Contacts of the helix formed by residues 54 - 61 (chain F) in PDB entry 1GZ0
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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29F LYS* 5.2 11.5 - - - +
31F ARG* 4.4 18.2 - - - +
53F ALA* 1.3 79.8 + - - +
55F ARG* 1.3 62.3 + - - +
56F GLN* 3.3 15.9 - - + +
57F TYR* 3.6 11.1 - - + +
58F LEU* 2.9 31.9 + - - +
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Residues in contact with ARG 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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31F ARG* 5.6 9.1 - - - +
54F ASN* 1.3 73.0 - - - +
56F GLN* 1.3 60.0 + - - +
57F TYR 3.3 0.4 - - - -
58F LEU* 3.7 8.3 - - + -
59F ASP* 2.9 72.2 + - - +
67F HIS* 3.8 24.4 - - + +
68F GLN* 5.6 1.4 - - - +
69F GLY* 4.9 8.1 - - - +
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Residues in contact with GLN 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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54F ASN* 3.9 9.6 - - + +
55F ARG* 1.3 80.2 - - - +
57F TYR* 1.3 57.4 + - - +
59F ASP* 3.7 2.2 - - - -
60F GLU* 2.7 70.7 + - + +
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Residues in contact with TYR 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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26F PHE* 4.3 30.6 - + - -
53F ALA* 3.5 23.6 - - + -
54F ASN* 3.6 21.9 - - + +
56F GLN* 1.3 83.2 + - - +
58F LEU* 1.3 65.9 + - + +
60F GLU* 4.0 9.1 - - - +
61F LYS* 3.2 68.2 + - + +
71F ILE* 5.0 2.2 - - + -
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Residues in contact with LEU 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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26F PHE* 4.6 3.1 - - + -
27F ILE 4.9 8.3 - - - +
28F LEU* 5.2 3.1 - - + +
53F ALA* 3.9 21.8 - - + +
54F ASN 2.9 27.0 + - - +
55F ARG* 3.9 7.4 - - + +
56F GLN 3.3 0.2 - - - -
57F TYR* 1.3 81.1 - - + +
59F ASP* 1.3 52.1 + - - +
60F GLU 3.2 0.4 - - - -
61F LYS 3.6 1.6 - - - -
62F SER* 2.6 39.3 + - - -
67F HIS* 3.1 30.9 - - + +
69F GLY* 3.6 27.8 - - - +
71F ILE* 3.2 33.2 - - + +
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Residues in contact with ASP 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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55F ARG* 2.9 55.3 + - - +
56F GLN* 4.3 2.2 - - - +
58F LEU* 1.3 72.7 - - - +
60F GLU* 1.3 58.5 + - + +
62F SER* 2.9 8.1 + - - -
63F ASP* 3.9 0.2 - - - -
64F GLY* 2.6 40.8 + - - -
65F ALA 3.8 12.1 - - - +
67F HIS* 3.3 14.6 + - - -
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Residues in contact with GLU 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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56F GLN* 2.7 63.0 + - + +
57F TYR* 4.0 9.0 + - - +
59F ASP* 1.3 74.4 - - + +
61F LYS* 1.3 61.7 + - + +
62F SER 2.9 8.3 + - - -
63F ASP* 3.5 10.4 + - - -
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Residues in contact with LYS 61 (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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4F MSE 4.1 32.8 - - + +
6F TYR* 3.7 12.4 + - - -
26F PHE* 5.2 10.9 - - + -
57F TYR* 3.2 56.1 + - + +
58F LEU 3.6 1.3 - - - +
60F GLU* 1.3 79.7 - - + +
62F SER* 1.3 57.3 + - - +
63F ASP 3.7 0.4 - - - -
71F ILE* 4.9 9.9 - - + +
73F ARG* 5.9 3.6 - - - +
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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