Contacts of the helix formed by residues 1353 - 1359 (chain A) in PDB entry 1WUF
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 ASP1353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1327A ASP 4.5 2.2 - - - +
1328A ILE* 3.5 6.7 + - - +
1329A VAL 3.0 10.9 + - - +
1330A THR* 2.7 35.1 + - - +
1352A LEU* 1.3 68.1 - - - +
1354A LEU* 1.3 52.9 + - - +
1355A LYS* 2.6 41.9 + - - +
1356A VAL* 3.3 34.7 - - + +
1357A LEU* 2.8 20.9 + - - +
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Residues in contact with LEU1354 (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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1009A ILE* 6.5 0.4 - - + -
1035A GLU* 6.2 0.2 - - - +
1352A LEU* 2.8 28.8 + - + +
1353A ASP* 1.3 70.9 - - - +
1355A LYS* 1.3 64.5 + - + +
1357A LEU* 3.8 20.0 - - + +
1358A LYS* 3.0 39.8 + - - +
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Residues in contact with LYS1355 (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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1330A THR* 3.8 13.3 - - - +
1352A LEU 4.4 1.0 + - - -
1353A ASP* 2.6 44.8 + - - +
1354A LEU* 1.3 78.6 - - + +
1356A VAL* 1.3 69.4 + - + +
1357A LEU 3.1 1.6 + - - -
1358A LYS* 3.1 23.3 + - - +
1359A LYS* 3.7 6.3 + - - +
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Residues in contact with VAL1356 (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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1013A LEU* 6.0 0.2 - - + -
1326A GLU* 3.9 24.9 - - + +
1327A ASP 3.1 26.7 - - - +
1328A ILE* 4.6 2.9 - - + -
1353A ASP* 2.9 36.1 + - + +
1355A LYS* 1.3 80.5 - - + +
1357A LEU* 1.3 65.4 + - - +
1359A LYS* 3.1 28.0 - - - +
1360A TYR* 3.3 25.9 - - + -
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Residues in contact with LEU1357 (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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1009A ILE* 4.5 21.3 - - + -
1011A ALA* 4.1 18.2 - - + -
1033A ILE* 5.3 4.3 - - + -
1328A ILE* 4.1 35.3 - - + +
1352A LEU* 3.8 37.0 - - + -
1353A ASP 2.8 18.3 + - - +
1354A LEU* 3.8 15.5 - - + +
1356A VAL* 1.3 72.8 - - - +
1358A LYS* 1.3 53.9 + - + +
1360A TYR* 2.7 29.2 + - + +
1361A THR* 2.8 29.7 + - - +
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Residues in contact with LYS1358 (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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1354A LEU* 3.0 26.0 + - - +
1355A LYS* 3.1 13.3 + - - +
1357A LEU* 1.3 78.9 - - - +
1359A LYS* 1.3 58.7 + - - +
1360A TYR 3.2 4.3 + - - -
1361A THR* 3.4 22.1 + - - +
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Residues in contact with LYS1359 (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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1326A GLU* 2.8 37.9 + - - -
1355A LYS 3.7 3.8 + - - +
1356A VAL* 3.1 25.5 + - - +
1357A LEU 2.9 0.2 + - - -
1358A LYS* 1.3 76.5 - - - +
1360A TYR* 1.3 84.3 + - + +
1361A THR 5.2 0.4 - - - -
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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