Contacts of the helix formed by residues 865 - 874 (chain A) in PDB entry 5J3V
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 865 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A LYS 2.9 14.7 + - - +
862A ASN* 4.0 6.1 + - - -
863A GLN 3.6 1.4 - - - -
864A VAL* 1.3 79.2 - - - +
866A ASP* 1.3 61.2 + - - -
867A GLU* 3.1 3.6 - - - -
869A TRP* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A LYS* 2.8 34.0 + - - +
862A ASN* 5.0 4.2 - - - +
865A GLY* 1.3 74.5 - - - -
867A GLU* 1.3 64.5 + - + +
869A TRP* 4.0 8.3 - - - +
870A ARG* 3.3 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLY* 3.1 0.8 - - - -
866A ASP* 1.3 85.4 - - + +
868A ASN* 1.3 65.4 + - - +
870A ARG* 3.4 29.2 - - - +
871A ARG* 3.5 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A VAL* 2.8 42.8 + - + +
865A GLY 3.4 2.0 + - - -
867A GLU* 1.3 75.3 - - - +
869A TRP* 1.3 62.3 + - - +
870A ARG 3.2 0.2 - - - -
871A ARG* 2.4 41.0 + - - +
872A PHE* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A PHE* 4.7 3.6 - + - -
836A CYS* 4.6 11.9 - - - -
857A LEU* 4.8 17.7 - - + -
860A PHE* 3.8 23.1 - + - -
861A LYS* 3.6 47.0 - - + +
864A VAL* 3.9 6.4 - - + +
865A GLY 3.0 19.1 + - - +
866A ASP 4.2 5.2 - - - +
868A ASN* 1.3 75.9 - - - +
870A ARG* 1.3 56.3 + - - +
872A PHE* 3.5 41.2 - + - -
873A SER* 2.8 53.8 + - - -
876A PHE* 5.5 0.9 - + - -
884A LEU* 5.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A ASP 3.3 15.4 + - - +
867A GLU* 3.4 24.2 - - - +
868A ASN 3.2 0.2 - - - -
869A TRP* 1.3 81.2 - - - +
871A ARG* 1.3 63.0 + - + +
873A SER* 3.0 15.8 + - - -
874A ASP* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A GLU* 3.5 17.6 + - - +
868A ASN* 2.4 37.0 + - - +
870A ARG* 1.3 84.3 - - + +
872A PHE* 1.3 61.1 + - - +
874A ASP* 3.6 20.5 + - - +
875A GLN* 4.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A PHE* 4.1 13.9 - + + -
833A ILE* 3.5 37.5 - - + -
836A CYS* 4.3 0.7 - - - -
860A PHE* 3.8 20.4 - + + -
864A VAL* 6.1 0.4 - - + -
868A ASN 3.0 18.7 + - - +
869A TRP* 3.5 39.5 - + - +
870A ARG 3.2 0.2 - - - -
871A ARG* 1.3 79.1 - - - +
873A SER* 1.3 56.3 + - - +
874A ASP 3.2 0.9 - - - -
875A GLN* 3.2 50.8 - - - +
876A PHE* 3.4 22.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A TRP* 2.8 47.2 + - - -
870A ARG* 3.0 12.8 + - - -
872A PHE* 1.3 74.9 - - - +
874A ASP* 1.3 63.5 + - - +
875A GLN 3.3 1.6 - - - -
876A PHE* 3.4 24.9 - - - +
881A LYS* 3.2 29.2 - - - +
884A LEU* 6.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A ARG* 2.9 39.5 + - - +
871A ARG* 3.8 14.6 - - - +
872A PHE 3.2 1.2 - - - -
873A SER* 1.3 79.8 + - - +
875A GLN* 1.3 59.0 + - - +
876A PHE 3.1 11.9 + - - +
881A LYS* 3.8 22.8 + - - +
----------------------------------------------------------
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