Contacts of the helix formed by residues 563 - 584 (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 ASN 563 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562C ILE* 1.3 74.0 - - - +
564C ASP* 1.3 60.1 + - - +
565C GLU* 3.0 29.5 + - + +
566C ASP* 3.0 32.0 + - - +
567C LYS* 2.9 26.7 + - - +
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Residues in contact with ASP 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C ILE 4.4 4.2 - - - +
563C ASN* 1.3 73.4 - - - +
565C GLU* 1.3 56.8 + - - +
567C LYS* 3.7 32.8 + - + +
568C GLN* 3.0 27.9 + - - +
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Residues in contact with GLU 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C ASN* 3.0 18.6 + - - +
564C ASP* 1.3 78.5 - - - +
566C ASP* 1.3 62.6 + - - +
568C GLN* 3.3 6.2 + - - +
569C LYS* 3.2 37.3 + - - +
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Residues in contact with ASP 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C ILE* 3.9 11.4 - - + -
563C ASN* 3.0 30.2 + - - +
565C GLU* 1.3 77.7 - - - +
567C LYS* 1.3 64.6 + - - +
569C LYS* 3.4 26.4 + - - +
570C ILE* 3.4 14.7 + - - +
606C ILE* 3.2 36.0 - - + +
609C LYS* 3.9 26.0 + - - +
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Residues in contact with LYS 567 (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* 3.4 29.3 - - + +
554C GLU* 3.1 44.2 + - - +
559C GLN* 4.5 19.2 - - - +
562C ILE* 3.7 25.0 - - + +
563C ASN 2.9 16.5 + - - +
564C ASP* 3.7 30.9 + - - +
566C ASP* 1.3 80.4 - - - +
568C GLN* 1.3 60.3 + - - +
570C ILE* 3.7 3.6 + - - +
571C LEU* 3.5 24.2 + - - +
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Residues in contact with GLN 568 (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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564C ASP 3.0 20.0 + - - +
565C GLU* 3.6 7.2 - - - +
566C ASP 3.2 0.4 - - - -
567C LYS* 1.3 76.3 - - - +
569C LYS* 1.3 57.5 + - - +
571C LEU* 3.5 21.1 + - - +
572C ASP* 2.6 59.3 + - - +
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Residues in contact with LYS 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C GLU* 3.2 24.9 + - - +
566C ASP* 3.5 33.1 + - - +
567C LYS 3.4 0.2 - - - -
568C GLN* 1.3 76.3 - - + +
570C ILE* 1.3 63.9 + - - +
572C ASP* 3.7 10.8 - - + +
573C LYS* 3.3 23.2 + - - +
602C VAL* 4.1 15.8 - - + +
606C ILE* 3.7 14.4 - - + -
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Residues in contact with ILE 570 (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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549C MET* 3.8 29.2 - - + +
550C LYS* 4.9 0.4 - - - +
553C VAL* 4.0 26.0 - - + -
562C ILE* 5.2 0.2 - - + -
566C ASP 3.4 14.8 + - - +
567C LYS 4.0 6.5 - - - +
568C GLN 3.3 0.4 - - - -
569C LYS* 1.3 75.2 - - - +
571C LEU* 1.3 66.8 + - - +
572C ASP 3.2 0.2 + - - -
573C LYS* 3.2 2.2 + - - +
574C CYS* 3.0 30.4 + - - -
602C VAL* 4.5 5.2 - - + +
603C CYS* 3.5 40.4 - - + +
606C ILE* 3.6 28.3 - - + -
607C ILE* 6.3 0.7 - - + -
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Residues in contact with LEU 571 (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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550C LYS* 3.8 46.2 - - + +
553C VAL* 4.1 7.0 - - + -
554C GLU* 3.8 24.0 - - + +
567C LYS 3.5 13.2 + - - +
568C GLN* 3.5 28.2 + - - +
569C LYS 3.4 0.4 - - - -
570C ILE* 1.3 77.6 - - - +
572C ASP* 1.3 56.2 + - - +
574C CYS* 3.5 1.2 + - - +
575C ASN* 2.5 46.9 + - - +
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Residues in contact with ASP 572 (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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568C GLN* 2.6 45.0 + - - +
569C LYS* 3.7 10.8 - - + +
571C LEU* 1.3 81.0 - - - +
573C LYS* 1.3 59.6 + - - +
575C ASN* 3.2 8.6 + - - +
576C GLU* 2.8 30.5 + - - +
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Residues in contact with LYS 573 (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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569C LYS 3.3 12.9 + - - +
570C ILE* 3.2 4.4 + - - +
572C ASP* 1.3 80.5 - - - +
574C CYS* 1.3 57.1 + - - +
576C GLU* 2.9 38.1 + - - +
577C ILE* 3.0 41.7 + - + +
598C GLU* 4.1 43.0 + - - +
599C LEU* 3.5 21.8 - - + +
602C VAL* 4.1 28.0 - - + -
603C CYS* 6.0 0.4 - - - -
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Residues in contact with CYS 574 (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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546C ALA* 3.4 29.3 - - - +
549C MET* 3.9 19.3 - - - -
550C LYS* 3.4 27.6 - - + -
570C ILE* 3.0 27.8 + - - +
573C LYS* 1.3 76.5 - - - +
575C ASN* 1.3 58.9 + - - +
577C ILE* 3.2 2.1 + - - +
578C ILE* 2.9 36.5 + - - +
599C LEU* 4.2 15.9 - - - -
603C CYS* 5.1 0.9 - - - -
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Residues in contact with ASN 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C LYS* 2.7 32.4 + - - +
571C LEU* 2.5 40.4 + - - +
572C ASP* 3.6 7.1 + - - +
574C CYS* 1.3 75.4 - - - +
576C GLU* 1.3 62.0 + - - +
578C ILE* 4.1 7.7 - - - +
579C ASN* 3.2 24.8 + - - +
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Residues in contact with GLU 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ASP* 2.8 16.5 + - - +
573C LYS* 2.9 45.2 + - - +
574C CYS 3.2 0.2 - - - -
575C ASN* 1.3 76.7 - - - +
577C ILE* 1.3 65.9 + - + +
579C ASN* 3.5 6.5 + - - +
580C TRP* 3.1 21.9 + - + +
595C GLN* 5.2 6.0 - - - +
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Residues in contact with ILE 577 (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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542C LEU* 4.1 31.0 - - + -
546C ALA* 5.0 4.9 - - + -
573C LYS* 3.0 36.4 + - + +
574C CYS 3.2 3.6 + - - +
576C GLU* 1.3 75.3 - - - +
578C ILE* 1.3 65.4 + - - +
580C TRP* 3.2 6.5 + - + +
581C LEU* 3.2 25.2 + - + +
595C GLN* 3.2 50.0 - - + +
598C GLU* 5.2 0.7 - - + -
599C LEU* 3.8 28.7 - - + -
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Residues in contact with ILE 578 (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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543C GLU* 4.6 11.6 - - + +
546C ALA* 3.6 22.9 - - + -
547C PHE* 3.6 56.5 - - + +
550C LYS* 4.5 10.1 - - + +
574C CYS 2.9 24.0 + - - +
575C ASN* 4.1 6.1 - - - +
577C ILE* 1.3 74.7 - - - +
579C ASN* 1.3 65.6 + - - +
581C LEU* 3.1 20.2 + - - +
582C ASP* 3.1 24.3 + - - +
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Residues in contact with ASN 579 (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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575C ASN 3.2 17.9 + - - +
576C GLU* 3.5 7.7 + - - +
578C ILE* 1.3 79.0 - - - +
580C TRP* 1.3 62.6 + - - +
582C ASP* 3.1 29.3 + - - +
583C LYS* 3.5 7.6 + - - +
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Residues in contact with TRP 580 (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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542C LEU* 5.8 0.4 - - + -
576C GLU 3.1 11.9 + - - +
577C ILE 3.5 8.7 - - - +
579C ASN* 1.3 80.1 - - - +
581C LEU* 1.3 91.9 + - + +
583C LYS* 3.3 2.4 + - - +
584C ASN* 2.9 65.7 + - + +
587C ALA* 3.9 24.5 - - + -
591C GLU* 3.8 30.5 - - + -
592C PHE* 4.1 12.6 - + + -
595C GLN* 3.7 47.3 - - + +
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Residues in contact with LEU 581 (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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539C GLU* 4.1 37.4 - - + +
542C LEU* 4.2 14.6 - - + -
543C GLU* 3.9 46.0 - - + +
577C ILE* 3.2 15.0 + - + +
578C ILE* 3.1 10.1 + - - +
580C TRP* 1.3 105.1 - - + +
582C ASP* 1.3 65.5 + - - +
583C LYS 3.3 0.3 + - - -
584C ASN 3.8 7.4 + - - +
585C GLN* 3.4 22.0 + - - +
592C PHE* 4.2 13.2 - - + -
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Residues in contact with ASP 582 (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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543C GLU* 4.4 10.7 - - - +
578C ILE* 3.1 25.8 + - - +
579C ASN* 3.1 20.6 + - - +
581C LEU* 1.3 79.5 - - - +
583C LYS* 1.3 57.5 + - + +
585C GLN* 3.0 22.4 + - - +
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Residues in contact with LYS 583 (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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579C ASN 3.5 5.5 + - - +
580C TRP* 3.3 4.7 + - - +
582C ASP* 1.3 81.7 - - + +
584C ASN* 1.3 81.7 + - - +
585C GLN* 2.9 10.9 + - - +
586C THR* 5.3 0.7 + - - -
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Residues in contact with ASN 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C GLU* 5.7 0.3 - - - +
580C TRP* 2.9 62.3 + - + +
581C LEU* 4.1 7.7 - - - +
583C LYS* 1.3 97.0 - - - +
585C GLN* 1.3 59.4 + - - +
586C THR* 3.3 10.3 + - - +
587C ALA* 4.1 14.5 + - + +
591C GLU* 4.1 15.6 + - - -
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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
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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