Contacts of the strand formed by residues 1741 - 1747 (chain A) in PDB entry 3AU5
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 MET1741 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1730A ILE* 6.0 0.2 - - - -
1740A ASN* 1.3 77.1 - - - +
1742A PHE* 1.3 68.9 + - - +
1743A ALA* 5.9 0.2 - - - -
1788A LEU* 3.5 5.2 - - - +
1789A TYR* 2.6 46.4 + - - -
1790A CYS* 3.2 37.3 + - + +
1792A LEU* 4.9 4.0 - - + +
2035A ALA* 4.5 8.7 - - + +
2038A SER* 5.6 0.7 - - - +
2039A MET* 3.7 43.7 - - + -
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Residues in contact with PHE1742 (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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1726A VAL* 4.0 9.4 - - - +
1730A ILE* 3.8 24.8 - - + +
1735A MET* 3.6 35.7 - - + -
1738A SER* 3.3 31.4 - - - -
1740A ASN 4.1 5.2 - - - -
1741A MET* 1.3 90.3 - - - +
1743A ALA* 1.3 66.3 + - - +
1786A PHE* 3.4 30.7 - + + -
1787A LYS* 3.1 22.4 - - - +
1788A LEU* 3.3 35.4 - - + -
1789A TYR* 4.0 2.0 - - - -
1803A GLU* 4.0 6.5 - - + -
1806A PHE* 4.2 6.5 - + - -
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Residues in contact with ALA1743 (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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1726A VAL* 3.7 16.3 - - - +
1742A PHE* 1.3 79.6 - - - +
1744A LEU* 1.3 64.0 + - - +
1745A PHE* 3.4 14.0 - - + -
1754A ALA* 5.3 2.2 - - + -
1755A ILE 4.8 8.3 - - - +
1786A PHE* 3.6 6.6 - - - -
1787A LYS 3.0 27.8 + - - -
1789A TYR* 3.9 24.7 - - + -
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Residues in contact with LEU1744 (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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1704A VAL* 3.7 28.5 - - + -
1722A ALA* 4.3 21.7 - - + +
1725A VAL* 4.1 23.3 - - + -
1726A VAL* 3.5 17.4 - - + +
1729A LEU* 5.1 1.1 - - + -
1743A ALA* 1.3 77.0 - - - +
1745A PHE* 1.3 66.5 + - - +
1754A ALA* 3.8 1.0 - - - -
1755A ILE* 2.9 40.7 + - + -
1761A VAL* 4.5 11.7 - - + -
1784A PHE* 4.0 27.6 - - + -
1785A TYR 3.4 15.9 - - - +
1786A PHE* 4.5 3.6 - - + +
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Residues in contact with PHE1745 (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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1743A ALA* 3.4 25.8 - - + -
1744A LEU* 1.3 77.3 - - - +
1746A GLU* 1.3 63.7 + - - +
1747A TYR* 4.3 0.7 - - + -
1752A ASP* 3.0 35.7 - - - +
1753A LYS 3.3 15.0 - - - -
1754A ALA* 3.7 20.0 - - + -
1755A ILE* 4.3 3.1 - - - -
1783A LYS 3.4 0.2 - - - +
1784A PHE* 3.2 11.8 - - - -
1785A TYR* 2.8 41.4 + - + +
1787A LYS* 3.5 35.9 - - + -
1788A LEU 4.3 5.4 - - - -
1789A TYR* 3.5 30.3 - + + -
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Residues in contact with GLU1746 (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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1745A PHE* 1.3 75.5 - - - +
1747A TYR* 1.3 60.1 + - - +
1751A VAL 3.5 0.9 - - - +
1752A ASP* 3.3 10.2 - - - +
1753A LYS* 3.1 46.7 + - - +
1755A ILE* 3.9 21.8 - - + +
1764A VAL* 3.9 24.4 - - - +
1767A LYS* 2.8 36.0 + - - -
1768A PHE* 3.9 14.7 - - + -
1782A TRP* 3.6 18.6 - - + -
1783A LYS 3.5 4.5 - - - -
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Residues in contact with TYR1747 (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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1707A HIS* 3.6 18.4 + - - -
1745A PHE* 4.3 0.2 - - + -
1746A GLU* 1.3 72.8 - - - +
1748A ASN* 1.3 58.7 + - - +
1749A GLY* 4.1 26.0 - - - +
1750A HIS 5.0 2.5 - - - -
1751A VAL 3.4 13.9 - - - -
1752A ASP* 3.1 40.0 + - + +
1781A PRO 3.6 1.4 - - - +
1782A TRP* 3.1 7.9 - - - -
1783A LYS* 2.6 41.3 + - + +
1785A TYR* 3.4 48.2 - + + -
1787A LYS* 3.1 30.6 + - + -
1813A GLU* 4.0 11.4 + - - -
1817A HIS* 6.0 1.3 - - - -
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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