Contacts of the helix formed by residues 795 - 811 (chain D) in PDB entry 2BKU
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 795 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B GLU* 5.2 6.6 - - - +
752D GLU* 4.6 11.3 - - - +
791D GLN 4.0 13.2 - - - +
792D LEU 3.1 14.7 + - - +
793D TYR 3.5 3.9 - - - +
794D SER* 1.3 81.2 + - - +
796D ASP* 1.3 67.2 + - - +
797D ALA* 3.4 9.3 + - - +
798D THR* 3.1 15.3 + - - +
799D SER 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 796 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ALA* 3.5 14.7 - - + +
794D SER 3.4 4.8 + - - +
795D GLU* 1.3 73.3 + - - +
797D ALA* 1.3 64.1 - - - +
799D SER* 3.2 2.8 + - - -
800D ARG* 3.0 33.6 + - - +
839D LEU 4.9 5.8 - - - +
840D PHE* 3.4 17.4 - - + -
841D SER* 2.7 40.2 + - - -
844D THR* 2.4 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 797 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B ASP* 3.5 28.9 - - + +
797B ALA* 4.2 18.5 - - + +
800B ARG* 3.1 32.3 + - - +
841B SER* 5.1 0.4 - - - +
795D GLU* 3.4 8.8 + - - +
796D ASP* 1.3 79.0 + - - +
798D THR* 1.3 62.9 - - - +
800D ARG* 4.7 1.1 - - - +
801D ALA* 3.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 798 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752D GLU* 3.6 26.5 + - + +
755D LEU* 3.6 24.5 - - + +
782D PHE* 6.4 0.2 - - + -
786D VAL* 4.1 12.1 - - + -
792D LEU* 3.2 45.5 + - + +
795D GLU* 3.1 11.2 + - - +
797D ALA* 1.3 79.9 - - - +
799D SER* 1.3 56.9 + - - +
801D ALA* 3.5 0.6 + - - -
802D ALA* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 799 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793D TYR* 2.4 34.8 + - - +
795D GLU 3.0 7.1 + - - -
796D ASP 3.2 6.0 + - - -
798D THR* 1.3 75.2 - - - +
800D ARG* 1.3 59.2 + - - +
802D ALA* 3.3 0.7 + - - +
803D VAL* 2.8 36.1 + - - +
830D TYR* 2.9 24.6 + - - -
834D THR* 4.7 4.5 - - - -
840D PHE* 3.7 17.9 - - - -
844D THR* 4.5 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 800 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ALA* 3.1 32.1 + - - +
800B ARG* 3.4 51.0 - - - +
801B ALA 3.8 2.8 - - - +
796D ASP* 3.0 32.6 + - - +
799D SER* 1.3 76.2 - - - +
801D ALA* 1.3 57.0 + - - +
803D VAL* 3.3 9.7 - - - +
804D GLY* 2.8 26.9 + - - -
841D SER* 3.7 5.5 + - - -
843D ALA* 3.4 43.2 - - - +
844D THR* 3.1 30.6 + - + +
847D THR* 3.4 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 801 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ARG* 3.6 8.7 - - - +
841B SER* 6.0 1.6 - - - +
843B ALA* 4.2 13.0 - - + -
755D LEU* 3.8 22.2 - - + -
759D VAL* 4.2 10.7 - - + +
797D ALA 3.1 17.4 + - - +
798D THR* 3.8 3.8 - - - +
800D ARG* 1.3 74.5 - - - +
802D ALA* 1.3 66.6 + - - +
804D GLY* 3.0 2.9 + - - -
805D LEU* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 802 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755D LEU* 4.3 4.0 - - + +
783D ILE* 4.4 9.0 - - + +
786D VAL* 3.9 22.0 - - + -
798D THR 2.9 19.5 + - - +
799D SER 3.5 3.6 - - - +
801D ALA* 1.3 75.3 - - - +
803D VAL* 1.3 57.8 - - - +
805D LEU* 3.0 32.8 + - - +
806D ILE* 3.2 15.6 + - - +
830D TYR* 3.7 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 803 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799D SER 2.8 27.6 + - - +
800D ARG* 3.3 13.5 - - - +
802D ALA* 1.3 73.4 - - - +
804D GLY* 1.3 63.1 + - - +
806D ILE* 3.4 12.4 - - + +
807D GLY 3.3 5.7 + - - -
830D TYR* 4.2 8.7 - - + -
831D ILE* 4.2 22.0 - - + -
834D THR* 4.4 11.4 - - + +
844D THR 4.6 0.2 - - - +
847D THR* 4.0 12.3 - - + +
848D ALA* 3.8 23.3 - - + +
851D ALA* 3.2 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 804 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800D ARG 2.8 18.1 + - - -
801D ALA* 3.0 5.4 + - - -
803D VAL* 1.3 76.2 - - - +
805D LEU* 1.3 58.7 + - - +
807D GLY* 3.3 2.1 + - - -
808D ASP* 2.8 40.1 + - - +
847D THR* 3.7 15.7 - - - -
850D TRP* 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 805 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755D LEU* 3.6 26.2 - - + -
758D TYR* 3.6 33.0 - - + +
759D VAL* 3.7 17.7 - - + -
762D VAL* 3.7 19.5 - - + -
779D ILE* 4.2 17.5 - - + -
782D PHE* 5.5 1.8 - - + -
783D ILE* 4.2 15.7 - - + -
801D ALA 2.8 14.0 + - - +
802D ALA* 3.2 10.8 - - - +
804D GLY* 1.3 73.5 - - - +
806D ILE* 1.3 67.6 + - - +
808D ASP* 4.5 3.4 - - + -
809D ILE* 2.8 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 806 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780D PHE* 4.4 9.9 - - + -
783D ILE* 3.9 25.6 - - + -
802D ALA 3.2 6.9 + - - +
803D VAL* 3.4 27.6 - - + +
805D LEU* 1.3 77.3 - - - +
807D GLY* 1.3 59.7 + - - +
809D ILE* 5.0 0.2 - - - -
810D ALA 3.4 0.5 + - - -
822D TYR* 2.5 54.1 + - + -
826D TRP* 5.8 0.7 - - + -
827D VAL* 4.1 23.6 - - + -
830D TYR* 3.8 24.2 - - + -
831D ILE* 4.2 17.5 - - + -
851D ALA* 4.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 807 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803D VAL 3.3 7.9 + - - -
804D GLY 3.3 2.0 + - - -
805D LEU 3.1 0.6 - - - -
806D ILE* 1.3 79.3 - - - +
808D ASP* 1.3 58.0 + - - +
810D ALA* 3.3 5.7 - - - +
811D ALA* 3.0 26.3 + - - +
850D TRP* 3.8 18.6 - - - -
851D ALA* 3.9 19.0 - - - +
854D GLN* 3.8 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 808 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762D VAL* 3.9 21.4 - - + +
766D HIS* 5.4 3.5 - - + -
804D GLY* 2.8 25.4 + - - +
805D LEU* 4.1 1.5 - - + +
807D GLY* 1.3 70.2 - - - +
809D ILE* 1.3 65.2 + - - +
811D ALA* 3.2 16.9 + - - +
812D MET* 3.4 17.5 + - - +
850D TRP* 3.3 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 809 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762D VAL* 3.6 33.9 - - + -
772D LEU* 4.6 6.1 - - + -
776D VAL* 4.4 9.2 - - + -
779D ILE* 3.8 32.8 - - + -
780D PHE* 4.1 18.8 - - + -
783D ILE* 5.2 0.2 - - + -
805D LEU* 2.8 26.9 + - + +
808D ASP* 1.3 70.2 - - - +
810D ALA* 1.3 63.7 + - - +
812D MET* 3.0 15.5 + - - +
813D PHE* 3.4 23.6 - - + -
818D ILE* 3.6 17.7 - - + -
822D TYR* 3.4 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 810 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806D ILE 3.4 3.6 + - - +
807D GLY 3.3 10.9 + - - +
809D ILE* 1.3 74.5 - - - +
811D ALA* 1.3 61.2 + - - +
812D MET 3.1 1.7 + - - -
813D PHE 3.2 9.0 + - - -
814D PRO* 4.1 2.1 - - - +
818D ILE* 4.6 0.4 - - - -
822D TYR* 2.7 35.5 + - + +
854D GLN* 3.8 26.2 - - + +
858D GLN* 2.9 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 811 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766D HIS* 4.6 18.7 + - + +
807D GLY 3.0 10.9 + - - +
808D ASP* 3.6 11.7 - - - +
809D ILE 3.2 1.0 - - - -
810D ALA* 1.3 75.1 - - - +
812D MET* 1.3 58.3 + - - +
814D PRO* 4.4 9.8 - - - +
850D TRP* 4.3 14.1 - - + -
854D GLN* 3.6 20.8 + - - +
----------------------------------------------------------
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