Contacts of the helix formed by residues 1734 - 1745 (chain A) in PDB entry 5NUG
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 ASP1734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1733A ILE* 1.3 77.4 - - - +
1735A PRO* 1.4 70.4 - - - +
1736A ASN* 3.0 39.0 + - - +
1737A THR* 3.5 18.7 - - + +
1738A TYR* 3.4 21.5 + - - +
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Residues in contact with PRO1735 (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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1733A ILE 3.8 7.4 - - - +
1734A ASP* 1.4 90.4 - - - +
1736A ASN* 1.3 67.0 + - - +
1737A THR 3.3 0.2 - - - -
1738A TYR* 3.9 3.3 - - + +
1739A ILE* 3.0 32.3 + - - +
1791A VAL* 3.8 32.5 - - + +
1794A ASP* 6.5 1.1 - - + -
1795A SER* 6.2 2.9 - - - -
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Residues in contact with ASN1736 (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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1734A ASP* 3.0 17.7 + - - +
1735A PRO* 1.3 87.7 - - - +
1737A THR* 1.3 58.8 + - - +
1739A ILE* 3.5 9.5 - - - +
1740A THR* 3.1 26.2 - - - +
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Residues in contact with THR1737 (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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1723A GLU* 5.6 0.2 + - - -
1727A PHE* 3.6 34.2 - - + -
1733A ILE* 5.5 0.2 - - + -
1734A ASP* 3.5 28.1 + - + +
1736A ASN* 1.3 75.5 - - - +
1738A TYR* 1.3 64.7 - - - +
1740A THR* 2.4 28.4 + - - -
1741A TRP* 2.9 15.1 + - - +
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Residues in contact with TYR1738 (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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1724A VAL* 5.9 2.9 - - + -
1727A PHE* 4.0 17.3 - + + -
1733A ILE* 3.7 27.4 - - + -
1734A ASP 3.4 14.8 + - - +
1735A PRO* 4.0 6.1 - - + +
1736A ASN 3.6 0.2 - - - -
1737A THR* 1.3 83.8 - - + +
1739A ILE* 1.3 57.3 + - - +
1741A TRP* 3.2 38.1 + + - +
1742A ILE* 2.9 58.7 + - + +
1754A ALA* 5.7 2.6 - - - +
1788A THR* 4.6 15.4 - - + +
1791A VAL* 4.7 12.1 - - + -
1792A LEU* 3.8 22.4 - - + -
1811A LEU* 3.9 12.2 - - + +
1815A LEU* 4.4 14.7 - - - +
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Residues in contact with ILE1739 (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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1735A PRO 3.0 25.5 + - - +
1736A ASN* 3.5 17.0 - - - +
1738A TYR* 1.3 78.8 - - - +
1740A THR* 1.3 63.6 + - + +
1742A ILE* 3.2 15.0 + - + +
1743A ASP* 2.9 36.4 + - - +
1795A SER* 5.0 9.4 - - - -
1800A GLN* 3.4 29.2 - - - +
1804A ARG* 3.6 29.6 - - - +
1808A LEU* 6.2 2.7 - - + -
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Residues in contact with THR1740 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1736A ASN 3.1 20.0 - - - +
1737A THR* 2.4 33.5 + - - -
1739A ILE* 1.3 85.8 - - + +
1741A TRP* 1.3 54.5 + - - +
1743A ASP* 3.2 10.6 + - - +
1744A LYS* 2.9 28.1 + - - +
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Residues in contact with TRP1741 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1720A SER* 2.8 34.9 + - - +
1723A GLU* 3.3 33.2 - - + +
1724A VAL* 3.5 24.5 - - + -
1727A PHE* 4.0 14.1 - + + -
1737A THR 2.9 12.1 + - - +
1738A TYR* 3.4 46.2 - + - +
1740A THR* 1.3 77.1 + - - +
1742A ILE* 1.3 86.5 + - + +
1744A LYS* 3.2 19.3 + - - +
1745A TYR* 3.3 23.9 + + - +
1750A VAL* 3.6 33.7 - - + -
1753A SER* 4.1 4.9 - - - -
1754A ALA* 5.1 4.7 - - + -
1811A LEU* 4.5 2.7 - - + -
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Residues in contact with ILE1742 (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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1738A TYR* 2.9 50.3 + - + +
1739A ILE* 3.4 13.2 - - + +
1741A TRP* 1.3 97.2 - - + +
1743A ASP* 1.3 66.4 + - - +
1745A TYR 3.1 18.2 + - - +
1750A VAL* 4.2 8.0 - - + +
1792A LEU* 4.4 1.8 - - + -
1804A ARG* 5.0 5.4 - - + -
1807A LYS* 3.2 37.7 + - + +
1808A LEU* 4.0 29.4 - - + -
1811A LEU* 4.5 7.2 - - + -
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Residues in contact with ASP1743 (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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1739A ILE* 2.9 20.3 + - - +
1740A THR* 3.4 11.6 - - - +
1742A ILE* 1.3 80.3 - - - +
1744A LYS* 1.3 62.5 + - - +
1745A TYR 3.5 3.6 + - - +
1746A GLN* 5.6 0.7 + - - -
1804A ARG* 2.8 50.8 + - - +
1807A LYS* 3.9 8.6 + - - +
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Residues in contact with LYS1744 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1716A LEU* 6.0 0.5 - - - +
1719A GLU* 4.5 6.3 + - - -
1723A GLU* 3.4 15.1 + - - +
1740A THR 2.9 13.2 + - - +
1741A TRP* 3.2 12.1 + - - +
1743A ASP* 1.3 78.2 - - - +
1745A TYR* 1.3 99.4 + - + +
1746A GLN* 4.0 11.3 + - - +
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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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1716A LEU* 3.4 52.3 - - + -
1719A GLU* 3.0 38.4 + - + +
1720A SER* 4.0 13.0 - - - +
1723A GLU* 3.4 20.3 + - - -
1741A TRP* 3.3 33.6 + + - -
1742A ILE 3.1 3.5 - - - +
1743A ASP 3.8 0.7 - - - +
1744A LYS* 1.3 107.5 + - + +
1746A GLN* 1.3 70.4 + - - +
1749A LEU* 4.9 4.5 - - + -
1750A VAL* 3.8 17.2 - - + +
1807A LYS* 2.9 25.3 + - - -
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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