Contacts of the strand formed by residues 83 - 88 (chain E) in PDB entry 4OA5
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 HIS 83 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D ASP* 5.9 3.6 - - + -
58E HIS 3.0 7.8 + - - +
59E SER* 3.4 6.2 - - - -
60E ILE 2.9 25.3 + - - +
78E LEU* 3.6 2.7 - - - +
81E LYS 4.6 3.6 - - - +
82E GLY* 1.3 74.5 + - - +
84E ILE* 1.3 84.3 - - - +
85E TYR* 3.2 40.1 - + + +
107E GLU 4.9 0.9 - - - -
108E ASP* 3.1 30.9 + - - -
109E LYS* 3.3 15.7 + - - -
110E ILE 3.9 0.9 - - - -
111E THR* 2.7 33.0 + - - -
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Residues in contact with ILE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ILE* 3.3 25.1 - - + +
62E GLU* 4.5 6.1 - - + -
71E ALA* 3.3 36.1 - - + +
74E MET* 3.7 15.3 - - + -
75E ALA* 3.5 25.6 - - + +
78E LEU* 3.6 12.8 - - + -
83E HIS* 1.3 83.5 - - - +
85E TYR* 1.3 70.0 + - - +
86E THR* 4.3 12.6 - - - -
109E LYS 2.7 12.7 + - - +
110E ILE* 3.4 7.2 - - + +
111E THR 2.9 28.2 + - - +
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Residues in contact with TYR 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E SER* 5.3 3.1 - - - -
60E ILE 2.8 14.2 + - - +
61E VAL* 3.3 5.6 - - - +
62E GLU 2.7 31.8 + - - +
83E HIS* 3.2 44.9 + + + +
84E ILE* 1.3 71.4 - - - +
86E THR* 1.3 54.6 + - - +
87E ILE* 5.1 1.3 - - - -
111E THR* 3.5 19.3 - - + -
113E LEU* 4.1 7.9 - - + -
124E LEU* 3.9 34.0 - - + +
127E MET* 3.5 28.9 - - + -
130E PHE* 3.8 29.2 - + - -
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Residues in contact with THR 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLU* 2.5 38.7 + - - +
65E THR* 2.6 38.5 + - + +
71E ALA* 4.4 1.8 - - + -
84E ILE* 4.3 4.9 - - - -
85E TYR* 1.3 75.2 - - - +
87E ILE* 1.3 55.9 + - - +
110E ILE* 3.8 22.7 - - + -
111E THR 3.0 15.7 + - - +
112E VAL* 3.3 7.9 - - + -
113E LEU* 2.7 33.4 + - - +
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Residues in contact with ILE 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL* 4.5 1.6 - - + -
62E GLU 2.9 17.8 + - - +
63E VAL* 4.6 9.9 - - + -
64E GLY* 2.9 25.1 + - - -
65E THR* 3.0 10.2 + - - -
85E TYR 4.9 0.2 - - - +
86E THR* 1.3 77.3 + - - +
88E GLU* 1.3 62.0 + - - +
113E LEU* 3.4 12.3 - - + +
115E GLY 3.6 17.7 - - - +
117E ALA* 3.8 15.9 - - + +
120E GLN* 3.7 32.1 - - + -
121E LEU* 3.7 37.9 - - + +
124E LEU* 4.2 11.4 - - + -
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Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E GLY* 4.2 3.5 - - - -
65E THR* 3.4 18.0 + - - +
66E CYS* 2.9 28.9 + - - +
87E ILE* 1.3 75.7 - - - +
89E LYS* 1.3 65.8 + - - +
90E ASP* 3.0 44.3 + - - +
93E ASN* 3.3 24.8 + - + -
94E VAL* 3.7 13.8 - - + +
112E VAL* 4.6 2.0 - - + -
113E LEU 2.9 7.4 + - - +
114E HIS* 3.3 10.7 - - - -
115E GLY 3.0 20.0 + - - -
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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