Contacts of the helix formed by residues 1921 - 1925 (chain J) in PDB entry 2BT4
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 TYR1921 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1884J SER 2.9 9.3 + - - +
1885J HIS 3.5 31.6 - - - -
1886J THR* 3.9 19.3 - - - -
1887J SER 3.9 15.9 - - - +
1888J VAL* 3.7 26.6 - - + +
1891J LEU* 3.5 22.4 - - + +
1919J HIS* 3.3 22.6 - + - -
1920J SER* 1.3 69.2 - - - +
1922J VAL* 1.3 68.0 + - + +
1924J GLN* 3.0 31.5 + - - +
2286L THR* 5.5 2.1 - - + +
2316L PHE* 4.0 29.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1922 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1878J ILE* 4.2 8.7 - - + -
1880J PRO* 3.8 18.2 - - + -
1883J TYR 5.0 2.5 - - - +
1884J SER* 4.0 8.0 + - - -
1887J SER 5.2 1.8 - - - +
1890J ILE* 3.8 29.8 - - + -
1891J LEU* 4.8 7.9 - - - +
1894J LEU* 3.7 20.9 - - + -
1904J GLU* 3.5 29.6 - - + +
1920J SER* 3.2 9.2 + - - +
1921J TYR* 1.3 78.4 - - - +
1923J SER* 1.4 58.8 + - - +
1925J ARG* 3.1 5.4 + - - +
1926J ALA* 2.9 27.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1923 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C ASN* 3.1 23.2 + - - +
511C HIS* 3.7 28.3 + - - +
512C GLN* 3.6 4.5 + - - +
1904J GLU* 2.6 25.0 + - - -
1920J SER* 3.2 23.5 + - - -
1921J TYR 3.2 1.2 - - - -
1922J VAL* 1.4 73.9 - - - +
1924J GLN* 1.3 59.4 + - - +
1925J ARG 3.2 1.2 + - - -
1926J ALA* 3.9 1.9 - - - +
1929J VAL* 3.5 21.3 - - - +
2412J GOL 4.3 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1924 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C HIS* 4.6 12.6 - - + +
512C GLN* 3.3 21.1 + - - +
1891J LEU* 4.0 10.3 - - + +
1895J ASN* 5.1 0.9 - - - +
1919J HIS* 3.2 32.5 + - - -
1920J SER 4.2 4.3 - - - +
1921J TYR* 3.0 27.1 + - - +
1923J SER* 1.3 76.3 - - - +
1925J ARG* 1.3 57.8 + - - +
2412J GOL 5.6 2.4 - - - +
2314L GLU* 5.1 3.5 - - - +
2316L PHE* 3.1 33.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1925 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C GLN* 3.5 6.0 + - - +
1891J LEU* 3.6 14.1 - - + +
1894J LEU* 3.4 35.6 + - + -
1895J ASN* 3.4 31.1 + - - +
1897J CYS* 3.0 23.0 + - - +
1898J ASP* 5.0 0.6 - - - +
1899J GLY 4.6 3.2 - - - +
1900J LEU 2.9 23.8 + - - +
1902J VAL* 3.8 14.0 - - + +
1922J VAL 3.1 4.4 + - - +
1924J GLN* 1.3 80.8 - - - +
1926J ALA* 1.3 70.0 + - - +
1927J ASP* 3.1 27.3 + - - +
----------------------------------------------------------
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