Contacts of the helix formed by residues 560 - 567 (chain A) in PDB entry 5Y36
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 THR 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A LYS* 5.2 4.3 - - + +
559A VAL* 1.3 86.1 - - - +
561A VAL* 1.3 63.5 + - - +
562A LYS* 4.0 8.9 + - - +
563A GLN* 3.2 41.8 + - - +
564A LEU* 3.4 12.1 + - - +
585A ASP 3.4 11.0 - - - +
586A ARG* 3.9 18.2 - - + +
587A PHE* 5.0 2.0 - - - -
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Residues in contact with VAL 561 (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* 1.3 68.0 - - - +
562A LYS* 1.4 60.2 + - - +
564A LEU* 3.2 11.9 + - + +
565A LYS* 2.9 60.2 + - + +
579A GLU* 5.3 1.3 - - - +
580A ILE* 4.3 26.5 - - + +
583A VAL* 5.1 2.9 - - + -
584A GLU 3.3 26.9 - - - +
585A ASP* 3.0 18.5 + - + +
586A ARG* 5.5 0.2 - - - -
587A PHE* 6.2 1.3 - - + -
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Residues in contact with LYS 562 (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* 3.4 8.2 + - - +
561A VAL* 1.4 77.6 - - - +
563A GLN* 1.4 57.7 + - + +
565A LYS* 4.5 6.5 - - - -
566A GLU* 2.8 54.0 + - + +
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Residues in contact with GLN 563 (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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552A LEU* 4.0 32.2 - - + +
555A THR* 5.4 0.5 + - - -
556A ASN* 4.1 20.2 - - - +
558A LYS 3.2 21.1 + - - +
559A VAL* 3.8 3.5 - - - -
560A THR* 3.2 45.6 + - - +
562A LYS* 1.4 75.8 - - + +
564A LEU* 1.4 58.3 + - - +
566A GLU* 5.1 0.7 - - - -
567A ASP* 3.0 42.4 + - - +
568A TYR 3.3 2.9 + - - -
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Residues in contact with LEU 564 (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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527A VAL* 5.4 4.0 - - + -
548A ILE* 3.9 30.5 - - + -
552A LEU* 3.6 20.9 - - + -
559A VAL* 4.2 3.1 - - + -
560A THR 3.4 9.4 + - - +
561A VAL* 3.2 12.2 + - + +
563A GLN* 1.4 76.4 - - - +
565A LYS* 1.4 57.1 + - - +
568A TYR* 3.5 14.7 + - + -
569A PHE* 3.0 39.6 + - + -
580A ILE* 3.8 36.1 - - + -
587A PHE* 3.9 27.1 - - + -
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Residues in contact with LYS 565 (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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561A VAL* 2.9 39.5 + - + +
562A LYS* 3.9 6.5 - - - +
564A LEU* 1.4 77.0 - - - +
566A GLU* 1.3 66.0 + - - +
570A LYS* 3.4 30.2 + - - +
578A VAL* 3.8 36.7 + - + +
579A GLU* 2.9 33.6 + - - -
580A ILE* 3.5 17.7 - - + -
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Residues in contact with GLU 566 (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 LYS* 2.8 45.9 + - + +
563A GLN* 5.1 0.2 - - - -
565A LYS* 1.3 80.4 - - + +
567A ASP* 1.3 69.8 + - - +
570A LYS* 2.9 50.8 + - - +
571A LYS* 4.6 5.0 - - - +
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Residues in contact with ASP 567 (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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551A LEU* 4.3 6.4 - - + +
552A LEU* 4.2 17.3 - - + +
563A GLN* 3.0 21.6 + - - +
566A GLU* 1.3 84.6 - - - +
568A TYR* 1.4 60.6 + - - +
569A PHE 3.7 0.2 - - - -
570A LYS 4.4 0.2 - - - -
571A LYS* 2.9 67.3 + - + +
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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