Contacts of the helix formed by residues 1722 - 1740 (chain B) in PDB entry 3LQJ
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 SER1722 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1605B GLU* 3.5 19.3 - - - -
1640B LEU* 4.2 10.2 - - - +
1644B LEU* 4.3 5.4 - - - +
1720B TYR* 3.5 2.4 - - - +
1721B THR* 1.3 86.2 + - - +
1723B VAL* 1.3 63.8 + - - +
1724B LEU* 3.8 3.4 + - - +
1725B GLU* 3.2 28.1 + - - +
1726B PHE* 3.6 17.3 + - - +
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Residues in contact with VAL1723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605B GLU* 3.0 16.6 + - - +
1609B ILE* 4.6 1.6 - - + -
1640B LEU* 3.7 14.6 - - + -
1644B LEU* 4.2 6.3 - - + -
1722B SER* 1.3 70.7 - - - +
1724B LEU* 1.3 61.2 + - - +
1726B PHE* 3.2 2.8 + - - +
1727B SER* 2.8 27.5 + - - -
1762B MET* 3.8 24.2 - - + -
1766B PHE* 3.5 42.2 - - + -
1768B TRP* 3.8 14.1 - - + -
1769B PHE* 3.7 24.5 - - + -
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Residues in contact with LEU1724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605B GLU* 3.2 15.3 + - - +
1722B SER* 3.4 5.4 - - - +
1723B VAL* 1.3 80.5 - - - +
1725B GLU* 1.3 57.6 + - - +
1727B SER* 3.8 0.3 - - - -
1728B ASP* 2.9 63.0 + - - +
1769B PHE* 3.8 25.1 - - + -
1773B LYS* 6.5 1.3 - - - -
1774B SER* 6.0 3.1 - - - -
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Residues in contact with GLU1725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704B GLN* 5.6 1.3 - - - +
1714B LYS* 2.7 38.0 + - - +
1719B ASN 3.9 9.5 - - - +
1720B TYR* 3.9 11.2 - - + -
1721B THR* 4.7 8.8 + - - -
1722B SER* 3.2 22.9 + - - +
1724B LEU* 1.3 77.7 - - - +
1726B PHE* 1.3 66.3 + - - +
1728B ASP* 3.6 4.9 + - - +
1729B ASP* 3.1 28.8 + - - +
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Residues in contact with PHE1726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644B LEU* 3.8 32.1 - - + -
1647B VAL* 3.7 34.5 - - + -
1648B LEU* 4.1 9.0 - - + -
1651B LEU* 5.0 0.9 - - + -
1711B VAL* 4.1 15.0 - - + -
1715B MET* 3.1 32.3 - - + -
1720B TYR* 3.5 28.8 - + + -
1722B SER 3.6 11.2 + - - +
1723B VAL 3.2 7.1 + - - +
1725B GLU* 1.3 79.5 - - - +
1727B SER* 1.3 64.2 + - - +
1729B ASP* 3.3 2.9 + - - +
1730B ILE* 3.2 42.8 + - + +
1758B PHE* 4.4 0.4 - + - -
1762B MET* 3.9 18.4 - - + -
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Residues in contact with SER1727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1723B VAL 2.8 19.3 + - - -
1724B LEU 3.8 1.1 - - - -
1726B PHE* 1.3 75.3 - - - +
1728B ASP* 1.3 59.8 + - - +
1730B ILE* 3.1 4.3 + - - +
1731B VAL* 2.8 33.4 + - - +
1758B PHE* 4.1 10.7 - - - -
1762B MET* 3.8 8.5 - - - -
1769B PHE* 3.4 33.1 - - - -
1771B VAL* 3.8 21.8 - - - +
1774B SER* 5.2 1.6 - - - -
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Residues in contact with ASP1728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724B LEU* 2.9 52.1 + - - +
1725B GLU* 4.0 5.1 - - - +
1727B SER* 1.3 73.2 + - - +
1729B ASP* 1.3 64.6 + - - +
1731B VAL* 3.7 4.3 - - - +
1732B LYS* 2.9 36.2 + - - +
1774B SER* 2.9 27.0 + - - -
1775B ARG 4.5 1.0 + - - -
1776B PHE* 3.3 30.9 - - + -
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Residues in contact with ASP1729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704B GLN* 3.3 22.7 + - - +
1705B PRO* 3.5 17.9 - - + +
1711B VAL* 4.6 7.6 - - + -
1714B LYS* 2.9 22.9 + - - -
1720B TYR* 2.6 29.7 + - - +
1725B GLU* 3.1 24.7 + - - +
1726B PHE 3.6 4.3 - - - +
1728B ASP* 1.3 76.2 - - - +
1730B ILE* 1.3 63.7 + - - +
1732B LYS* 3.5 10.6 + - - +
1733B ILE* 3.2 27.7 + - - +
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Residues in contact with ILE1730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1648B LEU* 5.1 2.2 - - + -
1651B LEU* 4.3 17.9 - - + -
1708B LEU* 5.1 8.7 - - + -
1711B VAL* 4.0 34.8 - - + -
1726B PHE* 3.2 24.7 - - + +
1727B SER 3.1 1.7 + - - +
1729B ASP* 1.3 75.6 - - - +
1731B VAL* 1.3 66.4 + - - +
1733B ILE* 3.0 10.1 + - + +
1734B ILE* 2.9 39.3 + - + +
1758B PHE* 3.4 44.4 - - + -
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Residues in contact with VAL1731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1727B SER* 2.8 25.4 + - - +
1728B ASP 3.7 4.5 - - - +
1730B ILE* 1.3 73.5 - - - +
1732B LYS* 1.3 52.8 + - - +
1734B ILE* 3.2 2.3 + - - +
1735B GLN* 2.6 38.1 + - - +
1758B PHE* 4.2 3.1 - - + -
1771B VAL* 4.0 13.2 - - + -
1774B SER* 3.6 21.8 - - - +
1776B PHE* 3.2 37.0 - - + +
1777B TRP* 3.6 42.1 - - + +
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Residues in contact with LYS1732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704B GLN* 2.4 37.2 - - - +
1705B PRO 5.8 1.8 - - - +
1728B ASP* 2.9 31.5 + - - +
1729B ASP* 3.8 11.4 + - - +
1731B VAL* 1.3 75.0 - - - +
1733B ILE* 1.3 58.6 + - + +
1735B GLN* 3.7 6.2 - - - +
1736B ALA* 2.9 29.8 + - - +
1776B PHE* 3.4 52.7 - - + +
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Residues in contact with ILE1733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660B LEU* 3.8 22.9 - - + +
1705B PRO* 3.6 18.2 - - + +
1706B LEU* 3.9 17.0 - - - +
1707B ASP* 3.4 34.3 - - - +
1708B LEU* 3.9 22.7 - - + +
1711B VAL* 3.6 20.6 - - + -
1729B ASP 3.2 14.0 + - - +
1730B ILE* 3.0 10.6 + - + +
1732B LYS* 1.3 76.2 - - + +
1734B ILE* 1.3 62.6 + - + +
1736B ALA* 3.3 6.9 + - - +
1737B ALA 3.2 17.2 + - - -
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Residues in contact with ILE1734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651B LEU* 6.1 0.9 - - + -
1660B LEU* 3.9 22.9 - - + -
1708B LEU* 6.2 0.4 - - + -
1730B ILE* 2.9 40.8 + - + +
1731B VAL 3.7 3.1 - - - +
1733B ILE* 1.3 75.2 - - + +
1735B GLN* 1.3 53.8 + - - +
1737B ALA* 3.4 4.0 + - - +
1738B ILE* 2.7 45.3 + - + +
1751B ASN* 4.7 0.2 + - - -
1754B VAL* 3.5 33.9 - - + +
1755B LYS* 4.2 7.4 - - - -
1758B PHE* 3.8 27.6 - - + -
1777B TRP* 3.9 20.9 - - + -
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Residues in contact with GLN1735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1731B VAL 2.6 22.0 + - - +
1732B LYS* 4.0 4.5 - - - +
1734B ILE* 1.3 73.0 - - - +
1736B ALA* 1.3 53.5 + - - +
1738B ILE* 3.6 18.6 - - - +
1739B ASN* 2.3 59.8 + - - +
1755B LYS* 5.3 0.9 + - - -
1776B PHE 3.5 15.2 + - - +
1777B TRP* 2.9 22.5 + - + -
1778B GLU* 2.5 51.4 + - - +
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Residues in contact with ALA1736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1663B TYR* 5.4 12.6 - - + +
1706B LEU 5.9 1.3 - - - +
1732B LYS 2.9 20.5 + - - +
1733B ILE* 3.4 9.4 - - - +
1734B ILE 3.1 0.2 - - - -
1735B GLN* 1.3 74.5 - - - +
1737B ALA* 1.3 57.2 + - - +
1738B ILE 3.0 1.1 - - - -
1739B ASN* 3.2 7.1 + - - +
1740B SER* 2.6 39.2 + - - +
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Residues in contact with ALA1737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1659B HIS* 4.4 7.0 - - + +
1660B LEU* 3.3 34.1 - - + -
1733B ILE 3.2 3.9 + - - +
1734B ILE 3.4 3.1 + - - +
1736B ALA* 1.3 78.6 - - - +
1738B ILE* 1.3 62.4 + - - +
1740B SER* 3.5 17.2 + - - +
1741B ASP* 3.9 7.8 - - - +
1747B ILE* 4.8 2.6 - - - +
1751B ASN* 3.3 21.0 + - - +
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Residues in contact with ILE1738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734B ILE* 2.7 41.1 + - + +
1735B GLN* 3.6 24.9 - - - +
1736B ALA 3.0 0.2 - - - -
1737B ALA* 1.3 79.9 - - - +
1739B ASN* 1.3 61.5 + - - +
1740B SER 3.2 0.2 - - - -
1741B ASP* 2.9 35.7 - - - +
1751B ASN* 2.6 27.6 - - - +
1752B SER* 6.0 0.4 - - - -
1755B LYS* 4.3 24.9 - - + +
1777B TRP* 4.5 0.9 - - + -
1778B GLU* 5.0 7.0 - - - +
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Residues in contact with ASN1739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1735B GLN* 2.3 51.6 + - - +
1736B ALA* 3.2 8.4 + - - +
1738B ILE* 1.3 78.3 - - - +
1740B SER* 1.3 56.0 + - - +
1741B ASP* 3.1 8.7 + - - +
1778B GLU* 3.7 19.2 - - - +
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Residues in contact with SER1740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1663B TYR* 5.6 3.6 + - - -
1736B ALA* 2.6 22.0 + - - +
1737B ALA* 3.9 12.7 - - - +
1738B ILE 3.2 1.2 - - - -
1739B ASN* 1.3 77.6 + - - +
1741B ASP* 1.3 62.2 + - - +
1742B GLY* 3.6 2.1 + - - -
1747B ILE* 4.7 4.0 - - - +
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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
------------------------------------------------------------
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