Contacts of the helix formed by residues 892 - 896 (chain C) in PDB entry 1ZXE
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 ALA 892 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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890C TYR 3.6 2.8 + - - -
891C VAL* 1.3 79.0 - - - +
893C THR* 1.3 63.7 + - - +
894C GLU* 3.3 17.0 - - - +
895C VAL* 3.1 20.2 + - + +
896C LEU* 3.7 5.4 + - - +
906C ILE* 3.6 35.7 + - + +
909C TYR* 3.4 14.7 - - + +
910C SER* 5.0 0.2 + - - -
936C ARG* 4.8 0.2 - - - -
969C ARG* 3.7 11.7 - - - +
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Residues in contact with THR 893 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891C VAL 4.6 0.2 - - - -
892C ALA* 1.3 72.7 - - - +
894C GLU* 1.3 66.1 + - - +
896C LEU* 3.2 26.0 + - - +
909C TYR* 3.8 17.9 - - + +
936C ARG* 4.2 13.7 - - + +
964C HIS* 3.3 65.9 + - + +
969C ARG* 4.3 1.7 + - - -
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Residues in contact with GLU 894 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892C ALA* 3.3 16.7 - - - +
893C THR* 1.3 78.4 + - - +
895C VAL* 1.3 62.2 + - - +
896C LEU 3.2 5.2 - - - +
897C ASP 3.9 8.1 - - - +
898C GLY* 4.0 8.5 - - - -
901C HIS 4.7 8.9 - - - +
902C TYR* 4.3 20.4 - - + -
903C ASN* 4.7 0.9 - - - +
906C ILE* 3.6 8.6 - - + +
964C HIS 4.4 1.4 - - - +
966C PRO* 3.2 31.4 - - + +
969C ARG* 2.9 30.5 + - - -
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Residues in contact with VAL 895 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859C ASN 4.3 18.3 - - - +
860C VAL* 4.3 14.1 - - + +
891C VAL* 3.4 25.4 - - + -
892C ALA* 3.1 25.6 + - + +
894C GLU* 1.3 79.2 - - - +
896C LEU* 1.3 64.9 + - + +
897C ASP 3.3 3.5 + - - -
898C GLY* 4.0 8.2 + - - +
900C GLY* 5.7 2.2 + - - -
901C HIS 5.6 0.2 - - - -
902C TYR* 4.1 26.2 - - + -
906C ILE* 4.2 19.3 - - + -
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Residues in contact with LEU 896 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860C VAL* 6.3 2.9 - - + -
888C ALA* 5.5 8.1 - - + +
891C VAL* 4.7 15.0 - - + -
892C ALA 3.7 8.9 + - - +
893C THR* 3.2 18.3 + - - +
894C GLU* 3.9 0.5 - - - +
895C VAL* 1.3 76.7 - - + +
897C ASP* 1.3 78.9 + - - +
936C ARG* 3.8 24.2 - - - +
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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