Contacts of the strand formed by residues 124 - 134 (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 GLY 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A PRO* 3.5 3.6 - - - +
121A VAL* 2.9 30.4 + - - +
122A ASP 3.4 1.8 + - - -
123A GLY* 1.3 79.7 - - - +
125A TYR* 1.3 77.5 + - - -
197A PHE* 4.0 2.1 - - - -
198A VAL 3.4 9.9 - - - -
200A GLY* 3.7 9.4 - - - -
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Residues in contact with TYR 125 (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* 3.9 25.4 - - + -
119A THR 3.1 7.2 - - - +
120A PRO* 3.6 37.2 - - + -
121A VAL* 4.1 3.0 - - - +
124A GLY* 1.3 82.9 - - - -
126A VAL* 1.3 63.8 + - - +
127A LEU* 4.2 0.9 - - + -
149A VAL* 4.1 10.5 - - + -
158A THR* 4.1 6.6 - - + +
159A PRO* 3.5 26.2 - - - +
162A LEU* 3.8 29.6 - - + +
196A ALA 3.8 0.2 - - - +
197A PHE* 3.4 5.1 - - - -
198A VAL* 2.7 43.8 + - + +
200A GLY* 4.9 4.3 - - - -
203A THR* 4.0 26.7 - - + -
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Residues in contact with VAL 126 (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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117A VAL 3.4 3.6 - - - +
118A ALA* 3.4 1.7 - - - -
119A THR* 2.7 48.4 + - - +
121A VAL* 3.8 27.1 - - + -
125A TYR* 1.3 76.1 - - - +
127A LEU* 1.3 63.0 + - - +
195A GLY* 3.7 25.6 - - - +
196A ALA 3.4 11.2 - - - +
197A PHE* 4.3 11.2 - - + +
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Residues in contact with LEU 127 (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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117A VAL 3.4 10.5 - - - +
118A ALA* 4.0 10.1 - - + -
125A TYR* 5.7 0.4 - - + -
126A VAL* 1.3 74.6 - - - +
128A LYS* 1.3 61.2 + - - +
131A TRP* 3.6 28.0 - - + -
145A LEU* 4.4 1.6 - - + -
147A ALA* 3.6 30.1 - - + -
164A VAL* 3.9 15.3 - - + -
166A LEU* 3.8 36.3 - - + -
193A VAL* 3.1 13.4 - - + +
195A GLY* 3.1 6.3 - - - -
196A ALA 2.8 34.5 + - - +
198A VAL* 4.3 9.0 - - + -
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Residues in contact with LYS 128 (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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116A GLY* 3.4 0.2 - - - -
117A VAL* 2.8 43.2 + - + +
127A LEU* 1.3 76.2 - - - +
129A GLY* 1.3 63.0 + - - +
131A TRP* 4.2 4.9 - - - -
193A VAL 3.3 14.1 - - - +
194A ASP* 3.6 24.9 - - - +
195A GLY* 4.9 0.7 - - - -
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Residues in contact with GLY 129 (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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115A MSE 4.1 2.0 - - - -
116A GLY* 4.1 6.3 - - - -
128A LYS* 1.3 78.9 - - - +
130A ARG* 1.3 59.4 + - - +
131A TRP* 3.3 17.7 - - - -
192A ILE* 3.4 5.2 - - - +
193A VAL 2.9 34.1 + - - +
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Residues in contact with ARG 130 (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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115A MSE 3.3 22.9 + - - +
129A GLY* 1.3 73.5 - - - +
131A TRP* 1.3 64.6 + - - +
174A VAL* 3.8 10.3 - - - +
177A THR* 3.4 24.0 - - - +
190A ASP* 2.8 35.0 + - + +
191A LEU 3.3 6.5 - - - +
192A ILE* 3.8 34.7 - - + +
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Residues in contact with TRP 131 (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* 3.7 32.3 - - + -
113A ALA 3.2 19.0 + - - -
115A MSE 3.4 16.4 - - + +
116A GLY* 3.4 30.3 - - - -
127A LEU* 3.6 32.5 - - + -
129A GLY* 3.3 24.5 - - - -
130A ARG* 1.3 77.4 - - - +
132A SER* 1.3 61.2 + - - +
134A SER* 6.1 0.2 - - - -
145A LEU* 3.9 24.7 - - + +
146A GLY 2.9 24.5 + - - -
190A ASP* 3.1 9.2 - - - +
191A LEU* 2.9 46.2 + - + +
193A VAL* 3.6 19.3 - - + -
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Residues in contact with SER 132 (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* 3.2 19.4 - - - +
115A MSE 5.1 5.6 - - - +
131A TRP* 1.3 74.7 - - - +
133A PHE* 1.3 74.8 + - - +
134A SER 3.4 2.7 - - - -
189A LYS 4.3 0.4 - - - -
190A ASP* 3.2 22.7 - - - +
344B HIS* 6.4 2.0 - - - -
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Residues in contact with PHE 133 (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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76A TRP* 3.7 33.9 - + - -
80A ILE* 5.9 0.7 - - + -
110A SER* 3.7 9.2 + - - -
111A PRO* 4.3 7.1 - - + +
132A SER* 1.3 81.4 - - - +
134A SER* 1.3 59.5 + - - +
135A SER* 3.1 27.7 + - - -
178A TRP* 3.9 28.2 - + + -
183A LEU* 4.8 5.2 - - + -
188A SER* 3.4 29.8 + - - -
189A LYS 3.8 0.4 + - - -
190A ASP* 4.3 0.2 + - - -
358A ALA* 4.7 11.4 - - + -
361A ALA 5.4 0.2 - - - -
362A HIS* 4.6 24.2 - + - -
340B GLY* 5.3 11.0 - - - -
343B LEU* 4.7 12.6 - - + -
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Residues in contact with SER 134 (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* 3.4 5.9 - - - +
110A SER* 2.7 29.5 + - - -
111A PRO* 4.2 3.1 - - - -
131A TRP 5.8 0.2 - - - -
132A SER 3.4 1.0 - - - -
133A PHE* 1.3 72.9 - - - +
135A SER* 1.3 62.7 + - - +
137A THR* 2.9 36.9 + - - +
187A GLY 3.5 0.9 - - - +
188A SER* 3.4 12.6 + - - -
189A LYS 3.1 20.6 + - - -
191A LEU* 3.7 17.6 - - - +
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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