Contacts of the strand formed by residues 1859 - 1862 (chain E) in PDB entry 6AJ4
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 VAL1859 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1847E GLU* 3.5 49.9 - - + +
1850E TYR* 3.2 39.3 - - + +
1851E GLY* 3.7 2.5 - - - +
1854E PHE* 4.3 4.5 - - + -
1855E GLY 3.8 7.6 - - - +
1856E GLU 3.7 11.2 + - - +
1858E VAL* 1.3 78.4 - - - +
1860E GLU* 1.3 72.5 + - - +
1861E VAL* 5.8 0.2 - - + -
1878E ALA* 3.2 17.5 - - + +
1880E ILE* 4.3 19.3 - - + -
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Residues in contact with GLU1860 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1847E GLU* 4.5 7.3 - - - +
1856E GLU 4.9 0.5 - - - +
1857E ASP* 4.2 11.6 - - - +
1858E VAL 4.6 0.2 - - - +
1859E VAL* 1.3 83.8 - - - +
1861E VAL* 1.3 65.8 + - - +
1863E LYS* 5.2 8.3 + - - +
1877E LYS* 2.6 46.8 + - + +
1878E ALA 2.7 9.3 + - - +
1879E TYR* 3.1 30.5 - - + -
1880E ILE* 3.0 23.2 + - - +
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Residues in contact with VAL1861 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1843E SER* 3.4 28.7 - - - +
1847E GLU* 3.4 37.4 + - + +
1859E VAL* 5.8 0.2 - - + -
1860E GLU* 1.3 76.7 + - - +
1862E ILE* 1.3 69.7 + - - +
1863E LYS* 3.1 31.1 + - + +
1879E TYR* 5.0 2.0 - - - -
1880E ILE* 3.3 17.0 - - + +
1882E ILE* 3.7 19.7 - - + -
28F PHE* 4.7 9.6 - - + -
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Residues in contact with ILE1862 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1817E TYR* 4.3 9.9 - - + -
1860E GLU 3.9 0.2 + - - -
1861E VAL* 1.3 74.2 - - - +
1863E LYS* 1.3 57.7 + - - +
1864E ASP* 2.8 34.7 + - + +
1868E VAL* 3.8 29.6 - - + -
1873E LEU* 4.7 9.2 - - + -
1879E TYR* 4.0 26.5 - - + -
1880E ILE 2.6 20.8 + - - +
1881E GLN* 3.9 28.5 - - + +
1882E ILE 4.2 6.4 + - - -
28F PHE* 4.2 4.2 - - - -
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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