Contacts of the helix formed by residues 54 - 60 (chain F) in PDB entry 1UW9
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 ASN 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226E TYR* 5.8 2.2 - - - -
229E GLN* 4.9 3.8 + - - +
53F SER* 1.3 82.9 - - - +
55F GLU* 1.3 66.3 + - - +
56F SER 3.3 2.9 - - - -
57F ALA* 3.0 20.9 + - + +
67F TYR* 5.7 1.8 - - - -
68F TYR* 3.9 8.2 - - - +
69F ASP* 3.5 2.9 - - - -
55J GLU 5.3 2.4 + - - -
56J SER* 5.4 4.4 + - - +
58J ILE* 3.7 24.5 - - + +
59J ARG* 2.9 47.2 + - + +
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Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ASN* 5.5 0.9 + - - -
49F LYS* 4.5 14.0 + - - -
53F SER* 2.4 34.8 + - - -
54F ASN* 1.3 72.1 - - - +
56F SER* 1.3 65.9 + - - +
57F ALA 3.3 0.7 + - - -
58F ILE* 3.3 24.8 + - - +
69F ASP* 3.2 16.9 + - - +
70F ASN* 4.6 4.9 + - - +
58J ILE* 4.0 8.3 - - - +
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Residues in contact with SER 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TYR* 3.5 29.6 - - - +
54C ASN* 5.5 4.0 - - - +
55F GLU* 1.3 75.5 - - - +
57F ALA* 1.3 55.8 + - - +
58F ILE* 3.0 7.4 - - - -
59F ARG* 2.9 32.2 + - - +
60F PHE* 3.8 7.4 - - - -
67F TYR* 3.4 17.6 + - - -
69F ASP* 2.7 33.3 + - - -
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F ASN* 3.0 19.6 + - + +
56F SER* 1.3 72.8 - - - +
58F ILE* 1.3 64.6 + - - +
59F ARG 3.0 2.5 - - - -
60F PHE* 3.0 44.8 + - + +
64F SER* 4.4 11.4 - - - -
67F TYR* 4.8 3.5 - - + -
58J ILE* 3.8 29.7 - - + +
59J ARG* 4.7 4.9 - - + +
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Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ASN* 4.0 36.3 - - + +
55C GLU* 4.1 7.9 - - - +
57C ALA* 3.9 16.8 - - + +
58C ILE* 3.7 44.6 - - + +
64C SER* 5.4 0.2 - - - -
55F GLU 3.3 20.3 + - - +
56F SER 3.0 1.0 - - - +
57F ALA* 1.3 78.9 - - - +
59F ARG* 1.3 64.3 + - + +
60F PHE 3.3 4.3 + - - +
58J ILE* 3.7 22.7 - - + +
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TYR* 3.0 43.8 + - - +
258B LYS 5.1 0.5 - - - +
259B GLU 3.9 1.2 - - - +
260B LEU 4.2 2.0 - - - +
261B GLY* 2.9 28.7 + - - -
54C ASN* 2.9 38.8 + - + +
57C ALA* 4.9 4.1 - - + +
62C SER* 5.8 2.8 - - - -
64C SER* 2.8 59.9 + - - +
66C LEU 4.0 1.2 - - - +
67C TYR* 2.9 22.8 + - - -
68C TYR* 3.6 22.8 + - - -
56F SER* 2.9 14.8 + - - +
58F ILE* 1.3 88.5 - - + +
60F PHE* 1.3 58.9 + - - +
61F GLY 4.3 0.2 + - - -
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Residues in contact with PHE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B THR* 4.1 1.6 - - + -
226B TYR* 4.1 9.4 - + - -
259B GLU 3.1 3.8 - - - +
260B LEU* 3.3 46.9 - - + -
61C GLY 5.0 5.6 - - - +
62C SER* 5.3 3.1 - - - -
56F SER* 3.8 12.6 - - - -
57F ALA* 3.0 32.9 + - + +
58F ILE 3.3 3.5 - - - +
59F ARG* 1.3 81.1 - - - +
61F GLY* 1.3 71.8 + - - +
63F VAL* 3.9 7.4 - - + -
64F SER* 4.0 18.2 - - - +
67F TYR* 3.6 57.2 - + + -
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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