Contacts of the helix formed by residues 79 - 86 (chain H) in PDB entry 3AOI
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 79 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78H PHE* 1.3 92.1 - - + +
80H GLN* 1.3 69.7 + - - +
81H ASP* 5.0 1.6 - - + +
82H GLU* 3.1 33.4 + - + +
83H CYS* 2.9 20.8 + - - -
90H TYR* 4.2 2.0 - - + -
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Residues in contact with GLN 80 (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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79H PRO* 1.3 70.1 - - - +
81H ASP* 1.3 65.6 + - - +
83H CYS* 2.5 35.0 + - - +
84H ARG* 3.2 19.0 + - - +
90H TYR* 3.0 44.8 + - + +
122H THR* 3.6 31.6 + - - +
123H GLU* 4.6 3.8 + - - +
128H ILE* 4.2 9.6 - - + -
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Residues in contact with ASP 81 (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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79H PRO* 3.6 1.3 - - + +
80H GLN* 1.3 91.3 + - - +
82H GLU* 1.3 65.3 + - + +
84H ARG* 3.0 18.3 + - - +
85H GLU* 2.9 24.6 + - - +
626H ARG* 4.6 10.0 - - - +
629H TYR* 3.5 35.1 + - + +
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Residues in contact with GLU 82 (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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78H PHE* 4.4 9.6 - - + +
79H PRO* 3.1 42.2 + - + +
80H GLN 3.0 0.4 - - - -
81H ASP* 1.3 79.6 - - + +
83H CYS* 1.3 64.7 + - - +
85H GLU* 3.1 25.7 - - - +
86H LYS* 3.0 54.5 + - + +
88H LEU* 4.5 0.8 - - - +
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Residues in contact with CYS 83 (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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78H PHE* 4.3 14.4 - - - -
79H PRO 2.9 25.5 + - - -
80H GLN 2.5 15.6 + - - +
82H GLU* 1.3 72.1 - - - +
84H ARG* 1.3 55.5 + - - -
87H ASP* 3.2 5.0 + - - -
88H LEU* 2.6 55.4 + - - +
89H THR 4.4 1.8 - - - -
90H TYR* 3.4 38.6 - - + -
128H ILE* 3.9 13.7 - - + -
131H GLY* 3.7 2.6 - - - -
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Residues in contact with ARG 84 (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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80H GLN* 3.2 22.8 + - - +
81H ASP* 3.0 16.5 + - - +
83H CYS* 1.3 75.5 - - - +
85H GLU* 1.3 64.1 + - - +
86H LYS 3.2 2.5 + - - -
87H ASP* 3.4 14.6 + - - +
122H THR* 4.9 9.9 + - - +
128H ILE* 3.3 30.0 - - + +
131H GLY* 3.1 26.6 - - - +
132H ALA* 5.9 0.2 - - - +
133H ASP* 2.7 41.0 + - - -
626H ARG* 4.7 18.4 - - - +
629H TYR* 5.8 7.9 - - - -
802H ARG* 5.3 2.4 + - - +
824H ARG* 5.0 1.9 + - - -
826H TYR* 5.8 0.2 + - - -
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Residues in contact with GLU 85 (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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81H ASP 2.9 14.8 + - - +
82H GLU* 3.1 25.3 - - - +
84H ARG* 1.3 77.3 - - - +
86H LYS* 1.3 70.3 + - + +
802H ARG* 4.2 24.3 + - - +
804H VAL* 4.1 23.5 - - + +
806H LEU* 4.8 2.1 - - + +
824H ARG* 2.8 23.4 + - - +
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Residues in contact with LYS 86 (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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82H GLU* 3.0 46.4 + - + +
85H GLU* 1.3 92.8 - - + +
87H ASP* 1.3 68.8 + - - +
88H LEU* 3.0 15.9 + - + +
806H LEU* 4.9 13.9 - - + +
811H PRO* 3.4 38.5 - - + +
812H GLY 5.0 3.4 - - - +
813H VAL* 3.0 44.4 - - + +
824H ARG* 4.3 2.5 - - - +
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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