Contacts of the strand formed by residues 2259 - 2262 (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 ALA2259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2212B MET* 4.1 15.0 - - + -
2235B ARG* 3.9 12.6 - - + -
2236B ILE 3.0 9.8 + - - +
2237B CYS* 3.1 31.5 - - + -
2238B LEU 3.3 4.9 + - - -
2257B CYS* 3.6 2.8 - - - -
2258B ARG* 1.3 81.9 - - - +
2260B ILE* 1.3 68.0 + - - +
2285B ILE* 3.9 1.7 - - - +
2286B LEU* 3.2 23.1 - - + +
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Residues in contact with ILE2260 (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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2237B CYS* 3.7 3.4 - - - -
2238B LEU* 4.1 3.6 - - + -
2242B ILE* 3.5 53.4 - - + -
2248B VAL* 4.4 12.6 - - + -
2257B CYS* 3.7 16.2 - - - -
2259B ALA* 1.3 82.6 - - - +
2261B ASN* 1.3 69.8 + - - +
2262B LEU* 3.2 15.2 + - + +
2276B ILE* 4.6 10.3 - - + -
2280B CYS* 4.2 13.5 - - - -
2285B ILE* 3.9 15.3 - - + -
2286B LEU 2.6 12.0 + - - +
2287B VAL* 3.6 4.2 - - + +
2288B TRP* 3.4 23.2 + - - -
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Residues in contact with ASN2261 (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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2162B LYS* 4.6 3.4 - - - +
2214B GLU* 3.0 30.3 + - - +
2237B CYS* 3.2 12.1 - - - -
2238B LEU 3.0 20.9 + - - +
2239B ASP* 4.3 4.7 - - + -
2260B ILE* 1.3 70.5 - - - +
2262B LEU* 1.3 56.6 + - - +
2263B LYS* 3.4 22.5 - - - +
2266B ARG* 2.8 32.2 + - - -
2288B TRP* 3.2 29.3 - - + +
2290B GLY* 3.2 22.0 - - - -
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Residues in contact with LEU2262 (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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2260B ILE* 3.2 7.7 + - + -
2261B ASN* 1.3 70.6 - - - +
2263B LYS* 1.3 67.2 + - - +
2264B LEU 4.2 0.7 + - - +
2266B ARG* 4.0 5.2 - - - +
2267B VAL* 3.6 37.7 - - + -
2273B ALA* 3.4 35.4 - - + +
2276B ILE* 4.1 12.8 - - + -
2277B ALA 4.4 0.7 - - - +
2287B VAL* 3.9 25.8 - - + -
2288B TRP 2.9 15.2 + - - +
2289B CYS* 3.2 10.7 - - - +
2290B GLY 3.0 18.2 + - - -
2305B LEU* 4.5 7.9 - - + +
2311B PHE* 3.9 13.9 - - + -
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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