Contacts of the strand formed by residues 142 - 149 (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 TRP 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL* 4.9 0.4 - - + -
98A GLU* 4.0 29.5 + - + -
99A ILE* 3.6 24.8 + - + +
106A THR* 3.6 26.6 - - + +
107A TRP 3.4 1.6 + - - -
108A MSE 3.3 20.7 - - + -
109A ALA* 2.8 21.9 + - - -
140A CYS* 3.6 3.5 - - - +
141A GLN* 1.3 95.6 + - + +
143A ALA* 1.3 58.8 + - - +
165A ILE* 3.4 27.8 - - + -
166A LEU 3.2 6.1 - - - -
167A PRO* 3.4 41.7 - - + -
171A TYR* 3.4 11.7 + - - -
202A ARG* 3.9 30.5 - - - -
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Residues in contact with ALA 143 (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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108A MSE 5.0 1.8 - - - -
109A ALA* 3.2 11.0 - - + +
142A TRP* 1.3 76.7 - - - +
144A PHE* 1.3 59.9 + - - +
145A LEU* 4.0 20.9 - - + +
164A VAL 3.4 1.4 - - - +
165A ILE* 3.3 7.5 - - - +
166A LEU* 2.8 32.1 + - + +
171A TYR* 3.6 25.4 - - + +
191A LEU* 4.0 13.0 - - + -
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Residues in contact with PHE 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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84A HIS* 4.0 30.3 - - + -
87A GLU* 3.6 30.3 - - + -
88A LEU* 4.1 15.9 - - + -
108A MSE 4.0 19.0 - - + +
109A ALA 2.7 13.6 + - - +
110A SER* 3.6 13.5 - - - -
111A PRO 3.3 12.5 - - - +
112A TYR* 3.8 23.5 + + + -
143A ALA* 1.3 71.6 - - - +
145A LEU* 1.3 60.4 + - - +
163A HIS* 3.6 29.4 - - + -
164A VAL 3.4 9.6 - - - -
165A ILE* 3.8 28.0 - - + +
204A LEU* 4.5 8.1 - - + -
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Residues in contact with LEU 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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110A SER 3.8 6.5 - - - +
111A PRO* 3.3 32.8 - - + +
112A TYR* 4.5 2.2 - - - -
127A LEU* 4.4 2.2 - - + -
131A TRP* 3.9 42.8 - - + +
143A ALA* 4.0 23.3 - - + +
144A PHE* 1.3 80.7 - - - +
146A GLY* 1.3 60.7 + - - +
163A HIS* 3.3 6.0 - - - -
164A VAL* 2.8 42.4 + - + +
166A LEU* 4.3 20.2 - - + -
171A TYR* 5.4 1.1 - - + -
191A LEU* 4.1 11.2 - - + -
193A VAL* 4.6 7.4 - - + -
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Residues in contact with GLY 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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111A PRO 3.3 10.9 + - - -
112A TYR* 3.2 22.4 + - - -
113A ALA 3.5 3.2 + - - +
114A PRO* 3.5 9.7 - - - +
115A MSE 3.6 0.7 + - - -
131A TRP* 2.9 26.5 + - - -
145A LEU* 1.3 73.1 - - - +
147A ALA* 1.3 63.6 + - - +
162A LEU 3.3 8.5 - - - -
163A HIS* 4.5 3.6 - - - -
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Residues in contact with ALA 147 (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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114A PRO* 3.8 7.8 - - - +
116A GLY 3.5 13.7 - - - +
118A ALA* 4.2 8.5 - - + -
127A LEU* 3.6 30.3 - - + -
146A GLY* 1.3 77.2 - - - +
148A MSE 1.3 66.0 + - - +
161A SER* 3.4 4.7 - - - -
162A LEU* 2.8 35.1 + - + +
164A VAL* 4.8 8.7 - - + -
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Residues in contact with MSE 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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114A PRO* 3.7 37.7 + - - +
116A GLY 3.0 11.2 + - - +
117A VAL* 3.5 10.2 - - + +
118A ALA* 2.9 24.9 + - - -
147A ALA* 1.3 73.8 - - - +
149A VAL* 1.3 66.1 + - - +
150A GLY 3.8 0.2 + - - -
160A SER* 3.7 25.8 - - - +
161A SER* 4.2 13.7 - - - -
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Residues in contact with VAL 149 (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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118A ALA 3.5 6.3 - - - +
120A PRO* 3.7 15.5 - - + -
125A TYR* 4.1 7.6 - - + -
148A MSE 1.3 75.9 - - - +
150A GLY* 1.3 76.8 + - - +
151A ASP* 5.0 1.0 - - - +
158A THR* 3.3 23.1 - - - +
159A PRO* 3.3 21.1 - - + +
160A SER* 2.9 17.9 + - - +
161A SER 4.5 0.2 - - - +
162A LEU* 3.6 37.2 - - + -
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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