Contacts of the helix formed by residues 105 - 111 (chain F) in PDB entry 3IZ0
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 GLU 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E PRO* 5.7 3.0 - - + +
103F ASP 4.5 1.8 - - - +
104F PHE* 1.3 88.1 - - - +
106F THR* 1.3 61.9 + - - +
107F ALA* 4.1 16.5 - - + +
108F ASP* 2.8 52.8 + - - +
113F LYS* 4.9 6.4 + - - -
116F ARG* 3.8 21.5 + - - +
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Residues in contact with THR 106 (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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136E LEU* 2.8 28.1 + - - +
137E CYS* 4.5 2.2 - - - -
138E PRO* 4.1 10.2 - - - +
195E HIS* 4.3 10.8 - - - +
199E LYS* 5.8 0.2 - - - +
85F PHE* 3.7 16.1 - - + -
89F VAL* 3.6 43.0 - - + +
104F PHE* 4.7 0.6 - - - -
105F GLU* 1.3 72.9 - - - +
107F ALA* 1.3 61.5 + - - +
109F ILE* 3.1 15.6 + - - +
110F LEU* 3.2 16.8 + - - +
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Residues in contact with ALA 107 (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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137E CYS* 4.1 23.3 - - + +
105F GLU* 3.1 17.4 + - - +
106F THR* 1.3 78.7 + - - +
108F ASP* 1.3 56.2 + - - +
109F ILE 3.2 0.2 - - - -
110F LEU* 4.3 2.9 - - - +
111F CYS* 2.6 43.7 + - + +
113F LYS* 4.1 16.2 - - - +
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Residues in contact with ASP 108 (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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45F LEU* 4.4 2.8 - - - +
49F TYR* 5.2 1.4 - - - +
104F PHE* 3.6 16.3 - - + -
105F GLU* 2.8 43.8 + - - +
107F ALA* 1.3 78.1 - - - +
109F ILE* 1.3 59.5 + - - +
111F CYS 4.6 2.7 - - - -
112F PRO* 3.4 25.8 - - - +
113F LYS* 4.9 6.6 + - - +
116F ARG* 3.1 37.2 + - - +
117F THR* 4.3 9.6 - - + +
120F PHE* 3.4 22.9 - - + -
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Residues in contact with ILE 109 (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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42F PRO* 3.5 26.3 - - - +
45F LEU* 5.7 2.4 - - + +
46F HIS* 4.2 23.3 - - + +
49F TYR* 3.6 33.0 - - + -
85F PHE* 4.0 22.7 - - + -
88F LEU* 3.8 10.1 - - + -
89F VAL* 4.2 17.3 - - + -
92F LEU* 3.6 8.3 - - + -
104F PHE* 3.6 29.2 - - + -
106F THR 3.1 6.7 + - - +
108F ASP* 1.3 79.4 - - - +
110F LEU* 1.3 64.2 + - + +
111F CYS 3.5 0.2 + - - -
112F PRO* 3.9 2.1 - - - +
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Residues in contact with LEU 110 (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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133E TYR* 3.2 33.7 - - + +
136E LEU* 5.1 2.0 - - + -
137E CYS* 3.4 20.6 - - - -
154E ILE* 6.1 0.2 - - + -
157E ASP* 3.9 40.5 - - + +
158E LEU* 3.7 21.1 - - + -
42F PRO* 4.7 3.8 - - - +
85F PHE* 3.4 45.1 - - + -
106F THR* 3.2 8.5 + - - +
107F ALA* 4.4 4.0 - - - +
109F ILE* 1.3 76.9 - - + +
111F CYS* 1.3 63.7 + - + +
112F PRO* 3.9 3.1 - - - +
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Residues in contact with CYS 111 (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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133E TYR* 5.9 0.9 - - - +
140E TYR* 6.6 0.2 - - - -
150E GLU* 5.3 8.7 - - - -
107F ALA* 2.6 21.5 + - + +
110F LEU* 1.3 80.9 - - + +
112F PRO* 1.4 66.2 - - - +
113F LYS* 2.7 42.5 + - - +
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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