Contacts of the strand formed by residues 92 - 95 (chain C) in PDB entry 5UHO
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 92 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 3.2 29.0 - - + +
62C CYS 3.1 13.4 + - - -
63C GLY* 3.8 11.1 - - - -
64C VAL 4.7 0.2 - - - -
85C LEU* 3.5 13.9 - - - +
91C ASN* 1.3 93.2 + - - +
93C TYR* 1.3 71.1 + - - +
131C ILE* 3.5 5.6 - - - +
132C GLU* 3.6 14.4 - - + -
134C ILE* 3.3 33.0 - - + -
311C LEU* 4.0 14.1 - - + -
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Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 3.5 15.5 - - + -
66C GLU* 3.2 34.1 + - + +
78C ARG* 3.8 9.1 + - + +
81C LEU* 3.7 24.2 - - + -
82C PHE* 3.5 26.0 - + + -
85C LEU* 4.3 3.4 - - + -
92C THR* 1.3 80.7 - - - +
94C LEU* 1.3 71.2 + - - +
95C TYR* 3.6 34.2 - + + -
122C LEU* 5.4 2.0 - - + -
131C ILE* 3.7 16.6 - - + -
132C GLU 3.0 6.1 + - - +
133C PHE* 3.8 30.7 - + - -
134C ILE* 3.0 25.5 + - - +
311C LEU* 4.8 0.2 - - - -
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL 3.2 8.9 + - - -
65C VAL* 3.6 22.6 - - + +
66C GLU 3.0 28.8 + - - -
93C TYR* 1.3 76.0 - - - +
95C TYR* 1.3 64.2 + - - +
96C ALA* 3.4 2.8 + - + -
134C ILE* 3.6 29.6 - - + +
136C ALA* 3.6 25.1 - - + -
170C ALA* 4.0 5.6 - - + -
172C LEU* 5.0 2.7 - - + -
213C LEU* 3.9 17.9 - - + -
248C LEU* 4.3 19.5 - - + -
278C TRP* 4.7 7.2 - - + -
311C LEU* 3.5 20.5 - - + +
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ARG* 3.6 27.4 + - - -
93C TYR* 3.6 26.9 + + + +
94C LEU* 1.3 68.4 - - - +
96C ALA* 1.4 58.1 + - - +
97C PRO* 3.7 14.8 - - + +
100C ASP* 2.9 38.2 + - - +
103C HIS* 4.5 5.8 - - - -
111C TYR* 4.0 6.4 + - - -
119C LEU* 4.9 13.6 - - + +
122C LEU* 5.0 5.4 - - + -
133C PHE* 4.0 21.8 - + + -
134C ILE 2.9 17.8 + - - +
135C TYR* 3.8 31.4 - + - -
136C ALA* 3.1 29.9 + - - +
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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
------------------------------------------------------------
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