Contacts of the helix formed by residues 72 - 81 (chain E) in PDB entry 2RAX
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 ASP 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E ALA* 4.5 4.5 - - + +
70E ASP 3.5 5.4 + - - +
71E ASP* 1.3 71.1 - - - +
73E PRO* 1.3 72.0 - - - +
74E ILE* 4.0 15.2 + - - +
75E GLU* 3.2 43.3 + - - +
76E GLU* 3.1 23.5 + - - +
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Residues in contact with PRO 73 (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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32E ALA 3.4 16.6 - - - +
33E CYS* 4.2 4.3 - - + -
37E ARG* 3.8 13.9 - - + +
38E MET* 3.6 30.7 - - - -
41E ALA* 3.7 21.3 - - + -
43E PHE* 4.0 8.0 - - + -
67E TRP* 4.2 13.9 - - + -
71E ASP 3.2 10.3 - - - +
72E ASP* 1.3 87.9 - - - +
74E ILE* 1.3 60.7 + - + +
76E GLU* 3.3 2.3 + - - +
77E HIS* 2.9 30.0 + - - +
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Residues in contact with ILE 74 (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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37E ARG 4.8 4.0 - - - +
40E GLU* 4.4 13.0 - - + +
41E ALA* 3.7 30.3 - - + +
72E ASP* 3.4 16.8 - - - +
73E PRO* 1.3 77.8 - - + +
75E GLU* 1.3 56.2 + - - +
77E HIS* 3.5 7.6 - - - +
78E LYS* 3.1 40.7 + - + +
86E PHE* 6.1 0.9 - - + -
87E LEU* 5.0 10.9 - - + +
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Residues in contact with GLU 75 (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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72E ASP* 3.2 36.2 + - - +
73E PRO 3.2 0.6 - - - -
74E ILE* 1.3 73.1 - - - +
76E GLU* 1.3 57.9 + - - +
77E HIS 3.1 1.6 - - - -
78E LYS* 3.0 14.1 + - + +
79E LYS* 2.7 61.8 + - + +
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Residues in contact with GLU 76 (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 LEU* 4.3 8.6 - - + +
66E GLY 5.3 1.9 - - - +
67E TRP* 3.7 32.8 - - + -
71E ASP* 3.2 24.7 - - + +
72E ASP 3.1 14.0 + - - +
73E PRO 3.6 6.3 - - - +
75E GLU* 1.3 81.5 - - - +
77E HIS* 1.3 53.9 + - - +
79E LYS* 4.2 11.9 - - - +
80E HIS* 2.8 67.3 + - - +
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Residues in contact with HIS 77 (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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41E ALA* 2.9 28.7 + - - +
43E PHE* 3.8 16.9 - + + -
57E CYS* 3.4 17.9 - - + -
60E CYS* 3.7 4.6 - - - -
62E LYS* 6.2 0.2 - - + -
64E LEU* 5.4 1.3 - - - -
73E PRO 2.9 17.0 + - - +
74E ILE* 3.5 9.4 - - - +
76E GLU* 1.3 73.1 - - - +
78E LYS* 1.3 58.5 + - - +
80E HIS* 5.3 0.4 - - - -
81E SER* 2.7 47.0 + - - +
84E CYS* 3.5 3.0 - - - -
86E PHE* 4.3 2.7 - + - -
87E LEU* 3.5 32.2 - - + +
341E ZN 2.1 36.5 - - - -
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Residues in contact with LYS 78 (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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74E ILE* 3.1 25.1 + - - +
75E GLU* 3.0 15.8 + - + +
77E HIS* 1.3 77.3 - - - +
79E LYS* 1.3 64.0 + - - +
82E SER* 3.3 29.2 + - - +
87E LEU* 3.9 21.3 - - + +
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Residues in contact with LYS 79 (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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75E GLU* 2.7 45.9 + - + +
76E GLU* 3.7 15.7 - - - +
78E LYS* 1.3 76.4 - - - +
80E HIS* 1.3 71.4 + - + +
82E SER* 4.6 1.2 + - - -
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Residues in contact with HIS 80 (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 LYS* 3.5 32.0 + - + +
64E LEU* 3.6 37.5 - - + +
76E GLU* 2.8 52.0 + - - +
77E HIS* 5.3 0.4 - - - -
79E LYS* 1.3 83.5 - - + +
81E SER* 1.3 60.4 + - - +
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Residues in contact with SER 81 (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 CYS* 3.5 35.9 - - - +
62E LYS* 4.1 17.7 - - - +
77E HIS* 2.7 29.0 + - - +
80E HIS* 1.3 76.8 - - - +
82E SER* 1.3 62.0 + - - +
83E GLY* 3.3 1.8 + - - +
84E CYS* 3.6 17.3 + - - +
87E LEU* 3.6 1.9 - - - +
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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
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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