Contacts of the helix formed by residues 149 - 160 (chain C) in PDB entry 2OTD
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 GLU 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C PRO* 4.0 24.0 - - + -
122C GLY* 5.5 0.9 - - - -
147C SER* 2.8 18.9 + - - +
148C PHE* 1.3 90.9 - - + +
150C ILE* 1.3 60.7 + - - +
151C ASP* 4.3 15.4 - - + +
152C ALA* 3.0 24.1 + - + -
153C LEU* 3.2 11.2 + - - +
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Residues in contact with ILE 150 (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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148C PHE 3.8 6.2 + - - +
149C GLU* 1.3 70.2 + - - +
151C ASP* 1.3 68.1 + - - +
152C ALA 3.2 0.2 + - - -
153C LEU* 3.3 6.7 + - - +
154C GLU* 2.8 46.4 + - + +
167C LEU* 4.0 21.8 - - + -
169C LEU* 6.2 0.2 - - + -
173C ARG* 3.4 31.2 - - - +
179C LEU* 3.6 21.1 - - + -
182C ARG* 4.1 13.7 - - - +
183C LEU* 4.8 5.2 - - + -
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Residues in contact with ASP 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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122C GLY* 4.0 18.0 - - - -
123C PRO* 3.5 29.2 - - - +
149C GLU* 4.3 16.3 - - + +
150C ILE* 1.3 74.2 + - - +
152C ALA* 1.3 59.9 + - - +
154C GLU* 3.4 11.8 + - - +
155C ALA* 3.0 28.2 + - - +
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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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115C ILE* 4.0 23.6 - - + -
117C PRO* 4.3 4.3 - - + -
122C GLY 3.3 22.7 - - - +
126C GLY* 3.6 5.5 - - - -
147C SER* 4.0 13.7 - - - +
149C GLU* 3.0 18.8 + - + +
151C ASP* 1.3 73.2 - - - +
153C LEU* 1.3 56.6 + - - +
155C ALA* 3.2 4.0 + - - +
156C ALA* 2.8 35.0 + - - +
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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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115C ILE* 5.0 6.5 - - + -
145C LEU 4.2 8.5 - - - +
146C SER 4.4 1.6 - - - -
147C SER* 3.6 32.1 - - - +
149C GLU 3.2 4.4 + - - +
150C ILE* 3.7 7.4 - - - +
152C ALA* 1.3 76.5 - - - +
154C GLU* 1.3 59.3 + - - +
156C ALA* 3.2 5.5 + - + +
157C GLN* 2.9 29.3 + - - +
165C ARG* 4.0 28.6 - - + -
166C GLY 3.6 27.6 - - - +
167C LEU* 3.8 24.2 - - + -
183C LEU* 4.3 20.6 - - + +
185C CYS* 5.0 2.7 - - - -
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Residues in contact with GLU 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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150C ILE* 2.8 34.0 + - - +
151C ASP* 3.6 9.5 - - - +
153C LEU* 1.3 71.5 - - - +
155C ALA* 1.3 63.2 + - - +
157C GLN* 3.2 14.5 + - - +
158C GLN* 3.2 27.1 + - - +
182C ARG* 3.1 30.8 + - - +
183C LEU* 3.9 17.7 - - + +
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Residues in contact with ALA 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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123C PRO* 3.3 34.1 - - + +
126C GLY 3.9 2.7 - - - -
127C LYS* 3.6 12.1 - - + +
151C ASP 3.0 18.2 + - - +
152C ALA 3.4 5.6 - - - +
154C GLU* 1.3 78.6 - - - +
156C ALA* 1.3 56.4 + - - +
158C GLN* 3.4 7.5 + - - +
159C ALA* 3.1 29.1 + - - +
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Residues in contact with ALA 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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115C ILE* 4.3 7.6 - - + -
126C GLY 3.6 16.5 + - - +
130C ALA* 3.9 12.3 - - + +
145C LEU* 4.1 16.6 - - + -
152C ALA 2.8 19.4 + - - +
153C LEU* 3.2 10.1 + - + +
155C ALA* 1.3 70.8 - - - +
157C GLN* 1.3 60.2 - - - +
160C ALA* 2.9 35.5 + - - +
165C ARG* 4.4 8.7 - - + -
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Residues in contact with GLN 157 (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 2.9 13.2 + - - +
154C GLU* 3.3 17.3 - - - +
156C ALA* 1.3 79.5 - - - +
158C GLN* 1.3 76.8 + - - +
161C PRO* 3.4 27.3 - - + +
165C ARG* 3.7 28.8 - - - +
182C ARG* 3.0 24.5 + - - +
183C LEU* 2.9 32.8 + - + +
184C GLY* 3.8 1.6 - - - +
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Residues in contact with GLN 158 (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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154C GLU* 3.2 11.4 + - + +
155C ALA* 3.4 8.7 + - - +
157C GLN* 1.3 100.2 + - - +
159C ALA* 1.3 62.3 + - - +
161C PRO* 4.2 8.2 - - - +
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Residues in contact with ALA 159 (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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127C LYS* 3.9 29.4 - - + +
130C ALA* 4.1 6.7 - - + -
131C LEU* 3.6 22.4 - - + +
134C ARG* 3.4 19.4 + - - -
155C ALA 3.1 18.4 + - - +
156C ALA 3.9 1.8 - - - +
158C GLN* 1.3 80.2 - - - +
160C ALA* 1.3 61.1 + - - +
161C PRO* 3.9 1.3 - - - +
135D GLN* 5.8 0.2 + - - -
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Residues in contact with ALA 160 (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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130C ALA* 4.1 20.0 - - + +
131C LEU 4.8 0.2 - - - +
134C ARG* 3.4 17.5 - - - +
145C LEU* 5.6 0.7 - - - +
156C ALA 2.9 11.6 + - - +
159C ALA* 1.3 80.2 - - - +
161C PRO* 1.3 69.2 - - - +
162C GLU* 3.0 7.0 + - - +
163C LEU* 3.1 39.9 + - + +
165C ARG* 4.0 1.6 + - - -
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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