Contacts of the strand formed by residues 1913 - 1918 (chain B) in PDB entry 4JKE
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 GLN1913 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1911A GLU* 2.9 30.3 + - - +
1912A PRO 4.1 6.7 + - - +
1913A GLN* 3.7 33.8 - - + +
1914A MET 4.9 2.4 + - - +
1915A VAL* 6.5 0.7 - - + -
1819B LEU 3.8 0.5 - - - +
1820B LYS* 3.5 4.0 - - - -
1821B ILE* 3.0 45.3 + - + +
1905B LEU* 4.9 3.6 - - - +
1909B ALA* 3.7 12.0 - - - +
1911B GLU* 3.1 11.7 + - - +
1912B PRO* 1.3 75.6 - - - +
1914B MET* 1.3 63.0 + - - +
1915B VAL* 3.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1914 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1914A MET* 3.6 31.4 + - + +
1915A VAL* 6.4 0.2 - - - -
1916A LEU* 3.5 40.6 - - + +
1818B PHE* 3.8 22.7 - - + -
1819B LEU 3.3 17.7 - - - +
1820B LYS* 3.9 26.9 - - + -
1848B LEU* 3.6 24.7 - - + -
1851B SER* 5.6 0.2 - - - +
1913B GLN* 1.3 79.4 - - - +
1915B VAL* 1.3 68.7 + - - +
1916B LEU* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1915 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1914A MET* 5.9 1.3 - - - -
1817B LEU 3.7 0.7 - - - +
1818B PHE* 3.8 0.9 - - - -
1819B LEU* 2.8 37.8 + - + +
1821B ILE* 5.2 1.1 - - + -
1905B LEU* 3.9 27.8 - - + -
1913B GLN* 3.8 24.9 - - + +
1914B MET* 1.3 80.1 - - - +
1916B LEU* 1.3 72.0 + - - +
1917B PHE* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1916 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818A PHE* 4.2 9.2 - - + -
1848A LEU* 4.0 9.6 - - + -
1851A SER* 3.6 27.1 - - - +
1852A LEU* 4.0 25.4 - - + -
1914A MET* 3.5 31.9 - - + +
1916A LEU* 5.0 3.1 - - + -
1816B GLN* 4.4 7.2 - - - +
1817B LEU 3.5 3.4 - - - +
1818B PHE* 3.4 40.8 - - + -
1914B MET* 4.3 9.9 - - + -
1915B VAL* 1.3 83.2 - - - +
1917B PHE* 1.3 71.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1917 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1851A SER* 3.4 12.9 - - - +
1816B GLN* 3.5 6.9 - - - +
1817B LEU* 2.9 40.3 + - + +
1819B LEU* 3.8 21.3 - - + -
1901B LYS* 4.0 28.9 - - + -
1902B PHE* 3.7 29.8 - + - -
1905B LEU* 4.2 13.2 - - + -
1915B VAL* 3.5 32.1 - - + -
1916B LEU* 1.3 80.5 - - - +
1918B ASN* 1.3 59.5 + - - +
1919B LEU* 3.9 11.7 - - + -
1967B ILE* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1918 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1850A ARG 4.5 8.3 + - - +
1851A SER* 3.5 19.9 + - - +
1852A LEU 4.5 11.8 + - - -
1853A PRO* 4.6 12.4 - - + +
1854A VAL* 5.7 0.6 - - - +
1814B THR 4.1 7.1 - - - +
1815B GLY 3.6 6.7 - - - +
1816B GLN* 4.8 0.2 - - - +
1917B PHE* 1.3 73.6 - - - +
1919B LEU* 1.3 62.0 + - - +
1920B TYR* 3.1 19.6 + - - +
1921B ASP* 2.8 46.7 + - - +
1922B ASP* 5.1 1.2 + - - -
1966B HIS* 6.0 0.4 - - - -
1967B ILE* 3.8 7.6 - - - +
----------------------------------------------------------
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