Contacts of the helix formed by residues 643 - 669 (chain A) in PDB entry 1R1H
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 643 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A TYR* 4.4 2.4 - - - +
638A LEU* 5.1 6.1 - - + +
639A ASN* 2.8 28.3 + - + +
640A GLY* 3.8 6.8 - - - -
642A ASN* 1.3 80.4 - - + +
644A LEU* 1.3 65.8 + - - +
645A GLY 3.3 2.0 - - - -
646A GLU* 3.2 3.5 + - - +
647A ASN* 2.9 44.4 + - - -
706A ILE 5.8 2.5 - - - +
709A ASP 4.3 5.6 - - - +
710A VAL 3.2 18.4 - - - +
711A HIS 4.0 16.2 - - - +
712A SER* 3.8 13.2 + - - +
713A PRO* 5.8 0.4 - - + -
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Residues in contact with LEU 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASN* 6.1 1.3 - - - +
591A ASP* 3.8 27.4 - - + +
618A SER* 3.8 34.8 - - - +
621A MET* 4.1 12.1 - - + -
622A VAL* 3.9 22.0 - - + +
640A GLY 3.5 11.4 + - - +
641A ILE* 3.2 19.8 + - + +
642A ASN 3.3 0.4 - - - -
643A THR* 1.3 77.3 - - - +
645A GLY* 1.3 60.1 + - - +
647A ASN* 3.1 4.7 + - - +
648A ILE* 2.8 47.5 + - + +
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Residues in contact with GLY 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A HIS* 4.4 2.5 - - - -
590A ASP* 3.7 22.9 - - - +
591A ASP* 3.2 22.0 + - - -
642A ASN 5.0 1.2 + - - -
643A THR 3.3 0.4 - - - -
644A LEU* 1.3 79.7 - - - +
646A GLU* 1.3 60.6 + - - +
648A ILE* 3.4 3.6 + - - +
649A ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A HIS* 3.0 11.0 + - + -
587A HIS* 3.3 12.1 - - - -
643A THR 3.2 3.8 + - - +
645A GLY* 1.3 75.9 - - - +
647A ASN* 1.3 60.3 + - - +
649A ALA* 3.4 3.0 + - - +
650A ASP* 2.9 35.0 + - - +
710A VAL* 3.0 43.3 - - + +
711A HIS* 3.1 33.5 + - + -
712A SER 4.8 0.4 - - - +
717A ARG* 5.3 0.4 - - - +
1001A ZN 2.0 38.4 - - - -
2001A BIR 3.3 9.4 + - - +
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Residues in contact with ASN 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A MET* 4.2 8.4 + - + -
625A TYR* 3.1 51.4 + - + +
640A GLY 4.9 1.2 + - - -
643A THR* 2.9 41.7 + - - +
644A LEU* 3.1 6.7 + - - +
646A GLU* 1.3 74.4 - - - +
648A ILE* 1.3 61.4 + - - +
650A ASP* 3.4 9.0 + - - +
651A ASN* 2.9 37.8 + - - +
712A SER* 2.8 23.1 + - - -
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Residues in contact with ILE 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR* 3.7 6.0 - - + +
590A ASP* 3.9 15.9 - - + -
591A ASP 4.2 10.1 - - - +
614A PHE* 4.0 24.0 - - + -
618A SER* 4.0 9.9 - - - -
621A MET* 4.0 17.7 - - - -
644A LEU* 2.8 42.8 + - + +
645A GLY 3.6 7.4 - - - +
647A ASN* 1.3 73.0 - - - +
649A ALA* 1.3 65.6 + - - +
651A ASN* 4.0 0.7 - - - +
652A GLY* 3.0 20.6 + - - -
748A VAL* 4.0 13.6 - - + +
749A TRP* 3.9 26.2 - - + +
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Residues in contact with ALA 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A HIS* 3.3 50.9 - - + +
586A THR* 3.8 12.7 - - - -
587A HIS* 4.0 13.0 - - + +
645A GLY 3.0 17.8 + - - +
646A GLU 3.6 0.2 - - - +
647A ASN 3.3 0.2 - - - -
648A ILE* 1.3 76.7 - - - +
650A ASP* 1.3 57.9 + - - +
653A GLY* 2.8 27.7 + - - -
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Residues in contact with ASP 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A MET* 2.9 24.4 - - + +
583A HIS* 2.8 16.7 + - - -
625A TYR* 5.2 0.6 + - - +
646A GLU* 2.9 21.5 + - - +
647A ASN* 3.7 10.2 - - - +
649A ALA* 1.3 77.0 - - - +
651A ASN* 1.3 58.4 + - - +
654A LEU* 2.9 27.9 + - - +
712A SER 5.8 0.2 + - - -
717A ARG* 2.7 58.2 + - - +
721A THR* 3.6 18.6 - - + +
2001A BIR 4.0 2.5 - - - -
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Residues in contact with ASN 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A MET* 3.7 22.6 - - + -
625A TYR* 3.1 28.3 + - - -
647A ASN 2.9 27.3 + - - +
648A ILE 4.1 0.9 - - - +
650A ASP* 1.3 74.0 - - - +
652A GLY* 1.3 66.4 + - - +
654A LEU* 3.6 4.2 + - - +
655A GLY* 3.3 17.3 + - - -
721A THR* 3.2 22.8 - - - +
724A ASN* 3.0 36.1 + - - +
746A CYS 5.6 0.4 - - - +
749A TRP* 4.8 3.1 - - - +
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Residues in contact with GLY 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR* 4.3 6.5 - - - -
621A MET* 5.6 0.2 - - - +
648A ILE 3.0 16.4 + - - -
649A ALA 4.1 0.2 - - - -
651A ASN* 1.3 74.4 - - - +
653A GLY* 1.3 64.2 + - - +
655A GLY* 3.1 3.1 + - - -
656A GLN* 2.9 40.3 + - - +
659A ARG* 5.1 0.2 + - - -
748A VAL* 5.8 0.4 - - - +
749A TRP* 4.0 23.3 + - - +
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Residues in contact with GLY 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A MET* 3.4 10.6 - - - +
582A GLY* 3.6 14.5 - - - -
583A HIS 3.6 2.7 - - - -
586A THR* 3.9 1.0 + - - -
649A ALA 2.8 22.0 + - - -
650A ASP 3.9 0.4 - - - -
652A GLY* 1.3 72.5 - - - +
654A LEU* 1.3 61.3 + - - +
656A GLN* 3.3 16.5 + - - +
657A ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A MET* 3.0 13.6 - - + -
650A ASP 2.9 18.7 + - - +
651A ASN 3.9 5.2 - - - +
653A GLY* 1.3 77.0 - - - +
655A GLY* 1.3 63.9 + - - +
657A ALA* 3.8 2.3 - - - +
658A TYR* 3.1 22.4 + - + +
685A PHE* 3.8 26.0 - - + -
686A PHE* 4.0 10.5 - - + -
689A PHE* 4.0 21.5 - - + -
721A THR* 3.8 34.1 - - - +
722A LEU* 4.0 16.6 - - + -
725A SER* 4.1 14.6 - - - +
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Residues in contact with GLY 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A ASN 3.3 8.1 + - - -
652A GLY 3.1 6.2 + - - -
654A LEU* 1.3 80.1 - - - +
656A GLN* 1.3 61.3 + - - +
658A TYR* 3.4 4.5 + - - +
659A ARG* 3.0 50.1 + - - +
727A GLU* 6.0 2.0 - - - -
749A TRP* 6.2 0.4 - - - -
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Residues in contact with GLN 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 4.4 16.1 - - + +
449A VAL* 3.6 9.7 - - + +
450A PHE* 3.4 44.2 - - + +
453A THR* 5.4 1.1 - - - +
582A GLY* 3.1 24.8 + - - -
585A ILE* 5.1 1.8 - - - +
586A THR* 3.1 27.6 + - - +
652A GLY* 2.9 21.5 + - - +
653A GLY* 3.3 7.3 - - - +
655A GLY* 1.3 77.0 - - - +
657A ALA* 1.3 62.3 + - - +
659A ARG* 3.4 15.3 + - - +
660A ALA* 3.0 23.0 + - - +
749A TRP* 4.1 9.4 - - - +
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Residues in contact with ALA 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 4.8 4.0 - - - +
574A TYR* 3.2 31.0 - - - +
578A GLY* 3.6 7.8 + - - -
579A MET* 3.5 16.4 - - + +
653A GLY 3.0 17.0 + - - +
654A LEU 3.8 3.6 - - - +
656A GLN* 1.3 76.0 - - - +
658A TYR* 1.3 58.4 + - - +
660A ALA* 3.1 9.0 + - - +
661A TYR* 2.9 27.5 + - - +
685A PHE* 4.0 6.8 - - + -
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Residues in contact with TYR 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A LEU* 3.1 18.1 + - + +
655A GLY* 3.9 5.2 - - - +
657A ALA* 1.3 73.2 - - - +
659A ARG* 1.3 61.9 + - + +
661A TYR* 3.1 8.2 + + - +
662A GLN* 2.8 60.5 + - + +
682A LYS* 2.8 48.8 + - + +
685A PHE* 3.6 39.4 - + + -
686A PHE* 3.9 24.3 - + + -
727A GLU* 3.5 38.9 + - + +
730A GLU* 5.2 2.8 + - - -
731A ALA* 5.3 1.2 - - - +
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Residues in contact with ARG 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A VAL* 3.7 12.6 - - + -
453A THR* 3.6 27.6 + - - +
456A ASP* 6.1 0.9 - - - -
652A GLY 5.1 0.4 + - - -
655A GLY* 3.0 43.0 + - - +
656A GLN* 3.5 14.5 - - - +
658A TYR* 1.3 77.5 - - + +
660A ALA* 1.3 57.0 + - - +
662A GLN* 3.1 20.8 + - - +
663A ASN* 2.9 37.8 + - - +
727A GLU* 5.4 9.3 + - - -
747A ARG* 3.2 38.5 - - - +
749A TRP* 4.4 4.6 + - - -
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Residues in contact with ALA 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 4.5 9.4 - - + +
446A ILE* 4.2 16.2 - - + -
449A VAL* 3.9 20.8 - - + +
574A TYR* 3.8 21.4 + - + -
656A GLN 3.0 13.8 + - - +
657A ALA 3.1 9.4 + - - +
659A ARG* 1.3 77.0 - - - +
661A TYR* 1.3 58.3 + - - +
663A ASN* 3.4 6.3 + - - +
664A TYR* 2.9 25.6 + - - +
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Residues in contact with TYR 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ASN* 3.8 6.5 - - + -
571A SER* 3.4 22.3 - - - -
574A TYR* 3.5 36.1 - + + -
657A ALA 2.9 12.7 + - - +
658A TYR* 3.1 17.2 + + - +
660A ALA* 1.3 74.3 - - - +
662A GLN* 1.3 67.7 + - - +
664A TYR* 2.9 17.4 + + - +
665A ILE* 2.9 45.2 + - + +
671A GLU* 2.8 31.3 + - - +
681A HIS* 3.2 32.1 - - - +
682A LYS* 4.5 7.9 - - + -
685A PHE* 4.2 16.8 - + + -
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Residues in contact with GLN 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A TYR* 2.8 40.9 + - + +
659A ARG* 3.1 29.0 + - - +
661A TYR* 1.3 77.7 - - + +
663A ASN* 1.3 62.2 + - - +
665A ILE* 3.2 8.2 + - - +
666A LYS* 3.0 28.5 + - - +
682A LYS* 3.6 26.1 - - - +
727A GLU* 5.1 4.5 - - - +
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Residues in contact with ASN 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A VAL* 4.0 20.8 - - - +
452A GLN* 4.7 11.3 + - - -
659A ARG* 2.9 20.3 + - - +
660A ALA* 3.6 8.1 - - - +
661A TYR 3.1 0.2 - - - -
662A GLN* 1.3 76.5 - - - +
664A TYR* 1.3 66.5 + - - +
666A LYS* 3.2 27.0 + - + +
667A LYS* 3.0 24.4 + - - +
----------------------------------------------------------
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Residues in contact with TYR 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 5.1 2.0 - - - +
570A ASN* 2.7 44.0 + - + -
574A TYR* 3.7 27.1 - + + +
660A ALA 2.9 13.8 + - - +
661A TYR* 2.9 25.9 + + - +
663A ASN* 1.3 75.9 - - - +
665A ILE* 1.3 61.9 + - + +
667A LYS* 3.2 2.6 + - - +
668A ASN* 2.8 75.5 + - + +
669A GLY 4.4 5.2 - - - -
671A GLU* 4.3 11.3 - - + +
----------------------------------------------------------
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Residues in contact with ILE 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A TYR* 2.9 55.7 + - + +
662A GLN* 3.6 9.4 - - - +
663A ASN 3.2 0.2 - - - -
664A TYR* 1.3 74.2 - - + +
666A LYS* 1.3 70.2 + - - +
669A GLY* 2.7 34.3 + - - +
670A GLU* 3.6 41.3 - - + +
671A GLU* 4.9 1.6 - - + +
681A HIS* 5.2 4.0 - - + -
682A LYS* 5.4 13.7 - - + -
----------------------------------------------------------
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Residues in contact with LYS 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A GLN 3.0 12.0 + - - +
663A ASN* 3.2 32.3 + - - +
665A ILE* 1.3 78.6 - - - +
667A LYS* 1.3 63.0 + - + +
669A GLY 4.3 1.4 + - - -
----------------------------------------------------------
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Residues in contact with LYS 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A ASN 3.0 15.3 + - - +
664A TYR* 4.8 0.7 - - - +
666A LYS* 1.3 80.1 - - + +
668A ASN* 1.3 88.4 + - - +
669A GLY 3.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ASN 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A TYR* 2.8 62.9 + - + +
667A LYS* 1.3 107.8 - - - +
669A GLY* 1.3 61.8 + - - +
670A GLU 5.3 0.2 - - - +
----------------------------------------------------------
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Residues in contact with GLY 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A TYR* 4.4 8.0 - - - -
665A ILE* 2.7 27.8 + - - +
666A LYS 4.3 1.4 + - - -
667A LYS 3.7 0.6 - - - -
668A ASN* 1.3 86.2 - - - +
670A GLU* 1.3 66.7 + - - +
671A GLU* 4.8 0.2 - - - +
----------------------------------------------------------
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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