Contacts of the helix formed by residues 1768 - 1779 (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 SER1768 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1767D LEU* 1.3 75.1 - - - +
1769D THR* 1.3 65.4 + - - +
1770D GLN* 3.6 5.9 + - - +
1771D GLN* 2.9 43.4 + - - +
1772D ILE* 2.8 23.0 + - - +
1804D ARG* 3.6 4.5 - - - +
1806D ASP* 3.7 26.2 - - - -
1809D GLN 3.6 14.9 + - - -
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Residues in contact with THR1769 (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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1768D SER* 1.3 71.7 - - - +
1770D GLN* 1.3 59.9 + - - +
1772D ILE* 3.2 1.7 + - - +
1773D VAL* 2.9 43.8 + - + +
1798D GLN* 5.1 12.3 - - + +
1801D LEU* 3.5 48.6 + - + +
1804D ARG* 3.6 8.3 + - - +
1806D ASP* 3.3 16.1 + - - -
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Residues in contact with GLN1770 (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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1768D SER* 3.1 9.9 + - - +
1769D THR* 1.3 80.4 - - - +
1771D GLN* 1.3 58.1 + - - +
1773D VAL* 3.4 5.3 + - - +
1774D LYS* 2.8 29.8 + - - +
1809D GLN* 3.6 22.1 + - - +
1810D LEU* 3.7 33.3 - - + +
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Residues in contact with GLN1771 (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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1694D LEU* 4.6 6.4 - - - +
1698D LEU* 3.9 23.1 - - + +
1739D PRO* 5.8 0.2 - - - +
1766D SER 4.5 1.7 - - - +
1767D LEU* 3.5 21.4 - - + +
1768D SER* 2.9 44.0 + - - +
1770D GLN* 1.3 73.9 - - - +
1772D ILE* 1.3 67.0 + - - +
1774D LYS* 3.6 1.3 - - - +
1775D ILE* 3.0 31.0 + - + +
1809D GLN 4.1 3.4 + - - -
1810D LEU* 2.8 34.4 + - + +
1811D LEU 4.6 0.4 + - - -
1812D LEU* 3.6 28.7 - - - +
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Residues in contact with ILE1772 (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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1746D LEU* 4.2 11.8 - - + +
1760D ILE* 4.1 21.3 - - + +
1761D CYS* 5.5 1.3 - - - -
1764D CYS* 3.6 29.8 - - + +
1767D LEU* 3.7 33.4 - - + +
1768D SER 2.8 11.0 + - - +
1769D THR* 3.6 6.5 - - - +
1771D GLN* 1.3 76.7 - - - +
1773D VAL* 1.3 63.3 + - - +
1775D ILE* 3.2 4.2 + - - +
1776D LEU* 3.0 39.7 + - + +
1797D ILE* 4.2 12.1 - - + -
1801D LEU* 3.8 22.7 - - + -
1804D ARG* 4.3 3.1 - - - +
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Residues in contact with VAL1773 (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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1769D THR* 2.9 24.8 + - + +
1770D GLN* 4.0 5.6 - - - +
1772D ILE* 1.3 73.7 - - - +
1774D LYS* 1.3 66.0 + - - +
1776D LEU* 3.4 7.1 + - - +
1777D ASN* 3.0 39.9 + - - +
1794D ILE* 4.0 19.1 - - + -
1797D ILE* 4.2 15.9 - - + -
1798D GLN* 4.0 33.2 - - + +
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Residues in contact with LYS1774 (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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1698D LEU* 3.0 38.2 + - + +
1699D LEU* 4.2 15.0 - - - +
1770D GLN 2.8 19.3 + - - +
1771D GLN 3.6 4.5 - - - +
1772D ILE 3.2 0.2 - - - -
1773D VAL* 1.3 78.0 - - - +
1775D ILE* 1.3 57.9 + - - +
1777D ASN* 3.1 11.0 + - + +
1778D LEU* 2.9 53.5 + - + +
1810D LEU* 3.9 29.3 - - + +
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Residues in contact with ILE1775 (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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1694D LEU* 4.5 4.7 - - + -
1697D LEU* 3.7 21.5 - - + +
1698D LEU* 3.9 17.3 - - + -
1704D CYS* 4.4 2.6 - - - -
1743D ALA* 3.9 27.6 - - + -
1746D LEU* 3.7 27.6 - - + -
1747D LEU* 3.7 27.8 - - + -
1751D LYS* 6.0 0.4 - - - -
1767D LEU* 4.6 5.2 - - + -
1771D GLN 3.0 23.0 + - - +
1772D ILE 3.7 4.0 - - - +
1774D LYS* 1.3 76.4 - - - +
1776D LEU* 1.3 61.0 + - + +
1778D LEU* 3.2 7.5 + - - +
1779D TYR* 2.9 27.6 + - + +
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Residues in contact with LEU1776 (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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1746D LEU* 4.0 20.2 - - + -
1751D LYS* 3.7 33.0 - - + -
1760D ILE* 4.5 3.6 - - + -
1772D ILE* 3.0 32.3 + - + +
1773D VAL* 3.8 4.9 - - - +
1775D ILE* 1.3 77.2 - - - +
1777D ASN* 1.3 61.8 + - - +
1779D TYR* 3.3 20.0 + - - +
1789D VAL* 3.4 22.4 + - + +
1793D PHE* 4.2 7.0 - - + -
1794D ILE* 4.2 17.5 - - + -
1797D ILE* 3.0 38.8 - - + -
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Residues in contact with ASN1777 (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* 3.0 36.9 + - - +
1774D LYS* 3.5 9.7 - - + +
1776D LEU* 1.3 75.7 - - - +
1778D LEU* 1.3 61.7 + - + +
1788D ARG* 3.3 23.6 + - - -
1789D VAL* 5.6 0.4 - - - +
1794D ILE* 2.9 25.6 - - - +
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Residues in contact with LEU1778 (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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1697D LEU 3.4 16.6 - - - +
1698D LEU* 3.5 21.1 - - - +
1699D LEU 5.3 1.6 - - - -
1700D ARG* 3.4 25.8 - - - +
1701D LYS* 4.0 19.3 - - + +
1704D CYS* 3.8 17.4 - - - +
1774D LYS* 2.9 38.5 + - + +
1775D ILE* 3.7 4.9 - - - +
1777D ASN* 1.3 80.1 - - + +
1779D TYR* 1.3 67.8 + - - +
1780D THR* 2.8 16.6 + - - -
1788D ARG* 4.0 2.6 + - - +
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Residues in contact with TYR1779 (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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76C ILE* 3.9 11.2 - - + +
1704D CYS* 3.5 11.0 - - - -
1705D SER* 3.5 19.2 - - - -
1706D TRP* 3.2 35.1 + - - +
1747D LEU* 3.4 32.9 + - + -
1751D LYS* 3.4 32.5 + - + -
1775D ILE 2.9 11.7 + - - +
1776D LEU* 3.3 19.3 + - - +
1777D ASN 4.4 0.2 - - - +
1778D LEU* 1.3 77.1 - - - +
1780D THR* 1.3 57.4 + - - +
1781D PRO* 3.9 27.8 - - + +
1786D GLU* 4.7 1.9 + - + -
1787D GLU 4.8 7.0 - - - -
1788D ARG* 3.4 23.9 + - - +
1789D VAL* 4.0 12.8 + - + -
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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