Contacts of the helix formed by residues 765 - 780 (chain A) in PDB entry 1OBH
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 THR 765 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A THR* 3.9 4.8 - - - +
718A ASP* 4.4 4.5 - - - +
758A TYR* 2.7 25.3 + - - +
762A ARG* 4.2 15.9 - - - +
763A PRO* 3.1 29.8 + - + +
764A VAL* 1.3 75.8 - - - +
766A PRO* 1.3 76.5 - - + +
767A VAL* 3.0 17.9 - - - +
768A TYR* 2.9 6.7 + - - +
769A ARG* 2.8 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A THR* 4.0 9.0 - - + -
706A SER* 3.1 28.3 - - - +
707A GLY 3.8 3.3 - - - +
708A VAL 3.5 22.7 - - - +
709A PHE* 4.0 12.1 - - + -
765A THR* 1.3 87.4 - - + +
767A VAL* 1.3 62.9 + - - +
769A ARG* 3.2 5.0 + - + +
770A THR* 3.0 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A PHE* 3.9 23.8 - - + +
714A LEU* 4.0 32.8 - - + -
718A ASP* 4.1 27.6 - - + +
721A LEU* 4.4 8.0 - - + +
722A TYR* 4.3 15.9 - - + +
725A LEU* 5.1 3.4 - - + +
758A TYR* 3.8 9.4 - - - +
765A THR* 3.0 21.1 - - - +
766A PRO* 1.3 79.5 - - - +
768A TYR* 1.3 58.1 + - - +
770A THR* 3.4 2.6 + - - -
771A ALA* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG* 3.1 26.3 + - - +
698A ASP* 2.6 35.7 + - + +
702A LEU* 4.1 5.8 - - + -
721A LEU* 4.1 7.2 - - + -
755A LEU* 3.7 30.1 - - + -
758A TYR* 3.7 26.5 - + + -
759A ARG* 3.6 19.1 - - + -
764A VAL* 3.9 24.9 - - + -
765A THR* 2.9 22.3 + - - +
767A VAL* 1.3 80.4 - - - +
769A ARG* 1.3 64.8 + - - +
771A ALA* 3.0 4.4 + - - +
772A ILE* 3.0 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A LEU* 2.7 58.5 + - + -
703A LEU* 4.3 7.5 + - - +
705A THR* 3.2 27.7 + - + -
706A SER 3.7 1.1 - - - -
707A GLY* 3.6 11.8 - - - +
765A THR 2.8 11.0 + - - +
766A PRO* 3.2 10.7 + - + +
768A TYR* 1.3 78.8 - - - +
770A THR* 1.3 56.6 + - - +
772A ILE* 3.3 4.7 + - - +
773A ARG* 3.0 25.6 + - - +
794A PHE* 4.0 23.4 + - - +
795A TRP* 3.5 25.7 - - + +
1502A SO4 2.9 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A GLY 2.9 27.0 + - - -
709A PHE* 3.4 18.6 - - + -
722A TYR* 6.1 0.7 - - + -
725A LEU* 4.4 9.2 - - + -
726A HIS* 6.5 0.2 - - + -
766A PRO 3.0 6.6 + - - -
767A VAL 3.7 7.9 - - - -
768A TYR 3.2 0.2 - - - -
769A ARG* 1.3 74.0 - - - +
771A ALA* 1.3 60.5 + - - +
773A ARG* 3.2 34.1 + - - +
774A TYR* 2.9 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 771 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU* 4.3 8.1 - - + -
725A LEU* 3.9 19.9 - - + +
751A PHE* 4.1 15.9 - - + -
755A LEU* 4.1 22.4 - - + -
767A VAL 3.0 14.5 + - - +
768A TYR* 3.0 11.2 + - - +
770A THR* 1.3 77.6 - - - +
772A ILE* 1.3 57.6 + - - +
774A TYR* 3.7 1.6 - - - +
775A TYR* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG* 4.8 3.1 - - + -
695A VAL* 4.4 28.0 - - + -
702A LEU* 4.4 18.6 - - + -
755A LEU* 4.0 21.3 - - + -
768A TYR* 3.0 53.5 + - + +
769A ARG* 3.5 8.1 - - - +
771A ALA* 1.3 73.7 - - - +
773A ARG* 1.3 64.9 + - - +
775A TYR* 3.2 5.8 + - + +
776A LEU* 3.1 39.0 + - + +
794A PHE* 5.0 1.8 - - + -
795A TRP* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A GLY* 4.7 2.0 + - - -
769A ARG 3.0 10.7 + - - +
770A THR* 3.5 37.5 + - - +
772A ILE* 1.3 79.3 - - - +
774A TYR* 1.3 84.4 + - - +
776A LEU* 3.3 0.9 + - - +
777A GLN* 3.2 33.5 + - - +
791A TRP* 3.5 31.0 - - + -
795A TRP* 3.5 42.6 - - + +
1502A SO4 2.9 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A LEU* 3.7 35.9 - - + -
726A HIS* 4.0 23.3 + + - -
729A LEU* 4.3 9.2 - - + -
770A THR* 2.9 27.1 + - + +
773A ARG* 1.3 98.9 + - - +
775A TYR* 1.3 61.8 + - - +
777A GLN* 3.2 17.7 + - - +
778A MET* 2.9 38.3 + - + +
805A PRO* 3.7 30.3 - - + -
806A GLU* 3.8 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A PHE* 3.4 23.2 - - - -
691A ILE* 3.9 28.7 - - + +
748A LEU* 2.7 46.8 + - + +
751A PHE* 3.5 28.9 - + - -
752A LEU* 3.6 18.2 - - + +
755A LEU* 4.2 11.0 - - + -
771A ALA 2.9 18.1 + - - +
772A ILE* 3.4 10.5 - - + +
773A ARG 3.2 0.2 - - - -
774A TYR* 1.3 76.3 - - - +
776A LEU* 1.3 67.8 + - + +
778A MET* 3.2 10.3 + - + +
779A LEU* 2.8 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A ILE* 4.9 2.7 - - + -
695A VAL* 5.1 5.2 - - + -
772A ILE* 3.1 26.3 + - + +
773A ARG 3.8 4.5 - - - +
774A TYR 3.3 0.2 - - - -
775A TYR* 1.3 86.6 - - + +
777A GLN* 1.3 61.5 + - - +
779A LEU* 3.4 8.5 + - + -
780A PHE* 3.0 21.0 + - - +
787A ALA* 3.6 24.0 - - - +
790A LEU* 3.9 33.7 - - + +
791A TRP* 3.8 39.7 - - + +
794A PHE* 5.1 1.6 - - + -
795A TRP* 4.1 15.5 - - + -
799A LEU* 3.7 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 3.2 22.9 - - + +
773A ARG* 3.2 25.5 + - - +
774A TYR* 3.2 20.2 + - - +
776A LEU* 1.3 78.2 - - - +
778A MET* 1.3 61.9 + - - +
779A LEU 3.4 0.5 + - - -
780A PHE* 3.4 8.0 + - - +
781A PRO* 3.5 0.2 - - - +
791A TRP* 3.8 10.8 - - + -
799A LEU* 3.7 24.2 - - + -
802A ALA* 3.5 17.7 + - + +
803A GLY 3.0 25.6 + - - +
804A TRP* 3.5 8.3 - - - -
805A PRO* 3.7 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A LEU* 4.4 12.3 - - + -
728A THR* 4.2 15.5 - - + -
729A LEU* 3.7 46.4 - - + +
732A VAL* 4.2 17.9 - - + -
748A LEU* 4.0 16.6 - - + +
751A PHE* 4.8 1.1 - - + -
774A TYR* 2.9 31.7 + - + +
775A TYR* 3.7 19.7 - - + +
777A GLN* 1.3 75.6 - - - +
779A LEU* 1.3 60.8 + - - +
781A PRO* 3.4 5.0 - - - +
782A PHE* 3.3 24.4 - - - -
804A TRP* 3.7 20.4 - - + -
805A PRO* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ILE* 5.3 0.2 - - + -
687A PHE* 4.4 11.4 - - + -
691A ILE* 3.8 42.4 - - + -
748A LEU* 4.2 19.0 - - + +
775A TYR* 2.8 25.0 + - + +
776A LEU* 3.8 9.9 - - + +
777A GLN 3.2 0.2 - - - -
778A MET* 1.3 78.3 - - - +
780A PHE* 1.3 64.0 + - - +
781A PRO 3.3 0.4 - - - -
782A PHE* 2.9 18.7 + - + -
783A ALA* 3.0 39.5 + - + +
786A LEU* 4.8 4.9 - - + -
787A ALA* 4.1 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TRP* 3.9 3.6 - + - -
64A ARG* 3.3 34.4 - - + -
68A MET* 3.6 22.2 - - + -
776A LEU 3.0 12.5 + - - +
777A GLN 3.5 10.1 - - - +
779A LEU* 1.3 75.8 - - - +
781A PRO* 1.3 68.0 - - + +
784A PRO* 3.1 50.6 - - + +
787A ALA* 3.8 6.3 - - - +
788A GLU* 3.5 22.7 - - - -
799A LEU* 3.3 31.4 - - + -
800A PHE* 3.6 40.2 - + - -
----------------------------------------------------------
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