Contacts of the strand formed by residues 1777 - 1782 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1725A LEU* 3.9 20.5 - - + +
1772A LEU* 3.6 1.6 - - - +
1773A VAL* 2.7 59.0 + - + +
1774A ASP* 3.2 29.4 + - - +
1776A ASN* 1.3 80.9 - - - +
1778A PHE* 1.3 59.8 + - - +
1779A THR* 5.4 0.4 + - - -
1790A THR* 4.5 12.7 + - - +
1791A PHE 3.3 16.4 - - - +
1792A MET* 4.5 6.4 - - + +
1796A CYS* 3.5 6.6 - - - -
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Residues in contact with PHE1778 (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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1734A ILE* 3.9 9.2 - - + -
1770A ILE* 4.7 3.1 - - + -
1771A CYS 3.1 13.0 - - - +
1772A LEU* 4.2 2.9 - - + -
1773A VAL* 4.1 3.6 - - - +
1777A GLN* 1.3 76.0 - - - +
1779A THR* 1.3 73.7 + - - +
1780A LEU* 3.9 20.2 - - + -
1790A THR* 3.3 5.6 - - - -
1791A PHE* 3.0 70.5 + + + +
1796A CYS* 3.6 19.5 - - + -
1799A ILE* 3.5 43.7 - - + -
1800A VAL* 3.5 25.8 - - + -
1803A ILE* 4.3 9.6 - - + -
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Residues in contact with THR1779 (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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1770A ILE* 3.5 4.2 - - - +
1771A CYS* 2.7 48.3 + - + +
1773A VAL* 4.1 12.2 - - - +
1777A GLN* 5.4 0.3 + - - -
1778A PHE* 1.3 84.9 + - - +
1780A LEU* 1.3 64.4 - - - +
1781A THR* 4.4 6.3 - - - +
1788A PRO* 3.8 24.0 - - + +
1789A LEU 3.2 9.2 - - - +
1790A THR* 3.7 17.7 - - - +
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Residues in contact with LEU1780 (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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1741A VAL* 4.6 14.6 - - + -
1762A TYR* 5.1 3.8 - - + -
1767A ILE* 3.6 33.2 - - + -
1769A GLU 3.6 7.0 - - - +
1770A ILE* 3.9 19.1 - - + -
1778A PHE* 3.9 15.2 - - + -
1779A THR* 1.3 72.2 - - - +
1781A THR* 1.3 63.5 + - - +
1782A ILE* 3.8 20.0 + - + -
1788A PRO* 3.5 1.9 - - - +
1789A LEU* 2.8 57.5 + - + +
1791A PHE* 4.6 9.0 - - + -
1803A ILE* 4.4 18.8 - - + -
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Residues in contact with THR1781 (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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1766A GLU 3.8 0.3 - - - +
1767A ILE* 3.8 0.5 - - - -
1768A GLU* 3.0 44.9 + - + +
1769A GLU* 2.9 42.4 + - + +
1779A THR* 4.3 6.4 - - - +
1780A LEU* 1.3 73.3 - - - +
1782A ILE* 1.3 67.5 + - - +
1785A GLN 5.0 5.6 - - - +
1786A GLY 5.4 3.6 - - - +
1788A PRO* 3.9 16.7 - - + +
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Residues in contact with ILE1782 (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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1762A TYR* 3.7 38.6 - - + -
1766A GLU* 3.3 28.0 - - + +
1767A ILE* 4.3 8.3 - - + -
1768A GLU* 4.4 3.0 - - - +
1780A LEU* 3.8 20.5 + - + +
1781A THR* 1.3 85.4 - - - +
1783A ALA* 1.3 79.1 + - - +
1784A ASN 3.4 0.3 + - - -
1785A GLN* 3.1 48.3 + - + +
1787A THR 5.7 0.4 + - - -
1788A PRO* 5.4 1.6 - - + +
1789A LEU* 3.9 20.2 - - + -
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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