Contacts of the strand formed by residues 748 - 752 (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 PHE 748 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726C THR* 3.6 31.4 - - + -
727C ILE 3.5 7.6 - - - -
728C PRO* 4.9 1.1 - - - -
733C LEU* 4.0 11.9 - - + -
745C VAL* 3.7 19.7 - - + +
746C SER 2.9 2.8 + - - -
747C ASP* 1.3 77.1 - - - +
749C THR* 1.3 78.8 + - - +
750C ILE* 3.9 18.6 - - + -
759C TYR* 4.0 0.5 - - - -
760C PHE* 2.8 54.3 + + + +
762C GLY 4.7 0.2 + - - -
764C VAL* 4.3 11.7 - - + -
766C LEU* 3.7 39.7 - - + -
771C LEU* 4.4 13.2 - - + -
798C LEU* 4.5 11.4 - - + -
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Residues in contact with THR 749 (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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725C TYR* 5.0 2.7 - - + +
726C THR* 3.0 10.3 - - - -
727C ILE* 2.8 67.1 + - + +
747C ASP 3.6 6.1 + - - -
748C PHE* 1.3 82.4 + - - +
750C ILE* 1.3 67.8 + - - +
757C SER* 4.8 9.9 - - - -
758C ILE 3.5 14.6 - - - +
759C TYR* 3.8 18.7 - - + -
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Residues in contact with ILE 750 (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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719C LEU* 3.9 12.6 - - + -
724C TYR* 4.7 7.2 - - + -
725C TYR* 3.4 12.3 - - - +
726C THR* 4.1 1.1 - - + +
748C PHE* 3.9 9.4 - - + -
749C THR* 1.3 74.7 - - - +
751C GLY* 1.3 59.4 + - - +
757C SER* 3.3 2.8 - - - -
758C ILE* 2.6 62.6 + - + +
760C PHE* 4.2 13.9 - - + -
771C LEU* 3.8 28.7 - - + -
775C VAL* 3.3 40.2 - - + -
777C ILE* 3.7 1.3 - - - +
798C LEU* 5.4 1.6 - - + -
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Residues in contact with GLY 751 (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* 3.3 4.1 - - - +
725C TYR* 2.8 58.2 + - - -
750C ILE* 1.3 78.2 - - - +
752C ARG* 1.3 58.2 + - - -
756C GLY 3.2 12.6 - - - -
757C SER* 3.7 3.1 - - - -
777C ILE* 3.5 9.9 - - - -
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Residues in contact with ARG 752 (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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721C LYS* 6.0 0.4 - - - +
722C VAL 4.8 3.5 + - - -
723C GLY* 3.0 33.0 - - - +
724C TYR* 2.9 50.7 + - + -
725C TYR* 4.1 1.3 - - - -
751C GLY* 1.3 74.8 - - - +
753C LYS* 1.3 69.2 + - - +
755C TYR* 3.0 65.4 + - + -
756C GLY 2.8 19.1 + - - +
777C ILE* 3.7 17.9 + - + +
778C ARG* 4.4 12.1 - - - +
807C ASP* 5.2 0.2 - - - +
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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