Contacts of the helix formed by residues 123 - 133 (chain F) in PDB entry 3WBR
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 123 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91F GLN* 4.8 0.5 + - - -
121F ILE* 3.5 7.0 - - - +
122F ASN* 1.3 89.0 - - + +
124F ARG* 1.3 60.1 + - - +
125F GLU* 2.9 43.2 + - - +
126F GLU* 3.1 17.8 + - - +
127F GLN* 3.0 23.4 + - - +
165H VAL* 3.7 14.1 - - + -
167H PHE* 4.5 0.9 - - - -
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Residues in contact with ARG 124 (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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123F THR* 1.3 70.8 - - - +
125F GLU* 1.3 115.4 + - - +
127F GLN* 3.1 2.8 + - - +
128F ASP* 2.9 37.6 + - - +
165H VAL* 3.8 7.8 - - + +
167H PHE* 3.7 26.0 - - + -
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Residues in contact with GLU 125 (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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90F PHE* 3.4 22.1 - - + -
91F GLN* 3.0 35.9 + - - +
123F THR* 2.9 30.9 + - - +
124F ARG* 1.3 111.1 + - - +
126F GLU* 1.3 55.2 + - - +
128F ASP* 3.6 5.1 + - - +
129F PHE* 3.1 21.5 + - - +
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Residues in contact with GLU 126 (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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90F PHE* 3.7 13.2 - - + -
91F GLN* 5.4 2.7 - - - +
95F TYR* 2.5 31.6 + - + +
119F VAL* 4.5 0.2 - - - +
120F VAL 3.1 11.3 - - - +
121F ILE* 4.1 2.5 - - + -
122F ASN* 2.9 34.7 + - - +
123F THR* 3.1 17.4 + - - +
124F ARG 3.1 0.4 - - - -
125F GLU* 1.3 78.5 - - - +
127F GLN* 1.3 64.9 + - - +
129F PHE* 3.3 1.9 + - - +
130F ILE* 3.0 40.8 + - + +
207F LYS* 2.6 24.6 + - - +
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Residues in contact with GLN 127 (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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121F ILE* 3.4 19.7 - - + +
123F THR 3.0 6.9 + - - +
124F ARG 3.4 8.3 - - - +
126F GLU* 1.3 75.0 - - - +
128F ASP* 1.3 69.4 + - - +
130F ILE* 3.3 7.1 + - - +
131F ILE* 3.1 33.9 + - + +
183F ILE* 3.8 18.0 - - - +
191F TRP* 4.9 4.6 + - - +
192F GLY* 4.7 7.5 - - - +
193F TRP* 3.1 24.2 + - - +
167H PHE* 3.4 56.8 - - + +
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Residues in contact with ASP 128 (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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124F ARG* 2.9 29.9 + - - +
125F GLU* 4.0 5.8 - - - +
127F GLN* 1.3 80.1 - - - +
129F PHE* 1.3 66.3 - - - +
131F ILE* 3.2 31.3 - - + +
132F GLN* 3.3 26.3 + - - +
167H PHE* 6.0 0.5 - - - -
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Residues in contact with PHE 129 (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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88F THR* 3.5 26.2 - - + -
89F SER 3.9 9.9 - - - -
90F PHE* 3.5 47.6 - + + -
95F TYR* 3.4 35.2 - + + -
125F GLU 3.1 18.8 + - - +
126F GLU 3.3 2.9 + - - +
128F ASP* 1.3 75.7 - - - +
130F ILE* 1.3 72.1 + - + +
132F GLN* 3.3 19.5 + - - +
133F ASN* 2.8 47.8 + - + -
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Residues in contact with ILE 130 (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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95F TYR* 4.2 20.2 - - + -
97F ILE* 5.4 1.3 - - + -
119F VAL* 3.7 18.2 - - + -
121F ILE* 3.7 35.0 - - + -
126F GLU* 3.0 32.4 + - + +
127F GLN* 3.3 4.9 + - - +
129F PHE* 1.3 81.6 - - + +
131F ILE* 1.3 57.7 + - - +
133F ASN* 2.9 24.9 + - - +
134F LEU* 3.3 20.3 + - + +
183F ILE* 4.9 7.9 - - + -
205F ILE* 3.9 31.2 - - + -
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Residues in contact with ILE 131 (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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127F GLN* 3.1 19.7 + - + +
128F ASP* 3.2 36.3 - - - +
130F ILE* 1.3 74.9 - - - +
132F GLN* 1.3 63.0 + - + +
133F ASN 3.3 0.2 - - - -
134F LEU* 3.5 22.9 + - + +
183F ILE* 3.8 25.1 - - + -
191F TRP* 3.7 55.1 + - + +
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Residues in contact with GLN 132 (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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128F ASP* 3.3 28.9 + - - +
129F PHE* 3.3 17.9 + - - +
130F ILE 3.1 1.0 - - - -
131F ILE* 1.3 81.0 - - + +
133F ASN* 1.3 63.3 + - - +
134F LEU 3.3 5.2 + - - +
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Residues in contact with ASN 133 (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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88F THR* 3.6 26.5 + - - +
95F TYR* 6.3 1.1 - - + -
97F ILE* 3.6 33.3 - - + +
129F PHE* 2.8 53.4 + - + -
130F ILE* 2.9 11.8 + - - +
132F GLN* 1.3 82.0 - - - +
134F LEU* 1.3 58.1 + - - +
135F LYS* 5.4 2.3 + - - +
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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