Contacts of the helix formed by residues 2319 - 2323 (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 ALA2319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2158B TYR* 5.8 0.2 + - - -
2318B SER* 1.3 84.0 + - - +
2320B SER* 1.3 68.2 + - - +
2321B ASN* 4.2 13.9 - - + +
2322B ARG* 2.9 21.6 + - + +
2323B PHE* 4.4 0.5 + - - -
2333B PHE* 2.9 32.3 - - - +
2335B LEU* 4.4 22.6 - - + +
2340B LEU* 4.3 5.1 - - + +
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Residues in contact with SER2320 (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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2299B ARG* 3.8 20.6 + - - +
2318B SER 3.4 2.8 + - - -
2319B ALA* 1.3 71.1 - - - +
2321B ASN* 1.3 58.6 + - - +
2322B ARG 2.8 12.0 + - - -
2323B PHE* 2.9 16.2 + - - +
2324B PHE* 2.9 19.7 + - - +
2326B GLU 5.5 0.4 - - - -
2327B ASP* 3.0 40.5 + - - +
2332B ALA* 5.1 5.2 - - - -
2333B PHE* 4.0 17.5 + - - +
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Residues in contact with ASN2321 (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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2016B LEU* 3.4 15.4 - - - +
2319B ALA* 2.9 13.1 + - + +
2320B SER* 1.3 82.8 + - - +
2322B ARG* 1.3 60.4 + - + +
2323B PHE 3.4 0.2 - - - -
2324B PHE 3.8 10.8 - - - -
2325B ALA 5.6 4.0 + - - -
2332B ALA* 4.9 10.2 - - - +
2333B PHE 4.5 4.2 - - - +
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Residues in contact with ARG2322 (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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2016B LEU* 4.1 8.5 - - - +
2135B VAL* 4.0 12.3 - - - +
2136B SER 5.4 2.0 + - - -
2153B TYR* 3.5 38.9 + - - -
2156B GLN* 4.8 4.9 + - - -
2158B TYR* 3.2 30.6 + - - +
2318B SER* 3.3 30.2 + - - +
2319B ALA* 2.9 20.3 + - + +
2320B SER 2.8 3.4 + - - -
2321B ASN* 1.3 77.7 - - + +
2323B PHE* 1.3 79.8 + - + +
2335B LEU* 5.9 0.9 - - + -
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Residues in contact with PHE2323 (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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2015B LEU* 3.6 18.3 - - + +
2016B LEU* 2.6 38.9 + - - +
2017B ALA 4.4 5.1 + - - +
2019B PHE* 4.7 15.5 - + - -
2293B LEU* 3.6 34.1 - - + -
2299B ARG* 5.6 7.2 - - - -
2318B SER* 4.4 18.2 - - - -
2320B SER* 2.9 3.6 + - - +
2322B ARG* 1.3 97.3 - - + +
2324B PHE* 1.3 71.5 + + + +
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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