Contacts of the helix formed by residues 917 - 925 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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915A TYR* 4.2 0.9 - - - +
916A ARG* 1.3 90.8 - - + +
918A VAL* 1.3 58.3 + - - +
919A SER* 3.6 9.6 + - - -
920A GLU* 2.8 29.0 + - - +
921A TRP* 2.9 29.8 + - - +
940A ASP 5.9 0.4 - - - -
941A THR* 6.3 0.2 - - - +
942A MET* 3.8 7.5 - - - +
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Residues in contact with VAL 918 (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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917A THR* 1.3 71.6 - - - +
919A SER* 1.3 52.9 + - - +
921A TRP* 3.3 10.3 + - + +
922A LEU* 2.7 46.5 + - + +
931A ILE* 3.9 20.0 - - + -
934A PHE* 4.3 17.3 - - + -
935A HIS* 5.5 3.1 - - + -
939A LEU 4.2 6.5 - - - +
940A ASP 3.9 17.4 + - - +
941A THR* 3.7 32.1 - - - +
942A MET* 3.7 15.3 - - - +
945A VAL* 4.3 8.1 - - + -
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Residues in contact with SER 919 (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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917A THR* 3.6 9.8 + - - -
918A VAL* 1.3 78.8 - - - +
920A GLU* 1.3 57.1 + - - -
922A LEU* 3.2 4.3 + - - +
923A GLU* 2.8 38.7 + - - +
928A LYS* 3.3 27.1 + - - +
931A ILE* 4.1 17.2 - - - +
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Residues in contact with GLU 920 (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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914A PRO 4.3 1.2 - - - +
915A TYR* 4.0 6.1 - - + -
916A ARG* 3.1 39.0 + - - +
917A THR* 2.8 20.7 + - - +
919A SER* 1.3 73.5 + - - +
921A TRP* 1.3 60.6 + - - +
923A GLU* 3.5 13.1 + - - +
924A SER* 2.8 29.5 + - - -
926B ARG* 2.5 33.3 + - - +
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Residues in contact with TRP 921 (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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915A TYR* 3.6 40.1 - + + +
917A THR 2.9 13.2 + - - +
918A VAL* 3.5 20.2 - - + +
920A GLU* 1.3 77.7 - - - +
922A LEU* 1.3 72.3 + - + +
924A SER* 3.2 12.1 + - - -
925A ILE* 3.3 24.6 + - + +
934A PHE* 3.7 30.7 - + - -
942A MET* 3.6 26.5 - - + -
945A VAL* 3.9 15.9 - - + -
967A ILE* 3.7 32.5 - - + -
970A SER* 2.9 21.6 + - - -
971A ILE* 3.9 21.5 - - + -
974A PHE* 3.7 9.4 - + - -
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Residues in contact with LEU 922 (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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918A VAL* 2.7 32.4 + - + +
919A SER 3.2 3.1 + - - +
921A TRP* 1.3 96.6 - - + +
923A GLU* 1.3 64.8 + - - +
925A ILE* 3.3 9.8 + - + +
926A ARG 3.0 4.2 + - - -
927A MET* 2.9 55.0 + - + +
928A LYS* 3.7 16.4 - - + -
931A ILE* 4.0 22.0 - - + +
934A PHE* 3.8 33.9 - - + -
967A ILE* 4.9 2.7 - - + -
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Residues in contact with GLU 923 (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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919A SER* 2.8 33.7 + - - +
920A GLU* 3.5 10.7 - - - +
922A LEU* 1.3 71.3 - - - +
924A SER* 1.3 64.8 + - - +
926A ARG* 2.9 31.6 + - - +
928A LYS* 3.6 34.7 + - + +
967E ASP* 5.2 0.9 - - - -
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Residues in contact with SER 924 (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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915A TYR* 3.1 33.1 - - - -
920A GLU* 2.8 16.7 + - - +
921A TRP 3.2 10.3 + - - -
923A GLU* 1.3 76.6 - - - +
925A ILE* 1.3 53.7 + - - +
926A ARG* 3.4 8.1 + - - +
915B TYR* 2.6 35.9 + - - -
924B SER* 3.6 17.5 + - - +
926B ARG* 3.9 10.0 + - - -
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Residues in contact with ILE 925 (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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915A TYR* 4.8 5.4 - - - +
921A TRP* 3.3 36.8 + - + +
922A LEU* 3.3 13.9 + - + +
923A GLU 3.2 0.2 - - - -
924A SER* 1.3 81.5 - - - +
926A ARG* 1.3 62.3 + - - +
927A MET* 3.5 12.1 - - + +
966A ARG* 2.7 45.9 + - - +
967A ILE* 4.1 31.6 - - + -
970A SER* 3.6 23.1 - - - +
915B TYR* 3.7 9.0 - - - +
925B ILE* 5.9 5.2 - - + -
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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