Contacts of the strand formed by residues 2043 - 2048 (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 HIS2043 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007B ARG* 4.5 4.6 + - - -
2035B GLU* 2.7 28.0 + - + +
2036B LEU 3.5 3.6 - - - +
2037B ILE* 3.4 37.0 - - + +
2041B GLY* 3.3 19.4 + - - -
2042B ILE* 1.3 75.4 - - - +
2044B GLY* 1.3 61.7 + - - +
2045B TYR* 3.4 25.5 - - + +
2110B ASP* 3.5 0.7 - - - +
2114B LYS* 3.0 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2044 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2034B ILE 3.4 0.5 - - - +
2035B GLU* 3.3 5.2 - - - -
2036B LEU* 2.7 40.8 + - - +
2042B ILE 4.0 0.8 + - - -
2043B HIS* 1.3 73.2 - - - +
2045B TYR* 1.3 61.1 + - - -
2107B ALA* 3.5 20.6 - - - -
2110B ASP* 3.3 7.4 - - - -
2111B ALA* 4.0 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2045 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2033B ILE* 4.4 6.7 - - + -
2034B ILE 3.4 1.8 - - - +
2035B GLU* 3.4 42.2 + - + -
2043B HIS* 3.4 31.9 - - + +
2044B GLY* 1.3 76.0 - - - -
2046B GLY* 1.3 59.5 + - - +
2106B LEU 3.8 0.2 - - - +
2107B ALA* 3.6 7.5 - - - -
2110B ASP* 2.9 22.5 + - - +
2114B LYS* 4.6 8.7 - - - -
2297B VAL* 3.8 18.8 - - + +
2301B HIS* 2.9 26.5 - - - -
2348B ILE* 4.3 13.0 - - + -
2350B VAL 5.4 4.3 - - - -
2351B THR* 6.2 3.6 - - + -
2352B LEU* 3.8 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2046 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2033B ILE* 3.5 9.7 - - - +
2034B ILE* 2.9 31.3 + - - +
2045B TYR* 1.3 74.4 - - - +
2047B GLU* 1.3 61.6 + - - +
2103B ALA 3.3 22.0 - - - -
2106B LEU* 4.5 2.5 - - - -
2107B ALA* 3.6 7.9 - - - +
2297B VAL* 4.0 5.2 - - - -
2301B HIS* 4.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2047 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2029B LYS* 3.7 6.2 + - - -
2031B PHE* 4.0 14.8 - - + -
2032B TYR 3.4 15.0 - - - +
2033B ILE* 4.1 3.2 - - + +
2034B ILE 4.8 0.2 - - - +
2046B GLY* 1.3 74.4 - - - +
2048B LEU* 1.3 61.8 + - - +
2049B GLU* 2.3 45.5 + - - +
2099B MET 5.2 0.3 - - - +
2102B ALA* 5.1 1.2 - - - +
2103B ALA* 3.7 16.8 + - - +
2106B LEU* 5.4 6.8 - - - +
2265B ALA* 5.7 1.4 - - - +
2295B ALA* 2.9 38.5 + - - +
2297B VAL* 3.6 9.2 - - + +
2298B GLY* 2.6 36.9 + - - +
2301B HIS* 5.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2048 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2031B PHE* 3.4 26.2 - - - +
2032B TYR* 3.0 25.5 + - + -
2034B ILE* 4.4 2.9 - - + +
2047B GLU* 1.3 68.9 - - - +
2049B GLU* 1.3 63.5 + - - +
2050B ALA* 4.1 7.4 - - + +
2061B LEU* 3.4 42.2 - - + +
2064B ALA* 3.8 18.8 - - + -
2065B ILE* 3.8 24.0 - - + +
2068B ILE* 4.3 2.7 - - + -
2099B MET 3.2 26.9 - - - +
2100B ALA* 4.0 4.9 - - - -
2103B ALA* 3.6 13.7 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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