Contacts of the helix formed by residues 903 - 916 (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 SER 903 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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901A ASP 3.5 2.9 + - - -
902A ALA* 1.3 77.5 - - - +
904A GLY* 1.3 58.8 + - - +
905A ASP* 3.5 7.7 + - - +
906A VAL* 3.1 29.7 + - - +
907A LYS* 2.8 26.5 + - - +
942A LEU* 5.6 0.6 - - - +
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Residues in contact with GLY 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902A ALA 3.8 0.6 + - - -
903A SER* 1.3 73.1 - - - +
905A ASP* 1.3 58.3 + - - +
907A LYS* 3.7 7.6 - - - +
908A GLU* 2.8 36.2 + - - +
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Residues in contact with ASP 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903A SER* 3.2 7.8 + - - +
904A GLY* 1.3 75.7 - - - +
906A VAL* 1.3 64.0 + - - +
908A GLU* 3.2 18.6 + - - +
909A ALA* 3.1 23.9 + - - +
933A LEU* 3.8 28.1 - - + +
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Residues in contact with VAL 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A ALA* 4.1 13.0 - - + -
903A SER* 3.1 25.4 + - - +
905A ASP* 1.3 79.8 - - - +
907A LYS* 1.3 62.0 + - - +
909A ALA* 3.2 3.0 + - - +
910A LEU* 2.9 39.8 + - + +
930A LEU* 4.1 5.5 - - + +
933A LEU* 4.0 28.0 - - + +
934A LEU* 3.9 34.1 - - + -
942A LEU* 4.4 8.5 - - + -
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Residues in contact with LYS 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897A ALA 3.5 10.8 - - - +
898A LEU* 3.4 45.3 + - + +
900A SER 2.7 30.1 + - - -
901A ASP* 4.2 2.6 - - - +
902A ALA* 3.1 26.2 + - + +
903A SER 2.8 18.5 + - - +
904A GLY* 4.0 5.8 - - - +
906A VAL* 1.3 76.8 - - - +
908A GLU* 1.3 61.9 + - - +
910A LEU* 4.1 3.1 - - + -
911A GLN* 3.0 24.5 + - - +
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Residues in contact with GLU 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904A GLY 2.8 22.2 + - - +
905A ASP* 3.2 20.6 + - - +
907A LYS* 1.3 71.7 - - - +
909A ALA* 1.3 59.2 + - - +
911A GLN* 3.3 7.2 + - - +
912A GLY* 3.1 23.2 + - - -
926A TYR* 4.3 6.9 - - + -
929A LYS* 5.4 5.2 + - - -
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Residues in contact with ALA 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905A ASP 3.1 11.7 + - - +
906A VAL 3.6 4.3 - - - +
908A GLU* 1.3 73.7 - - - +
910A LEU* 1.3 57.0 + - - +
912A GLY 3.2 0.3 + - - -
913A TRP* 2.7 37.4 + - - +
926A TYR* 3.6 18.2 - - + +
929A LYS* 4.3 17.9 - - + -
930A LEU* 3.3 25.4 - - + -
933A LEU* 4.0 11.9 - - + -
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Residues in contact with LEU 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A LEU* 6.5 0.2 - - + -
894A ALA* 3.9 29.6 - - + +
897A ALA* 3.5 33.0 - - + -
898A LEU* 4.0 12.6 - - + -
902A ALA* 5.3 0.4 - - + -
906A VAL* 2.9 31.3 + - + +
907A LYS* 3.6 7.2 - - + +
909A ALA* 1.3 77.2 - - - +
911A GLN* 1.3 56.4 + - - +
913A TRP* 3.7 6.7 - - + +
914A LEU* 2.9 35.9 + - - +
930A LEU* 3.8 28.8 - - + +
934A LEU* 5.4 0.4 - - + -
945A ILE* 4.5 16.6 - - + -
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Residues in contact with GLN 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898A LEU* 3.0 31.8 - - + +
907A LYS 3.0 18.4 + - - +
908A GLU* 3.5 7.6 - - - +
909A ALA 3.2 0.2 - - - -
910A LEU* 1.3 76.0 - - - +
912A GLY* 1.3 57.8 + - - +
914A LEU* 3.5 10.1 + - - +
915A ALA* 3.0 34.1 + - - +
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Residues in contact with GLY 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908A GLU 3.1 11.0 + - - -
909A ALA 3.2 0.2 + - - -
911A GLN* 1.3 73.9 - - - +
913A TRP* 1.3 65.8 + - - +
915A ALA* 3.4 6.5 + - - +
916A GLY* 3.1 19.6 + - - -
922A LYS* 4.9 0.5 - - - +
926A TYR* 3.4 43.4 - - - -
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Residues in contact with TRP 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887A ARG* 3.7 34.3 - - + -
890A LEU* 3.6 34.1 - - + -
891A ALA* 3.8 9.9 - - - -
894A ALA* 4.6 7.9 - - + -
909A ALA 2.7 17.8 + - - +
910A LEU* 3.7 4.0 - - + +
912A GLY* 1.3 77.9 - - - +
914A LEU* 1.3 71.6 - - + +
916A GLY 3.1 1.8 + - - -
917A LYS* 2.8 69.2 + - + -
922A LYS 5.2 1.8 - - - -
923A SER* 3.7 26.3 - - - -
926A TYR* 3.5 9.5 - - + +
927A GLY* 4.2 11.2 - - - -
930A LEU* 4.1 16.6 - - + -
952A TYR* 2.9 26.6 + + + +
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Residues in contact with LEU 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A ALA* 3.6 29.2 - - + +
894A ALA* 3.6 16.8 - - + +
895A ALA* 3.9 11.2 - - + +
898A LEU* 3.8 26.5 - - + -
910A LEU 2.9 20.9 + - - +
911A GLN* 3.8 10.1 - - - +
913A TRP* 1.3 99.8 - - + +
915A ALA* 1.3 62.3 + - - +
917A LYS* 3.2 25.5 - - - +
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Residues in contact with ALA 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A GLN* 3.0 25.5 + - - +
912A GLY* 3.8 7.0 - - - +
913A TRP 3.2 0.4 - - - -
914A LEU* 1.3 80.2 - - - +
916A GLY* 1.3 55.2 + - - +
917A LYS* 4.9 0.4 - - - +
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Residues in contact with GLY 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912A GLY 3.1 13.7 + - - -
913A TRP 3.4 2.5 - - - -
915A ALA* 1.3 77.1 - - - +
917A LYS* 1.3 60.3 + - - +
918A ASN 3.1 3.8 - - - -
919A ASP* 2.8 35.8 + - - +
922A LYS* 4.0 17.3 - - - -
923A SER* 3.3 9.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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