Contacts of the helix formed by residues 917 - 925 (chain B) in PDB entry 3KKA
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 THR 917 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915B TYR* 4.1 1.0 - - - +
916B ARG* 1.3 78.4 - - + +
918B VAL* 1.3 64.9 + - - +
919B SER* 3.5 10.4 + - - -
920B GLU* 2.7 35.4 + - + +
921B TRP* 3.0 19.6 + - - +
942B MET* 3.5 11.8 - - - +
907C THR* 3.2 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 918 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917B THR* 1.3 71.3 - - - +
919B SER* 1.3 57.3 + - - +
921B TRP* 3.4 12.0 - - + +
922B LEU* 3.0 47.4 + - + +
931B ILE* 4.0 11.7 - - + -
934B PHE* 4.1 19.5 - - + -
939B LEU 3.8 7.2 - - - +
940B ASP* 3.3 34.7 + - - +
941B THR 3.8 16.6 - - - +
942B MET* 3.6 14.6 - - - +
945B VAL* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 919 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917B THR* 3.1 9.4 + - - -
918B VAL* 1.3 80.2 - - - +
920B GLU* 1.3 56.2 + - - +
922B LEU* 3.5 3.7 + - - +
923B GLU* 3.0 29.5 + - - +
928B LYS* 3.7 25.6 + - - +
931B ILE* 4.2 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 920 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A ARG* 3.1 30.5 + - - +
914B PRO 4.7 0.5 - - - +
915B TYR* 4.1 5.4 - - + -
916B ARG* 3.4 41.4 + - - +
917B THR* 2.7 25.7 + - - +
919B SER* 1.3 72.3 + - - +
921B TRP* 1.3 67.5 + - - +
923B GLU* 3.5 4.6 + - - +
924B SER* 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 921 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915B TYR* 3.7 32.4 - + + +
917B THR 3.0 12.1 + - - +
918B VAL* 3.4 21.3 - - + +
920B GLU* 1.3 76.8 - - - +
922B LEU* 1.3 73.8 + - + +
924B SER* 3.0 19.2 + - - -
925B ILE* 3.2 22.8 + - + +
934B PHE* 3.5 42.0 - + - -
942B MET* 3.6 25.1 - - + -
945B VAL* 3.8 12.8 - - + -
967B ILE* 3.8 23.8 - - + -
970B SER* 2.9 26.1 + - - -
971B ILE* 3.9 21.8 - - + -
974B PHE* 3.5 10.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 922 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918B VAL* 3.0 36.7 + - + +
919B SER* 3.5 4.0 + - - +
920B GLU 3.3 0.2 - - - -
921B TRP* 1.3 102.1 - - + +
923B GLU* 1.3 58.6 + - - +
925B ILE* 3.3 8.5 + - + +
926B ARG 3.1 4.3 + - - -
927B MET* 2.6 61.0 + - + +
928B LYS* 3.7 5.6 - - - +
930B TYR* 5.0 0.4 - - + -
931B ILE* 4.0 33.9 - - + +
934B PHE* 4.0 23.8 - - + -
967B ILE* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 923 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919B SER 3.0 18.3 + - - +
920B GLU* 3.9 5.8 - - - +
922B LEU* 1.3 78.4 - - - +
924B SER* 1.3 61.0 + - - +
926B ARG* 3.1 32.4 + - - +
927B MET 4.7 0.2 - - - +
928B LYS* 4.2 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 924 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A TYR* 2.7 35.5 + - - -
924A SER* 3.6 15.3 + - - -
926A ARG* 3.5 16.5 + - - -
915B TYR* 3.1 34.1 - - - -
920B GLU* 3.1 9.7 + - - +
921B TRP 3.0 12.4 + - - -
923B GLU* 1.3 77.4 - - - +
925B ILE* 1.3 53.5 + - - +
926B ARG* 3.3 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 925 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A TYR* 3.8 11.2 - - - +
925A ILE* 5.9 4.7 - - + -
915B TYR* 5.0 5.6 - - - +
921B TRP* 3.4 42.4 - - + +
922B LEU* 3.6 9.9 - - + +
924B SER* 1.3 82.4 - - - +
926B ARG* 1.3 66.5 + - - +
927B MET* 3.3 22.0 - - + +
966B ARG* 3.0 36.3 + - - +
967B ILE* 4.1 17.9 - - + -
970B SER* 3.7 29.8 - - - +
----------------------------------------------------------
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