact with LYS 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A ASP* 3.5 22.3 + - - +
702A GLU* 3.3 38.1 + - - +
703A MET 3.3 0.4 - - - -
704A LYS* 1.3 77.6 - - + +
706A LEU* 1.3 65.8 + - + +
707A GLY 3.3 1.0 + - - -
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Residues in contact with LEU 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TYR* 3.7 23.3 - - - +
578A PHE* 3.7 41.8 - - + -
702A GLU* 3.5 14.6 + - + +
703A MET 3.1 7.1 + - - +
705A LYS* 1.3 81.9 - - + +
707A GLY* 1.3 60.2 + - - +
708A ILE* 3.4 10.7 + - - +
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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