Contacts of the helix formed by residues 855 - 866 (chain C) in PDB entry 2P5G
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 855 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811C TYR* 4.3 10.6 + - + +
815C ILE* 4.0 23.1 - - + -
821C ALA* 4.2 3.1 - - + +
822C PRO* 3.7 26.9 - - - +
853C GLU 3.3 5.2 + - - -
854C ILE* 1.3 73.4 - - - +
856C ASP* 1.3 62.9 + - - +
857C LEU* 3.6 23.4 - - + +
858C ILE* 3.2 26.7 + - + +
859C LYS 2.9 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 856 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854C ILE 3.4 1.7 + - - +
855C THR* 1.3 73.2 + - - +
857C LEU* 1.3 67.1 + - - +
858C ILE 3.1 0.7 + - - -
859C LYS* 3.4 32.0 + - - +
860C ASP* 4.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 857 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814C ALA 5.5 1.8 - - - +
815C ILE* 4.1 11.2 - - + -
818C ASN* 3.6 44.2 - - + +
821C ALA* 3.7 12.6 - - + -
855C THR* 3.6 18.4 - - + +
856C ASP* 1.3 79.6 - - + +
858C ILE* 1.3 66.3 + - + +
860C ASP* 5.4 0.7 + - - +
861C ASP* 5.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 858 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811C TYR* 3.7 32.3 - - + -
814C ALA* 4.1 25.6 - - + +
815C ILE* 4.7 3.4 - - + -
841C PHE* 4.0 20.2 - - + -
846C ILE* 4.0 14.6 - - + -
854C ILE* 3.8 20.2 - - + -
855C THR* 3.7 16.4 - - + +
857C LEU* 1.3 84.6 - - + +
859C LYS* 1.3 67.2 - - - +
860C ASP 3.3 3.4 - - - -
861C ASP* 3.1 10.4 + - - +
862C VAL* 3.1 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 859 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C TYR* 3.6 20.4 - - - +
853C GLU* 2.7 33.1 + - + +
854C ILE* 3.6 28.9 - - + +
855C THR 2.9 16.5 + - - +
856C ASP* 3.4 25.6 + - - +
858C ILE* 1.3 76.7 - - - +
860C ASP* 1.3 63.2 + - - +
862C VAL* 3.6 1.8 + - - +
863C LEU* 3.1 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 860 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856C ASP* 4.5 7.9 + - - +
857C LEU 5.4 0.6 + - - +
858C ILE 3.2 0.8 + - - -
859C LYS* 1.3 84.7 - - - +
861C ASP* 1.3 66.1 + - - +
863C LEU* 3.3 12.5 + - - +
864C HIS* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 861 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840C PRO* 3.8 23.1 - - + +
841C PHE* 3.4 27.0 - - + -
857C LEU 5.6 1.5 - - - +
858C ILE* 3.1 8.6 + - - +
860C ASP* 1.3 77.8 - - - +
862C VAL* 1.3 62.1 + - - +
864C HIS* 2.9 5.0 + - - +
865C TRP* 2.8 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 862 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C TYR* 5.1 0.9 - - + -
833C LEU* 4.1 24.0 - - + -
835C LEU* 4.3 4.9 - - + +
841C PHE* 3.7 19.9 - - + -
846C ILE* 4.0 27.6 - - + -
848C TRP* 4.9 1.3 - - + -
854C ILE* 3.8 32.5 - - + -
858C ILE* 3.1 16.5 + - + +
859C LYS* 3.8 4.9 - - - +
861C ASP* 1.3 75.3 - - - +
863C LEU* 1.3 66.6 + - + +
866C MSE 2.8 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 863 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C TYR* 3.7 48.0 - - + -
859C LYS* 3.1 42.3 + - + +
860C ASP* 3.6 13.5 - - - +
861C ASP 3.1 0.4 - - - -
862C VAL* 1.3 80.4 - - + +
864C HIS* 1.3 57.9 + - - +
865C TRP 3.5 0.2 - - - -
866C MSE 3.0 27.9 + - + +
868C TYR* 4.9 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 864 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836C ARG* 2.6 41.8 + - - -
860C ASP 3.1 13.1 + - - +
861C ASP* 2.9 7.6 + - - +
863C LEU* 1.3 78.0 - - - +
865C TRP* 1.3 89.0 + + + +
866C MSE 3.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 865 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835C LEU* 3.1 15.5 - - + -
836C ARG* 2.6 61.9 + - + +
837C GLU 3.3 21.3 - - - -
838C GLY 3.5 17.3 - - - -
839C ASN* 3.4 26.5 - - + -
840C PRO* 3.3 27.4 - - + +
841C PHE* 4.9 1.6 - - + -
861C ASP* 2.8 32.6 + - - +
864C HIS* 1.3 106.8 - + + +
866C MSE 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 866 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C TYR* 4.0 15.3 - - + -
779C ILE* 5.0 2.7 - - - -
833C LEU* 4.0 37.0 - - + -
834C PRO 3.4 9.2 - - - +
835C LEU* 4.2 1.1 - - + -
836C ARG* 2.9 20.8 + - - -
862C VAL* 2.8 25.4 + - + +
863C LEU* 3.0 46.7 - - + +
864C HIS 3.6 0.6 - - - -
865C TRP* 1.3 76.7 - - - +
867C ASP* 1.3 60.1 + - - +
868C TYR* 3.1 53.9 + - + +
871C LEU* 5.6 2.5 - - + -
----------------------------------------------------------
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