Contacts of the helix formed by residues 54 - 62 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28H LEU* 6.2 0.2 - - - -
29H LYS* 4.4 20.0 + - - +
31H ARG* 5.2 2.9 - - - +
53H ALA* 1.3 82.4 - - - +
55H ARG* 1.3 56.7 + - - +
56H GLN* 2.8 32.1 + - - +
57H TYR* 2.7 50.8 + - + +
58H LEU* 2.9 14.5 + - - +
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Residues in contact with ARG 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G THR* 4.8 15.2 + - - -
28H LEU* 6.2 3.9 - - - +
31H ARG* 3.2 52.4 - - - +
54H ASN* 1.3 72.6 - - - +
56H GLN* 1.3 60.2 + - + +
57H TYR 3.3 0.2 - - - -
58H LEU* 3.8 12.1 - - + +
59H ASP* 2.8 46.8 + - - +
67H HIS* 4.8 19.6 - - + -
69H GLY* 6.2 0.4 - - - +
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Residues in contact with GLN 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H ASN* 3.3 28.2 + - + +
55H ARG* 1.3 82.5 - - + +
57H TYR* 1.3 64.5 + - + +
59H ASP* 4.1 4.1 - - - +
60H GLU* 2.9 33.7 + - - +
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Residues in contact with TYR 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PHE* 5.8 5.6 - + - -
53H ALA* 3.5 28.3 - - + -
54H ASN* 2.7 38.4 + - + +
56H GLN* 1.3 83.5 - - + +
58H LEU* 1.3 59.7 + - + +
60H GLU* 3.2 10.2 + - - -
61H LYS* 2.9 45.7 + - + +
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Residues in contact with LEU 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PHE* 4.6 19.3 - - + +
27H ILE 4.9 4.5 - - - -
28H LEU* 4.5 14.1 - - + +
53H ALA* 4.3 17.9 - - + -
54H ASN 2.9 14.5 + - - +
55H ARG* 3.8 17.3 - - + +
56H GLN 3.4 0.2 - - - -
57H TYR* 1.3 81.0 - - + +
59H ASP* 1.3 55.1 + - - +
61H LYS* 4.8 0.2 - - - -
62H SER* 2.8 30.1 + - - -
67H HIS* 3.3 33.4 - - + +
69H GLY* 3.8 24.9 - - - +
71H ILE* 3.1 25.0 - - + +
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Residues in contact with ASP 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H ARG* 2.8 31.4 + - - +
56H GLN* 4.6 3.5 - - - +
58H LEU* 1.3 75.8 - - - +
60H GLU* 1.3 59.8 + - - +
61H LYS 3.3 0.4 - - - -
62H SER* 3.7 3.6 - - - -
63H ASP 3.2 6.8 + - - +
64H GLY* 3.0 34.7 + - - +
65H ALA 4.0 7.6 - - - +
67H HIS* 3.1 20.3 + - - -
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Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H GLN* 2.9 24.5 + - - +
57H TYR* 3.2 11.8 + - - +
59H ASP* 1.3 77.1 - - - +
61H LYS* 1.3 67.9 + - + +
63H ASP* 4.2 5.8 + - - +
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Residues in contact with LYS 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H MSE 3.7 53.1 - - + +
26H PHE* 4.2 18.5 - - + -
57H TYR* 2.9 32.8 + - + +
58H LEU 4.3 1.3 - - - +
60H GLU* 1.3 88.1 - - + +
62H SER* 1.3 57.7 + - - +
63H ASP* 3.0 7.5 + - - +
71H ILE* 4.4 10.5 - - + -
73H ARG* 5.9 2.6 - - - +
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Residues in contact with SER 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H MSE 5.8 0.7 - - - -
6H TYR* 4.2 30.9 - - - -
58H LEU 2.8 23.1 + - - -
59H ASP* 3.7 1.7 - - - -
61H LYS* 1.3 75.8 - - - +
63H ASP* 1.3 64.4 + - - +
64H GLY 2.9 8.4 + - - -
65H ALA* 3.2 36.3 + - - +
67H HIS* 3.4 8.3 - - - -
71H ILE* 3.6 15.3 - - - -
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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