Contacts of the helix formed by residues 840 - 848 (chain F) in PDB entry 1TU3
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 SER 840 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838F ALA 3.6 0.4 - - - -
839F ASP* 1.3 91.9 - - - +
841F LEU* 1.3 73.5 + - - +
842F GLU* 2.9 30.2 + - - +
843F ARG* 3.1 12.7 + - - +
844F ILE* 3.2 12.5 + - - +
841G LEU* 3.6 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 841 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840F SER* 1.3 75.9 + - - +
842F GLU* 1.3 64.8 + - - +
844F ILE* 3.7 7.6 - - + +
845F ARG* 3.1 32.0 + - - +
838G ALA 5.4 2.2 - - - +
839G ASP 3.7 21.1 - - - +
840G SER* 4.2 2.9 - - - -
841G LEU* 3.3 36.5 - - + +
844G ILE* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 842 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839F ASP* 5.6 0.9 - - - +
840F SER* 2.9 19.8 + - - +
841F LEU* 1.3 78.1 - - - +
843F ARG* 1.3 68.5 + - - +
844F ILE 3.0 1.2 + - - -
845F ARG* 3.0 14.2 - - - +
846F ALA* 3.0 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 843 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834F ARG* 3.7 14.5 + - - +
837F GLN* 3.7 13.3 + - - +
838F ALA* 3.6 23.0 - - + +
839F ASP* 3.5 31.3 + - - +
840F SER* 3.1 8.3 + - - +
842F GLU* 1.3 78.6 - - - +
844F ILE* 1.3 57.7 + - - +
846F ALA* 3.1 11.9 + - - +
847F ILE* 2.9 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 844 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835F ILE* 4.3 12.3 - - + +
838F ALA* 3.4 24.7 - - + +
840F SER 3.2 6.9 + - - +
841F LEU* 3.7 11.4 - - + +
842F GLU 3.0 0.8 + - - -
843F ARG* 1.3 78.2 - - - +
845F ARG* 1.3 57.8 + - + +
847F ILE* 3.0 10.2 + - - +
848F LEU* 2.7 52.1 + - + +
835G ILE* 4.4 8.5 - - + +
841G LEU* 4.0 18.8 - - + -
844G ILE* 3.2 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 845 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841F LEU* 3.1 20.8 + - - +
842F GLU* 3.0 22.9 - - - +
844F ILE* 1.3 81.9 - - + +
846F ALA* 1.3 61.8 + - + +
848F LEU* 3.5 11.2 + - - -
849F ASN* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 846 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842F GLU 3.0 13.0 + - - +
843F ARG* 3.1 20.0 - - - +
845F ARG* 1.3 81.2 - - + +
847F ILE* 1.3 59.2 + - + +
849F ASN* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 847 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831F GLN* 2.9 39.4 + - + +
834F ARG* 3.6 44.6 - - + +
835F ILE* 3.9 23.3 - - + +
838F ALA* 4.1 7.0 - - + -
843F ARG* 2.9 42.4 + - - +
844F ILE* 3.0 7.2 + - - +
846F ALA* 1.3 70.7 - - + +
848F LEU* 1.3 58.1 + - - +
849F ASN 2.8 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 848 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 4.8 8.1 + - - -
831F GLN* 4.0 11.7 - - - +
835F ILE* 3.8 28.5 - - + -
844F ILE* 2.7 52.2 + - + +
845F ARG* 3.9 9.4 - - - +
846F ALA 3.3 0.4 - - - -
847F ILE* 1.3 73.5 - - - +
849F ASN* 1.3 70.7 + - - +
832G LEU* 4.1 27.6 - - + +
835G ILE* 4.4 4.5 - - + -
836G ARG* 4.1 28.9 - - + +
----------------------------------------------------------
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