Contacts of the strand formed by residues 83 - 88 (chain B) in PDB entry 3UIO
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 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS* 3.4 29.2 + - + +
23B ALA* 3.7 21.3 - - + -
61B ARG 4.6 0.2 - - - +
62B PHE* 3.1 22.3 - - - -
81B GLU 3.4 10.7 + - - -
82B ASP* 1.3 72.9 - - - +
84B ILE* 1.3 75.1 + - - +
85B ASP* 4.2 12.2 + - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.3 17.9 - - + -
21B LYS 2.7 16.0 + - - +
22B VAL* 3.4 9.3 - - + +
23B ALA 2.9 26.5 + - - -
40B LEU* 4.2 16.4 - - + -
43B LEU* 4.2 23.6 - - + -
60B PHE* 4.1 20.2 - - + -
61B ARG 3.6 11.9 - - - +
62B PHE* 4.7 6.7 - - + -
67B ILE* 3.7 28.5 - - + -
78B MET* 4.8 6.3 - - - -
82B ASP 5.0 0.7 - - - +
83B THR* 1.3 77.2 - - - +
85B ASP* 1.3 70.3 + - - +
86B VAL 4.0 0.2 + - - -
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 3.7 17.2 - - - +
59B ARG 3.7 0.2 - - - +
60B PHE* 3.5 3.1 - - - -
61B ARG* 2.8 47.1 + - + +
62B PHE* 5.4 1.6 - - - -
63B ASP 5.6 1.6 + - - -
64B GLY 5.7 1.7 + - - -
83B THR* 4.4 12.0 - - - +
84B ILE* 1.3 78.4 - - - +
86B VAL* 1.3 63.1 + - - +
87B PHE* 3.6 26.6 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 3.5 20.4 - - + -
23B ALA 3.1 18.9 + - - +
24B GLY* 3.5 16.2 - - - -
25B GLN* 3.7 19.7 + - - +
47B TYR* 3.6 12.6 - - + +
58B ILE* 3.7 24.2 - - + -
59B ARG 3.4 10.5 - - - +
60B PHE* 3.5 30.5 - - + -
85B ASP* 1.3 74.1 - - - +
87B PHE* 1.3 70.6 + - - +
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 6.1 2.9 - - - -
118A GLU* 4.5 7.9 - - - -
25B GLN* 3.1 28.0 - - + +
58B ILE* 3.2 8.5 - - - +
59B ARG* 2.8 68.0 + - + +
61B ARG* 3.5 45.8 - - - -
85B ASP* 3.6 34.1 - - + -
86B VAL* 1.3 79.6 - - - +
88B GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 3.9 23.4 - - + +
102A ASP* 4.2 12.1 + - - +
104A ARG* 2.5 45.8 + - - +
107A ILE* 3.9 8.3 - - + +
111A GLN* 5.6 3.6 - - - +
118A GLU* 4.4 3.3 - - - +
25B GLN* 2.4 33.8 + - + +
57B GLN* 3.9 19.7 + - - +
58B ILE* 4.3 10.5 - - + +
59B ARG* 3.7 12.5 + - - -
87B PHE* 1.3 67.6 - - - +
89B GLN* 1.3 91.6 + - - +
90B GLN* 3.6 8.8 + - + +
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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