Contacts of the helix formed by residues 1790 - 1801 (chain D) in PDB entry 4LX0
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 THR1790 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1751D LYS 5.2 0.8 + - - -
1752D LYS 5.6 0.3 + - - -
1788D ARG 3.4 6.9 + - - +
1789D VAL* 1.3 80.0 - - - +
1791D VAL* 1.3 65.4 + - - +
1792D ALA* 3.6 9.4 + - - +
1793D PHE* 3.0 35.1 + - - +
1794D ILE* 3.1 13.4 + - - +
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Residues in contact with VAL1791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1789D VAL 4.0 0.6 + - - +
1790D THR* 1.3 74.3 - - - +
1792D ALA* 1.3 59.8 + - - +
1794D ILE* 3.3 12.4 + - + +
1795D ARG* 3.0 61.7 + - - +
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Residues in contact with ALA1792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1790D THR* 3.2 8.8 + - - +
1791D VAL* 1.3 82.5 - - - +
1793D PHE* 1.3 59.4 + - - +
1795D ARG* 3.4 11.2 + - - +
1796D THR* 3.0 28.1 + - - -
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Residues in contact with PHE1793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751D LYS* 3.7 28.9 - - + +
1752D LYS* 3.5 32.5 - - - +
1753D THR 3.1 25.1 - - - -
1756D ASP* 3.9 0.4 - - + -
1757D ALA* 3.5 29.2 - - + -
1760D ILE* 3.9 11.4 - - + -
1776D LEU* 4.2 4.3 - - + -
1789D VAL* 3.7 21.3 - - + -
1790D THR* 3.0 23.0 + - - +
1792D ALA* 1.3 74.0 - - - +
1794D ILE* 1.3 67.1 + - - +
1796D THR* 3.1 8.7 + - - -
1797D ILE* 2.9 43.3 + - + +
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Residues in contact with ILE1794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1773D VAL* 4.0 24.0 - - + -
1776D LEU* 4.2 14.8 - - + -
1777D ASN* 2.9 42.6 - - - +
1789D VAL* 4.0 21.8 - - + +
1790D THR 3.1 16.8 + - - +
1791D VAL* 3.6 11.9 - - + +
1793D PHE* 1.3 77.4 - - - +
1795D ARG* 1.3 57.8 + - + +
1797D ILE* 3.2 8.5 + - - +
1798D GLN* 2.9 40.6 + - + +
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Residues in contact with ARG1795 (chain D).
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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1791D VAL* 3.0 46.1 + - - +
1792D ALA* 3.9 9.4 - - - +
1793D PHE 3.2 0.2 - - - -
1794D ILE* 1.3 72.8 - - + +
1796D THR* 1.3 60.7 + - - +
1798D GLN* 3.4 19.4 + - - +
1799D ALA* 2.8 30.8 + - - +
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Residues in contact with THR1796 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1754D GLN* 3.4 42.2 + - - +
1757D ALA* 3.9 19.1 - - + -
1792D ALA 3.0 15.7 + - - -
1793D PHE* 3.1 12.8 + - - -
1795D ARG* 1.3 75.9 - - - +
1797D ILE* 1.3 63.1 + - - +
1799D ALA* 3.3 5.5 + - - +
1800D GLN* 2.9 28.4 + - + +
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Residues in contact with ILE1797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1757D ALA* 4.1 14.8 - - + +
1760D ILE* 4.5 9.6 - - + -
1761D CYS* 4.3 10.1 - - - -
1772D ILE* 4.2 13.5 - - + -
1773D VAL* 4.2 14.1 - - + -
1776D LEU* 3.0 26.9 - - + -
1793D PHE* 2.9 47.5 + - + +
1794D ILE* 3.5 9.0 - - - +
1795D ARG 3.2 0.2 - - - -
1796D THR* 1.3 75.6 - - - +
1798D GLN* 1.3 58.8 + - - +
1800D GLN* 3.1 8.1 + - - +
1801D LEU* 2.9 49.4 + - + +
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Residues in contact with GLN1798 (chain D).
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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1769D THR* 5.1 9.8 - - + +
1773D VAL* 4.0 26.6 - - + +
1794D ILE* 2.9 27.0 + - - +
1795D ARG* 3.5 27.6 - - - +
1797D ILE* 1.3 77.4 - - - +
1799D ALA* 1.3 61.3 - - - +
1801D LEU* 3.4 12.0 + - - +
1802D GLN* 3.4 12.1 + - - +
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Residues in contact with ALA1799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1795D ARG 2.8 19.9 + - - +
1796D THR* 3.8 5.8 - - - +
1798D GLN* 1.3 73.5 - - - +
1800D GLN* 1.3 58.4 + - - +
1802D GLN* 3.0 34.1 + - - +
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Residues in contact with GLN1800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1754D GLN* 4.3 11.1 + - - -
1757D ALA* 5.1 1.6 - - + +
1758D GLU* 3.7 37.2 + - + +
1761D CYS* 3.4 30.2 - - + +
1796D THR* 2.9 19.4 + - + +
1797D ILE* 3.4 4.7 - - - +
1799D ALA* 1.3 79.6 - - - +
1801D LEU* 1.3 57.9 + - - +
1802D GLN* 3.2 5.6 + - - +
1803D GLU* 4.6 2.8 + - - +
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Residues in contact with LEU1801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761D CYS* 3.4 33.4 - - + +
1769D THR* 3.5 39.9 + - + +
1772D ILE* 3.8 26.2 - - + -
1797D ILE* 2.9 33.4 + - + +
1798D GLN 3.4 2.9 + - - +
1799D ALA 3.3 0.2 - - - -
1800D GLN* 1.3 75.6 - - - +
1802D GLN* 1.3 57.2 + - - +
1803D GLU 3.2 3.1 - - - -
1804D ARG* 3.0 56.2 + - + +
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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