Contacts of the helix formed by residues 1744 - 1756 (chain B) in PDB entry 4J5L
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 LEU1744 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1693B PHE* 3.4 54.3 - - + +
1696B ILE* 5.0 4.0 - - + -
1697B GLY* 3.9 18.6 - - - +
1723B VAL* 4.2 21.5 - - + +
1726B LEU* 4.3 15.0 - - + -
1727B GLU* 5.1 3.6 - - + -
1740B ALA 3.9 9.9 - - - +
1741B LYS* 3.1 13.3 + - - +
1743B THR* 1.3 77.9 - - - +
1745B GLU* 1.3 59.5 + - - +
1746B PRO* 3.3 2.9 - - - -
1747B LEU* 3.0 17.2 + - + +
1748B ILE* 2.8 39.5 + - + +
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Residues in contact with GLU1745 (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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1741B LYS* 3.9 7.5 + - - +
1742B GLU* 3.5 24.0 + - + +
1744B LEU* 1.3 77.2 - - - +
1746B PRO* 1.4 69.5 - - + +
1748B ILE* 3.8 20.5 - - - +
1749B GLN* 2.9 59.8 + - - +
1773B ALA* 4.4 10.7 - - + +
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Residues in contact with PRO1746 (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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1701B LEU* 3.9 15.5 - - + -
1742B GLU 4.4 1.8 - - - +
1743B THR* 3.7 14.8 - - - +
1744B LEU 3.5 4.0 - - - -
1745B GLU* 1.4 94.9 - - + +
1747B LEU* 1.3 55.2 - - - +
1749B GLN* 3.9 0.3 - - - +
1750B ALA* 2.9 29.8 + - - +
1773B ALA* 3.9 19.5 - - + +
1774B LEU* 3.4 28.4 - - + +
1819B MET* 3.9 22.7 - - + -
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Residues in contact with LEU1747 (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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1629B MET* 4.3 8.7 - - + -
1696B ILE* 4.9 0.7 - - + +
1697B GLY* 4.3 23.8 - - - +
1700B THR* 3.6 39.5 - - + -
1701B LEU* 4.4 13.1 - - + +
1704B LEU* 4.4 9.2 - - + -
1719B ILE* 3.7 32.3 - - + -
1723B VAL* 4.3 13.2 - - + -
1726B LEU* 6.3 0.4 - - + -
1744B LEU* 3.0 16.2 + - + +
1746B PRO* 1.3 76.3 - - - +
1748B ILE* 1.3 61.8 + - - +
1750B ALA* 3.2 3.3 + - - +
1751B ALA* 2.8 26.7 + - - +
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Residues in contact with ILE1748 (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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1720B ARG* 3.6 26.5 - - + +
1723B VAL* 3.7 38.6 - - + -
1727B GLU* 4.2 11.2 - - - +
1741B LYS* 4.9 6.3 - - + +
1744B LEU* 2.8 30.2 + - + +
1745B GLU* 3.8 22.4 - - - +
1747B LEU* 1.3 76.1 - - - +
1749B GLN* 1.3 57.3 + - - +
1751B ALA* 3.1 8.1 + - - +
1752B GLN* 2.9 50.0 + - - +
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Residues in contact with GLN1749 (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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1745B GLU* 2.9 39.4 + - - +
1746B PRO 3.9 3.1 - - - +
1748B ILE* 1.3 75.8 - - - +
1750B ALA* 1.3 56.8 + - - +
1752B GLN* 3.3 17.9 + - - +
1753B LEU* 2.9 27.4 + - - +
1770B MET* 3.2 19.1 + - + +
1771B CYS* 3.2 12.6 - - - -
1772B ASN* 2.5 32.0 + - - -
1773B ALA* 2.8 40.1 + - - +
1774B LEU* 3.8 7.7 + - + -
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Residues in contact with ALA1750 (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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1701B LEU* 4.0 23.3 - - + -
1704B LEU* 4.3 11.0 - - + -
1746B PRO 2.9 19.2 + - - +
1747B LEU* 3.4 5.6 - - - +
1749B GLN* 1.3 78.3 - - - +
1751B ALA* 1.3 60.2 + - - +
1753B LEU* 3.2 9.3 + - - +
1754B LEU* 3.1 27.1 + - - +
1774B LEU* 3.8 14.3 - - + +
1782B VAL* 4.8 9.5 - - + +
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Residues in contact with ALA1751 (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 LEU* 5.2 0.6 - - - +
1716B GLY* 3.7 27.1 - - - +
1719B ILE* 3.9 23.1 - - + -
1720B ARG* 4.3 9.9 - - + -
1747B LEU 2.8 12.4 + - - +
1748B ILE* 3.4 10.1 - - - +
1750B ALA* 1.3 73.6 - - - +
1752B GLN* 1.3 65.8 + - - +
1754B LEU* 3.3 16.1 + - - +
1755B GLN* 3.4 20.1 + - - +
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Residues in contact with GLN1752 (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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1720B ARG* 2.9 38.5 + - - +
1748B ILE* 2.9 27.9 + - - +
1749B GLN* 3.5 15.8 - - - +
1750B ALA 3.3 0.2 - - - -
1751B ALA* 1.3 73.9 - - - +
1753B LEU* 1.3 59.7 + - - +
1755B GLN* 3.0 10.2 + - - +
1756B VAL* 3.0 34.3 + - + +
1770B MET* 3.1 37.0 - - - +
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Residues in contact with LEU1753 (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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1749B GLN 2.9 14.5 + - - +
1750B ALA 3.3 10.3 - - - +
1752B GLN* 1.3 78.0 - - - +
1754B LEU* 1.3 57.7 + - - +
1755B GLN 3.4 0.2 + - - -
1756B VAL* 3.5 8.0 - - + +
1758B LYS* 3.2 23.9 + - - -
1767B ILE* 3.7 43.5 - - + -
1770B MET* 3.9 3.1 - - + +
1771B CYS* 4.3 10.8 - - - -
1774B LEU* 4.8 5.2 - - + -
1779B ILE* 3.9 26.9 - - + +
1782B VAL* 3.7 34.5 - - + -
1783B LEU* 3.8 13.9 - - + -
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Residues in contact with LEU1754 (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 LEU* 4.1 22.2 - - + -
1710B MET 4.3 7.6 - - - +
1711B CYS* 3.8 29.2 - - + -
1712B SER 3.5 24.0 - - - +
1713B TRP* 3.4 17.6 - - - +
1715B LYS* 4.6 1.6 - - + -
1716B GLY* 3.9 17.9 - - - +
1719B ILE* 4.8 1.1 - - + -
1750B ALA 3.1 14.0 + - - +
1751B ALA* 3.5 8.7 - - - +
1752B GLN 3.2 0.2 - - - -
1753B LEU* 1.3 77.1 - - - +
1755B GLN* 1.3 60.3 + - - +
1758B LYS* 3.6 14.6 + - - +
1782B VAL* 3.6 25.8 - - + -
1786B TYR* 3.7 12.7 + - + -
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Residues in contact with GLN1755 (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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1713B TRP* 3.4 46.7 + - + +
1716B GLY 3.0 27.0 - - - +
1717B MET* 3.2 12.1 + - - +
1720B ARG* 4.2 18.9 - - - +
1751B ALA 3.4 12.8 - - - +
1752B GLN* 3.0 10.2 + - - +
1754B LEU* 1.3 79.8 - - - +
1756B VAL* 1.3 68.7 + - + +
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Residues in contact with VAL1756 (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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1752B GLN* 3.0 18.4 + - + +
1753B LEU* 3.5 22.0 - - - +
1754B LEU 4.6 0.2 - - - +
1755B GLN* 1.3 82.1 - - + +
1757B LYS* 1.3 68.5 + - + +
1758B LYS* 3.2 24.3 - - + -
1767B ILE* 4.1 24.7 - - + -
1770B MET* 4.1 21.1 - - + -
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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