Contacts of the strand formed by residues 1778 - 1788 (chain A) in PDB entry 4C6C
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 LYS1778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1716A THR* 4.2 9.9 - - - +
1758A TRP 3.6 6.7 - - - +
1759A THR* 4.0 17.0 - - - +
1776A GLY 3.5 7.2 + - - +
1777A GLN* 1.3 76.2 - - - +
1779A VAL* 1.3 65.5 + - - +
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Residues in contact with VAL1779 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1712A PRO* 4.1 11.9 - - + +
1713A LEU* 4.0 27.4 - - + -
1716A THR* 3.2 16.8 - - + +
1757A GLU* 3.4 5.2 - - - +
1758A TRP* 2.9 80.7 + - + +
1760A ILE* 4.0 18.8 - - + -
1777A GLN* 4.4 2.5 - - + +
1778A LYS* 1.3 80.9 - - - +
1780A LYS* 1.3 61.9 + - - +
1781A GLY 4.2 0.2 - - - -
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Residues in contact with LYS1780 (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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1715A LEU* 3.6 4.7 - - - +
1716A THR* 2.8 39.8 + - + +
1719A SER* 4.4 19.1 + - - +
1754A LEU* 3.3 21.0 - - - +
1755A GLU* 3.7 26.7 - - - +
1756A HIS 3.3 3.8 - - - -
1757A GLU* 4.0 22.3 + - + +
1779A VAL* 1.3 75.3 - - - +
1781A GLY* 1.3 60.7 + - - +
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Residues in contact with GLY1781 (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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1712A PRO* 3.7 14.8 - - - +
1715A LEU* 4.2 19.1 - - - -
1753A ASP 3.2 14.3 + - - -
1754A LEU* 4.1 6.2 + - - -
1756A HIS 3.0 11.8 + - - -
1758A TRP* 2.9 18.8 + - - -
1780A LYS* 1.3 77.8 + - - +
1782A THR* 1.3 60.6 + - - -
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Residues in contact with THR1782 (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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1712A PRO* 5.2 3.3 - - - +
1715A LEU* 4.3 3.4 - - - +
1752A VAL* 3.3 6.5 - - - +
1753A ASP* 2.9 41.3 + - + -
1756A HIS* 4.1 22.4 + - + +
1758A TRP* 3.8 20.1 + - - -
1781A GLY* 1.3 76.1 - - - -
1783A VAL* 1.3 67.1 + - - +
1784A ARG* 3.7 24.5 - - - -
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Residues in contact with VAL1783 (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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1494A ALA 3.6 22.9 - - - +
1495A GLY* 3.8 5.6 - - - -
1496A GLY* 3.7 14.8 - - - +
1711A LEU* 3.8 22.2 - - + -
1712A PRO* 5.4 6.6 - - + +
1715A LEU* 5.7 0.7 - - + -
1750A VAL* 4.2 9.4 - - + -
1751A GLU 3.9 2.7 - - - -
1752A VAL* 4.3 4.5 - - + -
1782A THR* 1.3 82.6 + - - +
1784A ARG* 1.3 63.5 + - - +
1785A ARG 4.2 1.6 - - - +
1786A VAL* 3.8 28.9 - - + -
1794A TYR* 3.7 25.5 + - + -
1796A ASP* 4.2 3.8 - - - +
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Residues in contact with ARG1784 (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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1461A LEU* 3.9 31.3 - - + +
1751A GLU 2.8 10.7 + - - +
1753A ASP* 3.6 36.4 + - + +
1782A THR* 3.7 22.9 - - - -
1783A VAL* 1.3 75.7 - - - +
1785A ARG* 1.3 64.5 + - + +
1794A TYR* 4.5 0.7 - - - -
1795A ILE* 3.3 7.3 - - - +
1796A ASP* 2.6 68.7 + - - +
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Residues in contact with ARG1785 (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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1461A LEU* 5.9 0.4 - - + -
1749A TYR* 2.8 37.0 + - - +
1750A VAL* 3.5 1.2 - - - +
1751A GLU* 2.8 66.6 + - + +
1783A VAL* 3.8 0.8 - - - +
1784A ARG* 1.3 83.6 - - + +
1786A VAL* 1.3 76.2 + - - +
1787A VAL* 3.8 15.3 - - - +
1792A VAL* 4.0 17.7 - - + +
1794A TYR 3.2 12.1 - - - +
1795A ILE* 3.8 22.2 - - + +
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Residues in contact with VAL1786 (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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1493A LEU* 3.4 39.3 - - + +
1496A GLY* 4.3 3.1 - - - -
1497A ILE 5.4 0.2 - - - +
1498A THR* 3.6 31.6 - - + -
1749A TYR 3.5 6.7 - - - +
1750A VAL* 4.3 9.6 - - + -
1783A VAL* 3.8 15.0 - - + -
1785A ARG* 1.3 78.8 - - - +
1787A VAL* 1.3 63.4 + - - +
1792A VAL* 3.7 4.0 - - - +
1793A ALA* 2.8 32.6 + - + -
1794A TYR* 2.9 24.3 + - + +
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Residues in contact with VAL1787 (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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1747A ASP* 3.5 17.7 - - - +
1748A THR* 3.2 6.6 - - - +
1749A TYR* 2.9 73.7 + - + +
1785A ARG* 3.8 24.2 - - - +
1786A VAL* 1.3 80.0 - - - +
1788A LEU* 1.3 62.4 + - - +
1790A GLY* 4.0 13.9 - - - +
1791A GLU 3.3 14.6 - - - +
1792A VAL* 4.5 8.1 - - + -
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Residues in contact with LEU1788 (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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1493A LEU* 4.6 5.8 - - + -
1498A THR* 4.1 8.7 - - + +
1528A ARG 3.7 22.7 - - - +
1529A CYS* 3.7 20.6 - - + -
1530A ASP* 3.6 12.6 - - - +
1745A GLN* 3.4 27.4 - - - +
1748A THR* 3.6 18.6 - - + +
1786A VAL* 4.1 1.0 + - + -
1787A VAL* 1.3 71.7 - - - +
1789A ARG* 1.3 66.1 + - + +
1790A GLY 3.2 1.1 - - - -
1791A GLU 2.9 15.1 + - - +
1793A ALA* 4.1 15.5 - - + +
1805A TYR* 2.7 43.5 + - + -
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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