Contacts of the helix formed by residues 921 - 925 (chain E) 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 TYR 921 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686D THR* 5.5 2.3 - - + +
716D PHE* 4.0 30.0 - + + +
884E SER 2.8 9.0 + - - +
885E HIS 3.5 26.5 - - - -
886E THR* 3.9 20.2 - - - -
887E SER 3.9 15.5 - - - +
888E VAL* 3.7 31.3 - - + +
891E LEU* 3.4 25.5 - - + +
919E HIS* 3.5 18.2 - + - -
920E SER* 1.3 69.7 - - - +
922E VAL* 1.3 66.1 + - + +
924E GLN* 3.1 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 922 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878E ILE* 4.5 4.9 - - + -
880E PRO* 3.7 25.6 - - + -
883E TYR 4.8 3.4 - - - +
884E SER* 4.4 8.1 - - - -
887E SER 5.2 1.8 - - - +
890E ILE* 3.8 26.7 - - + -
891E LEU* 4.9 8.3 - - - +
894E LEU* 3.8 20.0 - - + -
904E GLU* 3.7 27.8 - - + +
920E SER* 3.2 8.6 + - - +
921E TYR* 1.3 77.8 - - - +
923E SER* 1.3 57.7 + - - +
924E GLN 3.0 0.7 - - - -
925E ARG* 3.1 5.2 + - - +
926E ALA* 2.9 28.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 923 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904E GLU* 2.5 26.1 + - - -
920E SER* 3.3 23.6 + - - -
921E TYR 3.1 1.0 - - - -
922E VAL* 1.3 76.4 - - - +
924E GLN* 1.3 61.4 + - - +
925E ARG 3.1 0.8 + - - -
926E ALA 4.0 2.0 - - - +
929E VAL* 3.7 22.8 - - - +
2419E GOL 4.4 2.4 + - - -
2309L ASN* 3.1 25.6 + - - +
2311L HIS* 3.9 23.4 + - - +
2312L GLN* 3.4 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 924 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714D GLU* 5.4 3.2 - - - +
716D PHE* 3.1 36.8 - - - -
891E LEU* 3.8 13.4 - - + +
895E ASN* 5.1 1.4 - - - +
919E HIS* 3.1 26.3 + - - -
920E SER 4.2 4.9 - - - +
921E TYR* 3.4 23.6 - - - +
922E VAL 3.0 1.2 - - - -
923E SER* 1.3 79.8 - - - +
925E ARG* 1.3 57.9 + - - +
2419E GOL 4.7 5.4 - - - -
2311L HIS 4.6 11.4 - - - +
2312L GLN* 3.3 21.2 + - - +
2318L HIS* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 925 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891E LEU* 3.6 13.4 - - + +
894E LEU* 3.3 35.3 + - + -
895E ASN* 3.4 30.9 + - - +
897E CYS 3.1 22.0 + - - -
898E ASP* 5.0 0.8 - - - +
899E GLY 4.5 4.0 - - - +
900E LEU 3.0 24.2 + - - +
902E VAL* 3.8 13.9 - - + +
922E VAL 3.1 4.4 + - - +
924E GLN* 1.3 80.2 - - - +
926E ALA* 1.3 70.2 + - - +
927E ASP* 3.0 26.7 + - - +
2312L GLN* 3.3 6.8 + - - +
----------------------------------------------------------
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