Contacts of the helix formed by residues 629 - 660 (chain A) in PDB entry 3A8P
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 ASP 629 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LYS* 3.6 5.9 - - + +
628A GLU* 1.3 75.5 - - - +
630A THR* 1.3 62.9 + - - +
631A VAL* 3.8 6.9 + - - +
632A ARG* 3.4 41.8 + - + +
633A LEU* 3.2 20.4 + - - +
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Residues in contact with THR 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA* 3.5 31.6 + - + +
619A SER* 4.6 4.7 - - - +
622A ALA* 3.7 21.3 - - + +
628A GLU 3.2 8.8 + - - -
629A ASP* 1.3 72.5 + - - +
631A VAL* 1.3 64.0 + - - +
633A LEU* 3.1 4.2 + - + +
634A LEU* 2.9 33.2 + - + +
699A LEU* 3.7 26.0 - - + -
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Residues in contact with VAL 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ASP* 3.4 7.3 + - - +
630A THR* 1.3 75.1 - - - +
632A ARG* 1.3 60.0 + - - +
634A LEU* 3.4 3.8 + - - +
635A LYS* 3.0 55.1 + - + +
696A LEU* 3.9 15.3 - - + -
699A LEU* 4.3 19.7 - - + -
700A GLN* 3.9 21.8 - - + +
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Residues in contact with ARG 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ASP* 3.3 36.2 + - - +
630A THR 3.2 0.8 - - - -
631A VAL* 1.3 77.1 - - - +
633A LEU* 1.3 61.2 + - - +
635A LYS* 3.5 5.6 + - - -
636A SER* 2.9 29.3 + - - -
639A ARG* 3.8 11.7 + - - +
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A PHE* 3.8 22.2 - - + -
622A ALA* 3.4 35.9 - - + -
625A HIS* 3.8 34.5 - - + -
627A LYS* 4.1 21.5 - - + -
629A ASP 3.2 9.0 + - - +
630A THR* 3.1 8.8 + - + +
632A ARG* 1.3 79.4 - - - +
634A LEU* 1.3 58.1 + - - +
636A SER* 3.2 8.1 + - - -
637A GLN* 2.9 43.0 + - + +
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Residues in contact with LEU 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA* 4.4 1.1 - - + -
621A PHE* 4.0 19.7 - - + -
630A THR* 2.9 25.6 + - + +
631A VAL 3.6 4.0 - - - +
633A LEU* 1.3 77.2 - - + +
635A LYS* 1.3 56.9 - - - +
637A GLN* 3.2 6.8 + - - +
638A THR* 3.0 32.9 + - - +
692A MET* 3.8 25.6 - - - +
695A TYR* 3.7 22.0 - - + -
696A LEU* 3.5 50.9 - - + +
699A LEU* 4.1 15.7 - - + -
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Residues in contact with LYS 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A VAL* 3.0 36.8 + - + +
632A ARG* 3.9 6.1 - - - +
634A LEU* 1.3 73.6 - - - +
636A SER* 1.3 66.8 + - - +
638A THR* 2.7 23.4 + - - +
639A ARG* 3.1 27.0 + - - +
696A LEU* 4.0 18.4 - - + -
700A GLN* 4.2 18.7 - - - +
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Residues in contact with SER 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ARG* 2.9 20.0 + - - -
633A LEU* 3.5 11.2 - - - -
635A LYS* 1.3 77.3 - - - +
637A GLN* 1.3 62.4 + - - +
639A ARG* 3.3 28.3 + - - +
640A SER* 3.1 22.9 + - - -
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Residues in contact with GLN 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A PHE* 3.3 38.1 - - + -
625A HIS* 4.1 10.0 + - - -
633A LEU* 2.9 27.4 + - + +
634A LEU 3.4 8.1 - - - +
636A SER* 1.3 79.7 + - - +
638A THR* 1.3 57.8 + - - +
640A SER* 3.1 10.8 + - - -
641A LEU* 2.8 42.0 + - + +
692A MET* 3.8 17.3 - - + -
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Residues in contact with THR 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A LEU 3.0 14.0 + - - +
635A LYS* 2.7 23.4 + - - +
637A GLN* 1.3 75.9 - - - +
639A ARG* 1.3 64.1 + - - +
641A LEU* 4.6 1.6 - - - -
642A LEU* 3.0 35.1 + - - +
689A LEU* 3.8 22.3 - - + +
692A MET* 3.7 22.4 - - + -
693A ARG* 4.6 11.0 - - + -
696A LEU* 4.0 17.3 - - + +
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Residues in contact with ARG 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ARG* 3.8 13.9 + - - +
635A LYS* 3.1 21.4 + - - +
636A SER* 3.3 44.0 + - - +
638A THR* 1.3 83.2 + - - +
640A SER* 1.3 63.6 + - - +
642A LEU* 3.2 11.9 + - + +
643A GLN* 3.1 29.5 + - + +
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Residues in contact with SER 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A SER 3.1 10.9 + - - -
637A GLN* 3.5 17.3 + - - -
639A ARG* 1.3 77.9 - - - +
641A LEU* 1.3 66.5 + - - +
643A GLN* 3.0 12.8 + - - +
644A LYS* 3.0 43.6 + - - +
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Residues in contact with LEU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLN* 2.8 31.3 + - + +
638A THR* 3.9 4.5 - - - +
640A SER* 1.3 73.1 - - - +
642A LEU* 1.3 56.8 + - - +
644A LYS* 3.2 11.5 + - + +
645A ILE* 2.9 35.9 + - + +
685A PHE* 3.9 36.9 - - + +
688A ASP* 3.6 27.8 - - + +
689A LEU* 3.5 35.7 - - + +
692A MET* 3.9 13.0 - - + -
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Residues in contact with LEU 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A THR* 3.0 32.0 + - - +
639A ARG* 3.5 9.4 - - + +
640A SER 3.2 0.2 - - - -
641A LEU* 1.3 77.4 - - - +
643A GLN* 1.3 61.0 + - + +
645A ILE* 3.5 12.4 + - + +
646A ASP* 3.2 21.3 + - - +
689A LEU* 3.6 27.6 - - + -
693A ARG* 4.3 18.4 - - - +
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Residues in contact with GLN 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ARG* 3.1 15.4 + - + +
640A SER* 3.0 13.9 + - - +
642A LEU* 1.3 73.5 - - - +
644A LYS* 1.3 62.9 + - + +
646A ASP* 3.1 8.2 + - - +
647A MET* 2.9 29.0 + - - +
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Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A SER* 3.0 35.0 + - - +
641A LEU* 3.6 13.6 - - + +
643A GLN* 1.3 78.1 - - + +
645A ILE* 1.3 56.8 + - - +
647A MET* 4.3 6.1 - - - -
648A ASP* 2.9 36.9 + - - +
685A PHE* 4.0 40.5 - - + -
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Residues in contact with ILE 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU 2.9 21.7 + - - +
642A LEU* 3.7 11.4 - - + +
644A LYS* 1.3 77.1 - - - +
646A ASP* 1.3 57.7 + - - +
649A SER* 2.6 46.2 + - - +
682A LEU* 3.6 9.7 - - + +
685A PHE* 3.5 28.5 - - + +
686A HIS* 3.9 46.4 - - + +
689A LEU* 4.1 21.8 - - + -
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Residues in contact with ASP 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A LEU 3.2 10.7 + - - +
643A GLN* 3.1 11.2 + - - +
645A ILE* 1.3 81.2 - - - +
647A MET* 1.3 64.8 + - - +
649A SER* 3.7 4.9 - - - -
650A LYS* 3.2 55.7 + - - +
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Residues in contact with MET 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLN 2.9 16.3 + - - +
644A LYS* 3.8 7.9 - - - +
646A ASP* 1.3 81.3 + - - +
648A ASP* 1.3 65.3 + - - +
650A LYS* 3.3 10.1 + - - +
651A MET* 3.0 73.9 + - + +
678A TRP* 5.7 0.7 - - + -
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Residues in contact with ASP 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LYS* 2.9 23.9 + - - +
647A MET* 1.3 80.0 - - - +
649A SER* 1.3 63.9 + - - +
651A MET* 3.7 6.1 - - - +
652A LYS* 3.0 24.6 + - - +
678A TRP* 3.6 33.0 - - + +
681A ASN* 3.7 13.3 + - - +
682A LEU* 3.6 23.0 - - + +
685A PHE* 3.3 22.6 - - + -
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Residues in contact with SER 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ILE* 2.6 33.7 + - - +
646A ASP* 3.7 6.0 - - - -
647A MET 3.3 0.2 - - - -
648A ASP* 1.3 77.1 - - - +
650A LYS* 1.3 65.8 + - - +
652A LYS* 3.3 5.6 + - - +
653A LYS* 3.1 31.7 + - - +
682A LEU* 3.7 19.9 - - - +
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Residues in contact with LYS 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A ASP* 3.2 41.8 + - - +
647A MET* 3.6 10.3 - - - +
648A ASP 3.2 0.2 - - - -
649A SER* 1.3 77.3 - - - +
651A MET* 1.3 76.2 + - + +
653A LYS* 3.2 9.7 + - + +
654A MET* 3.0 22.2 + - - +
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Residues in contact with MET 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A MET* 3.0 56.8 + - + +
648A ASP 3.7 5.2 - - - +
649A SER 3.3 0.4 - - - -
650A LYS* 1.3 86.4 - - + +
652A LYS* 1.3 57.2 + - - +
654A MET* 3.2 11.3 + - + +
655A ALA* 2.9 28.9 + - - +
678A TRP* 3.5 42.3 + - + -
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Residues in contact with LYS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ASP 3.0 18.6 + - - +
649A SER* 3.5 6.5 - - - +
650A LYS 3.2 0.2 - - - -
651A MET* 1.3 77.6 - - - +
653A LYS* 1.3 61.0 + - + +
655A ALA* 3.5 2.4 + - - +
656A GLU* 3.0 58.7 + - - +
675A ILE* 4.1 15.7 - - + -
678A TRP* 4.0 20.4 - - + -
679A GLU* 3.8 42.9 + - - +
682A LEU* 4.0 20.0 - - + -
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Residues in contact with LYS 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A SER* 3.1 20.8 + - - +
650A LYS* 3.2 10.1 + - + +
652A LYS* 1.3 74.4 - - + +
654A MET* 1.3 66.1 + - - +
656A GLU* 3.3 18.6 + - - +
657A LEU* 2.9 23.0 + - - +
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Residues in contact with MET 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A LYS 3.0 13.4 + - - +
651A MET* 3.2 17.5 + - + +
653A LYS* 1.3 78.5 - - - +
655A ALA* 1.3 62.9 + - - +
657A LEU* 3.1 28.7 + - + +
658A GLN* 2.9 61.6 + - + +
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Residues in contact with ALA 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A MET 2.9 16.1 + - - +
652A LYS 3.7 4.9 - - - +
653A LYS 3.3 0.2 - - - -
654A MET* 1.3 76.0 - - - +
656A GLU* 1.3 56.8 + - - +
658A GLN* 3.1 11.5 + - - +
659A LEU* 2.9 27.7 + - - +
671A ILE* 3.8 9.4 - - + +
674A GLN* 4.2 21.8 - - - +
675A ILE* 3.9 19.1 - - + -
678A TRP* 4.2 7.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A LYS* 3.0 53.0 + - - +
653A LYS* 3.5 23.6 + - - +
654A MET 3.2 0.2 - - - -
655A ALA* 1.3 77.1 - - - +
657A LEU* 1.3 62.2 + - - +
659A LEU* 3.1 6.8 + - + +
660A SER* 3.0 22.5 + - - -
675A ILE* 3.7 29.3 - - + +
----------------------------------------------------------
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A LYS 2.9 13.9 + - - +
654A MET* 3.1 31.8 + - + +
656A GLU* 1.3 75.0 - - - +
658A GLN* 1.3 65.4 + - - +
660A SER* 2.6 32.8 + - - +
661A VAL* 4.3 3.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A MET* 2.9 60.2 + - + +
655A ALA* 3.5 9.2 - - - +
657A LEU* 1.3 84.2 - - - +
659A LEU* 1.3 60.6 + - - +
660A SER 3.4 0.5 + - - -
661A VAL* 3.5 21.9 - - - +
662A VAL* 3.5 10.0 - - - +
671A ILE* 4.7 9.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A ALA 2.9 12.7 + - - +
656A GLU* 3.1 11.2 + - + +
658A GLN* 1.3 77.8 - - - +
660A SER* 1.3 62.6 + - - +
662A VAL* 3.0 13.8 + - + -
668A ARG* 3.1 72.5 + - + +
671A ILE* 3.9 22.1 - - + +
672A GLU* 4.1 13.5 - - + +
675A ILE* 3.8 21.5 - - + -
----------------------------------------------------------
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Residues in contact with SER 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A GLU 3.0 10.0 + - - -
657A LEU* 2.6 31.6 + - - +
659A LEU* 1.3 77.1 - - - +
661A VAL* 1.3 66.6 + - - +
668A ARG* 4.1 12.6 + - - +
----------------------------------------------------------
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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