Contacts of the helix formed by residues 1795 - 1806 (chain A) in PDB entry 5JCY
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 SER1795 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1756A LYS 5.1 1.6 + - - -
1792A GLU* 5.7 4.7 - - - -
1793A ARG 3.6 3.7 + - - -
1794A VAL* 1.3 78.0 - - - +
1796A VAL* 1.3 62.0 - - - +
1797A SER* 3.1 11.8 + - - -
1798A PHE* 3.0 34.6 + - - +
1799A ILE* 3.2 15.2 + - - +
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Residues in contact with VAL1796 (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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1782A ASN* 5.9 2.2 - - - +
1794A VAL 5.4 1.6 - - - +
1795A SER* 1.3 73.4 - - - +
1797A SER* 1.3 57.0 + - - +
1799A ILE* 3.5 13.9 + - + +
1800A ARG* 3.1 52.6 + - - +
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Residues in contact with SER1797 (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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1795A SER* 3.1 13.7 + - - -
1796A VAL* 1.3 76.9 - - - +
1798A PHE* 1.3 63.2 + - - +
1800A ARG* 3.3 9.8 + - - +
1801A THR* 2.9 27.4 + - - -
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Residues in contact with PHE1798 (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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1756A LYS* 3.6 37.9 - - + +
1757A LYS* 3.5 19.1 - - - +
1758A THR 3.3 24.5 - - - -
1759A ASP* 6.0 0.4 - - - -
1761A ASP 4.2 0.2 - - - -
1762A ALA* 3.7 21.5 - - + -
1765A ILE* 3.6 25.1 - - + -
1781A LEU* 4.1 6.1 - - + -
1794A VAL* 3.7 16.8 - - + -
1795A SER* 3.0 23.1 + - - +
1797A SER* 1.3 76.5 + - - +
1799A ILE* 1.3 65.1 + - - +
1801A THR* 3.1 17.2 + - + -
1802A ILE* 3.2 32.3 + - + +
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Residues in contact with ILE1799 (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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1778A VAL* 3.7 32.5 - - + +
1781A LEU* 4.2 10.3 - - + +
1782A ASN* 3.5 44.2 - - - +
1794A VAL* 3.9 19.5 - - + +
1795A SER 3.2 14.5 + - - +
1796A VAL* 3.7 16.6 - - + +
1797A SER 3.3 0.2 - - - -
1798A PHE* 1.3 76.7 - - - +
1800A ARG* 1.3 63.8 + - - +
1802A ILE* 3.2 10.0 + - - +
1803A GLN* 3.1 29.8 + - - +
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Residues in contact with ARG1800 (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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1796A VAL* 3.1 42.2 + - - +
1797A SER* 3.7 9.5 - - - +
1798A PHE 3.2 0.4 - - - -
1799A ILE* 1.3 78.7 - - - +
1801A THR* 1.3 56.2 + - - +
1803A GLN* 3.2 21.2 + - + +
1804A MET* 2.9 39.9 + - + +
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Residues in contact with THR1801 (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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1759A ASP* 3.8 21.8 + - - +
1762A ALA* 4.1 8.3 - - + -
1797A SER 2.9 15.7 + - - -
1798A PHE* 3.1 13.5 + - + -
1800A ARG* 1.3 77.8 - - - +
1802A ILE* 1.3 56.9 + - - +
1804A MET* 3.4 7.7 + - - +
1805A ARG* 3.0 55.1 + - + +
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Residues in contact with ILE1802 (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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1762A ALA* 4.2 16.8 - - + +
1765A ILE* 4.0 16.2 - - + -
1766A CYS* 4.0 11.9 - - - -
1774A THR* 5.5 0.4 - - + -
1777A ILE* 4.1 15.5 - - + -
1778A VAL* 5.2 8.1 - - + -
1781A LEU* 3.4 21.8 - - + -
1798A PHE* 3.2 39.7 + - + +
1799A ILE* 3.2 8.9 + - + +
1801A THR* 1.3 75.4 - - - +
1803A GLN* 1.3 65.6 + - - +
1805A ARG* 3.2 6.5 + - - +
1806A LEU* 3.0 44.5 + - + +
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Residues in contact with GLN1803 (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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1774A THR* 4.3 16.0 - - + +
1778A VAL* 3.8 34.4 - - + +
1799A ILE* 3.1 25.5 + - - +
1800A ARG* 3.2 28.0 + - + +
1802A ILE* 1.3 77.0 - - - +
1804A MET* 1.3 62.9 + - - +
1806A LEU 3.4 3.1 + - - -
1807A ARG* 3.3 21.9 + - - +
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Residues in contact with MET1804 (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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1800A ARG* 2.9 26.0 + - + +
1801A THR* 3.6 7.6 - - - +
1802A ILE 3.2 0.2 - - - -
1803A GLN* 1.3 78.1 - - + +
1805A ARG* 1.3 62.0 + - + +
1807A ARG* 3.2 58.8 + - - +
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Residues in contact with ARG1805 (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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1759A ASP* 3.6 39.4 + - - +
1762A ALA* 3.9 12.1 - - - +
1763A GLU* 2.6 37.4 + - - +
1766A CYS* 3.7 26.7 - - + -
1801A THR* 3.0 36.8 + - + +
1802A ILE 3.2 4.9 + - - +
1804A MET* 1.3 77.6 - - + +
1806A LEU* 1.3 61.5 + - - +
1807A ARG 3.3 2.0 + - - -
1808A ASP 5.1 1.2 + - - -
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Residues in contact with LEU1806 (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 CYS* 3.8 31.4 - - + +
1774A THR* 3.8 28.1 + - + +
1777A ILE* 3.8 25.4 - - + -
1802A ILE* 3.0 37.1 + - + +
1803A GLN 3.7 4.7 - - - +
1804A MET 3.2 0.4 - - - -
1805A ARG* 1.3 78.1 - - - +
1807A ARG* 1.3 62.5 + - - +
1808A ASP 3.4 2.2 - - - -
1809A ARG* 3.2 47.7 - - + +
1811A ASP* 5.6 0.2 - - - +
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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