Contacts of the helix formed by residues 942 - 946 (chain A) in PDB entry 1YO8
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 PRO 942 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A ASP 5.9 0.2 - - - +
934A ASP* 3.4 21.8 - - + +
935A ASP* 4.5 2.2 - - + -
940A ASN 3.7 8.0 - - - +
941A ILE* 1.3 94.1 - - + +
943A ASP* 1.3 67.5 + - - +
944A ILE* 4.1 15.0 - - + -
945A ASP* 3.0 34.4 + - + +
946A ASP* 3.2 6.8 + - - +
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Residues in contact with ASP 943 (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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668A LEU* 5.8 3.4 - - + +
672A SER* 4.1 11.6 + - - +
673A ASP* 3.2 23.0 + - - +
928A ARG* 2.3 36.5 + - - -
934A ASP 2.8 17.7 + - - +
935A ASP* 3.6 0.9 - - - +
936A PHE* 3.1 29.7 + - - +
937A ASP* 5.5 0.3 - - - +
941A ILE 3.7 0.8 + - - -
942A PRO* 1.3 68.9 - - - +
944A ILE* 1.4 57.8 + - - +
946A ASP* 2.9 33.5 + - - +
949A PRO* 4.2 17.8 - - + +
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Residues in contact with ILE 944 (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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668A LEU* 4.5 14.1 - - + -
673A ASP 4.1 3.1 + - - +
674A PRO* 3.5 37.4 - - + +
677A LYS* 4.6 26.3 + - + +
942A PRO* 4.1 16.6 - - + -
943A ASP* 1.4 74.6 - - - +
945A ASP* 1.3 85.8 + - - +
946A ASP 3.3 1.0 + - - +
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Residues in contact with ASP 945 (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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941A ILE* 3.8 17.3 - - + +
942A PRO* 3.0 18.8 + - + +
944A ILE* 1.3 98.7 - - - +
946A ASP* 1.3 59.4 + - - +
947A VAL* 3.8 3.7 + - - +
955A SER 3.5 11.8 - - - +
956A GLU* 5.7 0.9 - - - +
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Residues in contact with ASP 946 (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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937A ASP* 3.2 1.6 - - - +
939A ASP* 3.0 3.3 - - - +
941A ILE* 4.0 2.5 - - + +
942A PRO 3.3 15.3 - - - +
943A ASP 2.9 16.8 + - - +
944A ILE 3.3 1.4 - - - -
945A ASP* 1.3 78.6 - - - +
947A VAL* 1.3 63.0 + - - +
948A CYS 2.8 25.7 + - - -
949A PRO* 3.3 14.5 - - + +
954A ILE 3.1 4.2 - - - +
955A SER* 3.1 14.1 + - - -
1168A GLU* 5.7 0.3 - - - -
1182A CA 2.4 30.5 - - - -
1183A CA 2.5 25.7 - - - -
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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