Contacts of the helix formed by residues 1742 - 1754 (chain C) in PDB entry 5JCZ
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 LEU1742 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1691C PHE* 3.3 59.0 - - + +
1694C ILE* 4.9 4.7 - - + -
1695C GLY* 3.7 20.2 - - - +
1721C VAL* 3.9 28.9 - - + +
1724C LEU* 4.0 15.5 - - + -
1725C GLU* 5.4 1.1 - - + -
1738C ALA 4.0 2.2 - - - +
1739C LYS* 3.0 16.5 + - + +
1741C THR* 1.3 80.3 - - - +
1743C GLU* 1.3 56.4 + - - +
1744C PRO* 3.4 2.0 - - - -
1745C LEU* 3.2 14.9 + - + +
1746C ILE* 2.9 31.8 + - + +
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Residues in contact with GLU1743 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1739C LYS* 3.7 5.1 + - - +
1740C GLU* 3.3 19.6 + - - +
1742C LEU* 1.3 74.4 - - - +
1744C PRO* 1.3 71.1 - - + +
1746C ILE* 3.3 21.6 + - - +
1747C GLN* 3.0 64.1 + - - +
1750C GLN* 5.3 0.3 - - - +
1770C ASN* 5.2 0.4 - - - +
1771C ALA* 3.9 8.7 - - + -
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Residues in contact with PRO1744 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699C LEU* 4.0 5.2 - - + -
1740C GLU 4.0 4.5 - - - +
1741C THR* 3.5 16.6 - - - +
1742C LEU 3.7 0.2 - - - -
1743C GLU* 1.3 93.6 - - + +
1745C LEU* 1.3 55.8 + - - +
1747C GLN* 3.4 0.6 + - + -
1748C ALA* 3.0 24.3 + - - +
1771C ALA* 3.8 29.2 - - + +
1772C LEU* 3.3 24.9 - - + +
1817C MET* 4.0 26.9 - - + -
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Residues in contact with LEU1745 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1627C MET* 4.3 7.4 - - + -
1695C GLY* 4.2 21.8 - - - +
1698C THR* 3.7 38.6 - - + -
1699C LEU* 4.0 23.0 - - + +
1702C LEU* 4.5 11.9 - - + -
1717C ILE* 4.0 15.0 - - + -
1721C VAL* 3.8 22.9 - - + -
1741C THR 5.2 0.6 + - - +
1742C LEU* 3.2 17.8 + - + +
1744C PRO* 1.3 75.9 - - - +
1746C ILE* 1.3 59.0 + - - +
1748C ALA* 3.2 4.5 + - - +
1749C ALA* 2.9 27.4 + - - +
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Residues in contact with ILE1746 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1718C ARG* 3.9 34.5 - - - +
1721C VAL* 3.7 33.4 - - + -
1725C GLU* 4.6 9.4 - - - +
1739C LYS* 4.8 7.2 - - + -
1742C LEU* 2.9 25.7 + - + +
1743C GLU* 3.6 26.5 - - - +
1744C PRO 3.3 0.2 - - - -
1745C LEU* 1.3 76.9 - - - +
1747C GLN* 1.3 57.6 + - - +
1749C ALA* 3.1 8.6 + - - +
1750C GLN* 2.9 45.6 + - - +
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Residues in contact with GLN1747 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1743C GLU* 3.0 40.7 + - - +
1744C PRO 3.9 3.8 - - - +
1746C ILE* 1.3 72.8 - - - +
1748C ALA* 1.3 59.7 + - - +
1750C GLN* 3.6 17.9 - - - +
1751C LEU* 2.9 28.8 + - - +
1768C MET 3.3 19.1 + - - +
1769C CYS* 3.2 12.8 - - - -
1770C ASN* 2.8 31.2 + - - +
1771C ALA* 2.8 36.9 + - - +
1772C LEU* 3.7 11.7 + - + -
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Residues in contact with ALA1748 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699C LEU* 3.7 24.5 - - + -
1702C LEU* 3.9 13.5 - - + -
1744C PRO 3.0 17.2 + - - +
1745C LEU* 3.5 5.4 - - - +
1746C ILE 3.2 0.2 - - - -
1747C GLN* 1.3 77.0 - - - +
1749C ALA* 1.3 60.5 + - - +
1751C LEU* 3.3 7.3 + - - +
1752C LEU* 3.1 28.3 + - - +
1772C LEU* 3.9 13.2 - - + +
1780C VAL* 4.8 9.4 - - + +
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Residues in contact with ALA1749 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1702C LEU* 4.8 0.4 - - - +
1714C GLY* 3.5 25.9 - - - +
1717C ILE* 3.8 21.3 - - + -
1718C ARG* 4.3 10.3 - - + +
1745C LEU 2.9 12.6 + - - +
1746C ILE* 3.1 11.4 + - - +
1748C ALA* 1.3 75.8 - - - +
1750C GLN* 1.3 62.2 + - - +
1752C LEU* 3.4 12.0 + - - +
1753C GLN* 3.0 25.6 + - - +
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Residues in contact with GLN1750 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1718C ARG* 5.0 6.7 - - - +
1743C GLU* 5.3 0.5 - - - +
1746C ILE* 2.9 32.9 + - + +
1747C GLN* 3.6 22.4 - - - +
1749C ALA* 1.3 75.2 - - - +
1751C LEU* 1.3 64.2 + - - +
1753C GLN* 3.0 24.5 + - - +
1754C VAL* 3.1 19.2 + - - +
1768C MET* 3.8 21.9 - - - +
44D ILE* 3.9 42.5 + - + +
47D GLU* 4.5 12.7 + - - -
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Residues in contact with LEU1751 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747C GLN 2.9 18.7 + - - +
1748C ALA* 3.5 5.8 - - - +
1750C GLN* 1.3 76.1 - - - +
1752C LEU* 1.3 59.8 + - - +
1753C GLN 3.3 0.3 + - - -
1754C VAL* 3.5 4.2 - - - +
1756C LYS* 3.1 24.8 + - - -
1765C ILE* 3.7 46.0 - - + -
1768C MET* 4.0 6.3 - - + -
1769C CYS* 4.3 11.0 - - - -
1772C LEU* 4.6 5.6 - - + -
1777C ILE* 3.9 26.7 - - + +
1780C VAL* 3.7 34.5 - - + -
1781C LEU* 4.1 12.6 - - + -
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Residues in contact with LEU1752 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1702C LEU* 4.0 19.7 - - + -
1708C MET 3.9 15.7 - - - +
1709C CYS* 3.7 29.4 - - + -
1710C SER 3.5 19.5 - - - +
1711C TRP* 3.3 16.4 - - - +
1714C GLY* 3.9 17.5 - - - +
1717C ILE* 4.5 2.0 - - + -
1748C ALA 3.1 18.4 + - - +
1749C ALA* 3.6 9.6 - - - +
1750C GLN 3.1 0.2 - - - -
1751C LEU* 1.3 75.4 - - - +
1753C GLN* 1.3 58.6 + - - +
1756C LYS* 3.2 15.9 + - - +
1780C VAL* 3.7 24.7 - - + -
1784C TYR* 3.4 15.3 - - + -
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Residues in contact with GLN1753 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1711C TRP* 3.8 25.8 - - + +
1714C GLY 3.6 12.6 + - - -
1715C MET* 3.3 24.0 - - + +
1718C ARG* 4.3 12.9 - - - +
1749C ALA 3.0 24.4 + - - +
1750C GLN* 3.0 14.0 + - - +
1752C LEU* 1.3 79.7 - - - +
1754C VAL* 1.3 68.0 + - - +
1755C LYS* 3.9 0.3 + - - +
1756C LYS* 4.2 0.7 + - - -
44D ILE 5.0 0.8 + - - -
45D GLY* 3.5 14.7 - - - -
46D VAL* 3.0 31.3 + - - +
76D ILE* 4.6 15.3 - - + +
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Residues in contact with VAL1754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750C GLN 3.3 13.2 - - - +
1751C LEU* 3.5 19.5 - - - +
1753C GLN* 1.3 79.4 - - + +
1755C LYS* 1.3 69.6 + - - +
1756C LYS* 2.5 32.8 + - - +
1764C ALA* 6.6 0.2 - - + -
1765C ILE* 3.9 23.6 - - + -
1768C MET* 4.0 11.7 - - + -
44D ILE* 3.6 26.5 - - + -
45D GLY 5.1 2.5 - - - +
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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