Contacts of the helix formed by residues 619 - 646 (chain A) in PDB entry 4MXP
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 619 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LYS* 4.1 0.2 - - - +
604A LEU 2.7 26.5 + - - +
605A ALA* 3.5 19.6 + - - +
606A LYS 3.9 0.9 - - - +
607A GLY* 3.9 11.4 - - - +
612A THR* 4.0 7.9 - - + -
617A LEU 3.5 0.2 + - - -
618A LYS* 1.3 79.1 - - - +
620A SER* 1.3 65.1 + - - +
622A VAL* 3.2 20.3 + - - +
623A SER* 3.2 22.2 + - - -
701A DB4 3.3 35.9 - - - +
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Residues in contact with SER 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A TYR* 3.9 9.9 - - - -
533A LYS 6.1 0.2 - - - -
534A TYR* 3.4 19.4 + - - -
618A LYS 3.9 0.4 + - - -
619A THR* 1.3 72.9 - - - +
621A SER* 1.3 57.4 + - - +
623A SER* 3.1 10.0 + - - -
624A SER* 2.9 29.5 + - - -
701A DB4 2.7 38.8 + - - -
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Residues in contact with SER 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A TYR* 3.8 14.1 - - - -
568A LYS* 3.5 9.8 - - - +
572A LEU* 3.6 20.4 - - - +
604A LEU* 3.1 38.1 + - - +
620A SER* 1.3 71.2 - - - +
622A VAL* 1.3 63.4 + - - +
624A SER* 3.2 9.8 + - - -
625A PHE* 2.9 20.3 + - - +
701A DB4 2.7 27.9 + - - -
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Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A TYR* 3.6 24.2 - - + +
604A LEU* 4.0 5.4 - - + -
605A ALA* 3.5 34.1 - - + +
618A LYS* 3.6 19.5 - - + -
619A THR* 3.2 23.0 + - - +
621A SER* 1.3 78.0 + - - +
623A SER* 1.3 57.9 + - - +
625A PHE* 3.3 7.7 + - - +
626A GLU* 3.0 49.0 + - + +
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Residues in contact with SER 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A LYS* 3.4 21.1 + - - +
619A THR 3.2 10.1 + - - -
620A SER* 3.1 13.4 + - - -
622A VAL* 1.3 76.9 - - - +
624A SER* 1.3 56.5 + - - +
626A GLU* 3.4 10.5 + - - +
627A LYS* 2.9 30.5 + - - +
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Residues in contact with SER 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU 3.6 13.0 - - - -
531A SER* 2.7 29.3 + - - -
532A TYR* 3.4 15.4 - - - +
572A LEU* 4.0 12.6 - - - -
620A SER 2.9 14.9 + - - -
621A SER 3.2 8.0 + - - -
623A SER* 1.3 77.1 - - - +
625A PHE* 1.3 63.0 + - - +
627A LYS* 3.2 8.1 + - - +
628A MET* 3.0 27.4 + - - +
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Residues in contact with PHE 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A LEU* 3.9 8.0 - - + +
575A PHE* 3.8 25.6 - + + -
579A LEU* 4.1 11.7 - - + -
592A VAL* 4.2 14.1 - - + -
595A LEU* 3.8 37.7 - - + -
596A LYS* 4.0 23.8 - - + -
601A TYR* 3.8 18.8 - + - -
604A LEU* 4.6 4.0 - - + -
621A SER 2.9 12.5 + - - +
622A VAL* 3.5 10.1 - - - +
624A SER* 1.3 76.2 - - - +
626A GLU* 1.3 65.5 + - + +
628A MET* 3.1 12.4 + - + +
629A VAL* 2.9 56.0 + - + +
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Residues in contact with GLU 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LYS* 5.3 5.6 + - - +
601A TYR* 4.6 4.8 + - - +
618A LYS* 2.8 38.8 + - - +
622A VAL* 3.0 33.0 + - + +
623A SER* 3.7 6.9 - - - +
625A PHE* 1.3 82.8 - - + +
627A LYS* 1.3 57.8 + - - +
629A VAL* 3.3 8.3 + - - +
630A GLU* 2.9 36.6 + - + +
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Residues in contact with LYS 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LYS* 5.2 10.3 - - - +
531A SER* 3.0 33.0 + - - +
623A SER 2.9 14.6 + - - +
624A SER* 3.2 10.7 + - - +
626A GLU* 1.3 77.7 - - - +
628A MET* 1.3 57.3 + - - +
630A GLU* 3.4 4.9 + - - +
631A GLU* 2.9 64.8 + - + +
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Residues in contact with MET 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU* 4.1 19.7 - - - +
531A SER* 4.6 9.2 - - - +
572A LEU* 4.0 29.2 - - + +
575A PHE* 5.0 0.2 - - + -
576A LYS* 3.6 51.1 - - + +
579A LEU* 3.8 13.7 - - + -
624A SER 3.0 13.6 + - - +
625A PHE* 3.1 23.8 + - + +
627A LYS* 1.3 73.9 - - - +
629A VAL* 1.3 56.3 - - - +
631A GLU* 3.4 9.7 + - - +
632A THR* 2.7 39.5 + - - +
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Residues in contact with VAL 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU* 4.0 9.4 - - + -
588A LEU* 4.0 4.2 - - + +
592A VAL* 3.8 30.1 - - + -
625A PHE* 2.9 51.4 + - + +
626A GLU* 3.6 9.6 - - - +
628A MET* 1.3 76.8 - - - +
630A GLU* 1.3 62.2 + - - +
632A THR* 3.2 6.1 + - - -
633A ARG* 2.9 50.8 + - - +
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Residues in contact with GLU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A GLU* 2.9 22.2 + - + +
627A LYS* 4.0 4.7 - - - +
629A VAL* 1.3 79.9 - - - +
631A GLU* 1.3 58.6 + - + +
633A ARG* 2.8 46.0 + - - +
634A GLU* 3.0 41.7 + - + +
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Residues in contact with GLU 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A HIS* 5.7 5.4 + - - -
499A ALA* 4.8 20.7 - - + +
503A LYS* 5.1 7.3 + - - +
531A SER* 4.9 2.6 + - - -
576A LYS* 5.7 2.1 + - - -
627A LYS* 2.9 57.8 + - + +
628A MET* 3.8 10.6 - - - +
630A GLU* 1.3 77.3 - - + +
632A THR* 1.3 55.6 + - - +
634A GLU* 3.5 5.4 + - - +
635A SER* 2.9 31.1 + - - -
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Residues in contact with THR 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ASN* 5.0 11.0 + - - +
579A LEU* 3.9 27.9 - - - +
582A ALA* 4.3 2.7 - - + +
588A LEU* 3.9 23.8 - - + -
628A MET* 2.7 23.4 + - - +
629A VAL* 3.5 4.9 - - - -
631A GLU* 1.3 74.5 - - - +
633A ARG* 1.3 59.8 + - - +
635A SER* 3.4 5.6 + - - -
636A ILE* 2.9 47.7 + - + +
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Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A GLU* 2.8 41.9 + - - +
588A LEU* 3.6 26.4 - - + +
589A LYS* 4.1 17.8 - - - +
592A VAL* 5.6 1.4 - - - +
629A VAL* 2.9 30.0 + - - +
630A GLU* 2.8 46.6 + - - +
632A THR* 1.3 77.5 - - - +
634A GLU* 1.3 63.2 + - - +
636A ILE* 3.4 5.0 + - - +
637A LYS* 3.0 53.4 + - - +
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Residues in contact with GLU 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ARG* 5.5 11.2 - - - +
630A GLU* 3.0 27.6 + - + +
631A GLU* 4.0 4.9 - - - +
633A ARG* 1.3 78.2 - - + +
635A SER* 1.3 60.6 + - - +
637A LYS* 3.4 32.8 + - - +
638A SER* 2.8 30.5 + - - -
641A ARG* 5.4 2.9 + - - -
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Residues in contact with SER 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ASN* 5.2 2.8 + - - -
498A ILE* 3.9 6.8 - - - +
499A ALA* 4.5 9.7 + - - -
502A GLN* 2.6 28.8 + - - -
631A GLU 2.9 19.5 + - - -
632A THR* 3.7 5.8 - - - -
634A GLU* 1.3 74.7 - - - +
636A ILE* 1.3 59.4 + - - +
638A SER* 3.2 1.7 + - - -
639A GLN* 2.9 55.6 + - - +
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Residues in contact with ILE 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA* 4.1 15.9 - - + +
583A THR 4.6 7.9 - - - +
584A ASP* 3.8 23.6 - - - +
585A GLU* 3.9 19.3 - - + +
588A LEU* 4.2 12.3 - - + -
632A THR* 2.9 36.6 + - + +
633A ARG* 3.5 5.6 - - - +
635A SER* 1.3 75.9 - - - +
637A LYS* 1.3 59.8 + - + +
639A GLN* 3.2 7.2 + - - +
640A GLU* 2.9 56.7 + - - +
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Residues in contact with LYS 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A GLU* 5.0 9.4 - - + +
633A ARG* 3.0 36.4 + - + +
634A GLU* 3.4 32.7 + - - +
636A ILE* 1.3 79.1 - - + +
638A SER* 1.3 56.4 + - - +
640A GLU* 3.5 5.6 + - - +
641A ARG* 3.1 45.5 + - - +
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Residues in contact with SER 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LYS* 5.9 1.4 + - - -
502A GLN* 3.7 26.2 + - - +
505A GLU* 5.6 0.7 + - - -
506A ARG* 5.9 2.9 + - - -
634A GLU 2.8 18.8 + - - -
635A SER* 3.5 5.2 - - - -
637A LYS* 1.3 77.2 - - - +
639A GLN* 1.3 61.1 + - - +
641A ARG* 3.5 31.4 + - - +
642A GLN* 3.3 18.5 + - - +
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Residues in contact with GLN 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 5.3 1.3 - - + -
473A GLN* 2.8 43.2 - - - +
476A LYS* 5.1 10.1 + - - +
495A ASN* 5.5 2.3 - - - +
498A ILE* 4.0 17.3 - - + +
502A GLN* 3.6 15.3 - - - +
635A SER* 2.9 40.7 + - - +
636A ILE* 4.1 5.1 + - - +
638A SER* 1.3 76.6 - - - +
640A GLU* 1.3 57.6 + - - +
642A GLN* 3.1 10.8 + - + +
643A THR* 2.9 27.8 + - - -
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Residues in contact with GLU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A THR 3.4 21.7 - - - +
584A ASP* 3.8 15.4 - - - +
585A GLU* 4.6 3.8 + - - +
636A ILE* 2.9 32.8 + - - +
637A LYS* 4.0 6.2 + - - +
639A GLN* 1.3 73.1 - - - +
641A ARG* 1.3 64.8 + - - +
642A GLN 3.1 0.7 - - - -
643A THR* 3.6 18.6 + - - +
644A ILE* 3.4 22.9 + - - +
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Residues in contact with ARG 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ARG* 6.3 1.0 - - - +
634A GLU* 5.4 2.8 + - - -
637A LYS* 3.1 36.9 + - - +
638A SER* 3.5 34.7 + - - +
639A GLN 3.3 0.2 - - - -
640A GLU* 1.3 76.5 - - - +
642A GLN* 1.3 63.1 + - - +
644A ILE* 3.5 20.1 + - + +
645A LYS* 3.2 21.6 - - + +
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Residues in contact with GLN 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLY 5.3 1.0 + - - -
466A LYS* 4.4 30.7 + - - +
473A GLN* 6.0 3.4 - - - +
638A SER 3.3 10.0 + - - +
639A GLN* 3.1 15.8 + - + +
641A ARG* 1.3 80.0 - - - +
643A THR* 1.3 61.1 + - - +
645A LYS* 3.0 29.6 + - - +
646A ILE* 3.0 52.8 + - + +
----------------------------------------------------------
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Residues in contact with THR 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A GLN 2.9 14.4 + - - -
640A GLU* 3.9 18.1 - - - +
641A ARG 3.4 0.6 - - - -
642A GLN* 1.3 74.8 - - - +
644A ILE* 1.3 63.0 + - - +
646A ILE* 3.3 30.9 + - + +
----------------------------------------------------------
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Residues in contact with ILE 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A GLU 3.4 17.9 - - - +
641A ARG* 3.5 15.5 + - + +
642A GLN 3.2 0.4 - - - -
643A THR* 1.3 77.6 - - - +
645A LYS* 1.3 63.5 + - + +
646A ILE 4.8 1.2 - - - -
----------------------------------------------------------
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Residues in contact with LYS 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LYS* 4.0 6.8 - - - +
641A ARG* 3.2 18.2 - - + +
642A GLN* 3.0 34.9 + - - +
644A ILE* 1.3 80.1 - - + +
646A ILE* 1.3 60.8 + - + +
----------------------------------------------------------
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Residues in contact with ILE 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 5.4 0.2 - - - +
362A LYS* 3.7 40.8 + - - +
363A GLY 3.5 20.6 - - - +
364A ASN* 3.6 49.3 + - + +
365A ILE 5.2 1.1 - - - +
366A SER* 5.5 2.0 - - - +
473A GLN* 5.8 3.6 - - - +
639A GLN 5.8 0.2 - - - +
642A GLN* 3.0 49.6 + - + +
643A THR* 3.3 24.6 + - + +
644A ILE 4.8 1.8 - - - -
645A LYS* 1.3 83.9 - - + +
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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