Contacts of the helix formed by residues 920 - 927 (chain C) 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 TYR 920 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912C LEU* 4.6 0.2 - - - -
917C MET* 3.1 19.8 + - + +
919C GLN* 1.3 98.0 + - + +
921C THR* 1.3 58.3 + - - +
922C GLU 3.4 1.6 - - - -
923C HIS* 3.1 21.8 + + + +
924C PHE* 2.9 54.3 + - + -
947C GLY 3.8 10.3 - - - -
948C VAL* 3.6 41.4 - - + +
949C ARG 4.4 5.2 + - - -
950C LEU* 4.0 8.8 - - - +
953C HIS* 2.8 46.6 - + + +
957C ILE* 4.3 8.3 - - + -
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Residues in contact with THR 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908C VAL* 6.0 0.7 - - + -
909C SER* 3.9 34.5 + - - +
912C LEU* 3.9 15.6 - - + +
917C MET 4.2 1.0 + - - -
918C GLN* 2.7 39.5 + - - +
919C GLN 3.4 0.8 - - - -
920C TYR* 1.3 75.8 - - - +
922C GLU* 1.3 63.5 + - + +
924C PHE* 3.0 6.6 + - - +
925C MET* 2.9 41.8 + - + +
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Residues in contact with GLU 922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918C GLN 4.9 0.2 + - - -
919C GLN 4.9 3.9 + - - +
920C TYR 3.4 0.2 - - - -
921C THR* 1.3 84.6 - - + +
923C HIS* 1.3 59.1 + - + +
925C MET* 4.1 9.9 - - + +
926C ALA* 3.0 29.1 + - - +
904E VAL 5.3 0.3 - - - +
906E PHE 4.3 5.6 - - - +
907E ARG* 3.6 22.9 - - - +
908E THR* 5.4 1.0 - - - -
932E ALA* 3.4 22.6 - - - +
933E ILE* 2.9 21.5 + - + +
934E GLU* 2.8 36.5 + - + +
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Residues in contact with HIS 923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919C GLN 4.1 18.6 - - - -
920C TYR* 3.1 26.2 + + + +
922C GLU* 1.3 78.8 - - + +
924C PHE* 1.3 64.5 + - - +
926C ALA* 3.4 6.4 + - - +
927C ALA 3.4 12.8 + - - -
946C ILE* 3.2 44.5 + - + +
947C GLY* 4.3 9.5 - - - -
907E ARG* 3.6 40.8 - - + +
908E THR* 4.3 15.0 - - + +
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Residues in contact with PHE 924 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908C VAL* 4.3 11.2 - - + -
911C TRP* 3.8 13.2 - + - -
912C LEU* 3.7 24.2 - - + -
920C TYR* 2.9 45.5 + - + -
921C THR 3.3 7.6 - - - +
923C HIS* 1.3 77.2 - - - +
925C MET* 1.3 59.0 + - + +
926C ALA 3.4 0.5 + - - -
927C ALA 3.5 3.8 + - - -
929C TYR* 3.1 42.2 + - + +
935C VAL* 5.0 0.2 - - + -
938C MET* 3.5 37.2 - - + -
943C ILE* 5.2 4.0 - - + -
946C ILE* 3.3 28.2 - - + +
948C VAL* 4.2 11.9 - - + -
957C ILE* 4.2 18.2 - - + -
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Residues in contact with MET 925 (chain C).
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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916B ARG* 5.6 11.7 - - + -
908C VAL* 5.6 4.9 - - + -
909C SER* 5.5 6.3 - - - -
921C THR* 2.9 32.7 + - + +
922C GLU* 4.1 9.6 - - + +
923C HIS 3.3 0.2 - - - -
924C PHE* 1.3 74.8 - - + +
926C ALA* 1.3 64.4 + - - +
928C GLY* 3.5 7.3 + - - -
929C TYR 4.6 1.3 - - - +
930C THR* 3.6 35.8 - - + +
903E GLY* 4.1 24.8 + - - +
904E VAL 4.0 11.4 - - - +
968E GLN* 4.9 14.6 - - - +
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Residues in contact with ALA 926 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C GLU 3.0 19.2 + - - +
923C HIS 3.7 5.4 - - - +
924C PHE 3.3 0.4 - - - -
925C MET* 1.3 73.6 - - - +
927C ALA* 1.3 57.6 + - - +
928C GLY* 3.1 9.6 + - - -
904E VAL 3.6 11.4 + - - +
905E PRO* 3.4 31.6 - - - +
906E PHE 4.2 0.2 - - - -
907E ARG* 3.9 22.4 - - + +
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Residues in contact with ALA 927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923C HIS 3.4 3.6 + - - +
924C PHE 3.5 0.2 + - - -
925C MET 3.5 0.2 - - - -
926C ALA* 1.3 77.0 - - - +
928C GLY* 1.3 57.6 + - - +
929C TYR* 3.3 21.3 + - + -
945C ARG* 5.9 4.9 - - - -
946C ILE* 3.5 36.8 - - + -
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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