Contacts of the helix formed by residues 893 - 899 (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 893 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768A GLN* 3.9 13.5 + - - +
783A ARG* 3.8 12.3 - - - +
853A ASP* 3.2 33.5 + - - +
887A LEU* 3.9 4.7 - - - -
892A ILE* 1.4 77.3 - - - +
894A GLN* 1.4 64.1 + - - +
895A ARG* 3.9 6.3 + - - +
896A LYS* 3.1 26.4 + - - +
897A PHE* 3.1 24.3 + - - +
911A LEU 6.1 0.7 - - - -
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Residues in contact with GLN 894 (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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887A LEU* 3.1 33.2 - - - +
893A THR* 1.4 73.4 - - - +
895A ARG* 1.4 57.3 + - - +
897A PHE* 3.5 11.0 + - - +
898A ASP* 2.9 69.1 + - - +
905A ARG* 4.8 2.0 - - - +
910A GLU* 3.1 38.0 + - + +
911A LEU 5.0 3.3 + - - +
913A LYS* 3.3 39.7 + - + +
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Residues in contact with ARG 895 (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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842A VAL* 5.5 9.3 - - - +
847A LEU* 4.4 29.1 + - - +
849A ASP* 3.9 26.4 + - - +
893A THR* 3.5 6.1 + - - +
894A GLN* 1.4 77.0 - - - +
896A LYS* 1.4 61.6 + - - +
898A ASP* 3.3 8.3 + - - -
899A ASN* 3.0 61.1 + - - +
909A SER* 6.4 1.1 - - - +
910A GLU* 5.1 4.8 + - - +
911A LEU* 4.0 32.2 + - + +
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Residues in contact with LYS 896 (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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783A ARG* 5.5 0.8 - - - +
813A LEU* 5.3 4.0 - - - +
816A LEU* 5.7 6.1 - - - +
817A GLN* 4.9 9.7 + - - +
822A MET* 4.1 28.1 - - + -
841A ILE* 3.9 19.6 - - + +
852A ILE 5.2 1.4 + - - -
853A ASP* 3.9 26.1 + - + +
855A LYS 4.0 19.1 + - - -
856A VAL* 5.3 2.2 - - - -
891A LEU 5.0 2.2 + - - -
892A ILE* 3.9 34.1 - - + +
893A THR* 3.1 24.6 + - - +
895A ARG* 1.4 78.4 - - - +
897A PHE* 1.4 61.3 + - - +
899A ASN* 3.7 13.3 + - - +
900A LEU* 3.7 17.6 - - + +
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Residues in contact with PHE 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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880A LYS* 3.6 43.5 - - + -
883A TRP* 3.5 33.2 - + + -
884A ARG* 3.8 22.2 - - + -
887A LEU* 5.4 8.3 - - + -
892A ILE* 4.3 11.4 - - + +
893A THR 3.1 17.7 + - - +
894A GLN* 3.6 14.8 - - - +
896A LYS* 1.4 73.7 - - - +
898A ASP* 1.4 79.0 + - - +
900A LEU* 3.0 24.4 + - - +
901A THR* 3.7 19.3 + - + +
905A ARG* 4.5 4.5 - - - -
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Residues in contact with ASP 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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894A GLN* 2.9 51.8 + - - +
895A ARG* 3.3 10.5 + - - +
897A PHE* 1.4 76.8 - - - +
899A ASN* 1.3 63.6 + - - +
901A THR* 2.9 21.2 + - - -
902A LYS* 3.1 10.4 + - - +
905A ARG* 2.7 30.4 + - - +
906A GLY 5.3 2.7 - - - +
908A LEU 5.6 0.7 - - - +
910A GLU* 3.0 18.6 - - - +
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Residues in contact with ASN 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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841A ILE* 3.7 32.9 - - + +
842A VAL* 5.0 8.5 - - + +
854A ASN* 5.5 3.2 + - - -
895A ARG* 3.0 59.8 + - - +
896A LYS* 3.9 10.5 - - - +
897A PHE 3.2 0.6 + - - -
898A ASP* 1.3 76.0 - - - +
900A LEU* 1.3 61.7 + - + +
901A THR 3.4 0.2 - - - -
902A LYS* 3.9 18.8 - - - +
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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