Contacts of the helix formed by residues 939 - 948 (chain A) in PDB entry 1KEK
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 ASP 939 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A GLN* 3.9 16.0 + - - +
938A LYS* 1.3 88.7 + - - +
940A GLY* 1.3 68.2 + - - +
941A LEU 3.8 0.5 + - - -
942A LEU* 3.9 2.3 + - - +
943A GLY 3.1 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 940 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A LYS 4.3 0.4 + - - -
939A ASP* 1.3 74.3 - - - +
941A LEU* 1.3 63.3 + - - -
943A GLY* 3.0 9.7 + - - -
944A GLN* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 941 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A LEU* 3.8 42.6 - - + +
896A LYS* 3.7 18.8 - - + +
897A ALA* 3.4 40.2 - - + +
900A SER* 4.9 8.1 - - - +
940A GLY* 1.3 70.7 - - - -
942A LEU* 1.3 64.3 + - + +
944A GLN* 3.1 16.9 + - - +
945A ILE* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A ALA* 4.0 26.9 - - + -
900A SER* 5.2 1.8 - - - +
902A ALA* 4.2 26.2 - - + -
903A SER 5.6 0.7 - - - +
906A VAL* 4.4 11.7 - - + -
910A LEU* 5.2 0.4 - - + -
934A LEU* 3.6 28.6 - - + +
937A GLN* 3.6 30.3 - - + +
939A ASP 3.9 1.5 + - - +
940A GLY 3.3 0.6 - - - -
941A LEU* 1.3 82.4 - - + +
943A GLY* 1.3 57.6 - - - +
945A ILE* 3.5 9.1 + - + +
946A ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A GLN* 3.6 25.1 - - - +
938A LYS* 4.1 8.9 - - - -
939A ASP 3.1 13.6 + - - -
940A GLY 3.0 8.4 + - - -
942A LEU* 1.3 77.2 - - - +
944A GLN* 1.3 61.8 + - - +
946A ALA* 3.6 2.3 + - - +
947A ALA* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A HIS* 4.3 10.0 + - - -
893A LEU* 4.1 27.8 - - + +
940A GLY 3.0 13.0 + - - +
941A LEU* 3.1 30.0 + - - +
943A GLY* 1.3 75.1 - - - +
945A ILE* 1.3 68.0 + - - +
947A ALA* 3.2 14.4 + - - +
948A MET* 3.4 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A LEU* 4.2 20.0 - - + -
893A LEU* 3.5 45.5 - - + +
894A ALA* 4.0 6.1 - - - +
897A ALA* 3.9 18.4 - - + -
910A LEU* 4.5 16.4 - - + -
930A LEU* 5.0 0.7 - - + -
934A LEU* 3.6 16.8 - - + -
941A LEU 2.9 22.0 + - - +
942A LEU* 3.7 8.1 - - + +
944A GLN* 1.3 79.0 - - - +
946A ALA* 1.3 62.9 + - - +
948A MET* 3.0 12.9 + - - +
952A TYR* 2.8 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A LEU* 3.9 26.5 - - + +
937A GLN* 3.8 16.2 - - + +
942A LEU 2.9 21.0 + - - +
943A GLY 3.8 6.3 - - - +
944A GLN 3.3 0.4 - - - -
945A ILE* 1.3 73.2 - - - +
947A ALA* 1.3 61.4 + - - +
948A MET 3.2 1.4 + - - -
949A SER* 3.4 20.1 + - - -
952A TYR* 3.5 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A GLY 3.2 16.6 + - - +
944A GLN* 3.2 6.3 + - - +
945A ILE 3.2 0.6 - - - -
946A ALA* 1.3 76.3 - - - +
948A MET* 1.3 60.4 + - + +
949A SER* 3.4 3.1 + - - -
950A ASP* 4.5 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A ARG* 4.3 14.6 - - + +
889A HIS* 3.5 39.5 - - + +
890A LEU* 3.9 25.6 - - + -
893A LEU* 3.7 22.7 - - + -
944A GLN* 3.5 11.7 - - - +
945A ILE 3.0 13.1 + - - +
947A ALA* 1.3 79.8 - - + +
949A SER* 1.4 58.0 + - - +
950A ASP* 3.2 8.3 - - - -
951A LEU* 2.9 40.7 + - + +
952A TYR* 3.6 6.9 - - - -
204B ARG* 6.5 0.7 - - - -
----------------------------------------------------------
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