Contacts of the helix formed by residues 1760 - 1771 (chain A) in PDB entry 4J5L
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 THR1760 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1759A LYS* 1.3 88.9 - - + +
1761A ASP* 1.3 61.6 + - - +
1762A ASP* 3.5 12.7 + - - +
1763A ASP* 3.0 30.5 + - - +
1764A ALA 3.0 21.8 + - - -
1800A PHE* 3.2 10.4 - - - -
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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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1759A LYS 5.3 0.7 - - - +
1760A THR* 1.3 73.9 - - - +
1762A ASP* 1.3 63.9 + - - +
1764A ALA* 3.1 9.0 + - - +
1765A GLU* 2.9 29.6 + - - +
1800A PHE* 6.0 0.5 - - - -
1803A THR* 4.4 17.6 + - + +
1807A ARG* 4.6 5.9 + - - +
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Residues in contact with ASP1762 (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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1760A THR* 3.2 11.8 + - - +
1761A ASP* 1.3 79.7 + - - +
1763A ASP* 1.3 59.7 - - - +
1765A GLU* 3.4 9.9 + - - +
1766A ALA* 3.0 27.2 + - - +
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Residues in contact with ASP1763 (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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1757A LYS* 3.3 53.1 - - - +
1759A LYS* 3.4 11.5 + - - +
1760A THR* 3.0 39.0 + - - +
1762A ASP* 1.3 79.0 - - - +
1764A ALA* 1.3 59.1 + - - +
1766A ALA* 3.4 7.5 + - - +
1767A ILE* 3.1 32.4 + - - +
1800A PHE* 4.2 3.6 - - + -
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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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1760A THR 3.0 11.7 + - - +
1761A ASP* 3.4 9.4 - - - +
1763A ASP* 1.3 75.5 - - - +
1765A GLU* 1.3 59.2 + - - +
1767A ILE 3.3 1.2 + - - -
1768A CYS* 3.0 34.7 + - - -
1800A PHE* 3.8 11.6 - - + -
1803A THR* 4.0 25.1 - - + -
1804A ILE* 3.5 24.3 - - + +
1807A ARG* 4.8 4.9 - - - -
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Residues in contact with GLU1765 (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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1761A ASP 2.9 12.8 + - - +
1762A ASP* 3.8 8.7 - - - +
1763A ASP 3.4 0.2 - - - -
1764A ALA* 1.3 77.1 - - - +
1766A ALA* 1.3 62.0 + - - +
1768A CYS* 3.4 3.0 + - - +
1769A SER* 3.1 33.8 + - - +
1807A ARG* 2.8 49.4 + - - +
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Residues in contact with ALA1766 (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 VAL* 6.4 1.8 - - + -
1762A ASP 3.0 17.5 + - - +
1763A ASP* 3.6 9.0 - - - +
1764A ALA 3.2 0.2 - - - -
1765A GLU* 1.3 78.7 - - - +
1767A ILE* 1.3 57.6 + - + +
1769A SER* 3.3 5.4 + - - +
1770A MET* 3.0 31.8 + - - +
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Residues in contact with ILE1767 (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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1753A LEU* 3.7 35.0 - - + -
1756A VAL* 4.0 17.3 - - + -
1757A LYS 4.1 9.0 - - - +
1758A LYS* 4.6 2.2 - - + -
1763A ASP 3.1 18.1 + - - +
1764A ALA 3.3 7.2 + - - +
1766A ALA* 1.3 78.5 - - + +
1768A CYS* 1.3 58.5 + - - +
1770A MET* 4.5 6.5 - - + -
1771A CYS* 3.1 37.2 + - + +
1779A ILE* 4.3 13.7 - - + -
1783A LEU* 4.4 6.3 - - + -
1800A PHE* 3.9 28.7 - - + -
1804A ILE* 4.0 12.8 - - + -
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Residues in contact with CYS1768 (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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1764A ALA 3.0 20.6 + - - +
1765A GLU* 3.4 7.4 + - - +
1766A ALA 3.3 0.2 - - - -
1767A ILE* 1.3 76.2 - - - +
1769A SER* 1.3 59.5 + - - +
1771A CYS* 4.5 6.1 + - - -
1772A ASN* 5.6 1.2 - - - +
1779A ILE* 5.8 1.6 - - - -
1804A ILE* 3.8 20.9 - - - -
1807A ARG* 3.9 25.6 - - + +
1808A LEU* 3.8 42.5 - - + +
1811A ARG* 4.9 7.1 + - - -
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Residues in contact with SER1769 (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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1765A GLU* 3.1 22.7 + - - +
1766A ALA* 3.3 5.4 + - - -
1767A ILE 3.1 0.6 - - - -
1768A CYS* 1.3 77.6 - - - +
1770A MET* 1.3 62.6 + - - +
1771A CYS 3.6 0.2 - - - -
1772A ASN* 4.7 12.4 + - - +
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Residues in contact with MET1770 (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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1749A GLN* 3.3 20.2 + - + +
1752A GLN* 3.4 34.8 - - + +
1753A LEU* 3.9 27.1 - - + +
1756A VAL* 4.1 22.9 - - + -
1766A ALA 3.0 15.5 + - - +
1767A ILE* 3.2 8.3 + - - +
1769A SER* 1.3 80.0 - - - +
1771A CYS* 1.3 77.3 + - - +
1772A ASN* 3.2 9.5 + - - +
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Residues in contact with CYS1771 (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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1749A GLN* 3.2 24.9 - - - +
1753A LEU* 4.3 11.2 - - - -
1767A ILE* 3.1 29.7 + - - +
1768A CYS* 5.0 4.0 - - - +
1769A SER 3.6 0.4 - - - -
1770A MET* 1.3 93.7 - - - +
1772A ASN* 1.3 59.6 + - - +
1773A ALA 3.2 6.0 + - - -
1774A LEU* 3.4 27.2 - - + +
1779A ILE* 3.7 22.7 - - + +
1811A ARG* 3.7 8.3 + - - -
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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