Contacts of the strand formed by residues 1772 - 1775 (chain B) in PDB entry 2H02
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 TYR1772 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1762B TYR* 3.5 6.6 - - - +
1763B ILE* 3.0 51.8 + - + +
1764B PRO 3.8 3.8 - - - -
1765B GLY* 3.5 23.3 - - - -
1770B ARG 4.3 1.9 - - - -
1771B GLU* 1.3 91.8 + - + +
1773B ILE* 1.3 67.5 + - - +
1774B VAL 4.0 0.4 - - - -
1888B ARG* 3.6 11.4 + - - -
1891B ILE* 5.2 1.1 - - + -
1899B PRO* 3.8 3.9 - - - +
1900B THR* 3.2 24.9 - - + +
1902B VAL* 4.2 9.0 - - + -
1914B PHE* 5.3 2.5 - + - -
1915B ILE* 3.6 43.1 - - + -
1918B ASP* 2.5 33.3 + - + +
1919B ARG* 3.7 14.1 - - + +
1922B GLN* 4.2 1.0 + - - -
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Residues in contact with ILE1773 (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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1744B VAL* 3.7 23.8 - - + -
1760B ALA* 3.9 0.4 - - + -
1761B SER 3.3 3.1 - - - -
1762B TYR* 3.8 14.4 - - + -
1772B TYR* 1.3 73.5 - - - +
1774B VAL* 1.3 73.2 + - - +
1775B THR* 4.7 0.9 - - - -
1789B MET* 3.8 33.7 - - + -
1793B GLN* 3.7 41.1 - - + +
1795B VAL* 4.6 7.0 - - + -
1899B PRO* 3.8 19.2 - - + +
1900B THR 2.9 6.7 + - - +
1901B VAL* 3.3 11.9 - - + +
1902B VAL 2.9 23.7 + - - +
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Residues in contact with VAL1774 (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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1760B ALA* 3.2 4.5 - - - +
1761B SER* 2.8 32.5 + - - +
1763B ILE* 3.7 21.8 - - + -
1772B TYR* 4.0 1.1 - - + -
1773B ILE* 1.3 75.4 - - - +
1775B THR* 1.3 65.4 + - - +
1902B VAL* 3.2 7.0 - - + +
1907B GLY 2.9 30.1 - - - +
1911B THR* 3.2 17.5 - - + -
1915B ILE* 3.2 35.4 - - + -
1943B ARG* 3.7 14.7 + - - +
1946B MET* 4.4 4.5 - - - -
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Residues in contact with THR1775 (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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1758B ILE* 4.4 7.6 - - - +
1759B ASN 2.7 22.7 + - - -
1760B ALA* 3.6 11.6 - - - +
1773B ILE* 4.7 0.2 - - - -
1774B VAL* 1.3 81.3 - - - +
1776B GLN* 1.3 69.6 + - - +
1778B PRO* 6.0 0.2 - - - +
1786B PHE* 4.0 18.0 - - + -
1789B MET* 4.3 8.5 - - + +
1901B VAL* 4.0 19.5 - - + -
1902B VAL 3.1 5.3 + - - -
1903B HIS* 3.1 34.4 - - + +
1907B GLY* 3.3 17.5 - - - -
1943B ARG* 4.3 3.4 - - - +
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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