Contacts of the helix formed by residues 1721 - 1733 (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 THR1721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1719A HIS 3.7 11.9 - - - +
1720A THR* 1.3 77.1 - - - +
1722A ALA* 1.3 64.9 + - - +
1723A GLY* 4.2 0.3 - - - -
1724A GLU* 3.1 32.2 + - - +
1725A VAL* 3.3 14.4 + - - +
1757A SER 3.4 14.1 + - - -
1758A ARG* 3.9 19.5 - - - +
1759A THR 3.3 7.2 - - - +
1760A VAL* 5.0 3.4 - - + -
1761A VAL* 3.9 2.5 - - - -
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Residues in contact with ALA1722 (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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1721A THR* 1.3 71.8 - - - +
1723A GLY* 1.3 58.7 + - - +
1725A VAL* 3.2 3.3 + - - +
1726A VAL* 2.8 36.0 + - + +
1744A LEU* 4.3 15.9 - - + +
1755A ILE* 3.4 36.1 - - + +
1756A GLU 3.5 11.7 - - - +
1757A SER* 3.5 1.3 + - - -
1759A THR 2.8 10.8 + - - +
1761A VAL* 3.8 12.4 - - + +
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Residues in contact with GLY1723 (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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1721A THR* 3.2 1.3 - - - -
1722A ALA* 1.3 78.4 - - - +
1724A GLU* 1.3 56.8 + - - +
1726A VAL* 3.3 8.6 + - - +
1727A GLU* 2.8 31.1 + - - +
1757A SER* 2.8 35.3 + - - +
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Residues in contact with GLU1724 (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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1720A THR* 3.9 21.5 + - + +
1721A THR* 3.1 25.5 + - - +
1723A GLY* 1.3 73.1 - - - +
1725A VAL* 1.3 62.1 + - - +
1727A GLU* 3.3 6.4 + - + +
1728A LYS* 2.8 36.1 + - + +
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Residues in contact with VAL1725 (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* 4.6 2.9 - - + -
1714A ILE* 4.4 22.0 - - + -
1715A THR 5.8 0.2 - - - +
1716A ILE* 4.4 10.1 - - + -
1720A THR* 4.0 18.2 - - + -
1721A THR 3.3 11.2 + - - +
1722A ALA 3.2 8.2 + - - +
1724A GLU* 1.3 75.5 - - - +
1726A VAL* 1.3 54.3 + - - +
1728A LYS* 3.0 8.6 + - - +
1729A LEU* 2.8 55.5 + - + +
1744A LEU* 4.1 17.9 - - + -
1761A VAL* 4.0 13.7 - - + -
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Residues in contact with VAL1726 (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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1722A ALA* 2.8 24.3 + - + +
1723A GLY* 3.5 8.3 - - - +
1725A VAL* 1.3 77.5 - - - +
1727A GLU* 1.3 57.1 + - - +
1729A LEU* 3.3 6.4 + - - +
1730A ILE* 2.9 44.4 + - + +
1742A PHE 4.0 21.8 - - - +
1743A ALA* 3.7 6.3 - - - +
1744A LEU* 3.5 35.4 - - + +
1786A PHE* 4.3 8.5 - - + -
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Residues in contact with GLU1727 (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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1723A GLY 2.8 19.9 + - - +
1724A GLU* 3.7 7.9 - - + +
1726A VAL* 1.3 75.8 - - - +
1728A LYS* 1.3 62.3 + - - +
1730A ILE* 3.4 8.9 + - - +
1731A ARG* 3.0 32.5 + - + +
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Residues in contact with LYS1728 (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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1724A GLU* 2.8 20.2 + - - +
1725A VAL* 3.3 12.1 - - - +
1727A GLU* 1.3 78.0 - - - +
1729A LEU* 1.3 57.9 + - + +
1731A ARG* 3.3 8.9 + - - +
1732A GLY* 2.9 25.5 + - - -
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Residues in contact with LEU1729 (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* 4.1 14.6 - - + -
1712A CYS* 3.7 34.8 - - + -
1714A ILE* 5.1 2.7 - - + -
1725A VAL* 2.8 42.5 + - + +
1726A VAL* 3.8 4.9 - - - +
1728A LYS* 1.3 70.6 - - + +
1730A ILE* 1.3 65.6 + - - +
1732A GLY* 4.4 1.8 - - - +
1733A LEU* 2.9 41.7 + - + +
1744A LEU* 5.1 1.8 - - + -
1786A PHE* 4.0 44.1 - - + -
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Residues in contact with ILE1730 (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* 2.9 29.9 + - + +
1727A GLU* 3.6 8.5 - - - +
1728A LYS 3.3 0.2 - - - -
1729A LEU* 1.3 77.9 - - - +
1731A ARG* 1.3 67.7 + - - +
1733A LEU 3.6 0.3 + - - -
1734A ALA 3.3 2.6 + - - -
1735A MET* 3.0 56.0 + - + +
1736A GLU* 3.9 8.3 - - - +
1738A SER* 6.3 0.4 - - - -
1740A ASN 5.8 0.9 - - - +
1742A PHE* 3.8 32.3 - - + +
1786A PHE* 3.9 18.2 - - + -
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Residues in contact with ARG1731 (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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1727A GLU* 3.0 19.7 + - + +
1728A LYS* 3.6 8.1 - - - +
1730A ILE* 1.3 78.7 - - - +
1732A GLY* 1.3 60.2 + - - +
1734A ALA* 2.8 23.0 + - - +
1736A GLU* 4.2 36.7 + - - +
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Residues in contact with GLY1732 (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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1728A LYS 2.9 14.5 + - - -
1729A LEU* 3.3 4.4 + - - -
1731A ARG* 1.3 77.9 - - - +
1733A LEU* 1.3 61.3 + - - +
1734A ALA* 2.9 8.5 + - - +
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Residues in contact with LEU1733 (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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1706A CYS* 5.3 6.1 - - - -
1712A CYS* 6.2 2.2 - - + -
1729A LEU* 2.9 37.9 + - + +
1732A GLY* 1.3 70.8 - - - +
1734A ALA* 1.3 73.4 + - - +
1735A MET* 3.6 18.8 - - + +
1786A PHE* 4.2 8.1 - - + -
1802A VAL* 3.5 25.9 - - + +
1806A PHE* 3.5 39.5 - - + -
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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