Contacts of the strand formed by residues 189 - 199 (chain A) in PDB entry 2OR0
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 LYS 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASP 6.0 0.4 - - - -
26A CYS* 4.5 16.2 - - - -
27A ARG* 4.9 7.5 - - - +
132A SER 4.3 0.2 - - - -
133A PHE 3.8 0.5 + - - -
134A SER* 3.1 33.5 + - - -
137A THR* 4.2 3.4 - - + -
138A ASP* 2.9 31.8 + - - +
173A ILE* 3.7 22.9 - - + -
174A VAL 3.6 8.7 - - - +
175A GLU* 3.0 35.2 + - - +
176A ASP 5.2 2.0 - - - +
177A THR* 3.4 17.0 - - - +
178A TRP* 4.1 16.8 - - + +
187A GLY 2.9 12.3 + - - +
188A SER* 1.3 72.9 - - - +
190A ASP* 1.3 66.6 + - - +
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Residues in contact with ASP 190 (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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130A ARG* 2.8 43.9 + - + +
131A TRP 3.1 14.1 - - - +
132A SER* 3.2 24.4 - - - +
133A PHE 4.3 0.9 + - - -
173A ILE* 3.6 4.0 - - - -
174A VAL* 2.8 34.2 + - + -
177A THR* 3.0 28.4 + - - +
188A SER 4.9 0.3 - - - +
189A LYS* 1.3 75.2 - - - +
191A LEU* 1.3 59.2 + - - +
344B HIS* 5.8 0.3 + - - -
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Residues in contact with LEU 191 (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 ALA* 5.2 0.2 - - + -
110A SER 4.1 0.2 - - - +
130A ARG* 3.3 4.9 - - - +
131A TRP* 2.9 45.4 + - + +
134A SER* 3.7 24.5 - - - +
137A THR* 3.4 23.6 - - + +
143A ALA* 4.0 19.1 - - + -
145A LEU* 4.1 17.0 - - + -
171A TYR* 3.9 28.7 - - + -
172A GLN 3.2 6.3 - - - +
173A ILE* 3.7 22.0 - - + -
189A LYS 3.9 0.2 + - - -
190A ASP* 1.3 81.5 - - - +
192A ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 192 (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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129A GLY 3.4 6.5 - - - +
130A ARG* 3.8 39.5 - - + +
171A TYR* 3.6 4.2 - - - +
172A GLN* 2.8 59.0 + - - +
174A VAL* 3.8 21.3 - - + +
191A LEU* 1.3 75.5 - - - +
193A VAL* 1.3 69.1 + - - +
194A ASP* 3.7 23.5 + - - +
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Residues in contact with VAL 193 (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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127A LEU* 3.1 26.5 - - + +
128A LYS* 3.3 7.3 - - - +
129A GLY 2.9 31.1 + - - +
131A TRP* 3.6 26.7 - - + -
145A LEU* 4.6 4.0 - - + -
166A LEU* 3.9 15.9 - - + -
170A ASP 4.0 5.2 - - - +
171A TYR* 3.6 22.0 - - + +
191A LEU* 5.6 0.9 - - + -
192A ILE* 1.3 78.5 - - - +
194A ASP* 1.3 64.7 + - - +
195A GLY 4.0 0.2 - - - +
196A ALA* 3.6 27.4 - - + +
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Residues in contact with ASP 194 (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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127A LEU 4.0 1.8 - - - -
128A LYS* 3.6 27.8 - - - +
172A GLN* 5.7 2.0 + - - -
192A ILE* 3.7 19.8 + - - +
193A VAL* 1.3 74.5 - - - +
195A GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 195 (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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126A VAL* 3.7 18.1 - - - +
127A LEU 3.1 11.3 + - - -
128A LYS* 4.9 0.7 - - - -
193A VAL* 4.0 0.4 - - - +
194A ASP* 1.3 80.4 - - - +
196A ALA* 1.3 60.6 + - - +
197A PHE 4.0 0.9 + - - -
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Residues in contact with ALA 196 (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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126A VAL* 3.4 2.4 - - - -
127A LEU* 2.8 35.1 + - - +
166A LEU* 4.0 14.6 - - + -
170A ASP* 3.8 28.9 - - + +
193A VAL* 3.6 20.2 - - + -
195A GLY* 1.3 75.5 - - - +
197A PHE* 1.3 64.7 + - - +
198A VAL* 3.5 1.4 + - - +
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Residues in contact with PHE 197 (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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121A VAL* 3.9 26.2 - - + -
122A ASP 4.2 5.6 - - - -
123A GLY* 3.8 21.3 - - - -
124A GLY 4.0 10.1 - - - -
125A TYR 3.4 16.2 - - - -
126A VAL* 4.3 10.0 - - + +
170A ASP* 4.3 13.3 + - - +
195A GLY 4.0 2.0 + - - -
196A ALA* 1.3 73.1 - - - +
198A VAL* 1.3 63.1 + - - +
199A PRO* 3.8 28.8 - - + +
202A ARG* 5.2 2.4 + - - -
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Residues in contact with VAL 198 (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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124A GLY* 3.4 0.3 - - - -
125A TYR* 2.7 45.9 + - + +
127A LEU* 4.3 11.4 - - + -
164A VAL* 4.2 12.3 - - + -
165A ILE 3.8 18.4 - - - +
166A LEU* 3.7 31.9 - - + -
196A ALA 3.9 9.6 - - - +
197A PHE* 1.3 79.7 - - - +
199A PRO* 1.3 75.8 - - + +
202A ARG* 3.9 9.2 - - + +
203A THR* 3.8 17.0 - - + -
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Residues in contact with PRO 199 (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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123A GLY 3.5 10.1 - - - +
197A PHE* 3.8 27.8 - - + +
198A VAL* 1.3 88.8 - - - +
200A GLY* 1.3 65.8 + - - +
201A TYR* 3.6 29.8 - - + +
202A ARG* 3.0 51.6 + - - +
203A THR* 3.5 9.4 - - - +
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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