Contacts of the helix formed by residues 894 - 905 (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 GLY 894 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C TRP* 3.4 32.9 - - - -
893C GLY* 1.3 72.2 - - - -
895C ILE* 1.3 60.2 + - - +
896C LYS 3.4 2.5 - - - -
897C GLU* 3.2 17.2 + - - -
898C LYS* 2.7 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 895 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C THR* 4.8 1.8 - - + -
892C VAL* 3.8 25.6 - - + +
893C GLY 4.0 2.0 - - - +
894C GLY* 1.3 77.2 - - - +
896C LYS* 1.3 59.8 + - - +
897C GLU* 4.3 0.2 + - - -
898C LYS* 3.8 5.1 - - + +
899C THR* 2.5 42.3 + - - +
912C LEU* 4.0 33.2 - - + -
916C ASN* 3.7 31.6 - - + +
919C ASP* 3.6 30.5 - - + +
920C PHE* 4.1 22.2 - - - +
923C LEU* 4.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 896 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C ILE* 1.3 73.2 - - - +
897C GLU* 1.3 83.7 + - + +
899C THR* 2.9 13.3 + - - -
900C ILE* 3.0 39.4 + - + +
923C LEU* 3.8 31.8 - - + +
927C ILE* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 897 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770C TRP* 4.1 24.2 + - + +
774C GLY* 3.8 35.7 - - - +
775C GLY* 3.5 14.0 + - - +
894C GLY* 3.2 19.3 + - - +
896C LYS* 1.3 94.2 - - + +
898C LYS* 1.3 66.5 + - + +
899C THR 3.1 0.2 + - - -
900C ILE* 3.4 8.0 + - + +
901C ALA 3.0 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 898 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C LEU* 3.4 47.2 - - + +
769C ALA 3.9 12.8 - - - +
770C TRP* 3.7 4.7 - - - +
852C ASP* 2.9 38.6 + - - -
855C SER* 3.3 3.0 + - - -
880C THR* 2.7 35.1 + - + +
892C VAL* 3.3 11.3 - - - +
893C GLY 2.9 24.5 + - - +
894C GLY 2.7 18.8 + - - +
895C ILE* 4.0 6.1 - - + +
897C GLU* 1.3 74.7 - - - +
899C THR* 1.3 57.7 + - - +
901C ALA* 3.5 4.7 + - - +
902C ALA* 3.0 21.3 + - - +
910C ILE* 6.1 0.2 - - - -
912C LEU* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 899 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C ILE* 2.5 34.8 + - - +
896C LYS 2.9 4.6 + - - -
898C LYS* 1.3 76.1 - - - +
900C ILE* 1.3 67.4 + - - +
902C ALA* 3.3 6.7 - - - +
903C LYS* 3.0 23.7 + - - +
910C ILE* 4.3 11.9 - - + +
912C LEU* 4.8 0.5 - - - +
920C PHE* 4.0 20.9 - - + -
923C LEU* 3.9 9.3 - - + +
927C ILE* 3.9 17.2 - - + +
928C THR* 4.6 1.1 - - - +
931C LEU* 3.6 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 900 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896C LYS* 3.0 39.2 + - + +
897C GLU* 3.9 7.6 - - - +
899C THR* 1.3 76.7 - - - +
901C ALA* 1.3 50.5 + - - +
903C LYS* 3.0 8.2 + - + +
904C ARG* 2.7 45.9 + - + +
927C ILE* 3.8 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 901 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C LEU* 5.1 0.4 - - + -
775C GLY 3.3 34.8 - - - -
776C SER* 3.4 14.8 - - - +
777C THR* 3.0 13.5 + - - +
897C GLU 3.0 11.2 + - - +
898C LYS* 3.8 4.5 - - - +
900C ILE* 1.3 74.2 - - - +
902C ALA* 1.3 65.8 + - - +
904C ARG* 3.2 26.2 + - - +
905C ALA* 3.1 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 902 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768C LEU* 4.1 9.8 - - + +
777C THR* 3.7 4.6 + - - -
898C LYS 3.0 15.8 + - - +
899C THR* 3.3 13.0 - - - +
901C ALA* 1.3 75.1 - - - +
903C LYS* 1.3 63.4 + - - +
905C ALA 3.0 6.1 + - - -
907C VAL* 2.9 47.2 + - + +
910C ILE* 4.0 20.4 - - + -
931C LEU* 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 903 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899C THR 3.0 10.6 + - - +
900C ILE* 3.6 9.2 - - + +
902C ALA* 1.3 78.0 - - - +
904C ARG* 1.3 64.9 + - - +
905C ALA 2.8 2.1 + - - -
906C GLY* 3.0 12.7 + - - -
907C VAL 4.6 7.0 - - - +
926C PHE* 4.1 13.9 - - + +
927C ILE* 2.9 27.6 - - - +
929C GLU 2.4 31.6 + - - +
930C GLY* 3.8 6.5 - - - -
931C LEU* 3.7 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 904 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C GLY* 2.6 31.3 + - - +
776C SER* 3.7 9.7 + - - +
777C THR* 4.7 1.2 + - - +
900C ILE* 2.7 27.9 + - + +
901C ALA* 3.2 46.3 + - - +
903C LYS* 1.3 73.3 - - - +
905C ALA* 1.3 55.8 + - + +
906C GLY 3.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 905 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755C ARG* 3.3 38.7 + - + +
777C THR* 3.8 23.6 - - + +
901C ALA 3.1 12.6 + - - +
902C ALA 3.0 7.0 + - - +
903C LYS 2.8 2.0 + - - -
904C ARG* 1.3 75.7 - - + +
906C GLY* 1.3 62.5 + - - +
907C VAL* 4.4 5.4 - - + -
----------------------------------------------------------
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