Contacts of the strand formed by residues 775 - 778 (chain C) in PDB entry 1KO6
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 775 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719C LEU* 5.3 1.1 - - + -
721C LYS* 2.9 23.6 + - - -
724C TYR* 3.5 6.3 - - + -
750C ILE* 3.3 37.5 - - + -
758C ILE* 4.3 13.2 - - + -
771C LEU* 2.9 31.6 + - + +
774C ILE* 1.3 74.5 - - + +
776C HIS* 1.3 65.2 + - - +
777C ILE* 3.9 26.7 - - + -
783C VAL 3.7 4.3 - - - +
784C VAL* 5.0 9.2 - - + -
798C LEU* 4.7 5.4 - - + -
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Residues in contact with HIS 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721C LYS* 4.0 9.4 + - - -
724C TYR* 3.4 6.7 + - - +
772C ASP 3.7 18.4 - - - -
773C ASP* 2.9 24.3 + - - -
774C ILE 3.6 11.4 - - - -
775C VAL* 1.3 76.5 - - - +
777C ILE* 1.3 62.2 - - - +
778C ARG* 3.9 15.5 + - - -
781C GLU 4.3 0.2 - - - +
782C VAL* 3.5 2.6 - - - +
783C VAL* 2.8 54.6 + - + +
786C LEU* 3.3 32.8 - - + +
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Residues in contact with ILE 777 (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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724C TYR* 2.8 23.2 + - + +
750C ILE 3.7 9.4 - - - +
751C GLY* 3.5 33.0 - - - +
752C ARG* 3.7 14.4 + - + +
755C TYR* 3.7 14.7 - - + +
756C GLY* 3.5 36.1 - - - +
757C SER* 4.1 4.9 - - - +
758C ILE* 4.2 5.6 - - + -
775C VAL* 3.9 18.6 - - + -
776C HIS* 1.3 74.0 - - - +
778C ARG* 1.3 61.5 + - - +
782C VAL* 3.5 23.8 - - + -
806C LEU* 4.6 6.1 - - + -
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Residues in contact with ARG 778 (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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752C ARG* 4.4 13.2 - - - +
755C TYR* 3.9 10.3 - - + -
776C HIS* 3.9 22.9 - - - -
777C ILE* 1.3 78.1 - - - +
779C ARG* 1.3 71.0 + - - +
780C LYS 3.0 0.7 + - - -
781C GLU* 2.6 66.7 + - - +
783C VAL* 5.4 3.2 - - - +
806C LEU* 4.3 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