Contacts of the strand formed by residues 150 - 156 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C GLY* 1.3 74.3 + - - -
151C VAL* 1.3 73.4 + - - +
152C ALA* 4.4 2.0 - - + +
171C TYR* 3.4 23.4 + - - +
178C GLU* 4.1 21.0 - - - +
179C THR* 3.1 29.0 + - - +
180C ALA* 4.4 7.9 - - - +
217C SER 5.2 0.4 - - - +
218C THR* 3.6 11.4 - - - -
219C TYR* 3.1 50.0 + - + +
220C GLY* 4.9 0.6 - - - -
221C PHE* 3.5 10.9 - - - -
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C VAL* 4.9 4.5 - - + -
139C TYR* 4.1 43.7 - - + +
150C ARG* 1.3 81.1 - - - +
152C ALA* 1.3 65.8 + - - +
153C LEU* 5.2 4.5 - - + -
178C GLU 3.6 0.5 - - - -
179C THR* 2.9 49.3 + - + +
181C ALA* 4.6 6.1 - - - -
216C LEU* 4.3 17.7 - - + -
217C SER 3.7 3.4 - - - -
218C THR* 4.2 9.0 - - + -
221C PHE* 4.0 17.9 - - + -
228C VAL* 5.3 0.2 - - + -
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ARG* 4.2 3.1 - - + -
151C VAL* 1.3 76.7 - - - +
153C LEU* 1.3 65.1 + - - +
170C PHE* 3.5 25.5 - - + -
171C TYR* 3.7 21.1 - - + +
177C VAL 3.3 11.0 - - - +
178C GLU* 4.3 3.6 - - + -
216C LEU* 3.5 7.3 - - - +
217C SER* 3.0 37.5 + - - +
219C TYR* 5.8 0.2 - - + -
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 4.0 27.6 - - + +
139C TYR* 4.6 13.0 - - + -
151C VAL* 5.2 4.3 - - + -
152C ALA* 1.3 82.1 - - - +
154C GLY* 1.3 57.3 + - - +
170C PHE* 3.5 4.9 - - - -
176C HIS* 3.1 4.3 - - - +
177C VAL* 2.8 48.5 + - + +
185C LYS* 5.0 5.6 - - + +
187C LEU* 3.9 21.0 - - + +
214C ILE* 5.4 4.9 - - + -
215C VAL 3.3 9.4 - - - +
216C LEU* 3.8 23.3 - - + -
231C LEU* 4.2 22.9 - - + -
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Residues in contact with GLY 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C LEU* 1.3 76.6 - - - +
155C PHE* 1.3 61.1 + - - +
170C PHE* 3.6 12.7 - - - -
173C LEU* 4.5 6.7 - - - -
175C LYS 3.2 11.0 - - - -
176C HIS* 4.1 2.7 - - - -
187C LEU* 4.0 4.7 - - - +
214C ILE* 3.6 6.2 - - - +
215C VAL* 2.8 37.7 + - - -
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Residues in contact with PHE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 4.5 5.8 - - + -
135C LEU* 5.8 0.2 - - + -
154C GLY* 1.3 74.8 - - - +
156C ASN* 1.3 68.9 + - - +
157C ASP* 3.6 23.6 - - + -
173C LEU* 4.3 5.4 - - - +
174C GLY* 4.1 7.4 + - - -
175C LYS* 3.0 33.7 + - + +
187C LEU* 4.3 2.7 - - + -
189C ILE* 3.3 50.0 - - + -
190C PRO* 4.5 11.7 - - + -
211C PHE* 3.8 19.3 - + - -
212C GLY* 3.7 14.8 - - - -
213C ARG 3.0 37.0 - - - -
214C ILE* 4.1 10.1 - - + -
215C VAL* 5.7 0.2 - - - -
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Residues in contact with ASN 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASN* 3.3 14.6 + - - +
243A THR* 4.0 9.1 + - - -
244A LYS* 5.3 1.2 - - - +
155C PHE* 1.3 79.1 - - - +
157C ASP* 1.3 60.5 + - - +
158C ASP 2.6 40.6 + - - +
161C ASP* 4.1 21.6 + - - +
162C THR 5.1 4.8 + - - -
173C LEU* 3.9 26.4 - - + +
174C GLY* 5.6 1.3 - - - +
212C GLY* 3.3 1.9 - - - -
213C ARG* 2.7 46.9 + - + +
215C VAL* 5.9 2.7 - - + -
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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