Contacts of the strand formed by residues 150 - 156 (chain B) in PDB entry 1OPO
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 ARG 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLY* 1.3 75.3 + - - +
151B VAL* 1.3 63.2 + - - +
178B GLU* 4.1 26.4 + - + +
179B THR* 3.3 16.4 - - - +
180B ALA* 3.7 21.6 - - - +
181B ALA 4.2 0.9 - - - +
218B THR* 3.6 2.8 - - - -
219B TYR* 2.8 71.4 + - + +
220B GLY* 5.8 0.2 - - - -
221B PHE* 3.4 7.4 - - - -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 4.6 11.7 - - + -
139B TYR* 4.1 41.7 - - + +
150B ARG* 1.3 79.3 - - - +
152B ALA* 1.3 65.3 + - - +
153B LEU* 4.9 6.7 - - + +
177B VAL 4.0 0.2 - - - +
178B GLU* 3.2 2.5 - - - +
179B THR* 2.8 51.9 + - + +
181B ALA* 4.2 13.5 - - - -
216B LEU* 3.8 22.9 - - + -
217B SER 3.7 2.5 - - - -
218B THR* 4.8 1.6 - - - +
221B PHE* 4.4 9.6 - - + -
228B VAL* 5.2 0.4 - - + -
231B LEU* 5.8 0.4 - - + -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B VAL* 1.3 75.8 - - - +
153B LEU* 1.3 64.0 + - - +
170B PHE* 3.5 23.5 - - + -
171B TYR* 5.0 0.7 - - - +
177B VAL 3.2 4.3 - - - -
178B GLU* 3.7 20.4 - - + -
215B VAL 3.8 0.2 - - - +
216B LEU* 3.4 8.5 - - - +
217B SER* 2.9 42.1 + - - +
219B TYR* 4.5 10.5 - - + +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B VAL* 4.1 28.0 - - + +
139B TYR* 4.7 16.8 - - + -
151B VAL* 4.9 4.9 - - + +
152B ALA* 1.3 84.0 - - - +
154B GLY* 1.3 58.7 + - - +
170B PHE* 3.6 4.5 - - - -
176B HIS* 3.0 4.2 - - - +
177B VAL* 2.8 39.9 + - + +
185B LYS* 5.1 3.6 - - + +
186B ASP 5.6 0.4 - - - -
187B LEU* 4.0 29.4 - - + +
214B ILE* 5.3 5.2 - - + -
215B VAL 3.3 9.6 - - - +
216B LEU* 3.7 21.5 - - + -
231B LEU* 3.7 18.8 - - + -
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Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 1.3 77.0 - - - +
155B PHE* 1.3 60.3 + - - +
170B PHE* 3.8 11.4 - - - -
173B LEU* 4.5 9.6 - - - -
175B LYS 3.2 12.1 - - - -
176B HIS* 4.0 2.7 - - - -
187B LEU* 4.1 5.6 - - - +
214B ILE* 3.5 6.8 - - - +
215B VAL* 2.8 34.4 + - - -
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 4.7 5.2 - - + -
154B GLY* 1.3 74.3 - - - +
156B ASN* 1.3 78.3 + - - +
157B ASP* 3.9 13.7 - - - -
173B LEU* 4.3 6.5 - - - +
174B GLY* 4.0 8.3 + - - -
175B LYS* 2.9 33.9 + - + +
187B LEU* 4.3 14.6 - - + -
189B ILE* 3.6 39.7 - - + -
190B PRO* 4.5 13.0 - - + -
211B PHE* 3.6 31.6 - + - -
212B GLY* 3.7 9.6 - - - -
213B ARG 3.2 29.6 - - - -
214B ILE* 4.2 3.8 - - + -
215B VAL* 5.8 0.2 - - - -
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Residues in contact with ASN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE* 1.3 80.8 - - - +
157B ASP* 1.3 82.2 + - - +
158B ASP* 2.7 19.4 + - - +
161B ASP* 4.0 24.7 + - - +
162B THR 5.2 4.0 + - - -
173B LEU* 3.9 18.9 - - + +
174B GLY* 5.6 0.7 - - - +
212B GLY* 3.0 4.0 - - - -
213B ARG* 2.8 48.4 + - + +
215B VAL* 6.1 2.5 - - + -
128C ASN* 3.5 9.2 + - - -
243C THR* 3.6 23.8 - - - +
244C LYS* 5.3 3.6 - - - +
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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