Contacts of the helix formed by residues 148 - 155 (chain A) in PDB entry 1OI4
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 ILE 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A CYS 3.6 22.7 - - - +
126A HIS* 4.0 22.2 - - + +
128A PRO* 4.4 8.5 - - + -
129A GLN* 3.7 44.0 - - + +
132A ILE* 5.3 0.9 - - + -
144A ALA* 3.8 15.9 - - + -
145A VAL* 3.1 17.9 + - + +
147A PRO* 1.3 80.0 - - + +
149A ILE* 1.3 67.2 + - - +
150A ILE 3.1 2.9 - - - -
151A ASP* 2.9 29.7 + - + +
152A VAL* 3.0 15.7 + - + +
299B ASP* 4.7 1.6 - - - +
302B ARG* 4.5 4.0 - - - +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA* 4.2 4.5 - - - +
145A VAL 3.5 9.5 + - - +
146A LYS* 3.1 38.3 + - + +
147A PRO 3.5 0.2 - - - -
148A ILE* 1.3 77.6 - - - +
150A ILE* 1.3 63.1 + - - +
152A VAL* 3.3 8.2 + - - +
153A LYS* 3.1 50.6 + - + +
159A PHE* 3.5 43.3 - - + -
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS 4.8 0.4 + - - -
147A PRO 4.0 8.1 - - - +
149A ILE* 1.3 81.7 - - - +
151A ASP* 1.3 59.8 + - - +
153A LYS* 3.4 11.6 + - + +
154A ASN* 2.9 48.5 + - - +
302B ARG* 3.3 29.4 - - - +
332B ILE* 4.0 18.4 - - + +
333B SER* 3.7 19.3 - - - +
335B ASP* 5.1 12.6 - - + +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN* 5.1 1.9 + - - +
132A ILE* 3.7 19.8 - - + +
148A ILE* 2.9 19.7 + - + +
150A ILE* 1.3 74.0 - - - +
152A VAL* 1.3 66.2 + - - +
154A ASN* 3.3 7.6 + - - +
155A ALA* 3.0 23.4 + - - +
302B ARG* 2.8 42.3 + - - -
329B GLN* 5.1 0.2 + - - -
332B ILE* 3.4 16.6 - - - +
351B ASP* 3.7 31.4 - - - +
354B ASN* 4.6 2.1 - - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 4.6 6.7 - - + -
132A ILE* 3.9 20.9 - - + -
137A ILE* 4.4 3.1 - - + -
142A LEU* 3.1 34.5 - - + -
144A ALA* 4.1 23.6 - - + -
148A ILE* 3.0 20.0 + - + +
149A ILE* 3.6 9.6 - - - +
151A ASP* 1.3 74.8 - - - +
153A LYS* 1.3 65.3 + - - +
155A ALA* 3.2 13.5 + - - +
157A ALA* 3.3 22.0 + - + +
159A PHE* 4.8 14.4 - - + -
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 3.1 37.4 + - + +
150A ILE* 3.7 12.8 - - + +
152A VAL* 1.3 72.9 - - - +
154A ASN* 1.3 59.8 + - - +
155A ALA 3.0 4.9 - - - -
156A GLY* 2.9 21.1 + - - -
157A ALA 3.9 12.1 + - - +
159A PHE* 3.6 37.5 - - + +
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Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ARG* 3.5 10.9 + - - -
150A ILE* 2.9 43.3 + - - +
151A ASP* 3.3 8.3 + - - +
153A LYS* 1.3 78.6 - - - +
155A ALA* 1.3 56.3 + - - +
156A GLY 3.1 3.0 + - - -
332B ILE* 4.0 6.8 - - - +
335B ASP* 5.2 6.1 + - - +
338B ARG* 4.4 10.5 - - - +
351B ASP* 4.7 1.2 - - - +
354B ASN* 3.5 43.5 + - + +
355B ALA* 3.5 21.2 - - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 4.2 12.8 - - + +
135A ASP* 4.6 9.1 - - - +
137A ILE* 3.8 21.8 - - + +
138A ARG* 3.4 31.4 + - - +
151A ASP 3.0 12.4 + - - +
152A VAL 3.4 10.8 - - - +
153A LYS 3.0 0.8 - - - -
154A ASN* 1.3 76.5 - - - +
156A GLY* 1.3 60.7 + - - +
157A ALA 3.3 1.0 + - - -
354B ASN* 3.5 17.3 - - - +
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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