Contacts of the helix formed by residues 629 - 660 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B LYS* 4.4 4.2 - - + +
628B GLU* 1.3 78.9 - - - +
630B THR* 1.3 61.9 + - - +
631B VAL* 3.6 9.5 + - - +
632B ARG* 3.2 41.6 + - + +
633B LEU* 3.1 20.9 + - - +
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Residues in contact with THR 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ALA* 3.6 30.5 + - + +
619B SER* 4.5 6.2 - - - +
622B ALA* 3.5 23.1 - - + +
628B GLU 3.2 9.1 + - - -
629B ASP* 1.3 72.8 + - - +
631B VAL* 1.3 63.1 + - - +
633B LEU* 3.2 4.7 + - + +
634B LEU* 3.0 32.6 + - + +
699B LEU* 3.7 26.2 - - + -
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Residues in contact with VAL 631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ASP* 3.4 7.5 + - - +
630B THR* 1.3 75.7 - - - +
632B ARG* 1.3 58.2 + - - +
634B LEU* 3.3 3.4 + - - +
635B LYS* 3.0 55.4 + - + +
696B LEU* 4.2 12.1 - - + -
699B LEU* 4.2 25.1 - - + -
700B GLN* 3.8 22.4 - - + +
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Residues in contact with ARG 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B ASP* 3.2 34.9 + - + +
631B VAL* 1.3 80.4 - - - +
633B LEU* 1.3 62.2 + - - +
635B LYS* 3.6 9.0 + - - +
636B SER* 3.1 25.3 + - - -
639B ARG* 4.9 4.3 + - - +
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Residues in contact with LEU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B PHE* 3.9 19.1 - - + -
622B ALA* 3.4 33.0 - - + -
625B HIS* 3.6 29.4 - - + -
627B LYS* 3.8 28.7 - - + -
629B ASP 3.1 13.0 + - - +
630B THR* 3.4 8.5 - - + +
632B ARG* 1.3 78.0 - - - +
634B LEU* 1.3 57.8 + - + +
636B SER* 3.3 7.2 + - - -
637B GLN* 2.9 38.7 + - + +
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Residues in contact with LEU 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B ALA* 4.3 1.8 - - + -
621B PHE* 4.1 17.9 - - + -
630B THR* 3.0 27.5 + - + +
631B VAL 3.7 1.3 - - - +
633B LEU* 1.3 76.2 - - + +
635B LYS* 1.3 56.8 + - - +
637B GLN* 3.2 6.9 + - - +
638B THR* 2.9 35.0 + - - +
692B MET* 3.7 26.9 - - - +
695B TYR* 3.9 31.9 - - + -
696B LEU* 3.5 31.2 - - + +
699B LEU* 3.8 25.8 - - + -
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Residues in contact with LYS 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B VAL* 3.0 43.0 + - + +
632B ARG* 3.9 7.2 - - - +
634B LEU* 1.3 75.7 - - - +
636B SER* 1.3 62.5 + - - +
638B THR* 2.6 22.7 + - - -
639B ARG* 3.1 38.3 + - - +
696B LEU* 4.1 18.3 - - + +
700B GLN* 4.0 20.0 + - - +
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Residues in contact with SER 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B ARG* 3.1 20.3 + - - -
633B LEU* 3.5 10.3 - - - +
634B LEU 3.2 0.2 - - - -
635B LYS* 1.3 74.9 - - - +
637B GLN* 1.3 64.2 + - - +
639B ARG* 3.0 20.6 + - - +
640B SER* 3.1 23.0 + - - -
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Residues in contact with GLN 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B PHE* 4.0 30.6 - - + -
625B HIS* 3.8 19.5 + - - -
633B LEU* 2.9 24.6 + - + +
634B LEU 3.2 7.8 + - - +
636B SER* 1.3 76.2 - - - +
638B THR* 1.3 57.3 + - - +
640B SER* 3.3 8.3 + - - -
641B LEU* 2.9 47.7 + - + +
692B MET* 3.8 16.2 - - + -
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Residues in contact with THR 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B LEU 2.9 14.3 + - - +
635B LYS* 2.6 24.9 + - - -
637B GLN* 1.3 76.6 - - - +
639B ARG* 1.3 57.1 + - - +
641B LEU* 3.4 3.6 + - - +
642B LEU* 2.9 39.5 + - - +
689B LEU* 3.9 21.9 - - + +
692B MET* 3.4 28.7 - - + -
693B ARG* 4.6 7.0 - - + +
696B LEU* 4.5 14.6 - - + +
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Residues in contact with ARG 639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B ARG* 4.9 4.4 + - - +
635B LYS* 3.1 41.3 + - - +
636B SER* 3.0 38.9 - - - +
638B THR* 1.3 77.5 + - - +
640B SER* 1.3 63.4 + - - +
642B LEU* 3.4 10.8 + - + +
643B GLN* 3.0 22.0 + - - +
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Residues in contact with SER 640 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B SER* 3.1 15.8 + - - -
637B GLN* 3.5 10.5 + - - -
639B ARG* 1.3 81.6 - - - +
641B LEU* 1.3 63.0 + - - +
643B GLN* 3.0 23.5 + - - +
644B LYS* 3.1 30.5 + - - +
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Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLN* 2.9 33.6 + - - +
638B THR* 3.8 4.9 - - - +
639B ARG 3.3 0.2 - - - -
640B SER* 1.3 76.3 - - - +
642B LEU* 1.3 58.3 + - - +
644B LYS* 3.2 11.2 + - + +
645B ILE* 2.9 35.3 + - - +
685B PHE* 4.1 30.3 - - + +
688B ASP* 3.8 26.9 - - + +
689B LEU* 3.6 38.6 - - + +
692B MET* 4.0 13.2 - - + -
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Residues in contact with LEU 642 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B THR* 2.9 26.7 + - - +
639B ARG* 3.7 9.4 - - + +
641B LEU* 1.3 77.5 - - - +
643B GLN* 1.3 58.2 + - - +
645B ILE* 3.8 10.6 - - + +
646B ASP* 2.9 29.3 + - - +
686B HIS* 6.3 0.2 - - + -
689B LEU* 3.7 29.2 - - + -
693B ARG* 4.0 21.3 - - - +
----------------------------------------------------------
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Residues in contact with GLN 643 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B ARG 3.0 13.2 + - - +
640B SER* 3.0 17.4 + - - +
642B LEU* 1.3 78.7 - - - +
644B LYS* 1.3 62.1 + - + +
646B ASP* 3.2 7.6 + - - +
647B MET* 3.0 29.1 + - + +
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B SER* 3.1 27.4 + - - +
641B LEU* 3.2 13.6 + - + +
643B GLN* 1.3 79.7 - - + +
645B ILE* 1.3 61.4 + - - +
647B MET* 3.4 6.6 + - - +
648B ASP* 3.0 30.1 + - - +
685B PHE* 3.4 43.9 - - + -
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Residues in contact with ILE 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU 2.9 22.3 + - - +
642B LEU* 3.8 11.4 - - + +
644B LYS* 1.3 73.2 - - - +
646B ASP* 1.3 66.8 + - - +
649B SER* 2.9 38.9 + - - +
682B LEU* 3.9 10.9 - - + +
685B PHE* 3.4 37.2 - - + +
686B HIS* 3.7 33.7 - - + +
689B LEU* 3.8 28.7 - - + -
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Residues in contact with ASP 646 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B LEU 2.9 19.7 + - - +
643B GLN* 3.2 8.3 + - - +
645B ILE* 1.3 78.1 - - - +
647B MET* 1.3 66.3 + - - +
649B SER* 3.7 3.8 - - - -
650B LYS* 3.0 62.5 + - - +
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Residues in contact with MET 647 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B GLN* 3.0 17.0 + - + +
644B LYS* 3.7 7.0 - - - +
645B ILE 3.3 0.2 - - - -
646B ASP* 1.3 80.7 + - - +
648B ASP* 1.3 72.6 + - - +
650B LYS* 4.6 11.7 - - + -
651B MET* 3.0 51.0 + - + +
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Residues in contact with ASP 648 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LYS* 3.0 16.3 + - - +
647B MET* 1.3 85.0 - - - +
649B SER* 1.3 57.5 + - - +
651B MET* 3.6 4.4 + - - +
652B LYS* 2.9 29.7 + - - +
678B TRP* 3.6 29.1 + - + +
681B ASN* 3.3 34.0 + - - +
682B LEU* 4.1 20.2 - - + -
685B PHE* 3.5 10.5 - - - -
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Residues in contact with SER 649 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B ILE* 2.9 30.2 + - - +
646B ASP* 3.7 4.5 - - - -
648B ASP* 1.3 74.9 - - - +
650B LYS* 1.3 61.9 + - - +
652B LYS* 3.0 8.5 + - - +
653B LYS* 2.8 29.9 + - - +
682B LEU* 3.7 18.7 - - - +
686B HIS* 5.3 1.0 + - - -
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Residues in contact with LYS 650 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B ASP* 3.0 48.9 + - - +
647B MET* 3.8 12.8 - - + +
649B SER* 1.3 77.0 - - - +
651B MET* 1.3 58.2 + - + +
653B LYS* 3.2 14.6 + - - +
654B MET* 2.9 33.3 + - + +
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Residues in contact with MET 651 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B MET* 3.0 48.3 + - + +
648B ASP* 4.0 3.8 - - - +
650B LYS* 1.3 76.4 - - - +
652B LYS* 1.3 57.5 + - - +
654B MET* 3.6 7.6 - - - +
655B ALA* 2.9 29.8 + - - +
678B TRP* 3.4 36.6 - - + -
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Residues in contact with LYS 652 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ASP 2.9 18.4 + - - +
649B SER* 3.3 6.5 - - - +
651B MET* 1.3 75.8 - - - +
653B LYS* 1.3 60.3 + - - +
655B ALA* 3.3 2.3 + - - +
656B GLU* 2.9 60.3 + - + +
675B ILE* 4.4 9.0 - - + -
678B TRP* 3.6 27.1 - - + -
679B GLU* 3.5 34.6 + - + -
682B LEU* 3.8 24.0 - - + -
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Residues in contact with LYS 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B SER 2.8 12.9 + - - +
650B LYS* 3.2 15.9 + - - +
652B LYS* 1.3 73.6 - - - +
654B MET* 1.3 78.1 + - - +
656B GLU* 2.9 17.7 + - - +
657B LEU* 2.9 56.8 + - + +
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Residues in contact with MET 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650B LYS* 2.9 18.6 + - + +
651B MET* 3.6 9.0 - - - +
653B LYS* 1.3 89.3 - - - +
655B ALA* 1.3 58.1 + - - +
657B LEU* 3.1 38.6 + - + +
658B GLN* 2.9 33.5 + - - +
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Residues in contact with ALA 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B MET 2.9 19.6 + - - +
652B LYS 3.5 4.3 - - - +
653B LYS 3.2 0.2 - - - -
654B MET* 1.3 76.7 - - - +
656B GLU* 1.3 56.9 + - - +
658B GLN* 3.2 7.2 + - - +
659B LEU 3.0 23.9 + - - -
671B ILE* 3.5 22.2 - - + +
674B GLN* 5.8 0.2 - - + -
675B ILE* 4.0 11.7 - - + -
678B TRP* 3.5 22.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B LYS* 2.9 57.9 + - - +
653B LYS* 2.9 18.0 + - + +
655B ALA* 1.3 75.9 - - - +
657B LEU* 1.3 65.5 + - + +
659B LEU* 3.4 17.2 + - + +
660B SER* 3.5 8.0 + - - -
675B ILE* 3.6 25.2 - - + +
679B GLU* 5.6 0.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B LYS* 2.9 49.3 + - + +
654B MET* 3.3 38.4 - - + +
656B GLU* 1.3 77.6 - - + +
658B GLN* 1.3 62.7 + - - +
660B SER* 2.5 27.8 + - - -
661B VAL* 3.8 6.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B MET* 2.9 16.6 + - - +
655B ALA* 3.2 11.9 + - - +
657B LEU* 1.3 77.9 - - - +
659B LEU* 1.3 62.6 + - - +
661B VAL* 3.1 24.5 + - - +
662B VAL* 3.0 25.1 + - - +
671B ILE* 3.9 13.3 - - + +
----------------------------------------------------------
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Residues in contact with LEU 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B ALA 3.0 12.8 + - - +
656B GLU* 3.5 13.0 - - + +
657B LEU 3.2 0.2 - - - -
658B GLN* 1.3 78.9 - - - +
660B SER* 1.3 60.5 + - - +
662B VAL* 3.2 7.0 - - + +
668B ARG* 2.7 70.5 + - + +
671B ILE* 4.1 10.7 - - + +
672B GLU* 3.0 33.0 - - + +
675B ILE* 4.5 16.6 - - + -
----------------------------------------------------------
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Residues in contact with SER 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B GLU 3.5 7.6 + - - -
657B LEU* 2.5 24.8 + - - -
659B LEU* 1.3 79.2 - - - +
661B VAL* 1.3 66.8 + - - +
662B VAL 3.7 0.4 - - - -
668B ARG* 5.0 2.5 - - - +
----------------------------------------------------------
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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