Contacts of the strand formed by residues 722 - 729 (chain C) in PDB entry 1XSK
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 THR 722 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717C ALA 3.6 1.4 - - - +
718C ARG* 3.3 2.0 - - - -
719C THR* 2.9 33.7 + - - -
720C GLY 5.0 3.4 - - - -
721C ASN* 1.3 84.3 + - - +
723C ILE* 1.3 64.5 + - - +
724C THR* 4.1 12.2 + - - +
769C THR* 3.7 27.6 - - + -
770C ILE 3.5 4.7 - - - +
771C THR* 4.5 11.1 + - - +
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Residues in contact with ILE 723 (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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690C LEU* 4.3 20.0 - - + -
693C LEU* 3.8 25.4 - - + +
716C ALA* 4.2 14.6 - - + -
717C ALA 3.3 5.6 - - - +
718C ARG* 3.9 18.6 - - + -
722C THR* 1.3 74.6 - - - +
724C THR* 1.3 64.9 + - - +
725C VAL* 3.9 9.0 + - + +
738C LEU* 5.4 3.6 - - + -
769C THR* 3.6 3.5 - - - +
770C ILE* 3.0 46.3 + - + +
772C LEU* 3.6 33.4 - - + -
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Residues in contact with THR 724 (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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715C LYS 3.3 4.5 - - - +
716C ALA* 3.6 1.0 - - - -
717C ALA* 3.0 36.7 + - - +
719C THR* 5.6 1.7 + - - -
722C THR* 4.2 13.0 + - - +
723C ILE* 1.3 74.2 - - - +
725C VAL* 1.3 63.1 + - - +
726C THR* 4.1 19.8 + - + +
767C ALA 5.7 0.7 - - - +
768C LEU 3.8 10.8 - - - +
769C THR* 4.3 9.5 + - - +
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Residues in contact with VAL 725 (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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714C LEU* 3.6 35.4 - - + -
715C LYS 3.3 4.5 - - - +
716C ALA* 4.8 5.8 - - + -
723C ILE* 4.5 14.8 - - + +
724C THR* 1.3 76.2 - - - +
726C THR* 1.3 70.7 + - - +
734C TRP* 4.6 9.2 - - + -
736C LEU* 5.2 14.1 - - + -
738C LEU* 6.6 0.2 - - + -
766C ASN* 5.0 1.9 - - - +
767C ALA* 4.4 3.1 + - - -
768C LEU* 3.1 63.4 + - + +
770C ILE* 5.3 1.1 - - + -
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Residues in contact with THR 726 (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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713C THR 4.0 0.2 - - - +
714C LEU* 3.4 5.4 - - - +
715C LYS* 2.8 49.0 + - - +
724C THR* 4.1 17.6 + - + +
725C VAL* 1.3 79.9 - - - +
727C GLY* 1.3 57.9 + - - +
766C ASN* 5.0 4.7 - - - +
767C ALA* 6.2 1.8 - - - -
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Residues in contact with GLY 727 (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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712C PHE* 4.0 12.8 - - - -
713C THR 3.0 11.0 - - - -
714C LEU* 3.9 13.1 - - - +
726C THR* 1.3 76.4 - - - +
728C ALA* 1.3 61.2 + - - +
734C TRP* 5.8 1.5 - - - -
766C ASN* 4.4 20.9 + - - +
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Residues in contact with ALA 728 (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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712C PHE* 3.1 4.5 - - - -
713C THR* 2.7 44.1 + - - +
727C GLY* 1.3 75.6 - - - -
729C GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 729 (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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711C ILE 3.3 11.2 - - - -
712C PHE* 3.4 11.0 - - - -
728C ALA* 1.3 74.4 - - - +
730C GLU* 1.3 61.2 + - - -
731C ALA 3.8 1.2 + - - -
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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