Contacts of the helix formed by residues 790 - 803 (chain A) in PDB entry 4K6J
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 790 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A LEU* 3.4 8.7 - - - -
769A LYS* 5.5 6.3 - - - +
786A LEU 5.3 0.4 - - - +
787A GLU 3.6 22.7 - - - +
788A ASN* 2.9 8.0 + - - -
789A ILE* 1.3 77.3 - - - +
791A THR* 1.3 60.0 + - - +
792A GLY* 3.6 3.6 + - - -
793A HIS* 3.3 25.3 + - - +
794A LEU* 3.1 30.3 + - - +
849A TRP* 5.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A GLN* 3.9 2.1 + - - +
717A SER* 3.0 39.1 + - - +
718A LEU* 3.2 22.5 + - - +
721A ALA* 4.2 4.6 - - + +
747A LEU* 3.4 31.2 - - + +
750A LEU* 4.4 11.0 - - + -
752A GLN* 5.9 2.7 - - - -
790A THR* 1.3 73.1 - - - +
792A GLY* 1.3 60.9 + - - +
795A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A LEU 4.6 6.5 + - - -
748A LEU* 4.1 0.7 - - - +
750A LEU 5.8 0.7 - - - -
790A THR* 3.4 4.3 + - - -
791A THR* 1.3 77.3 - - - +
793A HIS* 1.3 61.5 - - - +
795A ALA* 4.7 0.9 - - - -
796A MET* 3.1 23.6 + - - +
849A TRP* 4.3 5.2 - - - -
853A ARG* 3.4 39.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A LEU* 5.1 6.7 - - + -
787A GLU 5.2 0.6 + - - -
788A ASN* 3.0 67.3 + - + +
790A THR* 3.3 16.7 + - - +
791A THR 3.2 0.6 - - - -
792A GLY* 1.3 76.6 - - - +
794A LEU* 1.3 57.5 + - + +
796A MET* 3.2 14.4 + - + +
797A GLU* 2.8 43.0 + - + +
849A TRP* 3.2 43.9 - + - -
856A ARG* 5.4 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A LEU* 3.6 26.5 - - + -
721A ALA* 3.8 18.4 - - + -
722A ALA* 3.6 26.0 - - + +
725A TYR* 3.9 29.0 - - + +
772A ILE* 3.8 13.2 - - + -
776A CYS* 4.1 7.2 - - - -
784A LEU* 4.1 23.3 - - + -
788A ASN 5.0 0.7 - - - +
789A ILE* 4.3 6.5 - - + -
790A THR 3.1 17.2 + - - +
793A HIS* 1.3 74.6 - - - +
795A ALA* 1.3 55.7 + - - +
797A GLU* 3.9 3.9 - - + +
798A THR* 2.7 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ALA* 3.9 2.8 - - + +
744A MET* 3.7 28.2 - - - +
747A LEU* 4.0 5.8 - - + -
748A LEU* 3.8 31.9 - - - +
791A THR 2.9 17.7 + - - +
792A GLY 4.1 0.7 - - - +
794A LEU* 1.3 75.8 - - - +
796A MET* 1.3 63.3 + - - +
798A THR* 3.3 3.1 + - - -
799A LEU* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A LEU* 4.0 8.0 - - + +
792A GLY 3.1 20.3 + - - +
793A HIS* 3.4 9.4 - - + +
795A ALA* 1.3 77.4 - - - +
797A GLU* 1.3 78.1 + - - +
799A LEU* 3.1 5.6 + - - +
800A LEU* 2.9 45.2 + - + +
849A TRP* 4.0 13.7 - - + -
853A ARG* 3.7 41.3 - - + +
856A ARG* 3.3 50.3 - - + +
857A VAL* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A TYR* 3.5 29.6 + - + -
782A LYS* 3.5 36.4 + - - -
784A LEU* 4.3 19.7 - - + +
793A HIS* 2.8 28.9 + - + +
794A LEU* 3.9 6.1 - - + +
796A MET* 1.3 95.0 - - + +
798A THR* 1.3 58.4 + - - +
800A LEU* 3.8 13.4 - - - +
801A SER* 2.9 30.5 + - - -
856A ARG* 4.5 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ALA 3.4 5.5 + - - -
724A MET* 3.8 42.8 - - + +
725A TYR* 3.2 27.0 + - - +
728A SER* 4.3 0.8 + - - +
744A MET* 3.9 10.7 - - + -
794A LEU 2.7 22.0 + - - -
795A ALA* 3.4 6.6 - - - -
796A MET 3.1 0.4 - - - -
797A GLU* 1.3 77.5 - - - +
799A LEU* 1.3 58.5 + - - +
801A SER* 3.2 3.9 + - - -
802A LEU* 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A LEU* 4.5 13.2 - - + -
744A MET* 4.2 21.5 - - + +
745A ILE* 4.6 10.8 - - + -
748A LEU* 3.7 37.5 - - + -
795A ALA 3.0 20.2 + - - +
796A MET 3.1 3.8 + - - +
798A THR* 1.3 74.4 - - - +
800A LEU* 1.3 62.4 + - - +
802A LEU* 3.6 8.9 + - + -
803A THR* 2.8 31.9 + - - +
815A LEU* 4.5 26.9 - - + -
824A ILE* 4.9 1.1 - - + -
857A VAL* 3.8 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A LYS* 6.0 0.2 - - - +
796A MET* 2.9 49.3 + - + +
797A GLU* 3.8 16.6 - - - +
799A LEU* 1.3 75.0 - - - +
801A SER* 1.3 59.3 + - - +
803A THR* 3.2 4.7 + - - -
804A SER* 3.0 31.1 + - - -
856A ARG* 3.6 40.8 - - + +
857A VAL* 4.4 4.5 - - + -
859A GLU* 5.8 0.2 - - - +
860A SER* 3.7 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A TYR* 4.2 9.2 - - - -
728A SER* 2.8 44.3 + - - +
729A ARG* 4.7 0.2 - - - -
780A HIS* 3.9 7.6 + - - -
797A GLU 2.9 19.3 + - - -
798A THR 3.5 1.1 - - - -
800A LEU* 1.3 79.4 - - - +
802A LEU* 1.3 59.4 + - - +
804A SER* 3.1 21.5 + - - -
807A ALA* 3.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A MET* 4.6 2.9 - - - -
728A SER* 3.7 23.1 - - - +
730A ASP 5.4 1.1 - - - +
732A LEU* 3.9 20.6 - - + +
736A LEU* 3.8 18.8 - - + -
741A LEU* 4.3 19.5 - - + -
798A THR* 2.9 33.2 + - + +
799A LEU* 4.0 13.7 - - + +
800A LEU 3.3 0.4 - - - -
801A SER* 1.3 76.5 - - - +
803A THR* 1.3 61.2 + - + +
807A ALA* 3.1 17.5 - - + +
808A GLY 4.8 1.4 - - - +
811A PHE* 3.6 45.7 + - + +
812A LYS 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A LEU* 2.8 22.0 + - - +
800A LEU* 3.2 3.6 + - - -
802A LEU* 1.3 84.1 - - + +
804A SER* 1.3 64.4 + - - +
807A ALA* 4.5 0.2 - - - -
808A GLY 4.6 1.3 - - - -
811A PHE* 4.2 3.1 - - + -
812A LYS* 3.5 43.2 - - - +
815A LEU* 3.8 28.5 - - + -
857A VAL* 5.5 0.8 - - + +
860A SER* 2.7 35.3 + - - +
861A VAL* 4.0 10.3 - - + +
----------------------------------------------------------
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