Contacts of the helix formed by residues 2060 - 2071 (chain B) in PDB entry 1WUE
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 THR2060 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066A PHE* 4.8 3.7 - - - -
1067A ILE* 4.1 13.4 - - + +
1071A HIS* 4.4 2.7 - - - +
2050B ALA* 3.6 5.2 - - - -
2051B PHE 3.0 9.9 - - - -
2052B GLU* 4.3 7.0 - - - -
2053B GLN* 3.7 4.5 - - - -
2054B PRO* 3.6 33.2 - - + -
2058B GLN 3.6 8.1 - - - +
2059B GLU* 1.3 79.9 - - - +
2061B LEU* 1.3 65.4 + - - +
2062B VAL* 4.0 4.4 + - - +
2063B THR* 2.6 37.1 + - - +
2064B GLU* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2061 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2030B ALA* 3.4 41.7 - - + +
2031B PHE* 3.9 2.7 - - - +
2032B ASP* 3.8 15.7 - - - +
2048B LEU* 3.6 43.8 - - + +
2050B ALA* 3.5 18.7 - - - +
2051B PHE 2.8 11.0 + - - +
2052B GLU* 4.4 14.1 - - + +
2060B THR* 1.3 72.8 - - - +
2062B VAL* 1.3 60.7 + - + +
2064B GLU 3.4 0.2 + - - -
2065B ARG* 2.9 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2062 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066A PHE* 3.8 46.9 - - + -
2052B GLU* 5.9 6.7 - - + +
2060B THR* 3.5 2.5 + - - +
2061B LEU* 1.3 80.1 - - + +
2063B THR* 1.3 62.5 + - - +
2065B ARG* 3.4 27.9 + - - +
2066B PHE* 3.2 21.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2063 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A THR* 3.7 45.3 - - + +
1066A PHE* 3.9 18.8 - - + -
1067A ILE* 3.9 10.2 - - + +
1097A HIS* 5.0 4.8 + - - +
2059B GLU* 4.8 0.9 - - - -
2060B THR* 2.6 38.7 + - - +
2062B VAL* 1.3 73.9 - - + +
2064B GLU* 1.3 68.8 + - - +
2066B PHE* 3.2 6.1 + - - +
2067B ILE* 3.0 25.4 + - - +
2097B HIS* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2064 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2048B LEU* 3.8 27.1 - - + -
2050B ALA* 4.3 0.9 - - + -
2059B GLU* 3.6 30.6 - - + +
2060B THR 3.0 20.4 + - - +
2063B THR* 1.3 77.2 + - - +
2065B ARG* 1.3 67.7 + - - +
2067B ILE* 3.2 3.3 + - - +
2068B ILE* 2.9 27.7 + - - +
2097B HIS* 2.7 51.8 - - - +
2099B MET* 4.5 0.2 - - + -
2100B GLY* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2065 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2010B GLN* 3.5 40.8 + - - +
2032B ASP* 2.7 42.8 + - - +
2034B PHE* 5.6 3.9 - - + -
2048B LEU* 3.7 8.2 - - + +
2061B LEU* 2.9 38.0 + - - +
2062B VAL* 3.5 28.8 - - - +
2064B GLU* 1.3 77.0 - - - +
2066B PHE* 1.3 61.8 + - - +
2068B ILE* 3.5 7.5 + - - +
2069B GLN* 3.3 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2066 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052A GLU 5.9 0.7 - - - -
1060A THR* 4.5 8.7 - - - -
1062A VAL* 3.7 43.3 - - + -
1063A THR* 3.8 18.4 - - + -
2062B VAL* 3.2 10.5 + - + +
2063B THR* 3.4 7.9 - - - +
2064B GLU 3.1 0.4 - - - -
2065B ARG* 1.3 78.1 - - - +
2067B ILE* 1.3 66.0 + - + +
2068B ILE 3.2 0.2 + - - -
2069B GLN* 3.3 3.9 + - - +
2070B GLN* 2.8 74.2 + - + +
2071B HIS* 4.5 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2067 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A PRO* 4.6 0.9 - - + -
1060A THR* 4.0 15.7 - - + -
1063A THR* 4.2 13.5 - - + -
2063B THR 3.0 14.7 + - - +
2064B GLU* 3.2 7.8 + - - +
2066B PHE* 1.3 80.4 - - + +
2068B ILE* 1.3 57.5 + - - +
2071B HIS* 2.9 49.5 + - + -
2072B LEU* 3.0 25.1 + - + -
2094B VAL* 4.4 8.5 - - + -
2097B HIS* 3.6 52.9 - - + +
2100B GLY* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2068 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2034B PHE* 3.5 43.1 - - + -
2048B LEU* 4.0 14.8 - - + -
2064B GLU 2.9 19.1 + - - +
2065B ARG* 3.6 5.6 - - - +
2066B PHE 3.1 0.2 - - - -
2067B ILE* 1.3 79.3 - - - +
2069B GLN* 1.3 62.3 + - + +
2072B LEU* 3.5 11.2 + - + -
2073B ILE* 2.8 51.7 + - + +
2100B GLY* 3.6 33.4 - - - +
2103B ALA* 4.0 4.3 - - + -
2104B LEU* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2069 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008B THR* 4.8 6.2 - - - +
2034B PHE* 5.6 1.7 - - + -
2065B ARG* 3.3 28.6 + - - +
2066B PHE* 3.3 4.9 + - - +
2068B ILE* 1.3 79.3 - - + +
2070B GLN* 1.3 72.5 + - + +
2073B ILE* 4.3 7.5 - - + +
2074B PRO* 3.6 14.7 - - - +
2364B GLN* 4.5 18.5 + - - +
2366B ILE* 3.9 43.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2070 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A TYR* 4.3 6.9 - - - +
2066B PHE* 2.8 57.8 + - + +
2069B GLN* 1.3 89.0 + - + +
2071B HIS* 1.3 81.6 + - + +
2074B PRO* 3.7 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2071 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A TYR* 3.3 45.0 - + + +
1052A GLU 3.5 24.1 + - - -
1053A GLN* 3.7 11.7 - - - -
1054A PRO* 3.6 19.0 - - + +
1060A THR* 4.6 1.8 - - - +
2066B PHE* 4.5 7.6 - + - -
2067B ILE* 2.9 34.4 + - + +
2069B GLN 3.6 0.4 - - - -
2070B GLN* 1.3 95.4 + - + +
2072B LEU* 1.3 59.6 + - - +
2074B PRO* 3.4 7.2 - - - +
2075B LEU* 2.7 34.4 - - - +
2094B VAL* 4.4 8.7 - - + -
----------------------------------------------------------
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