Contacts of the helix formed by residues 846 - 861 (chain B) in PDB entry 2P0C
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 846 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B SER* 6.1 0.4 - - - -
780B LYS* 3.6 19.0 - - - +
783B VAL* 4.6 2.2 - - - -
845B PRO* 1.3 77.0 - - - +
847B PHE* 1.3 64.4 + - - +
848B SER* 3.1 23.0 + - - -
849B VAL* 3.2 15.0 + - + +
850B LEU* 3.1 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 847 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B ALA* 4.3 8.5 - - - +
711B MET* 3.5 53.6 - - + -
712B GLU* 3.8 22.2 - - + +
715B SER* 3.9 19.1 + - - -
779B SER* 3.9 4.9 - - - -
782B ASP* 3.6 17.7 - - + -
783B VAL* 3.6 36.3 - - + +
786B PHE* 3.6 30.5 - + + -
846B THR* 1.3 73.0 - - - +
848B SER* 1.3 57.5 + - - +
850B LEU* 3.6 13.5 - - + +
851B ARG* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B MG 3.8 9.9 - - - -
712B GLU* 3.1 34.1 - - - +
716B ASN* 5.7 0.7 - - - -
846B THR* 3.1 15.7 + - - -
847B PHE* 1.3 77.8 - - - +
849B VAL* 1.3 62.5 + - - +
851B ARG* 3.8 8.6 + - - +
852B LEU* 3.5 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B PRO* 3.7 20.4 - - + -
846B THR* 3.2 22.1 + - + +
848B SER* 1.3 78.8 + - - +
850B LEU* 1.3 65.8 + - - +
851B ARG 3.2 0.3 + - - -
852B LEU* 3.3 5.9 + - - +
853B GLN* 3.0 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B ALA* 5.2 1.1 - - + -
783B VAL* 3.9 26.5 - - + -
786B PHE* 4.0 21.3 - - + -
832B ILE* 3.7 24.7 - - + +
835B SER* 4.2 0.9 - - - +
836B CYS* 3.6 21.8 - - - -
845B PRO* 3.8 19.5 - - + +
846B THR 3.1 18.0 + - - +
847B PHE* 3.6 26.9 - - + +
849B VAL* 1.3 76.8 - - - +
851B ARG* 1.3 57.0 + - - +
853B GLN* 3.4 9.1 + - - +
854B LEU* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 851 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B VAL* 4.6 2.5 - - + +
708B ALA* 3.7 25.4 - - + +
709B LEU* 3.7 31.7 - - + +
712B GLU* 2.8 40.6 + - - +
847B PHE 2.8 21.4 + - - +
848B SER* 4.1 10.4 + - - +
849B VAL 3.2 0.2 - - - -
850B LEU* 1.3 73.0 - - - +
852B LEU* 1.3 79.0 + - - +
854B LEU* 3.4 3.7 + - - +
855B GLU* 2.9 65.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B SER 3.5 15.0 + - - +
849B VAL* 3.3 5.0 + - - +
851B ARG* 1.3 96.6 - - - +
853B GLN* 1.3 59.6 + - + +
855B GLU* 4.2 10.8 - - + +
856B LYS* 2.8 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 853 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B ILE* 4.1 33.9 - - + +
835B SER* 5.0 1.7 + - - -
845B PRO* 5.0 3.6 - - - +
849B VAL* 3.0 35.5 + - + +
850B LEU* 3.6 19.7 - - - +
852B LEU* 1.3 76.1 - - + +
854B LEU* 1.3 57.2 + - - +
856B LYS* 3.8 4.0 - - - +
857B LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 854 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B LEU* 4.6 9.5 - - + +
704B MET* 4.2 17.5 - - + +
705B VAL* 3.8 15.2 - - + +
708B ALA* 4.2 9.2 - - + -
786B PHE* 3.6 36.3 - - + -
790B MET* 3.7 25.4 - - + -
829B LEU* 4.0 10.3 - - + -
832B ILE* 3.8 20.0 - - + -
850B LEU 3.0 21.8 + - - +
851B ARG* 3.8 3.6 - - - +
853B GLN* 1.3 74.1 - - - +
855B GLU* 1.3 65.8 + - - +
857B LEU* 3.3 4.3 + - + +
858B LEU* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 855 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B VAL* 3.8 27.9 - - + +
709B LEU* 4.4 9.4 - - - +
851B ARG* 2.9 56.6 + - - +
852B LEU* 3.7 12.5 - - + +
854B LEU* 1.3 72.2 - - - +
856B LYS* 1.3 58.5 + - - +
858B LEU* 3.3 6.2 + - - +
859B GLU* 3.0 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 856 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B LEU* 2.8 34.1 + - + +
853B GLN* 3.9 4.5 - - - +
855B GLU* 1.3 75.5 - - - +
857B LEU* 1.3 64.2 + - - +
859B GLU* 3.5 10.8 + - + +
860B SER* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 857 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B LEU* 4.1 18.4 - - + -
826B LEU* 4.2 18.2 - - + -
828B GLU* 3.9 22.4 - - + -
829B LEU* 3.8 39.3 - - + +
832B ILE* 4.1 12.3 - - + -
853B GLN 2.9 18.4 + - - +
854B LEU* 3.7 7.0 - - + +
856B LYS* 1.3 77.5 - - - +
858B LEU* 1.3 62.8 + - - +
860B SER* 3.2 24.7 + - - +
861B LEU* 3.6 10.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B GLN* 3.3 42.3 - - + +
701B LEU* 3.8 18.3 - - + +
702B LYS* 3.8 37.7 - - + +
705B VAL* 4.4 8.7 - - + -
854B LEU 2.9 16.7 + - - +
855B GLU* 3.5 5.8 - - - +
857B LEU* 1.3 77.2 - - - +
859B GLU* 1.3 74.8 + - - +
861B LEU* 3.2 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B GLU* 3.0 24.6 + - + +
856B LYS* 4.0 12.1 - - + +
857B LEU 3.3 0.2 - - - -
858B LEU* 1.3 90.8 - - - +
860B SER* 1.3 60.4 + - - +
861B LEU 3.3 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B LYS* 3.2 17.0 + - - +
857B LEU* 3.3 20.0 - - - +
858B LEU 3.2 0.6 - - - -
859B GLU* 1.3 77.8 - - - +
861B LEU* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 861 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 3.9 23.6 - - + -
698B GLN* 4.2 37.8 + - + +
701B LEU* 3.5 32.3 - - + -
826B LEU* 4.3 22.2 - - + -
857B LEU* 3.7 11.2 - - + +
858B LEU* 3.2 13.2 + - - +
859B GLU 4.5 3.1 - - - -
860B SER* 1.3 82.5 - - - +
----------------------------------------------------------
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