Contacts of the strand formed by residues 895 - 901 (chain A) in PDB entry 6KZ1
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 895 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818A ARG* 3.4 61.5 + - + -
819A VAL 3.1 16.2 - - - +
820A LYS* 4.2 2.5 - - + -
821A LYS* 3.4 11.2 - - - +
868A ASN* 4.8 1.8 + - - +
887A ALA 4.5 1.2 - - - +
893A ARG* 3.3 55.3 + - + +
894A ASP* 1.3 97.6 - - - +
896A ILE* 1.3 67.7 + - - +
897A ASP* 3.5 19.9 + - + -
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Residues in contact with ILE 896 (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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817A VAL 3.6 1.7 - - - +
819A VAL* 2.9 35.0 + - + +
821A LYS* 4.1 4.9 - - + -
826A LEU* 4.4 7.2 - - + -
867A VAL* 3.9 19.3 - - + -
868A ASN* 3.8 6.5 - - - +
884A ILE* 4.0 7.0 - - + +
887A ALA* 3.6 18.6 - - + +
888A PHE* 3.5 45.1 - - + +
895A TYR* 1.3 77.6 - - - +
897A ASP* 1.3 73.5 + - - +
898A PHE* 3.7 36.0 + - + -
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Residues in contact with ASP 897 (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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816A LEU* 4.2 24.9 - - + +
817A VAL 3.5 2.2 - - - -
818A ARG* 2.8 58.3 + - - +
866A GLU 3.9 0.3 - - - +
867A VAL* 3.5 4.2 - - - -
868A ASN* 2.8 51.2 + - - +
869A GLY 5.3 0.4 - - - +
895A TYR* 3.5 9.0 - - - -
896A ILE* 1.3 73.4 - - - +
898A PHE* 1.3 61.5 + - - +
899A LEU 4.2 0.2 + - - -
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Residues in contact with PHE 898 (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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815A THR 3.6 1.4 - - - +
816A LEU* 3.6 3.3 - - - -
817A VAL* 2.8 35.9 + - - +
819A VAL* 3.7 30.5 - - + -
826A LEU* 3.7 33.2 - - + -
828A ILE* 5.0 2.9 - - + -
858A LEU* 4.2 14.4 - - + -
864A ILE* 3.9 30.1 - - + -
866A GLU 3.5 2.7 - - - +
867A VAL* 4.1 13.7 - - + -
884A ILE* 4.1 17.5 - - + -
896A ILE* 3.7 33.9 - - + -
897A ASP* 1.3 72.2 - - - +
899A LEU* 1.3 60.4 + - - +
900A VAL* 3.6 17.6 + - + +
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Residues in contact with LEU 899 (chain A).
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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814A SER* 3.7 26.9 - - - +
815A THR* 3.5 20.9 - - - +
816A LEU* 3.8 20.9 - - + +
864A ILE* 3.6 0.9 - - - -
865A LEU* 2.7 47.2 + - + -
866A GLU* 2.9 54.4 + - + +
897A ASP 4.2 0.2 - - - -
898A PHE* 1.3 70.6 - - - +
900A VAL* 1.3 57.6 + - - +
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Residues in contact with VAL 900 (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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814A SER* 3.2 5.0 - - - -
815A THR* 2.9 48.5 + - - +
817A VAL* 4.0 15.9 - - + -
858A LEU* 4.0 15.3 - - + -
862A HIS* 3.7 33.2 - - + +
863A VAL 3.2 11.7 - - - +
864A ILE* 4.3 13.0 - - + -
865A LEU* 4.2 3.6 - - - +
898A PHE* 3.8 21.8 - - + +
899A LEU* 1.3 80.0 - - - +
901A THR* 1.3 61.0 + - - +
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Residues in contact with THR 901 (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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813A GLY 2.9 21.4 + - - -
814A SER* 4.6 0.4 - - - -
861A GLY 4.3 0.2 - - - +
862A HIS* 3.5 10.3 - - - -
863A VAL* 2.9 47.0 + - + +
865A LEU* 4.0 19.1 - - + -
900A VAL* 1.3 75.2 - - - +
902A GLU* 1.3 61.0 + - - +
903A PHE* 3.1 36.9 + - + +
905A VAL* 4.0 13.7 - - + -
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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