Contacts of the strand formed by residues 133 - 138 (chain A) in PDB entry 1OH7
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 LEU 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLY* 3.6 14.8 + - - +
118A THR* 4.1 11.0 - - + -
132A LEU* 1.3 75.1 - - - +
134A ALA* 1.3 61.9 + - - +
147A THR* 3.3 2.6 - - - -
148A LEU* 2.8 43.7 + - + +
150A ILE* 6.1 0.9 - - + +
177A GLU* 3.6 44.2 - - + +
179A LEU* 4.1 15.5 - - + -
240A LEU* 3.3 39.8 - - + +
243A TYR* 3.9 17.3 - - + -
244A ALA* 4.7 6.1 - - + +
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Residues in contact with ALA 134 (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 LEU 4.0 0.2 - - - -
133A LEU* 1.3 74.5 - - - +
135A ALA* 1.3 60.4 + - - +
145A TYR* 3.3 33.2 - - + +
146A ALA 3.1 11.2 - - - +
147A THR* 4.2 4.0 - - + -
175A PRO* 3.5 20.0 - - + -
177A GLU 3.0 7.4 + - - +
178A LEU* 3.4 6.2 - - + -
179A LEU* 2.9 29.1 + - - +
240A LEU* 3.9 3.4 - - - -
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Residues in contact with ALA 135 (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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134A ALA* 1.3 74.8 - - - +
136A ILE* 1.3 62.4 + - - +
145A TYR* 3.3 7.7 - - - -
146A ALA 2.9 30.7 + - - +
178A LEU* 4.0 1.3 - - - -
179A LEU* 3.3 16.6 - - + +
204A PHE* 4.6 1.6 - - + -
236A ALA* 3.3 33.8 - - + +
239A CYS* 4.4 5.4 - - + -
240A LEU* 3.7 15.8 - - + +
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Residues in contact with ILE 136 (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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135A ALA* 1.3 76.9 - - - +
137A TRP* 1.3 70.9 + - - +
143A PHE* 4.9 0.4 - - + -
144A GLY 3.4 11.2 - - - +
145A TYR* 3.9 7.0 - - + -
166A MET* 3.6 34.5 - - + -
170A LEU* 4.3 4.3 - - + -
178A LEU* 3.4 25.8 - - + -
179A LEU 2.9 6.9 + - - -
180A TYR* 3.4 32.0 - - + -
181A ALA 3.5 0.3 + - - -
184A PHE* 3.7 20.9 - - + -
190A ILE* 3.5 26.2 - - + -
204A PHE* 3.3 12.1 - - - -
236A ALA* 4.7 0.7 - - - -
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Residues in contact with TRP 137 (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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136A ILE* 1.3 79.1 - - - +
138A GLN* 1.3 75.7 + - - +
139A ASP* 3.1 27.3 + - - -
143A PHE* 3.4 4.3 - - - +
144A GLY* 2.7 51.3 + - - +
181A ALA* 4.0 15.9 - - + -
183A ASP* 4.7 6.7 - - - -
184A PHE* 3.9 11.9 - - - -
201A LEU* 4.1 22.0 - - + -
204A PHE* 3.4 37.0 - + + -
232A ARG* 3.3 27.2 + - + +
235A CYS* 4.2 21.8 - - + -
236A ALA 4.6 3.4 - - - -
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Residues in contact with GLN 138 (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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137A TRP* 1.3 95.0 - - - +
139A ASP* 1.3 74.4 + - - +
142A GLY 3.5 12.1 - - - +
143A PHE* 3.5 26.0 - - + -
181A ALA* 5.3 1.0 - - - +
183A ASP* 4.6 11.3 + - - +
184A PHE* 3.6 21.9 - - + +
185A ALA* 3.2 23.4 + - - +
186A GLU* 2.9 38.6 + - - +
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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