Contacts of the helix formed by residues 939 - 948 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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937B GLN* 4.5 9.2 + - - +
938B LYS* 1.3 88.1 + - - +
940B GLY* 1.3 66.3 - - - +
942B LEU* 3.8 6.2 + - - +
943B GLY 3.0 16.7 + - - -
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Residues in contact with GLY 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939B ASP* 1.3 77.1 - - - +
941B LEU* 1.3 66.9 + - - -
944B GLN* 3.2 26.4 + - - +
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Residues in contact with LEU 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893B LEU* 3.8 45.3 - - + +
896B LYS* 3.8 19.5 - - + +
897B ALA* 3.6 37.7 - - + +
900B SER* 4.9 10.8 - - - +
940B GLY* 1.3 70.7 - - - -
942B LEU* 1.3 66.5 + - + +
944B GLN* 3.1 16.9 + - - +
945B ILE* 3.0 26.9 + - + +
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Residues in contact with LEU 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897B ALA* 4.1 24.9 - - + -
900B SER* 5.0 3.1 - - - +
902B ALA* 4.3 20.6 - - + -
903B SER 5.8 0.2 - - - +
906B VAL* 4.2 21.5 - - + -
910B LEU* 5.0 0.7 - - + -
934B LEU* 3.6 27.3 - - + +
937B GLN* 4.0 27.2 - - + +
939B ASP 3.8 4.4 + - - +
940B GLY 3.2 0.6 - - - -
941B LEU* 1.3 81.5 - - + +
943B GLY* 1.3 55.8 + - - +
945B ILE* 3.3 9.6 + - + +
946B ALA* 2.9 30.5 + - - +
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Residues in contact with GLY 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B GLN* 3.6 26.9 - - - +
938B LYS* 3.8 11.0 - - - -
939B ASP 3.0 19.6 + - - -
940B GLY 3.8 0.7 - - - -
942B LEU* 1.3 75.6 - - - +
944B GLN* 1.3 61.5 + - - +
946B ALA* 3.3 2.4 + - - +
947B ALA* 3.0 23.6 + - - +
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Residues in contact with GLN 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889B HIS* 4.6 7.4 + - - -
893B LEU* 3.8 32.5 - - + +
940B GLY* 3.2 17.6 + - - +
941B LEU* 3.1 23.4 + - - +
943B GLY* 1.3 74.8 - - - +
945B ILE* 1.3 64.5 + - - +
947B ALA* 3.2 14.5 + - - +
948B MET* 3.3 22.0 + - - +
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Residues in contact with ILE 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890B LEU* 4.2 20.4 - - + -
893B LEU* 3.7 44.4 - - + +
894B ALA* 4.0 5.8 - - + +
897B ALA* 3.8 18.6 - - + -
910B LEU* 4.5 15.0 - - + -
930B LEU* 5.0 1.1 - - + -
934B LEU* 3.8 14.1 - - + -
941B LEU* 3.0 23.1 + - + +
942B LEU* 3.7 9.0 - - + +
944B GLN* 1.3 78.6 - - - +
946B ALA* 1.3 61.5 + - - +
948B MET* 3.1 16.8 + - - +
952B TYR* 2.9 28.5 + - + +
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Residues in contact with ALA 946 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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934B LEU* 4.0 25.1 - - + +
937B GLN* 3.8 16.6 - - + +
942B LEU 2.9 17.6 + - - +
943B GLY 3.4 5.2 - - - +
945B ILE* 1.3 78.3 - - - +
947B ALA* 1.3 60.9 + - - +
948B MET 3.3 0.7 + - - -
949B SER* 3.3 21.5 + - - -
952B TYR* 3.6 9.4 - - - -
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Residues in contact with ALA 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943B GLY 3.0 17.1 + - - +
944B GLN* 3.7 8.1 - - - +
945B ILE 3.1 0.6 - - - -
946B ALA* 1.3 78.2 - - - +
948B MET* 1.3 58.7 + - + +
949B SER* 3.4 3.8 + - - -
950B ASP* 4.5 6.4 + - - +
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Residues in contact with MET 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886B ARG* 3.3 32.8 - - + +
889B HIS* 4.4 13.7 - - - +
890B LEU* 3.8 24.2 - - + +
893B LEU* 3.8 27.6 - - - -
944B GLN* 3.3 12.6 - - - +
945B ILE 3.1 14.1 + - - +
947B ALA* 1.3 78.6 - - + +
949B SER* 1.3 56.6 + - - +
950B ASP* 3.2 7.9 - - - -
951B LEU* 2.8 45.3 + - + +
952B TYR* 3.5 7.0 - - - -
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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