Contacts of the strand formed by residues 1777 - 1782 (chain B) in PDB entry 2D4Q
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 GLN1777 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1725B LEU* 3.7 13.3 - - - +
1773B VAL* 2.9 45.0 + - + +
1774B ASP* 3.1 27.4 + - - +
1776B ASN* 1.3 80.2 - - - +
1778B PHE* 1.3 66.8 + - - +
1779B THR* 5.5 1.1 - - + +
1790B THR* 4.5 9.2 + - - +
1791B PHE 3.2 16.4 - - - +
1792B MET* 3.2 34.3 - - + +
1796B CYS* 3.3 4.5 - - - -
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Residues in contact with PHE1778 (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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1734B ILE* 3.8 13.7 - - + -
1771B CYS 3.2 14.1 - - - +
1772B LEU* 4.3 1.3 - - - -
1773B VAL* 4.3 1.6 - - - +
1777B GLN* 1.3 74.8 - - - +
1779B THR* 1.3 79.1 + - - +
1780B LEU* 3.3 28.7 - - + -
1790B THR* 4.1 0.5 - - - -
1791B PHE* 2.9 70.3 + + + +
1796B CYS* 3.7 21.8 - - + -
1799B ILE* 3.6 33.0 - - + -
1800B VAL* 3.5 25.1 - - + -
1803B ILE* 4.2 9.6 - - + -
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Residues in contact with THR1779 (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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1769B GLU 4.0 0.4 - - - +
1771B CYS* 2.9 51.7 + - - +
1773B VAL* 4.2 17.5 - - + -
1777B GLN* 5.5 2.7 - - + +
1778B PHE* 1.3 82.2 - - - +
1780B LEU* 1.3 73.1 + - - +
1781B THR* 5.3 1.0 + - - -
1788B PRO* 4.4 12.3 - - + +
1789B LEU 3.1 10.5 - - - -
1790B THR* 3.6 21.5 - - + -
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Residues in contact with LEU1780 (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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1741B VAL* 4.6 13.5 - - + -
1743B VAL* 6.1 0.2 - - + -
1762B TYR* 5.5 3.1 - - + -
1767B ILE* 4.4 17.3 - - + -
1769B GLU 3.3 7.6 - - - +
1770B ILE* 4.2 21.1 - - + -
1778B PHE* 3.3 28.9 - - + -
1779B THR* 1.3 83.4 - - - +
1781B THR* 1.3 62.7 + - - +
1782B ILE* 3.8 18.9 + - + +
1788B PRO* 3.5 3.6 - - - +
1789B LEU* 2.9 42.5 + - + +
1791B PHE* 4.4 11.7 - - + -
1803B ILE* 4.2 19.3 - - + -
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Residues in contact with THR1781 (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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1767B ILE* 3.7 4.2 - - - +
1768B GLU* 2.9 46.6 + - + +
1769B GLU* 2.9 46.3 + - + +
1771B CYS* 5.1 3.6 - - - -
1779B THR* 4.4 1.1 + - - -
1780B LEU* 1.3 72.6 - - - +
1782B ILE* 1.3 65.3 + - - +
1785B GLN 4.9 7.2 - - - +
1786B GLY 6.1 0.7 - - - +
1788B PRO* 4.4 20.5 - - + +
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Residues in contact with ILE1782 (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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1762B TYR* 3.8 39.3 - - + -
1766B GLU* 3.4 22.7 - - + +
1767B ILE* 4.2 12.1 - - + -
1768B GLU* 4.4 4.7 - - - +
1780B LEU* 3.8 13.8 + - + +
1781B THR* 1.3 83.2 - - - +
1783B ALA* 1.3 78.5 + - - +
1784B ASN 3.3 0.2 + - - -
1785B GLN* 3.0 46.5 + - + +
1787B THR 5.5 3.3 + - - +
1788B PRO* 5.5 0.2 - - - +
1789B LEU* 3.6 29.8 - - + -
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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