Contacts of the helix formed by residues 119 - 130 (chain C) in PDB entry 3I5H
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 THR 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C LYS* 5.0 1.1 - - - -
118C ILE* 1.3 79.6 - - - +
120C GLU* 1.3 78.4 + - + +
121C ASP* 3.1 25.6 - - + +
122C GLN* 2.6 34.2 + - - -
123C CYS* 3.0 20.4 + - - +
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 5.1 2.4 + - - -
112C LYS* 2.6 47.1 + - - +
118C ILE 3.9 1.0 + - - -
119C THR* 1.3 76.1 - - + +
121C ASP* 1.3 61.3 + - - +
123C CYS* 3.2 12.1 + - - +
124C ASN* 2.5 46.3 + - - +
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C THR* 3.1 14.9 - - + +
120C GLU* 1.3 78.8 - - - +
122C GLN* 1.3 69.6 + - + +
123C CYS 2.8 2.3 + - - -
124C ASN* 2.8 23.4 + - - +
125C ASP* 2.5 42.9 + - - +
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Residues in contact with GLN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A ILE* 4.8 1.7 - - - +
792A ARG* 4.3 23.9 + - - +
795A LEU* 3.9 29.8 - - + +
118C ILE* 3.5 21.6 - - + +
119C THR* 2.6 47.3 + - - +
121C ASP* 1.3 83.8 + - + +
123C CYS* 1.3 61.6 + - - +
125C ASP* 4.1 2.9 - - - -
126C ILE* 3.2 24.1 + - - +
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Residues in contact with CYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 4.3 25.1 - - - +
111C LEU* 3.8 31.6 - - - -
112C LYS* 3.8 28.3 - - + -
118C ILE* 3.9 8.9 - - - +
119C THR 3.0 8.6 + - - +
120C GLU* 3.4 10.3 - - - +
121C ASP 2.8 4.2 + - - -
122C GLN* 1.3 71.0 - - - +
124C ASN* 1.3 63.3 + - - +
126C ILE* 2.8 27.0 - - - +
127C PHE* 3.1 11.2 + - - +
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Residues in contact with ASN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 3.0 29.1 + - - +
120C GLU* 2.5 49.9 + - - +
121C ASP* 2.8 14.4 + - - +
123C CYS* 1.3 71.1 - - - +
125C ASP* 1.3 58.1 + - - +
127C PHE* 2.9 6.7 + - - +
128C THR* 2.7 39.8 + - - +
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Residues in contact with ASP 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795A LEU* 4.3 8.6 - - + +
121C ASP* 2.5 34.6 + - - +
122C GLN* 4.0 6.7 + - - +
124C ASN* 1.3 82.8 - - - +
126C ILE* 1.3 64.8 + - - +
128C THR* 2.9 7.5 + - - +
129C PHE* 2.7 52.2 + - + -
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A ILE* 4.0 34.8 - - + -
794A TYR* 3.8 31.9 - - + -
795A LEU* 4.1 6.2 - - + +
111C LEU* 5.4 2.0 - - + -
122C GLN 3.2 13.3 + - - +
123C CYS* 2.8 30.1 - - - +
125C ASP* 1.3 79.3 - - - +
127C PHE* 1.3 72.6 + - + +
129C PHE* 3.2 3.9 + - - +
130C CYS* 3.0 50.2 + - - -
145C LEU* 4.8 5.8 - - + -
149C VAL* 4.4 15.3 - - + -
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Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE* 4.5 7.4 - - + -
108C ARG* 3.6 48.2 - - + +
111C LEU* 4.7 11.9 - - + -
123C CYS* 3.5 15.7 - - - +
124C ASN 2.9 8.9 + - - +
126C ILE* 1.3 84.8 - - + +
128C THR* 1.3 65.3 + - - +
129C PHE 3.5 0.2 + - - -
130C CYS 3.8 0.7 + - - -
131C ASP* 3.5 2.6 + - - -
132C ILE* 3.3 67.3 + - + +
140C ILE* 3.4 33.2 - - + -
145C LEU* 3.3 32.5 - - + -
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Residues in contact with THR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASN* 2.7 22.6 + - - +
125C ASP* 3.6 9.0 + - - -
127C PHE* 1.3 73.6 - - - +
129C PHE* 1.3 70.4 + - + +
131C ASP* 3.2 14.4 + - - +
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Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A TYR* 3.1 29.6 + + + +
795A LEU* 3.9 20.6 - - + -
798A LYS* 3.4 46.0 - - + -
125C ASP* 2.7 45.5 + - + +
126C ILE* 3.5 5.2 - - - +
128C THR* 1.3 83.4 - - + +
130C CYS* 1.3 57.7 + - - +
131C ASP* 3.0 8.9 + - - +
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Residues in contact with CYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794A TYR* 3.8 23.6 - - - +
126C ILE* 3.0 41.9 + - - +
129C PHE* 1.3 75.7 - - - +
131C ASP* 1.3 66.4 + - - +
132C ILE* 3.2 14.9 - - + +
148C LYS* 2.6 59.3 + - + +
149C VAL* 4.1 11.7 - - - -
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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