Contacts of the helix formed by residues 856 - 869 (chain C) in PDB entry 2X36
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 ALA 856 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C VAL* 5.5 4.5 - - + -
810C MET* 4.5 8.7 - - + -
813C SER* 5.6 0.4 - - - +
844C VAL* 4.9 7.9 - - + -
852C ASP 4.1 0.6 + - - +
853C GLY 3.2 14.5 + - - +
854C PRO 3.1 0.6 - - - -
855C SER* 1.4 77.7 + - - +
857C GLY* 1.3 62.5 + - - +
858C CYS 3.5 1.1 - - - -
859C THR* 3.2 15.0 + - - -
860C ILE* 3.0 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 857 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813C SER* 4.8 7.5 + - - -
817C ALA* 4.1 6.6 - - - +
854C PRO 3.1 13.1 + - - -
855C SER 3.2 2.2 - - - -
856C ALA* 1.3 76.7 - - - +
858C CYS* 1.3 63.1 + - - +
860C ILE* 3.1 18.7 + - - +
861C VAL* 3.2 17.5 + - - +
881C GLY 3.7 3.6 - - - -
883C VAL* 3.6 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 858 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855C SER 4.2 0.7 - - - -
857C GLY* 1.3 71.4 - - - +
859C THR* 1.3 69.7 + - - +
861C VAL* 3.6 2.6 + - - +
862C THR* 2.8 32.9 + - - -
879C MET* 3.5 23.3 - - - -
880C THR* 3.3 37.7 - - - -
881C GLY* 2.9 18.3 + - - +
883C VAL* 3.3 14.8 - - + +
889C ILE* 4.8 0.4 - - + -
939C TYR* 4.0 7.8 - - + -
942C ILE* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 859 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765C VAL* 3.8 19.7 - - + +
766C MET 3.9 1.1 - - - +
767C GLY* 3.7 24.8 - - - +
780C VAL* 3.5 26.5 - - + -
855C SER 4.6 0.3 + - - -
856C ALA* 3.2 15.9 + - - -
858C CYS* 1.3 80.8 - - - +
860C ILE* 1.3 57.4 + - - +
862C THR* 3.5 2.0 + - - -
863C ALA* 3.0 28.5 + - - +
879C MET* 3.5 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 860 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C VAL* 4.6 7.9 - - + -
810C MET* 5.0 4.5 - - + -
813C SER* 5.2 2.2 - - - +
814C ALA* 4.4 19.1 - - + +
817C ALA* 3.6 17.0 - - + -
842C LEU* 3.7 31.2 - - + -
844C VAL* 4.0 23.3 - - + -
856C ALA* 3.0 28.2 + - + +
857C GLY* 3.1 9.4 + - - +
859C THR* 1.3 74.3 - - - +
861C VAL* 1.3 65.4 + - - +
863C ALA* 3.4 6.2 + - - +
864C LEU* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 861 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817C ALA* 3.9 21.1 - - + +
820C PHE* 3.9 29.2 - - + -
821C ALA* 4.1 14.8 - - + -
857C GLY 3.2 14.5 + - - +
858C CYS 3.8 6.1 - - - +
860C ILE* 1.3 75.4 - - - +
862C THR* 1.3 60.2 + - - +
864C LEU* 3.1 3.2 + - - +
865C LEU* 2.7 42.2 + - + +
883C VAL* 4.6 12.3 - - + -
939C TYR* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 862 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765C VAL* 4.1 5.4 - - + -
858C CYS 2.8 21.5 + - - -
859C THR 3.6 4.5 - - - -
861C VAL* 1.3 80.9 - - - +
863C ALA* 1.3 57.6 + - - +
865C LEU* 4.5 1.8 - - - +
866C SER* 2.8 28.8 + - - -
873C VAL* 3.9 15.7 - - + -
879C MET* 3.4 19.7 - - + +
939C TYR* 2.9 20.0 + - - +
942C ILE* 4.2 0.3 - - - +
946C ALA* 4.0 10.3 - - + -
947C PHE* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 863 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763C GLY* 3.5 28.9 - - - +
765C VAL* 3.6 14.1 - - + +
780C VAL* 3.7 21.8 - - + -
782C THR* 3.5 12.7 + - + +
859C THR 3.0 14.8 + - - +
860C ILE 3.6 8.5 - - - +
862C THR* 1.3 74.6 - - - +
864C LEU* 1.3 58.2 + - - +
866C SER* 3.9 1.1 - - - -
867C LEU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 864 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C THR* 3.8 22.9 - - + -
800C LEU* 4.5 15.7 - - + -
817C ALA 4.0 4.0 - - - +
818C TYR* 3.7 42.8 - - + +
821C ALA* 3.9 17.5 - - + -
835C LEU* 4.0 11.1 - - + +
840C ILE* 4.3 26.2 - - + +
842C LEU* 5.2 0.9 - - + -
860C ILE* 3.0 25.4 + - + +
861C VAL 3.5 5.8 - - - +
863C ALA* 1.3 74.8 - - - +
865C LEU* 1.3 57.2 + - - +
867C LEU* 3.8 5.4 - - + +
868C ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 865 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821C ALA* 3.5 27.4 - - + +
824C PHE* 3.5 21.8 - - + -
825C LEU* 3.7 26.9 - - + -
835C LEU* 4.4 3.1 - - + -
861C VAL* 2.7 29.2 + - + +
862C THR 4.0 2.2 - - - +
864C LEU* 1.3 71.1 - - - +
866C SER* 1.3 60.3 + - - +
868C ALA* 3.2 4.6 + - - +
869C MET* 2.9 48.4 + - + +
939C TYR* 3.5 38.1 - - + +
943C PHE* 3.8 9.0 - - + -
947C PHE* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 866 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762C PRO* 3.4 3.8 - - - +
763C GLY* 2.8 20.2 + - - -
764C VAL 4.4 1.0 + - - -
862C THR 2.8 21.6 + - - -
863C ALA* 3.9 4.5 - - - -
865C LEU* 1.3 74.1 - - - +
867C LEU* 1.3 56.7 + - - +
869C MET* 3.5 1.7 + - - -
870C GLY* 3.0 7.3 + - - -
871C ARG 2.6 50.8 + - - +
872C PRO* 3.9 2.6 - - - +
873C VAL* 4.1 9.9 - - - +
947C PHE* 3.5 19.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 867 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762C PRO* 4.4 19.5 - - + +
763C GLY* 3.7 12.1 - - - +
782C THR* 3.7 20.0 - - - +
783C SER* 3.9 28.9 - - - +
784C LEU 4.9 1.8 - - - +
834C TYR* 3.4 33.3 - - + +
840C ILE* 4.2 11.0 - - + -
863C ALA 3.1 15.5 + - - +
864C LEU* 3.8 4.7 - - - +
866C SER* 1.3 81.9 + - - +
868C ALA* 1.3 62.9 + - - +
870C GLY* 3.3 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 868 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825C LEU* 4.0 11.4 - - + -
832C ASN* 2.9 22.3 + - - +
834C TYR* 3.3 40.6 - - + +
835C LEU* 3.9 15.7 - - + -
864C LEU 3.0 17.6 + - - +
865C LEU* 3.2 5.4 + - - +
867C LEU* 1.3 78.9 - - - +
869C MET* 1.3 56.4 + - - +
870C GLY 3.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 869 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825C LEU* 4.3 16.8 - - + -
828C HIS* 4.0 9.0 - - + -
829C ALA* 6.0 1.6 - - + -
832C ASN* 4.2 7.4 - - - +
865C LEU* 2.9 33.2 + - + +
866C SER 4.1 0.2 - - - +
868C ALA* 1.3 76.8 - - - +
870C GLY* 1.3 63.3 + - - +
871C ARG* 3.3 19.5 + - + +
943C PHE* 3.6 32.5 - - + -
947C PHE* 3.7 26.7 - - + -
950C GLU* 3.7 28.0 - - - +
----------------------------------------------------------
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