Contacts of the strand formed by residues 934 - 942 (chain A) in PDB entry 5KZX
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 VAL 934 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777A THR* 3.8 24.2 - - - +
779A PRO* 4.7 4.0 - - + -
905A THR* 3.6 29.6 - - + -
906A VAL 3.4 3.8 - - - +
907A LEU* 3.7 20.9 - - + -
927A THR* 3.8 1.4 + - - +
928A TYR* 3.4 6.1 - - - -
929A SER* 3.0 29.9 + - - -
932A THR* 3.3 33.0 - - - +
933A LYS* 1.3 77.6 - - - +
935A LEU* 1.3 64.1 + - - +
936A ASP* 4.6 4.7 - - + +
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Residues in contact with LEU 935 (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 VAL 3.7 1.7 - - - +
905A THR* 3.5 1.7 - - - +
906A VAL* 2.7 40.5 + - + +
909A VAL* 4.0 17.9 - - + -
913A PRO* 3.6 29.8 - - + -
916A VAL* 4.2 4.0 - - + -
926A PHE* 3.6 24.0 - - + -
927A THR 3.5 8.7 - - - +
928A TYR* 4.2 7.2 - - + -
933A LYS 4.0 1.0 + - - -
934A VAL* 1.3 72.5 - - - +
936A ASP* 1.3 59.5 + - - +
937A ILE* 3.9 21.8 - - + -
951A TRP* 3.8 42.0 - - + +
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Residues in contact with ASP 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A PRO* 3.2 27.2 - - + +
903A LYS* 3.6 24.8 + - - +
904A VAL 3.7 0.2 - - - -
905A THR* 2.7 29.8 + - + -
926A PHE* 3.1 6.1 - - - +
927A THR* 2.8 49.9 + - - +
934A VAL* 4.0 5.4 - - + +
935A LEU* 1.3 73.9 - - - +
937A ILE* 1.3 62.1 + - - +
938A CYS* 4.3 2.2 + - - -
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Residues in contact with ILE 937 (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 LYS* 3.4 7.7 - - - +
904A VAL* 2.8 52.6 + - + +
906A VAL* 4.2 11.7 - - + -
916A VAL* 3.7 33.2 - - + -
923A VAL* 3.9 10.8 - - + -
925A ASN 4.0 2.2 - - - -
926A PHE* 4.2 1.6 - - + -
935A LEU* 3.9 28.9 - - + +
936A ASP* 1.3 78.8 + - - +
938A CYS* 1.3 74.3 + - - +
939A VAL* 3.8 14.4 + - + +
949A VAL* 4.0 18.6 - - + -
951A TRP* 4.9 3.1 - - + -
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Residues in contact with CYS 938 (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 GLN 3.5 8.7 - - - +
903A LYS* 4.8 10.1 - - - +
923A VAL* 3.7 20.3 - - - +
924A SER* 4.0 19.1 + - - +
925A ASN* 2.9 37.7 + - + +
926A PHE* 5.8 0.2 - - - -
936A ASP* 4.3 2.2 - - - -
937A ILE* 1.3 72.5 - - - +
939A VAL* 1.3 65.4 + - - +
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Residues in contact with VAL 939 (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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901A LEU* 3.4 25.1 - - + +
902A GLN* 3.0 39.3 + - - +
903A LYS* 4.0 3.8 - - - +
904A VAL* 4.1 10.3 - - + -
918A SER* 4.1 22.2 - - - +
923A VAL* 5.6 0.2 - - - -
924A SER* 5.6 0.7 - - - -
937A ILE* 3.8 20.2 - - + +
938A CYS* 1.3 79.5 - - - +
940A SER* 1.3 64.8 + - - +
941A LEU* 3.9 22.4 - - + -
949A VAL* 4.5 8.7 - - + -
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Residues in contact with SER 940 (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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901A LEU 3.8 1.3 - - - -
902A GLN* 4.8 6.3 - - - -
918A SER* 5.2 1.0 + - - -
924A SER* 5.6 1.7 + - - -
939A VAL* 1.3 76.8 + - - +
941A LEU* 1.3 67.9 + - - +
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Residues in contact with LEU 941 (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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900A GLN* 3.5 7.4 - - - +
901A LEU* 2.8 44.6 + - + +
918A SER* 3.5 26.5 - - - +
919A ASN* 3.6 25.6 - - + +
939A VAL* 3.9 16.6 - - + -
940A SER* 1.3 82.9 - - - +
942A LEU* 1.3 69.0 + - - +
947A PHE* 3.9 26.2 - - + -
949A VAL* 3.8 22.2 - - + -
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Residues in contact with LEU 942 (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 4.5 16.6 - - - +
898A GLY* 4.6 2.7 - - - +
899A LEU 3.4 17.9 - - - +
900A GLN* 4.4 11.9 - - + -
901A LEU* 4.8 1.3 - - - -
941A LEU* 1.3 84.8 - - - +
943A MET* 1.3 65.4 + - - +
944A GLY 3.2 2.4 + - - +
945A GLU* 3.0 60.8 + - + +
947A PHE* 3.9 6.7 - - - -
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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