Contacts of the helix formed by residues 573 - 585 (chain A) in PDB entry 1WKB
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 SER 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A TYR* 2.9 17.5 + - - -
571A GLU 3.4 5.8 + - - -
572A PHE* 1.3 77.0 - - - +
574A GLU* 1.3 63.2 + - - +
575A ASP* 3.3 9.7 + - - +
576A LYS* 2.9 32.7 + - - +
577A GLU* 3.0 19.9 + - - +
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Residues in contact with GLU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A SER* 1.3 73.9 - - - +
575A ASP* 1.3 56.9 + - - +
577A GLU* 3.5 17.6 + - - +
578A LYS* 2.8 58.5 + - - +
588A ALA* 6.0 0.7 - - + -
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Residues in contact with ASP 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A SER* 3.1 7.7 - - - +
574A GLU* 1.3 77.9 - - - +
576A LYS* 1.3 60.2 + - - +
578A LYS* 3.1 17.1 + - - +
579A GLU* 2.8 35.6 + - - +
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Residues in contact with LYS 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A GLU* 3.3 31.7 + - - +
566A TYR* 4.0 11.0 - - + -
570A GLU* 3.5 31.6 + - - +
573A SER* 2.9 26.4 + - - +
575A ASP* 1.3 75.4 - - - +
577A GLU* 1.3 53.4 + - - +
579A GLU* 3.1 32.1 + - - +
580A LEU* 2.7 62.3 + - + +
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Residues in contact with GLU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A TYR* 2.4 37.7 + - + +
572A PHE* 4.2 0.2 - - - -
573A SER 3.0 20.4 + - - +
574A GLU* 3.6 17.4 - - - +
576A LYS* 1.3 78.4 - - - +
578A LYS* 1.3 51.9 + - - +
580A LEU* 3.3 7.5 + - - +
581A GLU* 2.7 34.3 + - - +
588A ALA* 3.7 21.5 - - + +
591A ILE* 3.9 15.3 - - + +
592A HIS* 2.6 47.4 + - - +
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Residues in contact with LYS 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A GLU* 2.8 62.0 + - - +
575A ASP* 3.1 20.3 + - - +
577A GLU* 1.3 77.2 - - - +
579A GLU* 1.3 62.4 + - - +
581A GLU* 3.2 19.5 + - - +
582A LYS* 3.3 32.2 + - - +
588A ALA* 4.1 15.5 - - + -
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Residues in contact with GLU 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A GLU* 4.1 0.9 - - - +
575A ASP* 2.8 24.1 + - - +
576A LYS* 3.1 48.0 + - + +
578A LYS* 1.3 70.0 - - - +
580A LEU* 1.3 66.0 + - + +
582A LYS* 3.3 17.5 + - + +
583A LYS* 3.1 48.8 + - - +
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Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A THR* 5.8 0.4 - - - +
562A GLU* 4.1 31.2 - - + +
563A PHE* 3.9 30.1 - - + +
566A TYR* 3.7 33.4 - - + -
576A LYS* 2.7 45.0 + - + +
577A GLU* 3.6 1.8 - - - +
579A GLU* 1.3 72.7 - - + +
581A GLU* 1.3 61.1 + - - +
583A LYS* 4.6 7.6 - - + +
584A THR* 2.7 40.7 + - + +
591A ILE* 3.6 15.0 - - + -
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Residues in contact with GLU 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A GLU 2.7 14.1 + - - +
578A LYS* 3.3 18.4 - - - +
579A GLU 3.2 0.2 - - - -
580A LEU* 1.3 77.7 - - - +
582A LYS* 1.3 58.4 + - + +
585A GLY* 2.8 29.1 + - - -
586A ILE 3.2 24.9 - - - +
587A PRO* 3.8 9.1 - - + +
588A ALA* 2.8 30.6 + - - +
589A GLU* 3.9 3.6 - - - +
591A ILE* 3.8 0.4 - - - +
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Residues in contact with LYS 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A LYS* 3.3 33.2 + - - +
579A GLU* 3.6 12.9 - - + +
580A LEU 3.3 0.4 - - - -
581A GLU* 1.3 82.3 - - + +
583A LYS* 1.3 64.4 + - + +
585A GLY* 4.1 3.6 + - - -
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Residues in contact with LYS 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A LYS* 3.5 29.0 - - - +
562A GLU* 2.8 39.3 + - - +
579A GLU* 3.1 35.9 + - - +
580A LEU* 4.0 8.9 - - + +
582A LYS* 1.3 80.9 - - + +
584A THR* 1.3 62.9 + - + +
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Residues in contact with THR 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A LYS 5.7 0.9 - - - +
554A LEU* 6.0 0.2 - - - +
555A ASP* 5.0 8.5 + - - +
558A LYS* 3.5 42.4 - - + +
559A LEU* 5.6 0.7 - - + -
563A PHE* 3.9 25.4 - - + -
580A LEU* 2.7 34.6 + - + +
583A LYS* 1.3 80.9 - - + +
585A GLY* 1.3 57.8 + - - +
586A ILE* 3.0 39.6 + - + +
591A ILE* 3.9 1.9 - - - +
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Residues in contact with GLY 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A LYS* 4.6 11.0 - - - +
581A GLU* 2.8 20.7 + - - -
582A LYS 4.1 3.0 + - - -
583A LYS 3.8 1.0 - - - -
584A THR* 1.3 73.0 - - - +
586A ILE* 1.3 61.7 + - - +
587A PRO* 3.7 7.8 - - - +
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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
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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