Contacts of the helix formed by residues 903 - 910 (chain D) in PDB entry 3BBT
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 GLU 903 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899D ILE* 4.5 5.4 - - + +
900D PRO* 3.3 40.4 + - + +
901D THR 3.0 1.2 - - - -
902D ARG* 1.3 77.4 - - - +
904D ILE* 1.3 60.7 - - - +
906D ASP* 3.0 23.6 - - - +
907D LEU* 3.3 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 904 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859D ILE* 5.0 9.6 - - + +
860D LYS* 3.6 46.4 - - + +
867D ILE* 5.7 0.4 - - + -
896D TYR* 4.3 33.2 - - + -
899D ILE* 4.3 10.1 - - + +
900D PRO 3.5 9.9 - - - +
901D THR* 3.5 19.3 - - + +
903D GLU* 1.3 77.0 - - - +
905D PRO* 1.4 69.3 - - + +
907D LEU* 3.1 9.7 + - + +
908D LEU* 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 905 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859D ILE* 5.2 3.4 - - + -
864D LEU* 3.6 13.4 - - + +
867D ILE* 4.6 21.1 - - + -
868D HIS* 4.2 24.5 - - + +
901D THR 3.5 12.1 - - - +
902D ARG* 3.5 17.3 - - - +
903D GLU 3.6 0.4 - - - -
904D ILE* 1.4 92.9 - - + +
906D ASP* 1.3 60.6 + - - +
908D LEU* 3.3 8.3 + - + +
909D GLU* 3.2 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 906 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902D ARG 3.9 2.6 - - - +
903D GLU* 3.0 29.1 - - - +
905D PRO* 1.3 78.8 - - - +
907D LEU* 1.3 62.7 + - - +
909D GLU* 3.3 18.1 + - + +
910D LYS* 3.2 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 907 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896D TYR* 5.8 4.7 - - + -
899D ILE* 3.7 35.9 - - + -
903D GLU* 3.3 35.2 + - + +
904D ILE* 3.1 14.0 + - + +
906D ASP* 1.3 77.4 - - - +
908D LEU* 1.3 63.4 + - + +
910D LYS* 3.4 18.8 + - + +
912D GLU* 3.3 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 908 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859D ILE 6.0 0.2 - - - +
862D MET 4.9 2.5 - - - +
864D LEU* 3.9 27.7 - - + +
867D ILE* 4.4 12.1 - - + -
879D TRP* 3.7 29.6 - - + -
896D TYR* 3.6 29.2 - - + +
904D ILE* 2.9 33.4 + - + +
905D PRO* 3.3 6.7 + - + +
907D LEU* 1.3 75.4 - - - +
909D GLU* 1.3 59.5 + - - +
911D GLY* 3.0 10.6 + - - -
912D GLU 3.8 14.4 - - - +
913D ARG* 2.8 34.0 + - - +
934D ILE* 5.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 909 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864D LEU* 4.0 21.8 - - + +
868D HIS* 4.3 17.3 + - - -
905D PRO 3.2 15.4 + - - +
906D ASP* 3.6 18.7 - - - +
907D LEU 3.3 0.4 - - - -
908D LEU* 1.3 76.2 - - - +
910D LYS* 1.3 57.8 + - + +
911D GLY* 3.1 5.0 + - - -
934D ILE* 5.5 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 910 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906D ASP* 3.2 34.4 + - - +
907D LEU* 3.7 18.7 - - + +
908D LEU 3.2 0.8 - - - -
909D GLU* 1.3 74.3 - - + +
911D GLY* 1.3 58.9 + - - +
912D GLU* 3.3 21.6 + - - +
----------------------------------------------------------
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