Contacts of the helix formed by residues 492 - 500 (chain A) in PDB entry 4WGK
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 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A LYS 3.5 3.3 + - - -
491A PRO* 1.3 77.2 - - - +
493A GLU* 1.3 63.2 + - - +
494A GLU* 3.6 15.8 + - - +
495A ILE* 3.2 28.1 + - - +
496A LYS* 3.3 9.0 - - - +
510A GLU* 2.7 33.5 + - - -
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Residues in contact with GLU 493 (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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490A LYS* 5.7 1.7 - - - -
491A PRO 5.0 0.3 - - - +
492A SER* 1.3 72.3 - - - +
494A GLU* 1.3 71.4 + - - +
496A LYS* 3.6 26.9 + - - +
497A GLU* 3.1 27.8 + - - +
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Residues in contact with GLU 494 (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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492A SER* 3.2 13.9 - - - +
493A GLU* 1.3 90.4 + - - +
495A ILE* 1.3 57.2 + - - +
497A GLU* 3.4 5.1 + - - +
498A CYS* 2.9 30.1 + - - +
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Residues in contact with ILE 495 (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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448A CYS* 5.1 0.2 - - + -
449A LYS* 3.6 36.6 - - + +
450A PRO 4.3 6.1 - - - +
451A ALA* 4.4 2.9 - - + -
491A PRO* 3.8 13.7 - - + -
492A SER* 3.2 34.8 + - - +
494A GLU* 1.3 77.2 - - - +
496A LYS* 1.3 65.5 + - - +
498A CYS* 3.7 4.7 + - - -
499A HIS* 3.0 47.7 + - + +
504A ILE* 3.7 5.7 - - + +
507A HIS* 4.2 17.0 - - + -
509A GLY* 5.0 0.4 - - - -
510A GLU* 3.8 19.1 - - + +
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Residues in contact with LYS 496 (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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484A ARG* 4.3 16.4 - - - +
490A LYS* 3.8 24.5 - - - +
491A PRO* 3.3 43.8 + - + +
492A SER 3.3 12.6 - - - +
493A GLU* 3.8 27.3 + - - +
494A GLU 3.3 0.4 - - - -
495A ILE* 1.3 78.0 - - - +
497A GLU* 1.3 62.7 + - - +
499A HIS* 3.5 2.8 + - - +
500A LYS* 3.2 32.9 + - - +
502A LYS 4.8 3.0 - - - +
504A ILE* 4.2 12.8 - - + -
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Residues in contact with GLU 497 (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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493A GLU* 3.1 21.3 + - + +
494A GLU* 3.8 4.9 - - - +
496A LYS* 1.3 76.6 - - - +
498A CYS* 1.3 63.5 + - - +
499A HIS 3.4 0.2 + - - -
500A LYS* 3.3 46.9 + - - +
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Residues in contact with CYS 498 (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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446A LYS* 3.9 22.7 - - - +
447A THR 3.8 7.9 - - - -
448A CYS* 2.0 63.9 - - + -
494A GLU 2.9 18.2 + - - +
495A ILE* 3.9 5.8 - - - +
497A GLU* 1.3 79.5 - - - +
499A HIS* 1.3 56.9 + - - +
500A LYS 3.7 0.7 + - - +
600A PRO* 3.3 17.0 - - - +
601A HIS* 5.7 0.2 - - - -
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Residues in contact with HIS 499 (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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448A CYS* 3.3 13.5 - - + +
449A LYS 2.7 21.6 + - - -
451A ALA* 3.4 20.7 - - + +
495A ILE* 3.0 37.7 + - + +
496A LYS 3.5 2.2 + - - +
497A GLU 3.3 0.6 - - - -
498A CYS* 1.3 75.8 - - - +
500A LYS* 1.3 67.9 + - - +
502A LYS* 2.9 45.8 + - + +
504A ILE* 4.2 5.2 - - + -
586A TYR* 2.5 27.0 + - - +
597A ILE 3.0 27.1 - - - -
599A GLY* 3.7 10.8 - - - -
600A PRO* 4.2 0.4 - - - -
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Residues in contact with LYS 500 (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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496A LYS* 3.2 21.0 + - - +
497A GLU* 3.3 48.0 - - - +
498A CYS 3.4 1.5 - - - +
499A HIS* 1.3 81.1 - - - +
501A PRO* 1.3 68.3 - - + +
502A LYS 3.4 3.1 - - - +
586A TYR* 3.8 5.9 - - - -
587A GLN* 5.1 0.3 + - - -
600A PRO* 3.9 11.1 - - - +
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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