Contacts of the helix formed by residues 2085 - 2091 (chain B) 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 GLU2085 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2083B LYS* 3.5 26.6 - - + +
2084B PRO* 1.3 105.1 - - - +
2086B GLU* 1.3 61.7 + - - +
2087B ILE 3.0 3.2 + - - -
2088B GLN* 3.6 13.2 + - - +
2089B GLU* 3.9 15.8 + - - +
2109B TRP* 3.9 15.1 - - - -
2271B SER* 3.3 23.8 - - - +
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Residues in contact with GLU2086 (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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2080B LYS 3.7 4.9 - - - +
2081B ILE* 3.2 16.4 - - + +
2082B ARG* 2.6 61.2 + - - +
2083B LYS* 2.9 29.0 + - + +
2085B GLU* 1.3 79.0 - - + +
2087B ILE* 1.3 60.1 + - - +
2088B GLN 3.4 0.2 - - - -
2089B GLU* 3.2 27.0 + - - +
2090B LEU* 2.9 25.2 + - + +
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Residues in contact with ILE2087 (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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2076B LEU* 3.7 29.4 - - + -
2081B ILE* 4.3 15.5 - - + -
2084B PRO 3.3 17.0 - - - +
2085B GLU 3.0 0.6 - - - -
2086B GLU* 1.3 76.1 - - - +
2088B GLN* 1.3 65.8 + - - +
2089B GLU 3.2 0.3 + - - -
2090B LEU* 3.5 12.5 + - + +
2091B PHE* 3.3 46.8 + - + -
2105B GLU* 3.3 29.4 - - + -
2108B VAL* 3.7 32.8 - - + -
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Residues in contact with GLN2088 (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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2085B GLU 3.6 9.9 + - - +
2086B GLU 3.4 0.6 - - - -
2087B ILE* 1.3 78.7 - - - +
2089B GLU* 1.3 59.0 + - + +
2091B PHE* 3.3 7.8 + - - +
2092B SER* 2.8 28.6 + - - -
2101B LYS* 5.2 2.4 + - + +
2105B GLU* 4.7 7.1 + - - +
2244B SER* 6.0 3.0 - - - -
2268B GLY 5.7 4.4 + - - +
2271B SER* 3.8 22.6 - - - -
2272B SER* 3.5 28.0 + - - +
2275B LYS* 3.3 34.1 + - - +
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Residues in contact with GLU2089 (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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2085B GLU* 3.9 15.7 - - - +
2086B GLU* 3.2 20.4 + - - +
2087B ILE 3.1 0.2 - - - -
2088B GLN* 1.3 76.8 - - + +
2090B LEU* 1.3 59.0 + - - +
2091B PHE 3.0 4.5 - - - -
2092B SER* 2.4 36.3 + - - -
2093B TRP* 5.3 0.2 - - - -
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Residues in contact with LEU2090 (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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1023A TYR* 5.5 0.3 + - - -
2075B LEU* 3.6 36.7 - - + +
2076B LEU* 4.3 10.8 - - + -
2079B ARG* 3.5 33.2 - - - +
2081B ILE* 5.1 3.4 - - + -
2086B GLU* 2.9 38.6 + - + +
2087B ILE* 3.6 22.9 - - + +
2089B GLU* 1.3 78.2 - - - +
2091B PHE* 1.3 66.2 + - + +
2092B SER 3.3 0.2 - - - -
2093B TRP* 3.2 26.9 + - - -
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Residues in contact with PHE2091 (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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2072B LEU* 3.8 39.5 - - + -
2075B LEU* 3.7 26.2 - - + -
2076B LEU* 4.4 6.7 - - + -
2087B ILE* 3.3 38.6 + - + +
2088B GLN* 3.3 6.9 + - - +
2089B GLU 3.0 1.2 - - - -
2090B LEU* 1.3 91.5 - - + +
2092B SER* 1.3 60.4 + - - +
2093B TRP 3.3 3.1 - - - -
2094B ILE* 2.9 15.5 + - - +
2101B LYS* 2.6 68.9 + - + -
2104B VAL* 4.0 20.9 - - + -
2105B GLU* 5.1 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