Contacts of the strand formed by residues 1759 - 1763 (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 ASN1759 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1626A HIS 5.8 0.5 + - - -
1660A ASN* 3.0 39.9 + - - +
1661A CYS 3.0 12.5 + - - +
1662A ASN* 3.4 15.2 - - - +
1735A LYS* 6.0 0.2 - - - -
1742A GLN* 3.0 36.4 + - - +
1743A VAL 3.7 2.7 - - - +
1744A THR* 2.8 30.1 + - + +
1758A LEU* 1.3 74.9 - - - +
1760A ASP* 1.3 61.1 + - - +
1761A ILE* 3.8 18.7 + - - +
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Residues in contact with ASP1760 (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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1662A ASN* 3.2 9.4 - - - +
1663A SER* 2.6 52.2 + - - -
1664A TRP 4.4 0.9 + - - -
1724A LYS* 4.8 7.4 + - - -
1741A VAL 4.0 0.2 - - - +
1742A GLN* 3.2 3.3 - - - -
1743A VAL* 2.6 48.8 + - + +
1758A LEU* 5.3 3.0 - - - +
1759A ASN* 1.3 72.8 - - - +
1761A ILE* 1.3 60.6 + - - +
1762A TYR* 3.5 30.5 + - + +
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Residues in contact with ILE1761 (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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1625A THR* 3.8 27.8 - - + -
1626A HIS* 3.2 35.0 + - + +
1660A ASN* 3.9 10.1 - - - +
1662A ASN* 5.5 0.6 - - - +
1712A LEU* 4.3 11.2 - - + -
1740A ALA* 4.3 10.3 - - + -
1741A VAL 3.5 7.2 - - - +
1742A GLN* 4.2 11.9 - - + +
1759A ASN* 3.8 29.6 + - - +
1760A ASP* 1.3 79.1 - - - +
1762A TYR* 1.3 72.7 + - - +
1763A TYR* 4.1 27.1 - - + -
1766A GLU* 3.9 0.7 - - - +
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Residues in contact with TYR1762 (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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1724A LYS* 4.7 5.4 + - - -
1740A ALA* 4.1 2.7 - - - -
1741A VAL* 2.8 54.5 + - + +
1743A VAL* 3.8 28.5 - - + +
1760A ASP* 3.5 32.6 + - + +
1761A ILE* 1.3 78.8 - - - +
1763A TYR* 1.3 63.9 + - - +
1766A GLU* 3.4 8.1 - - - +
1767A ILE* 4.2 9.0 - - + +
1780A LEU* 5.1 2.9 - - + -
1782A ILE* 3.7 41.1 - - + -
1785A GLN* 4.2 17.6 + - - -
1789A LEU* 3.5 31.8 - - + +
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Residues in contact with TYR1763 (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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1590A ARG* 3.4 15.9 + - - -
1625A THR* 5.0 0.2 - - - +
1626A HIS* 3.3 49.5 + + + +
1712A LEU* 4.8 12.1 - - + -
1739A THR* 3.7 7.6 - - - +
1740A ALA* 4.1 13.2 - - + -
1761A ILE* 4.1 9.9 - - + -
1762A TYR* 1.3 75.2 - - - +
1764A ALA* 1.3 69.0 + - - +
1765A SER* 3.5 20.9 - - - +
1766A GLU* 2.7 31.0 + - + +
1767A ILE* 3.4 7.8 + - - +
1813B SER 5.8 2.9 - - - -
1814B GLN 5.0 7.0 - - - -
1815B PRO* 5.1 4.9 - - + -
1816B ASP* 2.7 32.0 + - - -
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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