Contacts of the helix formed by residues 138 - 149 (chain B) in PDB entry 3UO9
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 SER 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B PRO* 1.3 80.3 - - - +
139B LEU* 1.3 61.4 + - - +
140B GLU* 3.1 16.5 + - - +
141B ASP* 3.4 37.2 + - - +
142B LEU* 2.9 29.8 + - - +
201B LYS* 3.7 15.4 + - - -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO 3.6 1.4 + - - -
138B SER* 1.3 72.8 + - - +
140B GLU* 1.3 71.0 + - - +
142B LEU* 3.4 16.2 + - + +
143B LEU* 3.2 20.3 + - - +
208B ILE* 4.0 21.3 - - + -
209B VAL* 5.2 11.7 - - + +
212B THR* 3.2 40.2 - - + +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B SER* 3.1 14.5 + - - +
139B LEU* 1.3 80.3 + - - +
141B ASP* 1.3 56.2 + - - +
143B LEU* 3.4 0.7 + - - +
144B PHE* 2.9 29.0 + - - +
200B PHE* 3.7 6.3 - - - -
201B LYS* 3.9 41.1 + - + -
204B VAL* 4.0 15.0 - - + -
205B GLN* 3.4 24.7 - - - +
208B ILE* 3.7 37.3 - - + +
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Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO 5.5 1.8 - - - -
138B SER* 3.3 32.0 + - - +
140B GLU* 1.3 75.0 - - - +
142B LEU* 1.3 65.4 + - + +
144B PHE* 3.2 8.2 + - - +
145B TYR* 2.9 45.7 + - + -
197B LYS* 3.6 33.4 + - + +
201B LYS* 4.5 12.0 - - - +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 3.5 18.4 - - + +
138B SER 2.9 21.7 + - - +
139B LEU* 3.5 18.8 - - + +
141B ASP* 1.3 76.1 - - + +
143B LEU* 1.3 62.7 + - - +
145B TYR* 3.3 13.3 + - + +
146B THR* 3.2 28.9 + - + +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 3.2 10.6 + - + +
140B GLU 3.7 7.9 - - - +
142B LEU* 1.3 75.7 - - - +
144B PHE* 1.3 64.5 + - - +
146B THR* 2.9 25.3 + - - +
147B ILE* 3.1 20.4 + - + +
159B PHE* 5.4 0.7 - - + -
200B PHE* 4.0 18.8 - - + -
204B VAL* 5.0 0.2 - - + -
208B ILE* 3.7 24.7 - - + -
211B LEU* 4.0 23.8 - - + -
212B THR* 4.2 16.6 - - + +
215B PHE* 3.7 37.9 - - + -
216B ARG* 5.5 4.3 - - - +
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLU 2.9 18.6 + - - +
141B ASP* 3.4 8.3 - - - +
143B LEU* 1.3 78.1 - - - +
145B TYR* 1.3 77.9 + + - +
148B ALA* 2.9 40.9 + - + +
151B GLN 4.9 2.5 - - - -
152B GLU 4.1 18.6 - - - -
153B LYS* 4.4 3.4 - - - -
154B ILE* 3.4 35.0 - - + +
195B LEU 4.2 3.4 - - - -
196B ASP* 3.7 8.1 - - - -
197B LYS* 3.5 48.7 - - + +
200B PHE* 3.6 30.4 - + + -
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ASP* 2.9 42.1 + - + +
142B LEU* 3.3 12.1 + - + +
144B PHE* 1.3 94.1 - + - +
146B THR* 1.4 62.6 + - + +
148B ALA* 3.4 5.0 + - + +
149B GLU* 3.1 21.5 + - - -
150B GLY* 4.0 7.2 + - - +
197B LYS* 4.3 16.9 - - + +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LEU* 3.2 15.5 + - + +
143B LEU* 2.9 28.3 + - - +
145B TYR* 1.4 75.7 - - + +
147B ILE* 1.3 61.8 + - - +
149B GLU* 3.9 15.2 + - - +
215B PHE* 5.4 1.4 - - - +
216B ARG* 4.2 28.3 + - - +
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.1 29.1 + - + +
146B THR* 1.3 80.0 - - - +
148B ALA* 1.3 63.1 + - - +
149B GLU* 3.2 4.7 + - - +
154B ILE* 3.9 28.0 - - + -
158B LYS* 2.9 28.0 + - + +
159B PHE* 3.8 30.3 - - + +
162B ALA* 4.9 9.6 - - + -
200B PHE* 4.1 4.7 - - + -
215B PHE* 3.7 41.7 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE* 2.9 30.3 + - + +
145B TYR* 3.6 7.9 - - + +
147B ILE* 1.3 79.1 - - - +
149B GLU* 1.3 66.2 + - - +
150B GLY* 4.2 3.1 - - - +
151B GLN* 3.4 37.3 + - - +
153B LYS 5.0 2.9 - - - +
154B ILE* 3.7 19.0 - - + +
158B LYS* 4.0 8.1 + - - +
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TYR 3.1 8.7 + - - -
146B THR* 3.9 11.0 + - - +
147B ILE 3.2 6.8 - - - +
148B ALA* 1.3 82.0 - - - +
150B GLY* 1.4 59.5 + - - +
151B GLN* 3.2 4.9 + - - +
158B LYS* 5.0 4.0 - - - +
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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