Contacts of the helix formed by residues 569 - 576 (chain A) in PDB entry 5XA0
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 LYS 569 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A ARG* 4.3 23.8 - - + +
564A GLN* 5.3 0.7 - - - +
567A TYR* 3.3 6.7 - - + -
568A ARG* 1.3 75.1 - - - +
570A ASN* 1.3 67.8 + - - +
571A GLN 3.1 2.5 - - - -
572A GLU* 2.9 26.1 + - - +
573A TYR 4.2 0.7 + - - -
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Residues in contact with ASN 570 (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 LEU* 4.5 13.0 - - + -
564A GLN* 2.6 38.7 - - - +
569A LYS* 1.3 77.9 - - - +
571A GLN* 1.3 64.3 + - - +
573A TYR* 2.8 27.8 + - + +
574A ILE 4.3 0.2 + - - -
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Residues in contact with GLN 571 (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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564A GLN* 4.5 1.2 - - - +
568A ARG* 3.8 17.7 + - + +
569A LYS 3.0 0.8 + - - -
570A ASN* 1.3 77.2 - - - +
572A GLU* 1.3 63.4 + - - +
574A ILE* 2.9 25.7 + - - +
575A ALA 4.7 0.2 + - - -
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Residues in contact with GLU 572 (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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568A ARG 4.8 0.4 + - - -
569A LYS* 2.9 15.7 + - - +
571A GLN* 1.3 78.7 - - - +
573A TYR* 1.3 61.4 + - - +
574A ILE 3.0 1.1 + - - -
575A ALA* 3.4 16.9 + - - +
576A LYS 4.7 0.5 + - - -
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Residues in contact with TYR 573 (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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569A LYS 4.2 0.4 + - - -
570A ASN* 2.8 21.5 + - + +
572A GLU* 1.3 77.8 - - - +
574A ILE* 1.3 53.9 + - - +
575A ALA 3.1 1.0 + - - -
576A LYS 3.4 1.4 + - - -
577A GLN* 2.6 50.9 + - + +
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Residues in contact with ILE 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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571A GLN 2.9 15.3 + - - +
573A TYR* 1.3 78.5 - - - +
575A ALA* 1.3 58.8 + - - +
578A PHE* 2.7 37.9 - - + +
607A GLU* 5.5 11.9 - - + -
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Residues in contact with ALA 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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572A GLU 3.4 11.6 + - - +
573A TYR 3.1 1.8 + - - -
574A ILE* 1.3 80.8 - - - +
576A LYS* 1.3 59.5 + - + +
578A PHE* 4.7 2.6 - - - +
579A GLY 5.3 0.9 + - - -
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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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572A GLU 4.7 0.6 + - - -
573A TYR 3.4 1.4 + - - -
575A ALA* 1.3 78.3 - - + +
577A GLN* 1.3 66.0 + - - +
578A PHE 3.2 2.6 + - - -
579A GLY* 3.5 11.4 + - - -
580A PHE 4.6 0.9 + - - -
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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
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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