Contacts of the helix formed by residues 588 - 612 (chain C) in PDB entry 4KBQ
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 GLU 588 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C THR 2.8 20.7 - - - +
587C ALA* 1.3 79.1 - - - +
589C LYS* 1.3 69.9 + - + +
590C GLU* 3.3 4.0 - - + +
591C GLU* 2.9 18.8 + - + +
592C PHE* 2.9 21.7 + - - +
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Residues in contact with LYS 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C ASP* 5.6 10.5 - - + +
538C THR* 5.2 12.9 - - - +
588C GLU* 1.3 77.4 - - + +
590C GLU* 1.3 59.9 + - + +
592C PHE* 3.2 8.7 + - - +
593C GLU* 2.9 40.5 + - + +
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Residues in contact with GLU 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C GLU* 3.3 3.2 - - + +
589C LYS* 1.3 79.5 - - + +
591C GLU* 1.3 58.0 + - - +
593C GLU* 3.2 19.8 + - - +
594C HIS* 2.9 29.5 + - - +
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Residues in contact with GLU 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C TRP* 3.8 11.2 + - + -
584C ASN* 4.1 12.6 + - - -
587C ALA* 3.3 22.8 - - + +
588C GLU* 2.9 34.4 + - + +
590C GLU* 1.3 79.0 - - - +
592C PHE* 1.3 62.0 + - - +
594C HIS* 3.4 13.6 + - - +
595C GLN* 3.5 18.5 + - - +
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Residues in contact with PHE 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C THR* 3.5 39.9 - - - -
539C GLU* 3.9 16.8 - - + -
541C SER* 5.4 0.2 - - - -
542C LEU* 3.3 38.9 - - + +
580C TRP* 4.1 13.4 - + + -
581C LEU* 4.2 16.8 - - + -
587C ALA* 6.1 1.1 - - + +
588C GLU 2.9 12.2 + - - +
589C LYS* 3.2 11.6 + - - +
591C GLU* 1.3 77.2 - - - +
593C GLU* 1.3 71.3 + - + +
595C GLN* 3.2 6.4 + - - +
596C GLN* 3.2 36.8 + - - +
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Residues in contact with GLU 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589C LYS* 2.9 26.2 + - + +
590C GLU* 3.2 24.2 + - - +
592C PHE* 1.3 80.0 - - + +
594C HIS* 1.3 64.7 + - - +
596C GLN* 3.4 17.9 + - - +
597C LYS* 3.1 49.6 + - - +
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Residues in contact with HIS 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590C GLU* 2.9 15.6 + - - +
591C GLU* 3.8 7.9 - - - +
592C PHE 3.2 0.4 - - - -
593C GLU* 1.3 77.2 - - - +
595C GLN* 1.3 72.1 + - - +
597C LYS* 3.4 11.5 + - + +
598C GLU* 3.0 65.0 + - + +
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Residues in contact with GLN 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LEU* 4.8 7.4 - - + -
576C GLU* 5.2 5.0 - - - +
577C ILE* 3.2 37.4 - - + +
580C TRP* 3.7 56.1 - - + +
591C GLU 3.5 14.1 + - - +
592C PHE 3.2 7.3 + - - +
594C HIS* 1.3 93.9 + - - +
596C GLN* 1.3 56.7 + - - +
598C GLU* 3.5 6.1 + - - +
599C LEU* 3.0 24.3 + - - +
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Residues in contact with GLN 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C SER* 5.6 3.4 + - - -
542C LEU* 4.6 27.0 - - + +
545C TYR* 6.1 0.2 - - - -
592C PHE* 3.2 26.7 + - + +
593C GLU* 3.5 24.3 - - - +
594C HIS 3.2 0.2 - - - -
595C GLN* 1.3 77.0 - - - +
597C LYS* 1.3 69.8 + - + +
599C LEU* 3.1 12.8 + - - +
600C GLU* 3.2 31.4 + - - +
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Residues in contact with LYS 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C GLU* 3.1 40.7 + - - +
594C HIS* 3.8 10.1 - - + +
596C GLN* 1.3 82.6 + - + +
598C GLU* 1.3 63.2 + - + +
600C GLU* 3.6 13.9 + - - +
601C LYS* 3.0 51.3 + - - +
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Residues in contact with GLU 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C LYS* 4.1 25.6 + - - +
577C ILE* 5.2 1.1 - - + -
594C HIS* 3.0 56.6 + - + +
595C GLN* 3.6 9.9 - - - +
597C LYS* 1.3 78.9 - - - +
599C LEU* 1.3 62.0 + - - +
601C LYS* 3.1 24.1 + - - +
602C VAL* 3.5 12.8 + - - +
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Residues in contact with LEU 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LEU* 4.0 17.9 - - + -
545C TYR* 3.8 32.5 - - + -
546C ALA* 4.6 11.4 - - + -
573C LYS* 3.5 45.8 - - + +
574C CYS* 4.1 8.7 - - - +
577C ILE* 3.8 17.3 - - + -
595C GLN 3.0 17.4 + - - +
596C GLN 3.1 5.1 + - - +
598C GLU* 1.3 76.0 - - - +
600C GLU* 1.3 61.0 + - - +
601C LYS 3.4 0.2 + - - -
602C VAL* 3.4 4.0 + - - +
603C CYS* 3.3 37.2 + - - -
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Residues in contact with GLU 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 4.1 14.4 - - - +
545C TYR* 4.5 15.7 - - + +
596C GLN* 3.2 33.0 + - - +
597C LYS* 3.6 21.1 + - - +
599C LEU* 1.3 75.3 - - - +
601C LYS* 1.3 70.4 + - + +
602C VAL 3.2 0.9 - - - -
603C CYS* 3.9 8.5 - - - +
604C ASN* 3.2 43.2 + - - +
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Residues in contact with LYS 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.7 22.3 + - - +
597C LYS* 3.0 41.8 + - - +
598C GLU* 3.1 21.8 + - - +
600C GLU* 1.3 87.0 + - + +
602C VAL* 1.3 59.9 + - + +
604C ASN* 5.8 0.4 - - - +
605C PRO* 3.5 19.9 - - - +
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Residues in contact with VAL 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C LYS* 4.1 39.5 - - + +
570C ILE* 4.8 6.3 - - + -
573C LYS* 4.1 27.6 - - + -
598C GLU 3.9 11.2 - - - +
599C LEU 3.4 6.7 + - - +
601C LYS* 1.3 82.9 - - + +
603C CYS* 1.3 64.5 + - - +
604C ASN 3.6 0.7 - - - -
605C PRO* 3.6 8.8 - - - +
606C ILE* 3.7 16.9 + - + +
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Residues in contact with CYS 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C TYR* 3.9 20.6 - - - +
549C MET* 4.1 18.8 - - - -
570C ILE* 3.5 29.3 - - + +
573C LYS* 6.0 0.4 - - - -
574C CYS* 5.1 0.7 - - - -
599C LEU* 3.3 33.9 + - - +
600C GLU* 3.8 2.0 + - - -
602C VAL* 1.3 81.7 - - - +
604C ASN* 1.3 55.4 + - - +
605C PRO 3.3 0.4 - - - -
606C ILE* 3.1 3.5 + - - +
607C ILE* 2.6 45.4 + - + +
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Residues in contact with ASN 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.9 20.5 + - - +
27A GLN* 3.9 22.7 - - + +
28A GLU* 4.0 20.4 + - - +
31A GLU* 5.1 2.6 + - - +
545C TYR* 4.7 2.3 + - - -
600C GLU* 3.2 31.9 + - - +
601C LYS* 5.8 1.0 - - - +
603C CYS* 1.3 79.7 - - - +
605C PRO* 1.3 61.7 - - + +
607C ILE* 3.0 20.1 + - - +
608C THR* 2.7 33.7 + - - -
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Residues in contact with PRO 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C LYS* 3.5 26.7 - - - +
602C VAL 3.6 10.3 - - - +
604C ASN* 1.3 94.3 - - + +
606C ILE* 1.3 63.3 + - + +
608C THR* 3.3 8.7 + - - +
609C LYS* 3.1 39.0 + - - +
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Residues in contact with ILE 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C VAL* 5.5 1.8 - - + -
562C ILE* 3.6 28.5 - - + -
566C ASP* 3.2 46.4 - - + +
569C LYS* 3.7 19.5 - - + -
570C ILE* 3.6 24.7 - - + -
602C VAL* 3.7 11.4 - - + +
603C CYS 3.1 7.6 + - - +
605C PRO* 1.3 75.0 - - + +
607C ILE* 1.3 69.3 + - + +
609C LYS* 3.2 12.3 + - + +
610C LEU* 3.2 21.6 + - + +
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Residues in contact with ILE 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLN* 3.8 33.9 - - - +
31A GLU* 6.0 0.4 - - - +
545C TYR* 4.5 4.3 - - + +
549C MET* 4.5 22.7 - - + -
603C CYS* 2.6 32.5 + - + +
604C ASN* 3.3 23.8 - - - +
606C ILE* 1.3 72.9 - - + +
608C THR* 1.3 54.6 + - - +
610C LEU* 2.8 44.7 + - + +
611C TYR* 3.4 16.0 + - + +
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Residues in contact with THR 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 5.6 1.8 - - + +
27A GLN* 4.0 18.7 + - - +
56A ASN* 3.7 26.0 - - - +
59A VAL* 4.0 14.6 - - + -
62A TYR* 4.1 10.5 + - - +
604C ASN 2.7 19.5 + - - -
605C PRO* 3.4 9.7 - - - +
606C ILE 3.2 0.2 - - - -
607C ILE* 1.3 78.5 - - - +
609C LYS* 1.3 58.6 - - + +
611C TYR* 3.5 13.8 - - - +
612C GLN* 3.3 24.9 + - - +
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Residues in contact with LYS 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C LYS 4.6 5.6 - - - +
566C ASP* 3.9 22.0 + - - +
605C PRO* 3.1 26.8 + - - +
606C ILE* 3.7 13.5 - - + +
607C ILE 3.1 0.4 - - - -
608C THR* 1.3 77.1 - - + +
610C LEU* 1.3 64.7 + - - +
611C TYR 3.2 0.2 - - - -
612C GLN* 3.3 30.6 + - + +
613C SER* 3.6 10.2 + - - -
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Residues in contact with LEU 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C THR* 5.5 4.9 - - + -
553C VAL* 5.7 5.4 - - + -
558C LEU* 4.2 21.3 - - + -
561C LYS* 3.6 36.8 - - + +
562C ILE* 4.5 13.0 - - + -
606C ILE* 3.2 21.3 + - + +
607C ILE* 2.8 21.1 + - + +
609C LYS* 1.3 76.8 - - - +
611C TYR* 1.3 60.4 + - + +
613C SER* 2.6 27.4 + - - -
616C GLY 3.3 7.9 - - - +
617C MET* 4.0 32.8 - - + +
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Residues in contact with TYR 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLN* 3.7 26.8 + - - -
30A LYS* 3.4 18.3 + - + -
59A VAL* 3.7 21.3 - - + -
60A ALA* 5.6 4.8 + - - +
61A VAL* 3.9 26.7 - - + +
62A TYR* 5.0 4.3 - + - -
90A ASP* 5.1 1.9 - - - +
607C ILE* 3.4 20.7 + - + +
608C THR* 3.5 13.5 - - - +
610C LEU* 1.3 80.8 - - + +
612C GLN* 1.3 56.4 + - - +
613C SER 3.0 7.2 + - - +
616C GLY* 3.3 18.8 - - - -
617C MET* 3.3 41.7 - - + -
646C ASP 2.9 24.7 + - - -
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Residues in contact with GLN 612 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 4.2 7.7 + - - +
58A LEU* 3.3 40.3 + - - +
59A VAL* 4.2 15.6 - - + +
60A ALA 6.0 1.1 - - - +
608C THR* 3.3 17.0 - - - +
609C LYS* 3.3 33.4 + - - +
610C LEU 3.2 1.2 - - - -
611C TYR* 1.3 71.9 - - - +
613C SER* 1.3 60.9 + - - +
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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
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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) + - + + + + + -
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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