Contacts of the strand formed by residues 815 - 819 (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 ASN 815 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A LEU 3.9 0.3 - - - +
752A ILE* 3.6 1.2 - - - -
753A THR* 3.0 40.0 + - - +
763A VAL* 4.0 4.8 - - - +
776A GLN* 5.1 0.4 - - - +
794A ARG* 2.9 31.6 + - - +
807A LEU* 3.7 31.9 - - + +
808A PRO 3.0 22.6 + - - -
809A ALA* 3.6 17.2 - - - +
813A THR* 4.9 0.9 - - - -
814A ILE* 1.3 75.8 - - - +
816A VAL* 1.3 64.5 + - - +
817A HIS* 3.6 15.4 - - + -
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Residues in contact with VAL 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A PHE* 3.8 37.9 - - + -
701A LEU* 4.5 8.3 - - + -
750A LEU* 4.1 15.0 - - + -
751A LEU 3.3 8.1 - - - +
752A ILE* 4.3 8.7 - - + -
774A ASP* 4.0 5.4 + - - +
775A LEU* 3.0 52.8 + - + +
776A GLN* 4.7 1.2 + - - +
814A ILE* 3.4 18.2 + - + +
815A ASN* 1.3 81.1 - - - +
817A HIS* 1.3 66.8 + - - +
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Residues in contact with HIS 817 (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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749A ALA 3.5 1.4 - - - +
750A LEU* 3.4 8.2 - - - +
751A LEU* 2.8 44.5 + - + +
753A THR* 5.3 1.6 + - - -
767A PHE* 3.8 28.9 - + + -
772A TRP* 3.7 28.4 - - + -
773A TYR 3.1 15.7 - - - +
774A ASP* 3.6 27.3 + - + +
775A LEU* 4.4 0.7 - - - +
794A ARG* 4.9 0.4 + - - -
795A GLU 5.0 1.4 + - - -
798A ILE* 3.4 21.6 - - + +
807A LEU* 4.2 3.0 - - + +
815A ASN* 3.6 32.2 - - + +
816A VAL* 1.3 79.9 + - - +
818A LEU* 1.3 60.3 + - - +
819A ARG 4.1 0.2 - - - -
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Residues in contact with LEU 818 (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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749A ALA* 3.5 24.0 - - + +
750A LEU* 4.0 13.2 - - + -
772A TRP* 3.6 1.7 - - - -
773A TYR* 2.8 45.8 + - + +
775A LEU* 4.3 15.7 - - + +
817A HIS* 1.3 72.2 - - - +
819A ARG* 1.3 66.0 + - - +
820A ALA 3.5 1.4 + - - -
822A TYR* 4.4 4.0 - - + +
824A ILE* 3.5 34.5 - - + -
844A ALA* 4.2 23.6 - - + +
846A ALA* 3.8 23.3 - - + +
907A LEU* 4.2 10.3 - - + -
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Residues in contact with ARG 819 (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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730A GLU* 2.8 37.0 + - - +
731A PHE* 3.4 26.6 - - - -
748A GLU 3.0 21.6 + - - -
749A ALA* 2.8 23.4 + - - +
769A LEU 5.8 0.6 + - - -
770A GLY* 6.4 1.6 - - - -
771A THR 3.9 3.1 - - - +
772A TRP* 3.6 32.7 - - + -
818A LEU* 1.3 71.1 - - - +
820A ALA* 1.3 75.5 + - - +
822A TYR* 3.4 45.6 + - + +
846A ALA* 3.5 7.6 - - - +
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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