Contacts of the strand formed by residues 769 - 772 (chain F) 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 769 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722F THR* 3.2 35.2 - - + -
723F ILE 3.5 6.4 + - - +
724F THR* 4.6 9.8 + - - +
746F GLY 4.0 0.5 - - - +
747F LEU* 3.5 1.7 - - - -
748F GLN* 2.7 53.5 + - + +
767F ALA* 3.3 15.8 + - - +
768F LEU* 1.3 72.2 - - - +
770F ILE* 1.3 62.5 + - - +
771F THR* 5.3 2.5 - - + +
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Residues in contact with ILE 770 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722F THR* 3.3 3.6 - - - +
723F ILE* 2.8 50.3 + - + +
725F VAL* 5.1 5.4 - - + -
736F LEU* 6.1 2.2 - - + -
738F LEU* 4.3 26.2 - - + -
744F VAL* 3.4 18.4 - - + -
746F GLY 3.3 9.2 - - - +
747F LEU* 4.5 10.1 - - + -
761F VAL* 5.0 5.8 - - + -
768F LEU* 4.1 23.6 - - + +
769F THR* 1.3 79.7 - - - +
771F THR* 1.3 63.5 + - - +
772F LEU* 3.4 35.2 - - + +
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Residues in contact with THR 771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721F ASN* 3.4 11.8 + - - +
722F THR* 4.2 12.2 + - - -
744F VAL* 2.8 24.3 - - - +
745F ASN* 2.8 26.1 + - + +
746F GLY* 2.9 39.4 + - - +
748F GLN* 6.4 1.1 - - + -
769F THR* 5.3 2.5 - - + +
770F ILE* 1.3 75.3 - - - +
772F LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 772 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693F LEU 5.7 0.2 - - - +
718F ARG* 3.6 42.2 - - - +
721F ASN* 3.0 30.5 + - - +
723F ILE* 3.7 19.7 - - + -
738F LEU* 5.4 4.3 - - + -
741F VAL* 4.6 25.4 - - + -
743F LYS 5.6 0.4 - - - -
744F VAL* 4.1 4.3 - - + +
745F ASN* 3.8 2.6 - - - +
770F ILE* 3.4 21.3 - - + -
771F THR* 1.3 81.4 + - - +
773F HIS* 1.3 62.3 + - - +
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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