Contacts of the helix formed by residues 1835 - 1839 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1582B ARG* 6.1 0.4 - - + -
1583B GLN* 5.2 6.3 - - + +
1586B HIS* 5.7 0.2 - - - -
1833B SER 3.3 6.2 + - - +
1834B LEU* 1.3 70.2 - - - +
1836B LEU* 1.3 65.3 + - - +
1837B GLU* 3.3 28.0 - - - +
1838B THR* 2.6 40.0 + - + +
1839B ILE* 3.5 8.2 + - - +
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Residues in contact with LEU1836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473B GLY* 3.9 10.3 - - - +
1509B TYR* 4.0 17.9 - - + -
1512B PHE* 3.9 22.4 - - + -
1513B MET* 3.5 37.6 - - + +
1516B ARG* 3.7 31.9 - - - +
1569B TYR* 3.9 26.1 + - + +
1583B GLN* 6.1 0.4 - - - +
1586B HIS* 3.7 16.6 + - - +
1834B LEU 3.5 5.5 + - - +
1835B ALA* 1.3 71.8 - - - +
1837B GLU* 1.3 63.1 + - - +
1838B THR 3.1 1.5 + - - -
1839B ILE* 3.3 28.6 + - + +
1852B ARG* 5.5 0.3 + - - -
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Residues in contact with GLU1837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471B PHE* 3.3 36.0 - - + +
1473B GLY* 3.8 13.4 - - - +
1582B ARG* 3.3 27.9 - - - +
1586B HIS* 3.1 20.3 - - + +
1835B ALA* 3.3 28.1 - - - +
1836B LEU* 1.3 74.1 + - - +
1838B THR* 1.3 58.2 + - + +
1852B ARG* 2.4 29.7 + - - +
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Residues in contact with THR1838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1835B ALA* 2.6 39.6 + - + +
1837B GLU* 1.3 93.0 - - + +
1839B ILE* 1.3 64.9 + - - +
1840B GLN* 3.2 13.0 + - - +
1852B ARG* 3.7 3.7 + - - +
96D HIS* 5.6 13.1 + - + +
100D GLU* 5.1 10.1 - - - +
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Residues in contact with ILE1839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503B ILE* 5.6 3.1 - - + -
1506B LEU* 4.0 21.3 - - + -
1509B TYR* 3.7 32.8 - - + -
1510B ILE* 5.0 4.5 - - + -
1513B MET* 4.1 23.5 - - - +
1834B LEU* 4.6 14.8 - - + -
1835B ALA 3.6 12.6 - - - +
1836B LEU* 3.3 35.2 + - + +
1838B THR* 1.3 78.6 - - - +
1840B GLN* 1.3 71.5 + - - +
1841B ILE* 4.3 4.8 - - + +
1852B ARG* 3.7 15.4 + - - -
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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