Contacts of the helix formed by residues 1835 - 1839 (chain C) in PDB entry 5JCZ
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 ALA1835 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1569C TYR* 5.3 0.2 - - - -
1582C ARG* 5.7 0.7 - - - -
1583C GLN* 5.2 6.3 - - + +
1586C HIS* 5.7 0.4 - - - -
1833C SER 3.2 6.6 + - - +
1834C LEU* 1.3 73.1 - - - +
1836C LEU* 1.3 64.8 + - - +
1837C GLU* 3.1 27.8 - - - +
1838C THR* 2.7 36.5 + - + +
1839C ILE* 3.6 7.4 + - - +
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Residues in contact with LEU1836 (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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1473C GLY* 3.4 15.2 - - - +
1509C TYR* 4.0 28.9 - - + +
1512C PHE* 3.9 20.0 - - + -
1513C MET* 3.4 35.8 - - + +
1516C ARG* 3.7 31.9 - - - +
1569C TYR* 4.0 31.4 + - + +
1586C HIS* 3.9 13.7 + - - +
1834C LEU 3.6 2.5 + - - +
1835C ALA* 1.3 71.2 - - - +
1837C GLU* 1.3 61.6 + - - +
1838C THR 3.1 1.5 + - - -
1839C ILE* 3.4 18.7 + - + +
1852C ARG* 5.6 0.3 + - - -
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Residues in contact with GLU1837 (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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1471C PHE* 3.5 28.8 + - - +
1472C GLN 4.2 0.4 - - - -
1473C GLY* 3.6 14.3 - - - +
1582C ARG* 3.2 37.6 + - - +
1586C HIS* 3.1 23.6 - - + +
1835C ALA* 3.3 29.1 - - - +
1836C LEU* 1.3 74.0 + - - +
1838C THR* 1.3 62.2 + - + +
1852C ARG* 2.6 27.9 + - - +
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Residues in contact with THR1838 (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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96A HIS* 5.3 14.0 + - + +
100A GLU* 5.3 8.3 - - - +
1834C LEU* 5.8 2.1 - - - +
1835C ALA* 2.7 27.9 + - + +
1837C GLU* 1.3 101.3 - - + +
1839C ILE* 1.3 65.9 + - - +
1840C GLN* 3.5 14.4 + - - +
1852C ARG* 3.6 7.1 + - - +
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Residues in contact with ILE1839 (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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1475C LEU* 5.6 1.2 - - - +
1503C ILE* 4.7 6.5 - - + -
1506C LEU* 4.1 18.6 - - + -
1509C TYR* 3.8 35.7 - - + -
1510C ILE* 5.1 3.4 - - + -
1513C MET* 3.9 25.9 - - + +
1834C LEU* 4.6 18.8 - - + -
1835C ALA 3.7 11.9 - - - +
1836C LEU* 3.4 28.1 + - + +
1838C THR* 1.3 79.4 - - - +
1840C GLN* 1.3 70.9 + - - +
1841C ILE* 5.6 1.4 - - + +
1852C ARG* 3.7 16.6 + - - +
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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