Contacts of the helix formed by residues 1737 - 1742 (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 GLY1737 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1688C LYS* 3.9 12.7 - - - +
1733C LEU 4.8 0.2 + - - -
1734C MET 4.9 1.4 + - - -
1735C ASN* 3.3 4.6 - - - +
1736C SER* 1.3 78.3 - - - +
1738C ALA* 1.3 62.9 + - - +
1740C GLU* 3.2 30.1 + - - +
1741C THR* 3.2 18.4 + - - +
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Residues in contact with ALA1738 (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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1687C VAL* 3.9 4.5 - - + -
1688C LYS* 3.8 22.2 - - - +
1691C PHE* 3.7 29.6 - - + +
1728C LEU* 3.8 14.8 - - + -
1736C SER* 3.2 18.1 + - - +
1737C GLY* 1.3 75.7 - - - +
1739C LYS* 1.3 64.9 + - - +
1741C THR* 2.6 26.5 + - - -
1742C LEU 3.8 1.4 + - - -
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Residues in contact with LYS1739 (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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1725C GLU* 3.3 42.4 - - + +
1728C LEU* 3.7 19.4 - - + +
1733C LEU 5.6 0.4 + - - -
1734C MET* 5.4 10.3 - - + +
1737C GLY 3.4 0.4 - - - -
1738C ALA* 1.3 78.2 - - - +
1740C GLU* 1.3 70.9 + - + +
1742C LEU* 3.0 28.2 + - + +
1743C GLU* 3.7 6.3 + - - +
1746C ILE* 4.8 10.4 - - + +
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Residues in contact with GLU1740 (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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1734C MET 4.8 7.9 - - - +
1737C GLY* 3.2 31.2 + - - +
1738C ALA 3.2 0.2 - - - -
1739C LYS* 1.3 88.2 + - - +
1741C THR* 1.3 61.7 + - + +
1742C LEU 3.3 0.9 + - - -
1743C GLU* 3.3 22.3 + - - +
1744C PRO* 4.0 3.6 - - - +
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Residues in contact with THR1741 (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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1688C LYS* 3.8 33.9 - - + +
1691C PHE* 3.6 20.3 + - - +
1692C TYR* 4.1 24.3 - - + -
1695C GLY* 5.1 5.7 - - - -
1737C GLY 3.2 17.9 - - - +
1738C ALA 2.6 17.1 + - - +
1740C GLU* 1.3 77.4 - - + +
1742C LEU* 1.3 62.0 + - - +
1743C GLU 3.3 0.2 - - - -
1744C PRO* 3.5 12.7 - - - +
1745C LEU* 5.2 0.7 + - - +
1823C PHE* 4.7 4.9 - - + -
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Residues in contact with LEU1742 (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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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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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