Contacts of the helix formed by residues 896 - 901 (chain A) in PDB entry 1OY6
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 896 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894A SER* 3.1 17.7 + - - -
895A TRP* 1.3 80.4 - - - +
897A ILE* 1.3 75.2 + - - +
898A PRO 3.4 0.9 - - - -
899A PHE* 3.5 2.7 + - - +
900A SER* 3.2 17.9 + - - -
1028A VAL* 5.8 0.8 - - - -
1031A ARG* 3.7 20.4 - - - +
1032A ARG* 3.5 49.5 + - - +
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Residues in contact with ILE 897 (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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888A LEU* 3.1 19.9 - - + +
892A TYR* 3.2 48.7 - - + +
893A GLU 4.9 1.3 - - - +
894A SER* 3.2 20.2 + - - +
896A SER* 1.3 79.3 + - - +
898A PRO* 1.3 65.8 - - + +
899A PHE 3.0 9.7 + - - -
900A SER* 3.0 18.1 + - - -
901A VAL* 3.6 1.4 + - + +
943A ILE* 5.7 3.4 - - + -
946A VAL* 3.4 35.7 - - + -
950A LYS* 4.2 24.5 - - + -
1028A VAL* 6.5 0.4 - - + -
1032A ARG* 5.6 0.7 - - - +
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Residues in contact with PRO 898 (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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885A PHE* 3.3 42.5 - - + +
888A LEU* 3.4 34.6 - - + +
889A ALA* 4.5 1.1 - - + -
892A TYR 3.6 7.6 - - - +
895A TRP* 3.5 29.2 - - + +
896A SER 3.4 11.9 - - - +
897A ILE* 1.3 93.8 - - + +
899A PHE* 1.3 59.9 + - + +
902A MET* 3.1 19.2 - - - +
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Residues in contact with PHE 899 (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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885A PHE* 3.4 36.6 - + - -
895A TRP* 3.1 46.7 - + + -
896A SER 3.5 2.6 + - - +
897A ILE 3.0 0.8 - - - -
898A PRO* 1.3 77.5 - - - +
900A SER* 1.3 65.8 + - - +
901A VAL 3.6 0.9 - - - -
902A MET* 3.5 22.9 - - + +
903A LEU* 4.0 6.4 - - - +
1031A ARG* 3.6 30.2 + - + +
1035A ARG* 6.3 1.6 - - - -
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Residues in contact with SER 900 (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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896A SER 3.2 13.0 + - - -
897A ILE* 3.0 14.9 + - - -
899A PHE* 1.3 73.3 - - - +
901A VAL* 1.3 63.5 + - - +
902A MET 3.1 4.9 + - - -
903A LEU* 3.4 6.8 + - - +
904A VAL* 4.5 1.7 + - - +
942A ALA* 5.1 3.1 + - - +
946A VAL* 3.2 29.0 - - - +
1024A VAL* 5.5 1.4 + - - +
1027A VAL* 3.2 45.8 - - - +
1028A VAL* 4.7 6.5 - - - -
1031A ARG* 4.5 1.8 - - - +
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Residues in contact with VAL 901 (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 VAL* 5.0 1.1 - - + -
884A VAL* 4.5 12.6 - - + -
888A LEU* 3.4 35.2 - - + -
897A ILE* 3.6 4.3 + - + +
899A PHE 3.6 0.2 - - - -
900A SER* 1.3 76.5 + - - +
902A MET* 1.3 59.2 + - - +
903A LEU 3.0 8.7 + - - -
904A VAL* 3.0 25.0 + - - +
905A VAL* 3.8 7.4 - - + +
939A ALA* 3.7 32.1 - - + +
942A ALA* 3.4 28.0 - - + -
943A ILE* 3.7 14.8 - - + +
946A VAL* 6.1 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