Contacts of the helix formed by residues 1758 - 1769 (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 THR1758 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1757A LYS* 1.3 79.3 - - + +
1759A ASP* 1.3 61.6 + - - +
1760A ASP* 3.2 11.4 + - - +
1761A ASP* 2.9 37.5 + - - +
1762A ALA* 2.9 22.2 + - - +
1798A PHE* 3.3 8.5 - - - -
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Residues in contact with ASP1759 (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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1758A THR* 1.3 73.3 - - - +
1760A ASP* 1.3 63.4 + - - +
1762A ALA* 3.7 3.9 - - - +
1763A GLU* 2.9 29.5 + - - +
1798A PHE* 6.0 0.9 - - - -
1801A THR* 3.8 22.3 + - - +
1805A ARG* 3.6 19.2 + - - +
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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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1758A THR* 3.2 8.4 + - - +
1759A ASP* 1.3 79.9 - - - +
1761A ASP* 1.3 64.7 + - - +
1763A GLU* 3.5 5.7 + - - +
1764A ALA* 3.1 24.3 + - - +
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Residues in contact with ASP1761 (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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1754A VAL* 5.6 0.2 - - - +
1755A LYS* 3.3 53.7 - - - +
1757A LYS* 3.0 16.8 + - - +
1758A THR* 2.9 46.5 + - - +
1760A ASP* 1.3 78.6 - - - +
1762A ALA* 1.3 61.1 + - - +
1764A ALA* 3.5 6.4 + - - +
1765A ILE* 3.1 27.5 + - - +
1798A PHE* 4.2 3.6 - - + -
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Residues in contact with ALA1762 (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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1758A THR 2.9 12.8 + - - +
1759A ASP* 3.7 9.2 - - - +
1760A ASP 3.3 0.4 - - - -
1761A ASP* 1.3 74.7 - - - +
1763A GLU* 1.3 63.4 - - - +
1765A ILE* 3.2 4.3 + - - +
1766A CYS* 3.1 26.7 + - - -
1798A PHE* 3.7 21.5 - - + -
1801A THR* 4.1 16.8 - - + -
1802A ILE* 4.2 10.7 - - + +
1805A ARG* 3.9 14.8 - - - +
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Residues in contact with GLU1763 (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 2.9 17.8 + - - +
1760A ASP* 3.9 7.0 - - - +
1762A ALA* 1.3 76.0 - - - +
1764A ALA* 1.3 57.9 + - - +
1766A CYS* 3.3 7.2 + - - +
1767A SER* 2.9 32.6 + - - -
1805A ARG* 2.6 40.5 + - - +
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Residues in contact with ALA1764 (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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1754A VAL* 6.3 3.8 - - + -
1760A ASP 3.1 17.9 + - - +
1761A ASP* 3.6 7.6 - - - +
1762A ALA 3.2 0.2 - - - -
1763A GLU* 1.3 78.5 - - - +
1765A ILE* 1.3 57.7 + - + +
1767A SER* 3.3 6.2 + - - -
1768A MET* 2.8 35.8 + - - +
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Residues in contact with ILE1765 (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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1751A LEU* 3.7 34.5 - - + -
1754A VAL* 3.9 14.1 - - + -
1755A LYS 4.1 10.5 - - - +
1756A LYS* 4.8 1.3 - - + -
1761A ASP 3.1 20.6 + - - +
1762A ALA 3.2 6.7 + - - +
1764A ALA* 1.3 75.7 - - + +
1766A CYS* 1.3 59.0 + - - +
1768A MET* 4.3 7.4 - - + -
1769A CYS* 3.0 35.3 + - + +
1777A ILE* 3.9 22.9 - - + -
1781A LEU* 4.5 5.4 - - + -
1798A PHE* 3.6 30.7 - - + -
1802A ILE* 4.0 11.7 - - + -
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Residues in contact with CYS1766 (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 ALA 3.1 17.2 + - - +
1763A GLU* 3.7 12.8 - - - +
1765A ILE* 1.3 80.1 - - - +
1767A SER* 1.3 59.2 + - - +
1769A CYS* 4.0 5.5 + - - -
1770A ASN* 4.9 1.6 + - - +
1777A ILE* 5.9 0.4 - - - -
1802A ILE* 4.0 17.3 - - - -
1805A ARG* 3.7 33.7 - - + -
1806A LEU* 3.8 35.8 - - + +
1809A ARG* 4.6 8.2 + - - +
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Residues in contact with SER1767 (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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1763A GLU* 2.9 21.8 + - - -
1764A ALA* 3.7 6.7 - - - -
1766A CYS* 1.3 77.2 - - - +
1768A MET* 1.3 61.2 + - - +
1770A ASN* 4.5 10.4 + - - +
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Residues in contact with MET1768 (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 GLN* 3.4 19.5 + - + +
1750A GLN* 3.9 31.9 - - + +
1751A LEU* 3.8 33.9 - - + +
1754A VAL* 4.0 27.1 - - + -
1764A ALA* 2.8 18.6 + - - +
1765A ILE* 3.3 6.7 + - - +
1767A SER* 1.3 79.2 - - - +
1769A CYS* 1.3 79.2 + - - +
1770A ASN* 3.3 7.6 + - - +
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Residues in contact with CYS1769 (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 GLN* 3.2 14.1 - - - +
1751A LEU* 4.3 12.1 - - - -
1765A ILE* 3.0 28.9 + - - +
1766A CYS 4.0 2.0 + - - -
1767A SER 3.5 1.4 - - - -
1768A MET* 1.3 101.3 - - - +
1770A ASN* 1.3 61.0 + - - +
1771A ALA 3.3 0.7 + - - -
1772A LEU* 3.3 28.1 + - + +
1777A ILE* 3.7 20.2 - - + -
1809A ARG* 2.9 18.2 + - - +
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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