Contacts of the helix formed by residues 904 - 909 (chain A) in PDB entry 3IJE
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 TRP 904 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A PRO* 4.3 18.4 - - + -
772A VAL* 3.3 28.7 - - + -
807A THR* 3.7 33.8 + - + +
808A LEU 2.6 20.7 + - - +
810A TYR* 4.1 23.1 - + + -
831A LEU* 3.4 33.9 - - + -
833A ILE* 4.2 6.3 - - + -
902A LEU 3.5 2.3 + - - +
903A LEU* 1.3 70.2 - - - +
905A THR* 1.3 65.2 + - - +
906A GLU* 3.2 45.3 + - + +
907A THR* 3.4 29.2 + - - -
908A PHE* 3.2 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A LEU* 4.6 8.3 - - + -
757A ILE* 4.1 32.3 - - + -
760A TRP* 2.8 31.4 + - - +
772A VAL 2.6 24.3 + - - +
773A GLY* 4.2 6.5 - - - -
774A PRO* 4.3 2.5 - - + -
903A LEU* 3.1 27.7 + - + +
904A TRP* 1.3 69.8 - - - +
906A GLU* 1.3 68.2 + - - +
908A PHE* 2.7 18.7 + - - +
909A MET* 3.1 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A TRP* 3.7 21.5 - - + -
762A HIS* 3.0 38.8 + - + -
763A LYS 3.6 14.2 + - - +
764A GLU 5.2 1.0 - - - +
766A PRO* 5.2 4.0 - - - +
771A ASP 6.0 1.1 - - - +
772A VAL* 5.8 1.3 - - - +
904A TRP* 3.2 37.5 + - + +
905A THR* 1.3 77.8 + - - +
907A THR* 1.3 63.2 + - - +
909A MET* 3.3 19.6 + - - +
911A LYS* 5.1 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A TYR* 5.9 2.2 - - + -
806A ASN* 3.2 44.5 - - + +
807A THR 3.5 5.7 + - - -
808A LEU* 4.0 18.8 + - + -
904A TRP* 3.4 27.0 + - - -
905A THR 2.8 3.8 + - - -
906A GLU* 1.3 76.2 - - - +
908A PHE* 1.3 68.2 + - + +
909A MET 3.2 1.0 + - - +
910A ASN* 3.0 32.1 + - - +
911A LYS 4.7 0.2 + - - -
912A GLU* 4.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A LEU* 3.5 29.6 - - + +
808A LEU* 3.6 40.8 - - + -
903A LEU* 3.3 34.8 - - + -
904A TRP 3.2 24.0 - - - -
905A THR 2.7 8.7 + - - +
907A THR* 1.3 72.5 - - + +
909A MET* 1.3 54.7 + - - +
910A ASN* 2.8 27.2 + - - +
914A GLN 3.6 7.6 - - - +
915A ASN* 4.6 1.0 - - - +
918A TYR* 3.8 31.8 - + + -
920A LEU* 4.0 27.4 - - + -
951A VAL* 4.2 14.1 - - + -
953A TRP* 4.4 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A LEU* 4.7 15.0 - - - +
757A ILE* 5.2 4.5 - - + -
760A TRP* 3.7 37.0 - - + -
905A THR* 3.1 13.9 + - - +
906A GLU* 3.4 9.7 - - - +
907A THR 3.1 2.6 - - - -
908A PHE* 1.3 74.0 - - - +
910A ASN* 1.3 52.1 + - - +
911A LYS* 2.7 37.7 + - + +
914A GLN 3.9 3.6 - - - -
953A TRP* 3.8 35.2 - - + -
965A TRP* 5.4 2.0 - - + -
----------------------------------------------------------
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