Contacts of the strand formed by residues 1900 - 1903 (chain A) in PDB entry 2H04
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 THR1900 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1771A GLU* 2.9 14.4 + - - +
1772A TYR* 3.1 18.0 - - + +
1773A ILE 2.8 23.8 + - - +
1797A ASN* 3.8 22.1 + - + +
1799A VAL* 4.1 17.0 - - + -
1887A VAL* 4.9 0.9 - - + -
1891A ILE* 3.6 37.1 - - + +
1898A GLY 3.6 2.4 + - - -
1899A PRO* 1.3 71.0 - - - +
1901A VAL* 1.3 74.6 + - - +
1902A VAL* 4.3 5.8 - - + -
1914A PHE* 5.9 0.7 - - + -
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Residues in contact with VAL1901 (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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1773A ILE* 3.2 25.1 - - + +
1775A THR* 4.2 9.2 - - + -
1786A PHE* 4.0 24.0 - - + -
1789A MET* 4.7 4.9 - - + -
1790A VAL* 4.4 10.5 - - + -
1795A VAL* 3.7 29.8 - - + -
1797A ASN 3.1 11.9 + - - +
1798A ILE* 3.5 17.1 - - + -
1799A VAL* 2.8 30.3 + - - +
1899A PRO 3.7 1.2 + - - -
1900A THR* 1.3 74.6 - - - +
1902A VAL* 1.3 67.9 + - - +
1903A HIS* 4.5 1.1 - - + -
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Residues in contact with VAL1902 (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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1772A TYR* 3.9 28.7 - - + -
1773A ILE 3.0 5.3 + - - +
1774A VAL* 3.3 27.9 - - + +
1775A THR 3.4 1.6 + - - -
1799A VAL* 3.3 15.7 - - + +
1801A VAL* 5.1 2.0 - - + -
1900A THR* 4.2 8.5 - - + +
1901A VAL* 1.3 81.3 - - - +
1903A HIS* 1.3 68.3 + - - +
1911A THR* 3.8 31.2 - - + +
1914A PHE* 3.8 31.0 - - + -
1915A ILE* 4.0 7.2 - - + -
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Residues in contact with HIS1903 (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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1775A THR* 2.9 33.2 - - + +
1776A GLN 4.1 4.3 - - - +
1777A GLY* 3.7 3.8 - - - -
1778A PRO* 4.1 2.2 - - + -
1786A PHE* 4.5 6.7 - + - -
1798A ILE* 4.2 10.3 - - + -
1799A VAL 2.9 17.8 + - - +
1800A MET* 3.4 28.5 - - + +
1801A VAL* 3.1 24.6 + - - +
1802A THR* 4.6 0.2 - - + -
1812A CYS* 3.7 12.1 - - - -
1815A TYR* 2.7 42.6 + + - -
1901A VAL* 4.5 6.1 - - + -
1902A VAL* 1.3 75.5 - - - +
1904A CYS* 1.3 69.6 + - - +
1911A THR* 3.0 11.5 + - - -
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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