Contacts of the strand formed by residues 143 - 148 (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 PHE 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ILE* 4.8 0.4 - - + -
137A TRP 3.4 5.4 - - - +
138A GLN* 3.5 40.6 - - + -
142A GLY* 1.3 80.5 - - - -
144A GLY* 1.3 59.8 + - - +
159A GLU* 3.3 13.2 - - - -
160A PRO* 3.3 13.9 + - + +
162A ASP* 3.4 36.6 - - - -
163A ARG* 3.5 8.1 - - + -
166A MET* 3.6 32.8 - - + -
184A PHE* 4.0 15.7 - + - -
186A GLU* 4.7 4.3 - - + -
189A LEU* 3.6 28.7 - - + -
232A ARG* 3.2 26.5 + - - +
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Residues in contact with GLY 144 (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* 3.4 5.7 - - - +
137A TRP* 2.7 49.2 + - - +
143A PHE* 1.3 75.0 - - - +
145A TYR* 1.3 61.6 - - - +
158A SER 3.8 4.7 - - - -
232A ARG 3.9 16.8 - - - -
233A GLY 4.2 0.2 - - - -
236A ALA* 4.0 6.7 - - - -
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Residues in contact with TYR 145 (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* 3.3 32.3 - - + +
135A ALA 3.3 13.0 - - - -
136A ILE* 3.9 11.0 - - + -
144A GLY* 1.3 72.7 - - - +
146A ALA* 1.3 71.1 + - - +
147A THR* 3.4 19.7 - - + -
157A LEU* 3.7 1.2 - - - -
158A SER* 3.1 40.8 + - - +
160A PRO* 4.3 6.5 - - + -
166A MET* 3.5 24.9 - - + -
169A GLU* 3.9 20.2 - - - -
170A LEU* 3.5 22.6 - - + +
173A THR* 2.6 32.8 + - + -
175A PRO* 3.5 10.7 - - - +
178A LEU* 4.3 0.4 - - + -
233A GLY* 4.4 4.2 - - - +
236A ALA* 3.9 3.9 - - - +
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Residues in contact with ALA 146 (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* 3.1 6.9 - - - +
135A ALA 2.9 30.2 + - - +
145A TYR* 1.3 81.2 - - - +
147A THR* 1.3 62.9 + - - +
155A PHE* 4.8 1.8 - - + -
156A ARG 3.2 15.9 - - - +
157A LEU* 4.4 0.9 - - - +
158A SER* 5.6 0.2 - - - -
233A GLY 4.6 0.9 - - - +
236A ALA* 4.0 4.9 - - + -
237A ALA* 3.7 36.6 - - + +
240A LEU* 3.3 8.5 - - + +
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Residues in contact with THR 147 (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* 3.9 19.6 - - + +
133A LEU 3.3 5.4 - - - -
134A ALA* 4.2 4.5 - - + -
145A TYR* 3.4 37.7 - - + +
146A ALA* 1.3 75.2 - - - +
148A LEU* 1.3 60.9 + - - +
154A ARG 3.9 1.1 - - - +
155A PHE* 3.5 3.5 - - - -
156A ARG* 2.8 49.6 + - - +
172A ARG* 5.9 0.2 + - - -
173A THR* 3.8 20.3 - - + +
240A LEU* 3.9 2.0 - - - -
261A GLU* 5.3 1.7 + - - -
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Residues in contact with LEU 148 (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* 3.7 4.8 - - - -
133A LEU* 2.8 38.2 + - + +
147A THR* 1.3 74.9 - - - +
149A ASP* 1.3 70.4 + - - +
150A ILE* 4.0 15.9 + - + +
153A GLY 4.3 1.8 - - - -
154A ARG 3.4 17.0 - - - +
155A PHE* 4.0 20.6 - - + -
240A LEU* 3.3 32.3 - - + +
241A LEU* 5.9 0.9 - - + -
244A ALA* 4.0 17.9 - - + -
255A ILE* 3.6 37.9 - - + -
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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