Contacts of the helix formed by residues 73 - 80 (chain C) in PDB entry 3UED
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 PRO 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA 4.1 5.8 - - - +
33C CYS* 3.8 15.7 - - + -
37C ARG* 3.8 23.6 - - + +
38C MET* 3.6 31.4 - - - +
41C ALA* 3.7 20.2 - - + -
43C PHE* 3.7 5.5 - - + -
67C TRP* 4.2 11.9 - - + -
71C ASP 3.4 10.1 - - - +
72C ASP* 1.3 86.5 - - - +
74C ILE* 1.3 57.7 + - + +
76C GLU* 3.3 2.3 + - - +
77C HIS* 2.8 31.0 + - - +
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 5.4 8.7 - - - +
40C GLU* 4.6 19.5 - - + +
41C ALA* 4.2 21.1 - - + +
72C ASP* 3.1 13.7 + - - +
73C PRO* 1.3 76.6 - - + +
75C GLU* 1.3 59.0 + - - +
77C HIS* 3.3 4.4 + - - +
78C LYS* 2.9 55.5 + - + +
87C LEU* 4.9 9.6 - - + -
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ASP* 2.7 30.8 + - + +
74C ILE* 1.3 73.8 - - - +
76C GLU* 1.3 64.0 + - - +
78C LYS* 3.6 10.4 - - + +
79C LYS* 2.8 31.7 + - - +
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 4.5 2.5 - - + -
67C TRP* 3.7 31.6 - - + -
71C ASP* 4.0 17.6 - - + +
72C ASP 2.9 19.8 + - - +
73C PRO 3.6 6.7 - - - +
75C GLU* 1.3 83.3 - - - +
77C HIS* 1.3 57.2 + - - +
79C LYS* 4.5 3.8 - - - +
80C HIS* 2.8 48.4 + - + +
1D ALA* 2.9 34.3 + - + +
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Residues in contact with HIS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA 2.8 25.8 + - - +
43C PHE* 3.9 17.5 - + + -
57C CYS* 3.1 18.7 - - + +
60C CYS* 3.6 1.8 - - - -
62C LYS* 5.5 2.0 - - + -
64C LEU* 5.0 2.2 - - + -
73C PRO 2.8 17.8 + - - +
74C ILE* 3.6 5.6 - - - +
76C GLU* 1.3 76.7 - - - +
78C LYS* 1.3 56.7 + - - +
80C HIS* 5.1 0.2 - - - -
81C SER* 2.7 50.5 + - - +
84C CYS* 3.4 6.3 - - - -
86C PHE* 4.6 2.5 - + - -
87C LEU* 3.6 20.6 - - + +
143C ZN 2.0 38.8 - - - -
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ILE* 2.9 39.2 + - + +
75C GLU* 3.6 8.7 - - - +
77C HIS* 1.3 78.1 - - - +
79C LYS* 1.3 64.3 + - - +
82C SER* 3.3 24.7 - - - +
87C LEU* 3.9 29.7 + - + +
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Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLU 2.8 21.1 + - - +
76C GLU* 3.8 7.6 - - - +
78C LYS* 1.3 76.6 - - - +
80C HIS* 1.3 69.4 + - + +
82C SER* 4.3 4.5 + - - -
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Residues in contact with HIS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LYS* 3.6 18.8 + - + +
64C LEU* 3.7 35.0 - - + +
76C GLU* 2.8 44.5 + - + +
77C HIS* 4.5 0.4 - - - +
79C LYS* 1.3 78.6 - - + +
81C SER* 1.3 58.4 + - - +
82C SER 3.9 0.2 - - - -
1D ALA 2.7 29.3 + - - -
2D ARG* 3.8 14.1 - - + -
3D TPO 2.7 33.2 + - - +
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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