Contacts of the helix formed by residues 889 - 896 (chain B) in PDB entry 1DJL
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 889 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B PRO* 1.3 75.4 - - - +
890B TYR* 1.3 67.8 + - - -
892B LEU* 2.9 17.7 + - - +
893B CYS* 3.6 6.1 + - - -
923B ALA* 4.5 0.7 - - - -
924B GLY 4.5 0.9 - - - -
930B LEU* 4.1 11.5 - - - +
963B ILE 2.9 11.1 + - - -
964B GLY 3.0 14.7 - - - -
965B ALA* 3.8 4.0 - - - -
2136B NAP 3.2 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 890 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889B GLY* 1.3 71.1 - - - -
891B GLY* 1.3 65.6 + - - +
893B CYS* 3.2 9.7 + - + +
894B ALA* 3.0 45.2 + - + +
924B GLY* 3.8 11.4 - - - +
925B ARG* 3.1 71.8 - - + +
929B GLN* 4.7 6.7 - - - -
964B GLY 3.1 1.0 + - - -
2136B NAP 2.7 36.3 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 891 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B TYR* 1.3 74.5 - - - +
892B LEU* 1.3 60.1 + - - -
895B ALA* 3.1 25.8 + - - +
964B GLY* 2.8 21.8 + - - -
1026B ALA* 4.0 3.2 - - - +
2136B NAP 3.4 45.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 892 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B PRO* 3.6 23.1 - - + -
889B GLY 2.9 12.4 + - - +
891B GLY* 1.3 76.5 - - - +
893B CYS* 1.3 68.1 + - - +
895B ALA 3.4 0.3 + - - -
896B LYS 3.0 17.5 + - - -
897B ALA* 3.0 22.5 + - + +
898B GLN* 3.6 34.7 - - + +
901B ILE* 4.3 24.7 - - + -
917B PHE* 5.6 0.7 - - + -
930B LEU* 3.8 16.8 - - + -
933B LEU* 5.1 0.7 - - + -
934B LEU* 4.5 8.1 - - + -
963B ILE* 3.7 24.9 - - + +
964B GLY* 3.9 4.2 - - - -
1026B ALA* 4.5 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 893 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889B GLY 3.9 4.7 - - - -
890B TYR* 3.2 12.1 + - + +
892B LEU* 1.3 79.7 - - - +
894B ALA* 1.3 58.8 + - - +
896B LYS* 2.8 34.1 + - - +
898B GLN* 4.3 2.8 + - - +
929B GLN* 3.7 22.2 - - - +
930B LEU* 3.6 37.9 - - - -
933B LEU* 3.5 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 894 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B TYR* 3.0 43.8 + - + +
891B GLY 3.9 4.5 - - - +
893B CYS* 1.3 75.9 - - - +
895B ALA* 1.3 58.0 + - - +
896B LYS* 3.3 18.4 - - - +
2136B NAP 4.1 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 895 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B GLY 3.1 15.4 + - - +
892B LEU 4.1 1.1 - - - +
894B ALA* 1.3 75.8 - - - +
896B LYS* 1.3 70.9 + - - +
897B ALA 4.4 0.2 - - - +
1025B ASP* 3.6 12.3 - - - +
1026B ALA* 3.8 6.1 - - + -
1027B LYS* 3.2 37.5 - - - +
2136B NAP 3.4 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 896 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892B LEU 3.0 0.6 + - - -
893B CYS 2.8 22.1 + - - +
894B ALA* 3.3 15.9 - - - +
895B ALA* 1.3 80.8 - - - +
897B ALA* 1.3 59.4 + - - +
898B GLN* 2.8 29.1 + - - +
899B TYR* 3.9 18.9 - - + -
900B PRO* 4.2 2.8 - - - +
933B LEU* 6.3 0.8 - - - +
1027B LYS* 4.0 15.6 - - + +
----------------------------------------------------------
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