Contacts of the strand formed by residues 2212 - 2214 (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 MET2212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2187B MET* 3.4 21.7 - - + +
2188B ALA 2.9 25.3 + - - +
2210B LEU* 3.1 3.3 - - - +
2211B GLU* 1.3 81.1 - - + +
2213B ILE* 1.3 66.5 + - - +
2214B GLU* 5.6 0.2 - - - -
2234B THR* 3.6 3.8 - - - -
2235B ARG* 3.2 22.7 - - + +
2237B CYS* 3.7 24.0 - - + -
2259B ALA* 4.1 4.7 - - + -
2286B LEU* 3.6 27.4 - - + -
2288B TRP* 3.2 43.5 - - + +
2313B PHE* 3.9 18.4 - - + -
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Residues in contact with ILE2213 (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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2165B ILE* 6.2 0.9 - - + -
2188B ALA* 3.2 12.3 - - + +
2190B ALA* 4.5 10.8 - - + -
2202B LEU* 4.3 24.7 - - + +
2205B LEU* 4.2 32.1 - - + -
2206B ASP* 5.4 0.4 - - - +
2210B LEU* 3.9 11.0 - - + -
2212B MET* 1.3 77.7 - - - +
2214B GLU* 1.3 62.0 + - - +
2215B GLN 3.7 0.3 + - - -
2216B PRO* 3.8 21.0 - - + +
2232B LEU* 4.6 13.5 - - + -
2234B THR* 3.8 19.7 - - + +
2235B ARG 3.0 8.6 + - - +
2236B ILE* 3.6 12.7 - - + +
2237B CYS* 3.0 19.6 + - - -
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Residues in contact with GLU2214 (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* 4.2 1.7 + - - +
2187B MET* 5.3 4.7 - - - -
2188B ALA 2.7 13.6 + - - +
2189B ASP* 3.0 30.3 - - + +
2190B ALA* 2.9 26.0 + - - +
2191B ASN 3.9 0.7 + - - -
2212B MET* 4.1 1.4 - - - +
2213B ILE* 1.3 70.2 - - - +
2215B GLN* 1.3 78.7 + - + +
2216B PRO 3.3 1.1 - - - -
2237B CYS* 3.4 19.9 - - + +
2239B ASP* 2.9 19.1 - - + +
2261B ASN* 3.0 26.7 + - - -
2263B LYS* 5.2 0.2 + - - -
2288B TRP* 3.7 11.8 - - - -
5002B MG 2.4 25.1 - - - -
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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
------------------------------------------------------------
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