Contacts of the helix formed by residues 90 - 98 (chain E) in PDB entry 2UX1
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 90 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E SER* 1.3 82.1 - - - +
91E LEU* 1.3 65.2 + - - +
92E LYS* 3.2 31.4 - - - +
93E GLU* 3.0 22.9 + - - +
94E PHE* 3.0 28.7 + - - -
41G SER* 3.9 0.4 - - - -
45G GLN* 4.0 1.3 - - - +
102G GLU* 3.4 28.9 - - + +
103G VAL 3.2 32.3 - - - +
104G LEU* 4.5 0.2 - - + -
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Residues in contact with LEU 91 (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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90E THR* 1.3 71.6 - - - +
92E LYS* 1.3 53.7 + - - +
94E PHE* 3.3 19.8 + - + +
95E SER* 2.8 38.4 + - - -
37G SER* 4.7 7.4 - - - +
38G VAL* 4.0 16.8 - - + -
41G SER* 3.8 22.0 - - - +
91G LEU* 4.0 29.7 - - + +
94G PHE* 3.8 35.2 - - + -
95G SER* 4.3 12.6 - - - +
102G GLU* 2.9 20.9 + - - +
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Residues in contact with LYS 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E THR* 3.2 26.7 - - - +
91E LEU* 1.3 77.4 - - - +
93E GLU* 1.3 66.1 + - + +
95E SER* 4.6 3.8 - - - -
96E GLU* 3.0 43.1 + - - +
95G SER* 4.7 9.8 + - - +
102G GLU* 3.2 29.3 + - + +
103G VAL* 4.3 3.2 - - - +
104G LEU* 3.8 20.8 - - - +
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Residues in contact with GLU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ALA* 4.4 0.7 - - - +
87E PRO 4.9 1.2 - - - +
88E PHE* 3.6 38.0 - - + -
89E SER* 3.0 24.8 + - - -
90E THR* 3.0 26.3 + - - +
92E LYS* 1.3 83.2 - - + +
94E PHE* 1.3 65.4 + - - +
96E GLU* 4.9 0.9 - - - -
97E ASN* 2.9 36.7 + - - +
104G LEU* 3.6 30.8 - - + +
105G GLY 5.1 0.5 + - - -
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Residues in contact with PHE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E VAL* 3.8 7.9 - - + -
34E ALA* 3.8 14.9 - - - +
37E SER* 3.6 35.9 - - - -
38E VAL* 4.2 1.8 - - - -
88E PHE* 3.2 40.8 - - + -
89E SER* 3.8 13.0 - - - -
90E THR 3.0 17.7 + - - -
91E LEU* 3.5 28.3 - - + +
93E GLU* 1.3 76.4 - - - +
95E SER* 1.3 63.1 + - - +
98E SER* 3.0 29.8 + - - -
41G SER* 4.1 8.1 - - - -
48G TRP* 4.6 11.2 - + - -
91G LEU* 3.6 12.3 - - + -
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Residues in contact with SER 95 (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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38E VAL* 4.4 10.0 - - - +
91E LEU 2.8 20.9 + - - -
92E LYS* 4.0 4.9 - - - -
94E PHE* 1.3 74.1 - - - +
96E GLU* 1.3 64.5 + - - +
98E SER* 3.9 12.3 + - - +
100E LEU 5.2 2.3 - - - +
102E GLU* 4.8 3.8 + - - -
91G LEU* 4.1 17.5 - - - +
92G LYS* 4.7 10.8 + - - +
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Residues in contact with GLU 96 (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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92E LYS* 3.0 31.6 + - - +
93E GLU* 4.3 2.0 - - - +
95E SER* 1.3 81.4 - - - +
97E ASN* 1.3 67.7 + - - +
98E SER 3.5 4.7 + - - +
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Residues in contact with ASN 97 (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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31E GLN* 3.0 27.4 + - - +
34E ALA* 4.0 4.7 - - + -
88E PHE* 3.3 44.5 - - + -
93E GLU* 2.9 34.7 + - - +
96E GLU* 1.3 80.8 - - - +
98E SER* 1.3 62.5 + - - +
99E GLN* 3.7 3.1 + - - +
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Residues in contact with SER 98 (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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31E GLN* 4.0 1.3 - - - +
34E ALA* 3.8 7.6 - - - -
35E ASP* 2.7 23.0 + - - -
38E VAL* 3.5 28.6 - - - +
94E PHE 3.0 21.2 + - - -
95E SER 4.0 11.1 - - - +
96E GLU 3.3 5.1 - - - +
97E ASN* 1.3 80.1 - - - +
99E GLN* 1.3 60.3 + - - +
100E LEU* 3.2 17.0 + - - +
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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