Contacts of the helix formed by residues 647 - 671 (chain A) in PDB entry 3F7F
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 PHE 647 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A ILE* 3.6 33.2 - - + -
580A PRO* 3.8 29.2 - - + -
583A LEU* 3.9 4.7 - - + -
637A PHE* 3.6 30.7 - + + -
642A LEU* 4.0 27.6 - - + -
643A ASP 3.0 21.4 + - - +
644A THR 4.1 1.3 - - - -
646A ILE* 1.3 96.0 - - + +
648A GLY* 1.3 54.9 + - - +
649A GLN 3.1 2.9 - - - -
650A HIS* 3.2 23.6 + + + +
651A ILE* 2.7 40.1 + - + +
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Residues in contact with GLY 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A THR 3.2 20.5 + - - -
645A GLU* 3.2 9.2 + - - -
646A ILE 3.1 5.7 - - - -
647A PHE* 1.3 76.1 - - - +
649A GLN* 1.3 61.0 + - - +
651A ILE* 3.9 4.8 - - - +
652A SER* 3.1 24.6 + - - -
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Residues in contact with GLN 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A GLU 4.8 0.4 + - - -
646A ILE 4.3 5.4 + - - +
647A PHE 3.1 1.0 - - - -
648A GLY* 1.3 75.5 - - - +
650A HIS* 1.3 66.3 + - + +
652A SER* 3.0 15.5 + - - -
653A THR* 2.9 52.2 + - - +
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Residues in contact with HIS 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A PRO* 4.4 5.3 + - + +
583A LEU* 4.2 15.0 - - + +
584A ASN* 4.1 39.2 + - - -
587A ILE* 3.4 30.9 - - + +
588A ASN* 4.2 9.9 - - - -
637A PHE* 5.0 0.9 - - + -
646A ILE 5.7 1.3 - - - -
647A PHE* 3.2 36.0 + + + +
649A GLN* 1.3 85.7 - - + +
651A ILE* 1.3 58.3 + - - +
653A THR* 3.2 4.6 + - - -
654A LEU* 2.8 41.1 + - + +
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Residues in contact with ILE 651 (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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546A THR* 4.4 8.7 - - + +
550A PHE* 3.7 31.6 - - + -
634A LEU* 4.1 4.2 - - + +
637A PHE* 3.9 34.3 - - + -
642A LEU 5.4 1.6 - - - +
644A THR* 4.0 27.6 - - - +
647A PHE* 2.7 37.5 + - + +
648A GLY* 3.9 5.4 - - - +
650A HIS* 1.3 73.1 - - - +
652A SER* 1.3 58.5 + - - +
654A LEU* 3.7 8.2 - - - +
655A LEU* 3.0 41.1 + - + +
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Residues in contact with SER 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A GLY 3.1 13.4 + - - -
649A GLN* 3.0 22.9 + - - -
651A ILE* 1.3 78.4 - - - +
653A THR* 1.3 64.2 + - - +
655A LEU* 4.1 8.2 - - - +
656A ASP* 3.2 23.2 + - - +
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Residues in contact with THR 653 (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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587A ILE* 3.8 27.6 - - + -
592A LYS* 3.9 30.2 + - + +
649A GLN* 2.9 38.2 + - - +
650A HIS* 3.7 7.5 + - - -
652A SER* 1.3 76.6 - - - +
654A LEU* 1.3 59.6 + - - +
656A ASP* 3.4 5.7 + - + +
657A LEU* 3.0 31.6 + - + +
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Residues in contact with LEU 654 (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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583A LEU* 5.2 0.7 - - + -
586A LEU* 5.7 1.6 - - + -
587A ILE* 3.7 30.3 - - + -
591A MET* 5.0 8.5 - - - -
630A THR* 3.7 22.4 - - + +
633A VAL* 3.8 31.9 - - + -
634A LEU* 3.5 25.1 - - + -
637A PHE* 4.0 13.2 - - + -
650A HIS* 2.8 27.7 + - + +
651A ILE* 3.7 0.7 - - - +
653A THR* 1.3 75.7 - - - +
655A LEU* 1.3 59.8 + - - +
656A ASP 3.1 0.2 - - - -
657A LEU* 3.0 9.0 + - + +
658A HIS* 2.7 32.4 + - - +
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Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A PHE* 3.6 44.4 - - + +
535A ILE* 4.1 28.0 - - + -
536A ILE* 3.6 20.3 - - + +
550A PHE* 4.7 4.9 - - + -
634A LEU* 3.7 19.5 - - + -
651A ILE* 3.0 38.7 + - + +
652A SER* 3.6 8.0 + - - +
654A LEU* 1.3 75.5 - - - +
656A ASP* 1.3 60.5 + - - +
658A HIS* 3.8 5.5 + - - +
659A TYR* 3.2 22.3 + - - +
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Residues in contact with ASP 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ILE* 4.4 10.0 - - + +
592A LYS* 6.0 0.9 - - - -
652A SER 3.2 19.0 + - - +
653A THR* 3.6 6.9 - - + +
654A LEU 3.1 0.6 - - - -
655A LEU* 1.3 77.4 - - - +
657A LEU* 1.3 69.0 + - - +
659A TYR* 3.5 4.2 + - - +
660A LYS* 2.6 62.1 + - - +
714A ILE* 3.7 14.9 - - - +
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ILE* 4.9 5.2 - - + -
591A MET* 4.5 22.9 - - + -
592A LYS* 4.3 22.0 - - + -
630A THR* 4.7 2.0 - - + -
653A THR* 3.0 38.8 + - + +
654A LEU* 3.0 9.4 + - + +
656A ASP* 1.3 81.4 - - - +
658A HIS* 1.3 61.3 + - - +
660A LYS* 3.4 4.0 + - + +
661A GLN* 2.9 45.2 + - - +
710A TYR* 3.4 50.9 - - + +
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Residues in contact with HIS 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A SER* 2.8 46.9 + - - -
532A PHE* 3.6 17.2 - - + +
533A LEU* 3.9 18.1 - - + +
627A TYR* 3.5 23.9 - + - -
630A THR* 3.7 9.4 - - + +
631A LEU* 3.7 22.7 - - + +
634A LEU* 3.9 13.5 - - + -
654A LEU 2.7 16.9 + - - +
655A LEU 3.8 5.1 + - - +
657A LEU* 1.3 76.9 - - - +
659A TYR* 1.3 58.4 + - - +
661A GLN* 3.1 15.2 + - - +
662A PHE* 2.8 30.5 + - + +
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Residues in contact with TYR 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A LEU* 3.5 26.9 - - + -
536A ILE* 3.6 34.9 - - + +
537A THR* 3.9 19.1 - - + +
655A LEU 3.2 15.8 + - - +
656A ASP* 3.7 5.8 - - - +
657A LEU 3.3 0.2 - - - -
658A HIS* 1.3 79.5 + - - +
660A LYS* 1.3 63.6 + - - +
662A PHE* 3.4 1.9 + - - +
663A LEU* 3.0 52.6 + - + +
714A ILE* 3.6 37.2 + - + -
716A GLU* 3.7 6.9 + - - -
725A ARG* 3.1 30.5 - - - +
729A ILE* 4.1 9.6 - - + -
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Residues in contact with LYS 660 (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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656A ASP* 2.6 48.9 + - - +
657A LEU* 3.9 4.0 - - + +
659A TYR* 1.3 80.1 - - + +
661A GLN* 1.3 57.4 + - - +
663A LEU* 3.4 2.6 + - - +
664A LEU* 2.9 31.1 + - - +
709A VAL* 3.6 27.6 - - + +
710A TYR* 2.9 34.9 + - + +
711A ASN 4.9 0.6 - - - -
712A ALA 3.5 20.7 + - - +
714A ILE* 3.9 27.4 - - + -
720B PHE* 4.0 13.1 - - + -
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Residues in contact with GLN 661 (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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591A MET* 3.5 9.1 - - - +
623A LEU* 4.1 20.8 - - + +
626A HIS* 3.7 1.2 + - - +
627A TYR* 3.2 33.8 - - + -
630A THR* 2.8 27.6 + - - -
657A LEU* 2.9 30.1 + - - +
658A HIS* 3.3 16.7 - - - +
660A LYS* 1.3 73.0 - - - +
662A PHE* 1.3 68.5 + - - +
664A LEU* 3.4 4.3 + - - +
665A LEU* 2.9 30.5 + - - +
710A TYR* 3.0 30.3 + - + +
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Residues in contact with PHE 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ILE* 5.0 3.8 - - + -
398A VAL* 4.1 28.4 - - + +
529A SER* 4.1 9.9 - - - -
533A LEU* 3.5 36.6 - - + -
627A TYR* 3.7 32.7 - + + -
658A HIS* 2.8 20.6 + - + +
659A TYR 3.6 4.0 - - - +
661A GLN* 1.3 72.1 - - - +
663A LEU* 1.3 67.0 + - - +
665A LEU* 2.9 8.5 + - - +
666A ASN* 2.7 43.5 + - + +
729A ILE* 3.8 28.0 - - + -
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 3.0 47.9 + - + +
660A LYS 3.6 4.3 - - - +
662A PHE* 1.3 79.0 - - + +
664A LEU* 1.3 57.7 + - - +
666A ASN* 2.9 9.6 + - - +
667A LEU* 2.8 35.6 + - + +
714A ILE* 4.9 2.2 - - + -
725A ARG* 5.3 1.8 - - + -
729A ILE* 3.3 40.4 - - + -
720B PHE* 3.7 34.1 - - + -
724B PHE* 4.2 23.6 - - + -
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LEU* 6.3 0.2 - - + -
619A LEU* 4.0 18.6 - - + +
620A HIS* 5.4 2.7 - - + -
623A LEU* 2.8 40.8 - - + -
660A LYS 2.9 20.3 + - - +
661A GLN 3.8 3.1 - - - +
663A LEU* 1.3 72.6 - - - +
665A LEU* 1.3 62.0 + - + +
667A LEU* 3.1 4.6 + - - +
668A TYR* 2.8 29.5 + - + +
675A LEU* 4.0 23.3 - - + -
679A LEU* 4.4 4.7 - - + -
709A VAL* 4.0 15.5 - - + -
719B PHE* 3.8 27.6 - - + -
720B PHE* 3.9 4.7 - - + -
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Residues in contact with LEU 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 3.8 31.4 - - + -
620A HIS* 3.4 27.6 - - + +
623A LEU* 4.3 10.3 - - + +
624A SER* 3.2 34.8 - - - +
627A TYR* 3.9 30.5 - - + -
661A GLN 2.9 19.0 + - - +
662A PHE* 2.9 4.8 + - - +
664A LEU* 1.3 78.4 - - + +
666A ASN* 1.3 61.2 + - - +
668A TYR* 3.4 4.6 + - - +
669A ARG* 3.0 36.2 + - - +
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Residues in contact with ASN 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 4.1 15.7 - - + +
400A LYS* 4.0 15.8 + - - +
662A PHE* 2.7 34.9 + - + +
663A LEU* 2.9 14.6 + - - +
665A LEU* 1.3 75.7 - - - +
667A LEU* 1.3 65.5 + - + +
669A ARG* 3.4 8.1 + - - +
670A GLN* 3.1 46.8 + - - +
728A ILE* 3.4 27.6 + - - +
729A ILE* 4.2 4.7 - - - +
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Residues in contact with LEU 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A LEU* 2.8 26.9 + - + +
664A LEU* 3.7 4.3 - - - +
666A ASN* 1.3 71.5 - - + +
668A TYR* 1.3 65.3 + - - +
670A GLN* 4.1 1.6 - - - -
671A ASP 3.1 21.7 + - - +
675A LEU* 4.2 17.4 - - + +
728A ILE* 4.2 11.2 - - + -
719B PHE* 4.5 2.7 - - + -
720B PHE* 3.8 29.6 - - + +
723B PHE* 3.5 65.3 - - + -
724B PHE* 3.9 20.6 - - + -
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Residues in contact with TYR 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL* 4.1 12.8 - - + +
616A LEU* 4.1 26.5 - - + -
617A GLU* 2.5 41.1 + - - -
620A HIS* 3.1 56.5 - + + -
664A LEU* 2.8 13.9 + - + +
665A LEU* 3.5 8.5 - - - +
667A LEU* 1.3 80.7 - - - +
669A ARG* 1.3 72.4 + - + +
672A LYS* 3.3 56.1 + - + +
675A LEU* 3.6 13.8 - - + +
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Residues in contact with ARG 669 (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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390A GLN* 5.0 5.1 + - - -
396A ASP* 3.0 31.7 + - - -
398A VAL* 3.5 14.6 - - - +
399A THR* 3.1 39.7 + - + +
400A LYS 5.7 0.7 - - - +
406A ARG* 5.5 3.5 + - - -
410A ASN* 5.7 3.2 - - - +
413A SER* 2.8 28.5 + - - +
414A ARG* 6.5 0.7 - - - -
620A HIS* 2.6 38.5 + - - -
624A SER* 4.5 1.6 + - - -
665A LEU* 3.0 28.7 + - - +
666A ASN* 3.8 10.5 - - - +
668A TYR* 1.3 86.9 - - + +
670A GLN* 1.3 61.0 + - - +
671A ASP 3.4 0.4 - - - -
672A LYS* 4.4 3.4 - - - +
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Residues in contact with GLN 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 3.5 15.1 - - - +
406A ARG* 3.8 33.3 - - - +
413A SER* 4.7 4.8 + - - -
666A ASN* 3.1 35.7 + - - +
667A LEU* 3.2 8.5 + - + +
669A ARG* 1.3 81.5 - - - +
671A ASP* 1.3 63.0 + - - +
728A ILE* 3.9 11.3 - - + +
723B PHE* 4.3 7.2 - - + -
727B TYR* 3.0 53.4 + - + +
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Residues in contact with ASP 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A SER* 5.3 2.0 - - - -
667A LEU 3.1 9.1 + - - -
669A ARG 3.4 1.0 - - - -
670A GLN* 1.3 82.3 - - - +
672A LYS* 1.3 61.9 + - - +
673A CYS* 3.4 8.7 + - - +
674A LEU* 3.0 29.9 + - - +
675A LEU* 3.0 18.7 + - - +
723B PHE* 3.8 16.0 - - + -
727B TYR* 3.9 15.7 - - + -
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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