Contacts of the helix formed by residues 824 - 829 (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 GLN 824 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823E ARG* 1.3 111.7 + - + +
825E PRO* 1.3 73.3 - - - +
826E GLU* 3.0 20.0 - - - +
827E ILE* 3.0 26.2 + - + +
828E TYR* 2.9 45.2 + - + -
913E ARG* 5.0 7.3 + - - +
960E CA2 5.3 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 825 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821E GLY 5.7 3.6 - - - +
823E ARG* 3.2 8.9 - - - +
824E GLN* 1.3 92.6 - - - +
826E GLU* 1.3 68.1 + - + +
829E GLY* 2.8 45.5 + - - +
830E SER* 4.4 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 826 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824E GLN* 3.0 28.8 - - - +
825E PRO* 1.3 86.1 - - + +
827E ILE* 1.3 81.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 827 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824E GLN* 3.0 33.3 + - - +
826E GLU* 1.3 99.0 - - + +
828E TYR* 1.3 76.2 + - + +
829E GLY 3.6 0.7 - - - -
907E ILE* 4.2 9.4 - - - +
908E SER* 3.8 31.4 - - - -
913E ARG* 4.7 14.6 - - - +
934E GLY* 5.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 828 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817E LEU* 6.1 0.2 - - + -
820E LEU* 3.8 23.2 - - + +
824E GLN* 2.9 40.2 + - + +
827E ILE* 1.3 88.4 - - + +
829E GLY* 1.3 64.9 + - - +
831E ASP 5.2 0.3 + - - +
907E ILE* 3.7 34.3 - - + +
908E SER* 4.0 7.2 - - - -
913E ARG* 2.7 32.5 + - - -
934E GLY* 6.2 0.2 - - - -
935E VAL* 4.7 9.0 + - - +
960E CA2 3.1 77.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 829 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821E GLY* 4.1 11.3 + - - -
823E ARG 4.7 1.7 - - - +
825E PRO* 2.8 30.6 + - - +
827E ILE 3.6 0.6 - - - -
828E TYR* 1.3 86.9 - - - +
830E SER* 1.3 60.8 + - - -
831E ASP* 3.5 4.7 - - - -
935E VAL* 6.2 0.2 - - - -
----------------------------------------------------------
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