Contacts of the strand formed by residues 2235 - 2238 (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 ARG2235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2211B GLU* 3.2 35.1 + - - +
2212B MET* 3.2 2.2 - - + -
2213B ILE* 3.0 23.0 + - - -
2229B GLN* 3.8 6.3 - - - +
2233B LYS 5.1 1.1 - - - +
2234B THR* 1.3 80.0 - - - +
2236B ILE* 1.3 61.3 + - - +
2258B ARG* 3.3 46.1 + - + +
2259B ALA* 3.9 9.9 - - + -
2284B GLU 4.9 5.1 + - - -
2286B LEU* 3.3 36.7 - - - +
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Residues in contact with ILE2236 (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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2213B ILE* 3.6 18.4 - - + +
2216B PRO* 4.0 10.1 - - + -
2225B HIS* 3.7 22.7 - - + +
2228B LEU* 3.8 25.8 - - + -
2229B GLN* 2.9 43.9 - - + +
2232B LEU* 3.8 15.5 - - + -
2235B ARG* 1.3 77.2 - - - +
2237B CYS* 1.3 67.6 + - - +
2238B LEU* 4.9 0.4 - - + -
2256B SER 3.7 18.6 - - - +
2257B CYS* 3.1 4.0 - - + +
2258B ARG 3.0 5.7 + - - -
2259B ALA* 3.0 23.3 + - - -
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Residues in contact with CYS2237 (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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2212B MET* 3.7 20.6 - - + -
2213B ILE 3.0 8.8 + - - +
2214B GLU* 3.4 15.8 - - - +
2215B GLN* 2.7 32.7 + - - -
2236B ILE* 1.3 76.4 - - - +
2238B LEU* 1.3 64.2 + - - +
2259B ALA* 3.1 9.4 - - + +
2260B ILE 3.7 0.9 - - - -
2261B ASN* 3.2 36.3 - - - -
2288B TRP* 3.6 21.8 - - - -
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Residues in contact with LEU2238 (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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2215B GLN* 3.3 21.3 - - - +
2221B ASP 4.4 0.4 - - - +
2222B PHE* 4.3 4.0 - - + -
2225B HIS* 3.8 34.3 - - + +
2236B ILE* 4.9 0.2 - - + -
2237B CYS* 1.3 77.0 - - - +
2239B ASP* 1.3 61.6 + - - +
2241B ASN* 3.9 16.2 - - - +
2242B ILE* 3.5 26.7 - - + +
2251B ALA* 3.9 28.3 - - + -
2256B SER* 4.2 9.0 - - - -
2257B CYS* 3.8 15.7 - - + -
2259B ALA 3.3 6.9 + - - -
2260B ILE* 4.0 4.6 - - + -
2261B ASN* 3.0 28.2 + - - +
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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