Contacts of the strand formed by residues 150 - 156 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLY* 1.3 75.0 + - - -
151A VAL* 1.3 79.8 + - - +
152A ALA* 4.2 2.0 - - + +
171A TYR* 3.8 16.7 + - - +
178A GLU* 4.1 16.7 - - - +
179A THR* 2.9 31.5 + - - +
180A ALA* 4.0 5.9 - - - +
217A SER 5.0 0.4 - - - +
218A THR* 3.4 14.4 - - - -
219A TYR* 2.9 49.7 + - + +
220A GLY* 4.9 0.2 - - - -
221A PHE* 3.3 16.8 - - - -
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Residues in contact with VAL 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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94A VAL* 4.8 5.6 - - + -
139A TYR* 4.2 41.7 - - + +
150A ARG* 1.3 80.5 - - - +
152A ALA* 1.3 65.7 + - - +
153A LEU* 5.3 3.6 - - + -
179A THR* 2.9 51.1 + - + +
181A ALA* 4.3 7.9 - - + -
216A LEU* 4.3 17.3 - - + -
217A SER 3.6 3.6 - - - -
218A THR* 4.3 7.6 - - + -
221A PHE* 3.8 17.9 - - + -
228A VAL* 5.2 0.7 - - + -
231A LEU* 6.2 0.4 - - + -
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ARG* 4.2 3.4 - - + -
151A VAL* 1.3 76.8 - - - +
153A LEU* 1.3 71.4 + - - +
170A PHE* 3.6 24.1 - - + -
171A TYR* 3.9 20.4 - - + +
177A VAL 3.3 13.0 - - - +
178A GLU* 4.1 4.0 - - - -
216A LEU* 3.5 0.9 - - - +
217A SER* 3.0 37.8 + - - +
219A TYR* 5.9 0.2 - - + -
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Residues in contact with LEU 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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137A VAL* 4.0 29.6 - - + +
139A TYR* 4.5 17.5 - - + +
151A VAL* 5.3 3.6 - - + -
152A ALA* 1.3 84.4 - - - +
154A GLY* 1.3 57.8 + - - +
170A PHE* 3.5 4.9 - - - -
176A HIS* 3.0 5.7 - - - +
177A VAL* 2.8 52.2 + - + +
185A LYS* 5.2 2.7 - - + +
187A LEU* 3.8 21.3 - - + +
214A ILE* 5.2 7.0 - - + -
215A VAL 3.4 9.9 - - - +
216A LEU* 3.6 22.0 - - + -
231A LEU* 3.9 17.3 - - + -
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Residues in contact with GLY 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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153A LEU* 1.3 76.8 - - - +
155A PHE* 1.3 60.6 + - - +
170A PHE* 3.7 8.9 - - - -
173A LEU* 4.4 11.0 - - - -
175A LYS 3.3 10.1 - - - -
176A HIS* 4.0 5.4 - - - -
187A LEU* 3.9 4.8 - - - +
214A ILE* 3.5 6.6 - - - +
215A VAL* 2.8 35.7 + - - -
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Residues in contact with PHE 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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109A VAL* 4.6 6.1 - - + -
135A LEU* 5.5 0.2 - - + -
154A GLY* 1.3 75.1 - - - +
156A ASN* 1.3 59.5 + - - +
157A ASP* 3.5 37.0 - - + -
173A LEU* 4.2 6.2 - - - +
174A GLY* 3.9 9.0 + - - -
175A LYS* 2.9 34.4 + - + +
187A LEU* 4.3 1.1 - - + -
189A ILE* 3.4 47.8 - - + -
190A PRO* 4.6 14.1 - - + -
211A PHE* 3.7 33.7 - + - -
212A GLY* 3.8 3.8 - - - -
213A ARG 3.3 30.5 - - - -
214A ILE* 4.2 6.3 - - + -
215A VAL* 6.0 0.2 - - - -
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Residues in contact with ASN 156 (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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155A PHE* 1.3 78.7 - - - +
157A ASP* 1.3 58.0 + - - +
158A ASP* 2.7 41.0 + - - +
161A ASP* 3.9 22.2 + - - +
162A THR 5.0 4.2 + - - -
173A LEU* 4.3 19.4 - - + +
174A GLY* 5.5 1.3 - - - +
212A GLY* 3.3 0.2 - - - -
213A ARG* 2.7 47.0 + - + +
215A VAL* 6.2 1.8 - - + -
128B ASN* 3.2 16.8 + - - +
243B THR* 3.9 16.5 + - - -
244B LYS* 5.0 0.6 - - - +
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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