Contacts of the helix formed by residues 566 - 569 (chain A) in PDB entry 4YOZ
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 LEU 566 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A PHE* 3.7 31.6 - - + -
520A PRO* 4.1 26.9 - - + -
523A ILE* 5.0 3.1 - - + -
530A PRO* 4.0 21.7 - - + +
561A GLN* 3.2 19.2 + - + +
562A ILE* 3.8 17.3 - - + -
565A SER* 1.3 88.0 + - - +
567A ALA* 1.3 61.7 + - - +
568A TRP 3.2 0.9 + - - -
569A SER* 3.4 21.3 + - - +
572A SER* 4.4 0.9 - - - -
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Residues in contact with ALA 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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530A PRO* 4.1 6.0 - - - +
531A PHE* 4.4 11.9 - - + -
562A ILE* 3.0 30.1 + - + +
566A LEU* 1.3 76.2 - - - +
568A TRP* 1.3 58.3 + - + +
569A SER 3.5 0.2 - - - -
572A SER* 2.6 29.3 + - - +
574A LEU* 3.5 13.9 - - - +
791A PHE* 3.6 30.3 - - + -
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Residues in contact with TRP 568 (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 ILE 4.3 0.9 - - - -
563A LEU 2.7 27.7 + - - -
564A GLU 3.8 6.5 - - - -
565A SER 2.8 17.5 + - - +
567A ALA* 1.3 78.8 - - - +
569A SER* 1.3 67.0 + - - +
574A LEU* 3.4 25.1 - - + -
575A TRP* 3.5 17.6 + + - +
578A LEU* 5.6 0.2 - - + -
791A PHE* 3.6 22.8 - + - -
792A TYR* 3.6 34.8 - + - -
795A VAL* 4.0 12.8 - - + -
828A LEU* 4.5 10.5 - - + -
832A PRO* 5.0 3.8 - - + -
835A MET* 3.4 56.9 - - + +
836A LYS* 3.3 8.5 - - - -
837A ASP 2.9 16.1 + - - -
838A ARG 4.4 1.3 - - - +
840A LEU* 4.1 12.3 - - + +
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Residues in contact with SER 569 (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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530A PRO* 5.9 0.5 - - - +
565A SER 3.7 3.7 + - - -
566A LEU* 3.4 17.4 + - - -
567A ALA 3.5 0.6 - - - -
568A TRP* 1.3 77.7 - - - +
570A HIS* 1.3 65.1 + - - +
571A ASP* 2.7 25.3 + - - -
572A SER* 2.9 17.5 + - - -
575A TRP* 2.9 15.8 + - - -
837A ASP* 3.2 17.0 - - - +
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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