Contacts of the helix formed by residues 1735 - 1753 (chain A) in PDB entry 5XJY
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 LEU1735 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1718A ILE* 5.1 13.0 - - + -
1722A ILE* 5.8 8.7 - - + -
1728A SER* 5.8 1.1 - - - -
1729A TYR 4.7 6.9 + - - +
1730A VAL 5.4 3.1 - - - +
1731A SER 3.4 10.3 + - - +
1732A SER* 5.2 2.5 - - - -
1734A ASN* 1.3 80.1 - - - +
1736A PRO* 1.4 68.5 - - + +
1738A LEU* 3.2 8.9 + - + +
1739A ALA* 3.0 40.0 + - + +
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Residues in contact with PRO1736 (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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1732A SER* 3.4 31.0 - - - +
1733A THR 4.3 1.8 - - - -
1734A ASN 3.9 2.9 - - - +
1735A LEU* 1.4 97.2 - - + +
1737A VAL* 1.3 66.2 + - + +
1739A ALA* 4.5 2.0 - - + +
1740A LEU* 2.9 50.9 + - + +
1846A TRP* 6.0 3.8 - - + -
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Residues in contact with VAL1737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1733A THR 3.5 26.2 - - - +
1734A ASN 4.3 2.0 - - - +
1736A PRO* 1.3 75.5 - - + +
1738A LEU* 1.3 59.1 + - - +
1740A LEU* 5.5 0.7 - - - -
1741A LEU* 3.2 29.9 - - - +
1821A ASP* 5.3 0.7 - - - +
1824A LYS* 3.7 30.4 - - + +
1845A SER* 3.5 36.6 - - - +
1846A TRP* 3.6 16.2 - - + +
1851A ARG* 4.2 13.0 - - + +
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Residues in contact with LEU1738 (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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1718A ILE* 4.5 22.9 - - + +
1721A PHE* 3.5 35.9 - - + -
1722A ILE* 6.5 0.4 - - + -
1727A LYS* 4.2 16.4 - - - -
1728A SER* 3.3 24.9 - - - +
1734A ASN 3.3 16.4 - - - +
1735A LEU* 3.2 7.3 + - + +
1736A PRO 3.1 0.4 - - - -
1737A VAL* 1.3 81.4 - - - +
1739A ALA* 1.3 60.1 + - + +
1740A LEU 3.5 0.2 - - - -
1741A LEU* 3.3 8.1 + - + +
1742A LEU* 2.9 44.6 + - + +
1817A ARG* 6.1 1.8 - - - +
1821A ASP* 4.5 7.2 - - - +
1824A LYS* 5.2 3.6 - - - +
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Residues in contact with ALA1739 (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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1718A ILE* 3.8 28.9 - - + -
1735A LEU* 3.0 28.2 + - + +
1736A PRO* 4.3 2.7 - - + +
1738A LEU* 1.3 77.1 - - + +
1740A LEU* 1.3 61.3 + - + +
1742A LEU* 2.9 18.6 + - - +
1743A LEU* 2.9 24.7 + - + +
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Residues in contact with LEU1740 (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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1736A PRO* 2.9 29.2 + - + +
1737A VAL* 5.5 0.2 - - - -
1739A ALA* 1.3 79.7 - - + +
1741A LEU* 1.3 53.5 + - - +
1743A LEU* 4.7 11.2 - - + +
1744A LEU* 2.7 43.9 + - + +
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Residues in contact with LEU1741 (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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1736A PRO 4.1 1.8 + - - -
1737A VAL* 3.2 25.5 - - - +
1738A LEU* 3.3 5.1 + - + +
1739A ALA 3.2 0.4 - - - -
1740A LEU* 1.3 79.3 - - - +
1742A LEU* 1.3 49.8 + - + +
1744A LEU* 4.7 6.1 - - + -
1745A TYR* 2.7 40.9 + - + +
1817A ARG* 3.6 45.5 - - + +
1820A ILE* 4.7 11.9 - - + -
1821A ASP* 4.3 16.2 - - + +
1824A LYS* 6.4 0.4 - - + -
1854A PHE* 3.8 28.3 - - + -
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Residues in contact with LEU1742 (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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1661A VAL* 5.2 2.7 - - + -
1665A MET* 4.2 17.7 - - + -
1710A TYR* 2.8 25.0 + - - +
1714A ALA* 4.4 14.1 - - + +
1717A VAL* 5.0 12.3 - - + -
1718A ILE* 3.8 30.5 - - + -
1721A PHE* 5.1 2.0 - - + -
1738A LEU* 2.9 33.5 + - + +
1739A ALA* 2.9 10.1 + - - +
1741A LEU* 1.3 74.9 - - + +
1743A LEU* 1.3 61.0 + - + +
1745A TYR* 2.9 14.6 + - - +
1746A GLY 2.9 2.8 + - - -
1817A ARG* 3.6 37.2 - - - +
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Residues in contact with LEU1743 (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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1707A MET* 3.4 23.2 - - + +
1710A TYR* 3.7 6.8 - - + -
1711A VAL* 4.4 24.2 - - + -
1714A ALA* 4.3 19.7 - - + -
1715A THR* 4.4 15.9 - - - +
1718A ILE* 5.3 6.5 - - + -
1739A ALA* 2.9 26.5 + - + +
1740A LEU* 4.7 11.2 - - + +
1742A LEU* 1.3 71.5 - - + +
1744A LEU* 1.3 58.9 + - - +
1746A GLY* 3.2 3.8 + - - -
1747A TRP 3.1 20.4 + - - -
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Residues in contact with LEU1744 (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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1707A MET* 5.3 0.2 - - - -
1740A LEU* 2.7 25.8 + - + +
1741A LEU* 3.8 5.8 - - + +
1743A LEU* 1.3 77.5 - - - +
1745A TYR* 1.3 57.0 + - - +
1746A GLY 3.5 0.2 - - - -
1747A TRP* 3.2 32.9 - - + +
1748A SER* 2.9 21.1 + - - -
1854A PHE 4.3 5.6 - - - +
1855A ALA* 4.4 11.2 - - + -
1858A VAL* 3.6 32.7 - - + +
1859A GLU* 3.6 14.1 - - + +
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Residues in contact with TYR1745 (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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1662A ILE* 3.3 12.3 - - + +
1665A MET* 3.6 21.0 + - + -
1666A SER 4.4 0.9 + - - -
1710A TYR* 3.8 15.5 - + - -
1741A LEU* 2.7 26.1 + - + +
1742A LEU* 2.9 5.1 + - + +
1744A LEU* 1.3 75.6 - - - +
1746A GLY* 1.3 59.4 + - - +
1747A TRP 3.2 0.2 - - - -
1748A SER* 2.3 46.0 + - - -
1749A ILE* 3.0 33.5 + - + +
1813A PHE 4.4 2.7 - - - -
1814A CYS* 2.8 43.7 - - - -
1817A ARG* 3.3 49.6 - - + -
1858A VAL* 5.3 2.9 - - + -
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Residues in contact with GLY1746 (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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1707A MET* 4.6 4.3 - - - -
1710A TYR* 3.5 37.7 - - - -
1742A LEU 2.9 11.5 + - - -
1743A LEU 3.2 0.8 + - - -
1745A TYR* 1.3 75.4 - - - +
1747A TRP* 1.3 55.8 + - - +
1748A SER 3.2 0.2 + - - -
1749A ILE* 4.5 2.9 - - - -
1750A THR* 2.6 42.7 + - - +
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Residues in contact with TRP1747 (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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1703A PHE* 3.9 32.3 - + - -
1707A MET* 3.9 32.2 - - + -
1743A LEU 3.1 8.0 + - - +
1744A LEU* 3.2 34.7 - - + +
1746A GLY* 1.3 73.9 - - - +
1748A SER* 1.3 58.3 + - - +
1750A THR* 4.1 4.0 - - - -
1751A PRO* 3.3 17.3 - - + +
1858A VAL 3.4 22.2 + - - -
1859A GLU* 4.7 4.9 + - - +
1861A VAL* 3.7 5.4 - - + +
1862A VAL* 4.2 30.9 - - + +
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Residues in contact with SER1748 (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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1744A LEU 2.9 8.3 + - - -
1745A TYR* 2.3 42.7 + - - -
1747A TRP* 1.3 79.1 - - - +
1749A ILE* 1.3 71.9 + - - +
1751A PRO* 3.7 5.5 - - - +
1752A LEU* 4.3 8.3 + - - +
1813A PHE* 4.1 19.4 + - - +
1858A VAL* 3.6 30.1 - - - -
1861A VAL* 3.8 16.8 - - - +
1864A PHE* 5.8 0.5 - - - +
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Residues in contact with ILE1749 (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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1665A MET 3.3 27.6 - - - +
1668A VAL* 5.3 1.8 - - + -
1669A PRO* 3.8 20.0 - - + -
1710A TYR* 6.1 0.2 - - + -
1745A TYR* 3.0 41.6 + - + +
1746A GLY* 4.5 3.4 - - - +
1748A SER* 1.3 85.6 + - - +
1750A THR* 1.3 58.7 + - + +
1752A LEU* 2.6 38.4 + - + -
1753A MET* 3.4 29.4 + - + -
1774A ASN* 4.5 6.7 - - - +
1813A PHE 5.7 0.2 - - - +
1814A CYS* 4.3 13.5 - - + -
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Residues in contact with THR1750 (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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1669A PRO* 4.7 11.9 - - + -
1672A PHE* 4.1 28.5 - - + -
1703A PHE* 3.3 20.5 - - - -
1706A ASP* 4.5 14.6 - - + +
1707A MET* 5.2 3.0 + - - -
1710A TYR* 5.3 4.7 - - + -
1746A GLY* 2.6 29.7 + - - +
1747A TRP* 4.1 0.5 - - - -
1749A ILE* 1.3 72.6 - - + +
1751A PRO* 1.3 67.4 - - - +
1753A MET* 4.1 9.3 + - - +
1754A TYR* 3.5 28.8 - - - -
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Residues in contact with PRO1751 (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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1703A PHE* 3.6 18.8 - - + -
1747A TRP* 3.3 20.4 - - + +
1748A SER 3.7 3.6 - - - +
1749A ILE 3.6 2.7 - - - -
1750A THR* 1.3 96.1 - - - +
1752A LEU* 1.3 56.9 + - - +
1753A MET 3.1 7.3 + - - -
1754A TYR* 3.1 21.7 + - + +
1755A PRO* 3.3 10.9 - - - +
1861A VAL 4.0 9.9 - - - +
1862A VAL* 5.5 0.4 - - - -
1864A PHE* 4.0 6.1 - - + +
1865A LEU* 3.6 40.6 - - + +
1868A VAL* 4.2 3.6 - - - +
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Residues in contact with LEU1752 (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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1748A SER 4.3 6.3 + - - +
1749A ILE* 2.6 21.3 + - + +
1751A PRO* 1.3 74.0 - - - +
1753A MET* 1.3 68.4 + - - +
1754A TYR 3.4 0.6 + - - -
1755A PRO* 4.0 8.8 - - - +
1756A ALA* 4.2 9.6 + - + +
1812A HIS* 6.5 0.9 - - + -
1813A PHE* 4.0 35.7 - - + +
1814A CYS* 6.5 1.6 - - + -
1864A PHE* 5.1 11.2 - - + -
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Residues in contact with MET1753 (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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1666A SER 5.9 0.2 - - - +
1669A PRO* 4.0 26.2 - - + +
1670A ALA* 4.9 2.2 - - + +
1673A VAL* 3.6 21.3 - - + +
1749A ILE* 3.6 33.7 - - + +
1750A THR* 4.5 6.7 - - - +
1751A PRO 3.1 1.4 + - - -
1752A LEU* 1.3 90.4 - - - +
1754A TYR* 1.3 68.1 + - + +
1755A PRO 3.6 0.2 - - - -
1756A ALA* 3.4 9.6 + - - +
1757A SER* 3.3 21.5 + - - -
1770A LEU* 3.7 46.4 - - + +
1774A ASN* 5.3 8.1 - - + +
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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