Contacts of the helix formed by residues 90 - 95 (chain E) in PDB entry 6MUO
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 ALA 90 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E TRP* 4.0 21.5 - - + -
87E GLN* 3.3 10.6 + - - +
89E GLN* 1.3 80.0 - - - +
91E LEU* 1.3 59.4 + - - +
93E ALA* 2.9 22.0 + - - +
94E LEU* 3.1 19.6 + - - +
81F VAL 4.2 3.6 - - - +
82F THR 3.7 26.9 - - - +
83F ALA* 4.6 3.2 - - - +
86F VAL* 4.1 10.4 - - + +
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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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67E PHE* 3.9 13.2 - - + +
68E SER* 3.4 33.9 - - - +
71E ALA* 4.2 25.4 - - + -
72E ARG* 4.4 14.4 - - + +
86E TRP* 4.3 28.9 - - + +
87E GLN 3.7 11.6 + - - +
88E ALA* 5.3 5.2 - - - -
89E GLN 3.3 0.4 - - - +
90E ALA* 1.3 77.8 - - - +
92E LEU* 1.3 61.7 + - + +
93E ALA 3.2 1.0 + - - -
94E LEU* 4.3 7.6 - - + +
95E GLN* 3.6 26.0 + - - +
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Residues in contact with LEU 92 (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 LEU* 4.1 15.0 - - + -
64E LYS* 4.0 31.0 - - + +
88E ALA 4.0 17.8 + - - +
89E GLN* 3.2 21.1 + - - +
90E ALA 3.2 0.6 - - - -
91E LEU* 1.3 77.4 - - + +
93E ALA* 1.3 58.9 + - - +
95E GLN* 3.8 24.7 - - + +
96E GLU* 3.7 15.3 - - + +
100F PHE* 3.1 21.5 - - + -
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Residues in contact with ALA 93 (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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89E GLN 2.8 12.4 + - - +
90E ALA* 2.9 15.7 + - - +
92E LEU* 1.3 79.2 - - - +
94E LEU* 1.3 66.0 + - - +
95E GLN 3.3 1.1 - - - -
96E GLU 3.6 1.4 + - - -
97E ALA* 3.5 14.6 + - - +
83F ALA* 5.2 4.0 - - - +
86F VAL* 4.0 21.4 - - + +
87F VAL* 5.4 1.1 - - + -
90F LEU* 4.8 0.2 - - - +
97F LEU* 3.7 16.4 - - + +
100F PHE* 3.6 22.2 - - + -
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Residues in contact with LEU 94 (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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67E PHE* 3.8 21.1 - - + -
71E ALA* 4.8 11.9 - - + -
86E TRP* 5.1 8.5 - - + -
90E ALA 3.1 15.1 + - - +
91E LEU* 4.1 6.5 + - + +
93E ALA* 1.3 75.8 - - - +
95E GLN* 1.3 54.3 + - - +
97E ALA* 2.7 7.0 + - + +
98E ALA* 2.5 36.1 + - + +
61F PHE* 5.3 4.5 - - + -
62F LEU* 4.0 24.0 - - + -
65F VAL* 3.7 31.0 - - + -
66F ILE* 4.5 17.5 - - + -
86F VAL* 4.0 18.2 - - + -
90F LEU* 5.0 4.5 - - + -
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Residues in contact with GLN 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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60E LEU* 3.4 43.8 - - + +
62E ILE* 2.6 33.1 + - + -
64E LYS* 3.9 17.2 - - - +
67E PHE* 3.6 27.5 - - + -
91E LEU 3.6 16.3 + - - +
92E LEU* 3.8 17.8 - - - +
93E ALA 3.3 0.6 - - - +
94E LEU* 1.3 78.8 - - - +
96E GLU* 1.3 60.8 + - + +
97E ALA 3.2 0.9 - - - -
98E ALA* 4.5 1.3 - - - +
99E GLU* 3.6 33.8 + - + +
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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