Contacts of the helix formed by residues 643 - 667 (chain A) in PDB entry 5FBQ
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A HIS 3.9 5.4 + - - +
639A GLY* 3.7 17.4 - - - -
640A SER* 2.8 34.2 + - - +
641A TYR 3.7 0.7 - - - +
642A THR* 1.3 77.0 + - - +
644A GLU* 1.3 64.7 + - - +
645A ALA* 3.8 7.5 + - - +
646A PHE* 3.1 26.2 - - + +
647A LEU* 3.4 22.7 + - - +
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Residues in contact with GLU 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A THR 4.1 1.3 + - - -
643A THR* 1.3 74.9 + - - +
645A ALA* 1.3 68.1 + - - +
646A PHE 3.0 0.7 + - - -
647A LEU* 3.1 3.0 + - - +
648A SER* 2.9 27.9 + - - -
52B SER* 3.2 23.6 + - - -
59B THR* 5.3 5.9 - - - +
61B LYS* 2.5 48.1 + - - +
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Residues in contact with ALA 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A HIS* 3.6 32.6 - - + +
643A THR* 3.9 4.9 + - + +
644A GLU* 1.3 78.0 - - - +
646A PHE* 1.3 56.0 + - - +
648A SER* 3.9 7.0 + - - -
649A ALA* 3.1 27.9 + - - +
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Residues in contact with PHE 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A LEU* 4.3 16.2 - - + -
634A PHE* 3.8 40.6 - + + -
635A LEU* 4.2 11.7 - - + -
638A HIS* 4.1 6.2 - - + +
639A GLY 3.6 15.0 - - - +
640A SER 3.3 20.4 - - - +
641A TYR* 3.1 36.8 - + + -
643A THR* 3.1 11.4 - - + +
644A GLU 3.1 0.8 - - - -
645A ALA* 1.3 75.0 - - - +
647A LEU* 1.3 60.0 + - + +
649A ALA* 2.9 4.7 + - - +
650A GLN* 2.6 65.5 + - + +
717A VAL* 4.8 3.8 - - + -
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Residues in contact with LEU 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A TYR* 3.3 26.2 - - + +
642A THR* 5.1 3.8 - - - +
643A THR 3.4 9.8 + - - +
644A GLU* 3.1 6.3 + - - +
646A PHE* 1.3 83.4 - - + +
648A SER* 1.3 58.6 + - - +
650A GLN* 3.6 22.4 - - - +
651A ARG* 2.9 29.1 + - - +
725A MET* 5.4 1.2 - - - +
11B LEU* 5.0 18.8 - - + -
61B LYS* 3.7 34.3 - - + +
63B GLN* 6.3 1.1 - - - +
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Residues in contact with SER 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A GLU 2.9 16.5 + - - -
645A ALA* 3.9 7.5 + - - -
647A LEU* 1.3 77.6 - - - +
649A ALA* 1.3 57.7 + - - +
651A ARG* 3.3 10.4 + - - +
652A ASN* 2.9 44.6 + - - +
682A GLU 5.0 0.2 + - - -
61B LYS* 5.2 1.6 - - - +
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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
----------------------------------------------------------
634A PHE* 3.7 22.1 - - + -
638A HIS* 3.9 21.5 - - + +
645A ALA 3.1 19.8 + - - +
646A PHE 2.9 6.1 + - - +
648A SER* 1.3 74.2 + - - +
650A GLN* 1.3 60.6 + - - +
652A ASN* 3.4 2.6 + - - +
653A PHE* 2.9 28.2 + - - +
682A GLU 3.3 20.0 - - - +
683A GLY* 3.8 2.1 - - - -
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Residues in contact with GLN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A PHE* 4.2 4.9 - - - -
646A PHE* 2.6 37.6 + - + +
647A LEU* 3.6 26.2 - - - +
649A ALA* 1.3 72.9 - - - +
651A ARG* 1.3 57.8 + - - +
653A PHE* 3.1 9.0 + - - +
654A VAL* 2.9 40.4 + - + +
717A VAL* 2.4 38.3 + - + +
718A MET 3.7 13.9 + - - -
719A GLY* 3.9 4.6 - - - +
725A MET* 3.8 22.8 - - + +
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Residues in contact with ARG 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A LEU 2.9 17.7 + - - +
648A SER* 3.4 9.9 - - - +
650A GLN* 1.3 76.5 - - - +
652A ASN* 1.3 63.9 + - - +
654A VAL* 3.3 2.3 + - - +
655A GLN* 3.1 53.8 + - + +
725A MET* 4.1 20.8 - - + +
728A TYR* 5.4 2.1 + - + -
33B ARG* 6.2 2.2 - - - +
48B PHE* 4.5 29.3 + - + -
49B ALA* 4.8 9.5 - - - +
50B THR* 3.8 25.7 + - - +
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Residues in contact with ASN 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A SER* 2.9 29.3 + - - +
649A ALA 3.6 0.9 - - - +
651A ARG* 1.3 79.9 - - - +
653A PHE* 1.3 62.1 + - - +
655A GLN* 4.1 11.0 - - - +
656A SER* 3.0 19.9 + - - -
682A GLU* 2.8 42.1 + - - +
683A GLY 3.9 1.1 - - - -
684A HIS* 3.1 42.4 + - + +
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Residues in contact with PHE 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A ILE* 6.4 0.4 - - + -
630A LEU* 4.1 19.5 - - + -
634A PHE* 3.8 18.8 - + + -
649A ALA 2.9 12.2 + - - +
650A GLN* 3.1 13.9 + - - +
652A ASN* 1.3 75.3 - - - +
654A VAL* 1.3 59.1 + - + +
656A SER* 2.7 18.0 + - - -
657A CYS* 2.9 41.5 + - - +
679A LEU* 4.5 2.0 - - + -
683A GLY 3.2 23.9 + - - +
685A ILE* 3.2 27.6 - - + -
714A PHE* 4.0 37.7 - + - -
717A VAL* 3.8 18.2 - - + -
718A MET* 4.3 11.0 - - + -
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Residues in contact with VAL 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A GLN* 2.9 22.8 + - + +
651A ARG 3.3 4.5 + - - +
653A PHE* 1.3 79.5 - - + +
655A GLN* 1.3 62.2 + - - +
657A CYS* 3.4 6.9 + - - +
658A ALA* 3.2 21.0 + - - +
718A MET* 3.9 26.0 - - + -
725A MET* 3.7 39.9 - - + +
728A TYR* 3.9 18.4 - - + -
729A TYR* 3.7 24.8 - - + -
732A LEU* 4.4 2.2 - - + -
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Residues in contact with GLN 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A PRO* 3.1 41.8 + - - +
593A LEU* 3.8 2.1 - - - -
594A TRP* 3.1 30.8 + - + +
651A ARG* 3.1 44.6 + - - +
652A ASN* 4.2 13.6 - - - +
654A VAL* 1.3 76.5 - - - +
656A SER* 1.3 61.8 + - - +
658A ALA* 3.7 1.1 + - - +
659A GLY 3.2 14.7 + - - -
684A HIS* 5.3 1.4 + - - -
728A TYR* 3.9 12.7 + - + -
732A LEU* 3.8 20.0 - - + -
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Residues in contact with SER 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A TRP* 3.2 28.1 - - - +
652A ASN 3.0 15.3 + - - -
653A PHE* 2.7 19.8 + - - -
655A GLN* 1.3 73.9 - - - +
657A CYS* 1.3 64.0 + - - +
658A ALA 3.4 0.2 - - - -
660A TYR* 3.2 31.5 + - - +
684A HIS* 3.5 0.8 - - - -
685A ILE* 3.0 43.0 + - - +
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Residues in contact with CYS 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A PHE* 2.9 47.0 + - - +
654A VAL 3.6 3.6 - - - +
655A GLN 3.3 0.2 - - - -
656A SER* 1.3 76.2 + - - +
658A ALA* 1.3 59.6 + - - +
660A TYR 3.5 0.3 + - - -
661A CYS* 3.0 31.0 + - - +
685A ILE* 3.7 23.3 - - - -
708A PHE* 4.2 8.3 - - + -
710A LEU* 5.3 0.9 - - - -
714A PHE* 4.0 12.6 - - - -
718A MET* 3.8 11.4 - - + -
729A TYR* 3.4 20.8 + - + +
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Residues in contact with ALA 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU* 3.6 23.6 - - + -
654A VAL 3.2 13.5 + - - +
655A GLN 4.0 1.1 - - - +
657A CYS* 1.3 77.1 - - - +
659A GLY* 1.3 65.4 + - - +
661A CYS* 3.5 3.0 - - - +
662A LEU* 3.2 27.9 + - - +
729A TYR* 3.3 22.6 - - + +
732A LEU* 3.9 5.8 - - + -
733A MET* 3.8 19.1 - - + +
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Residues in contact with GLY 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TRP* 3.7 2.9 - - - -
593A LEU* 4.1 20.9 - - - +
595A ILE* 3.8 20.4 - - - -
655A GLN 3.2 13.9 + - - -
656A SER 4.0 0.4 - - - -
658A ALA* 1.3 78.4 - - - +
660A TYR* 1.3 60.3 + - - +
662A LEU* 3.2 7.3 + - - +
663A VAL* 3.2 23.4 + - - +
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Residues in contact with TYR 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU* 4.9 7.0 - - + -
594A TRP* 4.2 2.0 - + - -
595A ILE* 3.9 25.1 - - + -
596A LYS* 3.0 37.7 + - - +
656A SER 3.2 26.0 + - - +
657A CYS 4.3 2.0 - - - +
659A GLY* 1.3 73.3 - - - +
661A CYS* 1.3 61.4 + - - +
663A VAL* 3.6 14.1 - - + +
664A CYS* 2.8 37.5 + - - -
685A ILE* 3.2 30.3 - - + -
686A ILE* 3.4 13.3 - - + +
687A HIS* 3.6 54.5 + + + +
690A PHE* 4.7 9.9 - + - -
708A PHE* 5.2 1.3 - - + -
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Residues in contact with CYS 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A CYS 3.0 19.3 + - - +
658A ALA 3.5 5.8 - - - +
660A TYR* 1.3 77.9 - - - +
662A LEU* 1.3 55.8 + - - +
664A CYS* 3.2 3.6 + - - +
665A TYR* 2.9 27.5 + - - +
708A PHE* 3.5 31.1 - - + +
729A TYR* 3.6 12.8 - - - +
733A MET* 3.4 31.4 - - - -
792A MET* 4.3 9.6 - - - -
796A SER* 5.8 4.5 - - - -
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Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TRP* 3.8 22.0 - - + -
593A LEU* 3.8 10.5 - - + -
658A ALA 3.2 10.4 + - - +
659A GLY 3.2 9.3 + - - +
661A CYS* 1.3 79.0 - - - +
663A VAL* 1.3 58.1 + - - +
665A TYR* 3.3 3.5 + - + +
666A LEU* 2.9 43.3 + - + +
733A MET* 3.5 49.1 - - + +
736A GLY 3.6 22.4 - - - +
737A LEU* 3.8 20.9 - - + +
740A ALA* 6.2 0.2 - - + -
789A VAL* 6.5 0.2 - - + -
792A MET* 4.3 10.5 - - + -
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Residues in contact with VAL 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU* 3.2 37.0 - - + -
582A LEU* 3.9 20.9 - - + -
586A TRP* 4.2 8.3 - - + -
595A ILE* 4.7 6.1 - - + -
659A GLY 3.2 15.4 + - - +
660A TYR* 3.6 13.9 - - + +
661A CYS 3.3 0.2 - - - -
662A LEU* 1.3 74.7 - - - +
664A CYS* 1.3 65.3 + - - +
666A LEU* 4.1 4.0 - - - +
667A LEU* 3.0 41.1 + - + +
669A VAL* 5.1 0.7 - - + -
690A PHE* 4.4 14.4 - - + -
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Residues in contact with CYS 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A TYR* 2.8 24.2 + - - +
661A CYS 3.5 4.9 - - - +
663A VAL* 1.3 78.0 - - - +
665A TYR* 1.3 57.4 + - - +
668A GLN* 2.8 9.7 + - - -
669A VAL* 2.7 52.2 + - + +
672A ARG* 4.5 2.5 - - - -
687A HIS* 3.9 29.8 - - - -
690A PHE* 6.0 1.3 - - - -
708A PHE* 3.6 33.0 - - + +
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Residues in contact with TYR 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A CYS* 2.9 13.4 + - - +
662A LEU* 3.7 4.3 - - + +
664A CYS* 1.3 74.5 - - - +
666A LEU* 1.3 81.1 + - + +
668A GLN* 2.8 44.4 + - - +
737A LEU* 5.0 10.5 - - + -
775A ARG* 3.1 36.2 + - + +
777A HIS* 2.5 35.1 + + - -
788A LEU* 4.5 6.2 - - + +
792A MET* 3.5 46.9 - - + -
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Residues in contact with LEU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A VAL* 6.3 1.1 - - + -
582A LEU* 4.1 35.2 - - + -
586A TRP* 5.5 1.6 - - + -
662A LEU* 2.9 33.0 + - + +
663A VAL* 4.1 2.9 - - - +
665A TYR* 1.3 88.4 - - + +
667A LEU* 1.3 60.9 + - + +
737A LEU* 4.7 12.1 - - + -
740A ALA* 4.9 6.5 - - + -
747A VAL* 6.3 0.4 - - + -
772A LEU* 3.2 13.7 - - + +
775A ARG* 2.9 44.4 + - + +
776A PHE* 4.1 36.3 - - + -
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Residues in contact with LEU 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LEU* 6.0 2.0 - - + -
575A ALA* 4.2 30.1 - - + +
578A VAL* 4.4 31.0 - - + -
579A LEU* 5.5 0.7 - - + -
582A LEU* 6.2 0.4 - - + -
663A VAL* 3.0 33.4 + - + +
666A LEU* 1.3 79.8 - - + +
668A GLN* 1.3 65.4 + - - +
669A VAL* 3.9 13.2 - - + -
690A PHE* 5.1 2.2 - - + -
693A ILE* 3.4 16.8 - - + +
694A LEU* 2.9 47.2 + - + +
751A VAL* 5.1 7.4 - - + -
772A LEU* 5.5 3.6 - - + -
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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