Contacts of the helix formed by residues 152 - 170 (chain B) in PDB entry 3UXO
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 ARG 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A LEU* 6.1 4.9 - - - -
301A LEU* 5.8 5.7 - - - +
303A VAL 4.8 2.4 + - - -
304A THR* 4.0 4.2 - - - +
305A GLY* 3.3 33.7 - - - +
150B ILE 4.6 0.4 - - - -
151B PRO* 1.3 72.0 - - - +
153B GLU* 1.3 58.0 + - - +
155B MET* 3.3 9.5 + - - +
156B LEU* 3.0 27.6 + - + +
181B PHE* 3.0 43.0 + - + +
184B GLY* 3.2 22.3 - - - -
185B ALA 3.1 26.5 + - - +
186B GLU* 2.9 24.4 + - - +
187B SER* 5.2 0.4 - - - +
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Residues in contact with GLU 153 (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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283A ARG* 3.8 33.6 + - - +
292A THR* 6.3 2.5 - - + -
293A ILE 4.8 3.3 - - - +
151B PRO* 3.2 5.8 - - + -
152B ARG* 1.3 74.7 - - - +
154B GLU* 1.3 59.1 + - - +
156B LEU* 3.4 8.9 + - + +
157B GLN* 3.0 44.5 + - + +
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Residues in contact with GLU 154 (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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150B ILE* 3.9 8.5 - - + -
151B PRO* 3.1 33.8 + - + +
153B GLU* 1.3 78.6 - - - +
155B MET* 1.3 57.3 + - - +
157B GLN* 3.4 11.0 + - - +
158B MET* 2.8 35.0 + - - +
241B LEU* 3.7 18.9 - - + +
250B TYR* 3.8 29.9 - - + +
251B PRO* 4.4 4.1 - - - +
253B ARG* 2.9 33.9 + - - +
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Residues in contact with MET 155 (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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150B ILE* 3.6 40.2 - - + +
151B PRO 3.1 14.5 + - - +
152B ARG* 3.7 4.9 - - - +
153B GLU 3.3 0.4 - - - -
154B GLU* 1.3 73.1 - - - +
156B LEU* 1.3 57.1 + - - +
158B MET* 3.4 13.6 - - - +
159B GLN* 2.7 36.2 + - - +
177B VAL* 4.2 7.1 - - + +
181B PHE* 3.3 44.3 - - + -
188B SER* 3.9 9.9 - - - +
190B ASP 3.7 17.3 - - - +
191B MET* 3.8 26.2 - - + +
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Residues in contact with LEU 156 (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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287A LEU* 5.9 0.2 - - + -
292A THR* 3.6 37.9 - - + +
299A ARG* 5.2 2.7 - - - +
301A LEU* 4.4 10.5 - - + -
305A GLY* 3.2 30.3 - - - +
307A ALA* 4.5 10.5 - - + -
152B ARG* 3.0 16.0 + - + +
153B GLU* 3.7 9.0 - - + +
154B GLU 3.3 0.2 - - - -
155B MET* 1.3 75.1 - - - +
157B GLN* 1.3 56.3 + - - +
159B GLN* 3.8 8.5 - - - +
160B ASP* 2.7 57.7 + - - +
181B PHE* 3.9 7.4 - - + -
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Residues in contact with GLN 157 (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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294A ASN* 5.3 9.4 - - - +
153B GLU* 3.0 31.5 + - + +
154B GLU* 3.5 23.3 - - - +
156B LEU* 1.3 76.3 - - + +
158B MET* 1.3 61.3 + - - +
160B ASP* 3.3 10.2 + - - +
161B ILE* 3.2 27.0 + - + +
241B LEU* 4.1 17.9 - - + +
250B TYR* 3.8 24.4 + - - -
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Residues in contact with MET 158 (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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150B ILE* 3.9 14.1 - - + -
154B GLU* 2.8 28.5 + - - +
155B MET* 3.4 28.5 - - - +
157B GLN* 1.3 73.0 - - - +
159B GLN* 1.3 63.5 + - - +
161B ILE* 3.3 5.3 + - - +
162B VAL* 3.1 27.0 + - - +
191B MET* 3.5 44.6 - - + -
223B PHE* 4.2 9.7 - - + -
239B CYS* 3.9 16.6 - - - -
241B LEU* 3.8 24.5 - - + +
253B ARG* 4.0 19.3 - - + -
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Residues in contact with GLN 159 (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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305A GLY 2.8 29.4 + - - +
306A VAL* 3.8 13.3 - - - +
307A ALA 4.4 2.4 + - - -
155B MET 2.7 18.3 + - - +
156B LEU* 3.3 9.4 + - - +
158B MET* 1.3 71.7 - - - +
160B ASP* 1.3 57.5 + - - +
162B VAL* 3.0 4.4 + - - +
163B LEU* 2.7 62.6 + - + +
177B VAL* 3.6 29.8 - - + +
181B PHE* 3.1 29.4 - - + -
191B MET* 4.5 3.1 - - - -
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Residues in contact with ASP 160 (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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294A ASN* 5.3 1.9 + - - -
299A ARG* 2.5 38.5 + - - -
307A ALA* 4.4 2.3 + - - +
156B LEU* 2.7 45.2 + - - +
157B GLN* 3.5 9.5 + - - +
159B GLN* 1.3 80.1 - - - +
161B ILE* 1.3 57.4 + - + +
163B LEU* 3.4 5.7 + - - +
164B ASN* 2.9 34.2 + - - +
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Residues in contact with ILE 161 (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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157B GLN 3.2 9.3 + - - +
158B MET 3.5 6.5 - - - +
159B GLN 3.2 0.2 - - - -
160B ASP* 1.3 77.1 - - + +
162B VAL* 1.3 65.2 + - - +
163B LEU 3.3 0.2 + - - -
164B ASN* 3.9 2.9 - - - -
165B GLU* 3.1 38.1 + - + +
218B LEU* 4.2 6.3 - - + -
221B VAL* 4.7 4.9 - - + -
223B PHE* 3.8 37.2 - - + -
241B LEU* 3.8 18.2 - - + -
242B PRO* 3.8 34.8 - - + -
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Residues in contact with VAL 162 (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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158B MET 3.1 13.4 + - - +
159B GLN* 3.0 9.0 + - - +
161B ILE* 1.3 75.7 - - - +
163B LEU* 1.3 64.9 + - + +
165B GLU* 4.0 1.0 - - - +
166B VAL* 3.0 38.2 + - + +
175B ALA* 5.3 0.9 - - + -
177B VAL* 6.0 0.2 - - + -
191B MET* 4.0 15.5 - - + -
193B VAL* 4.5 25.4 - - + -
214B VAL* 5.5 0.7 - - + -
218B LEU* 4.1 24.2 - - + +
223B PHE* 3.4 26.7 - - + -
255B ILE* 4.6 3.4 - - + -
257B ILE* 5.4 2.7 - - + -
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Residues in contact with LEU 163 (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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306A VAL* 5.4 9.4 - - + -
307A ALA 5.8 2.9 - - - +
159B GLN* 2.7 55.0 + - + +
160B ASP* 4.1 5.4 - - - +
162B VAL* 1.3 78.3 - - + +
164B ASN* 1.3 66.1 + - - +
166B VAL* 3.8 5.4 - - + +
167B LYS* 3.0 27.0 + - - +
175B ALA* 4.3 31.2 - - + +
176B THR* 5.4 0.4 - - - +
177B VAL* 5.0 6.7 - - + +
193B VAL* 5.9 0.4 - - + -
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Residues in contact with ASN 164 (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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160B ASP 2.9 19.0 + - - +
161B ILE* 4.0 3.6 - - - +
163B LEU* 1.3 77.4 - - - +
165B GLU* 1.3 75.5 + - - +
167B LYS* 3.1 27.3 + - - +
168B LYS* 3.0 43.0 + - - +
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Residues in contact with GLU 165 (chain B).
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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161B ILE* 3.1 25.1 + - + +
162B VAL 4.2 0.2 - - - +
164B ASN* 1.3 88.8 + - + +
166B VAL* 1.3 63.2 + - + +
168B LYS* 3.3 14.2 - - - +
169B LEU* 3.2 28.3 + - - +
217B GLN* 3.5 30.7 + - + +
218B LEU* 4.0 24.7 - - + -
221B VAL* 3.8 27.6 - - + +
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Residues in contact with VAL 166 (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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162B VAL* 3.0 35.0 + - + +
163B LEU* 3.8 6.1 - - + +
164B ASN 3.2 0.4 - - - -
165B GLU* 1.3 75.0 - - + +
167B LYS* 1.3 63.0 + - + +
169B LEU* 2.9 25.4 + - + +
170B ASP 3.1 11.6 + - - +
173B TYR* 3.4 35.9 - - + +
175B ALA* 4.7 9.9 - - + +
195B LEU* 4.3 11.7 - - + -
214B VAL* 3.9 33.4 - - + -
218B LEU* 5.6 1.3 - - + -
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Residues in contact with LYS 167 (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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309A GLU* 6.1 1.3 - - - -
163B LEU 3.0 15.8 + - - +
164B ASN* 3.1 29.8 + - - +
166B VAL* 1.3 78.4 - - + +
168B LYS* 1.3 86.3 + - - +
169B LEU 3.4 0.2 + - - -
170B ASP 3.6 8.5 + - - -
171B PRO* 3.5 34.1 - - + +
173B TYR* 5.5 2.2 - - - +
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Residues in contact with LYS 168 (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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164B ASN* 3.0 37.6 + - - +
165B GLU* 3.3 17.5 - - - +
166B VAL 3.1 0.2 - - - -
167B LYS* 1.3 109.8 - - - +
169B LEU* 1.3 69.0 + - + +
171B PRO* 5.4 0.9 - - - +
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Residues in contact with LEU 169 (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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165B GLU* 3.2 11.6 + - + +
166B VAL* 2.9 11.5 + - + +
168B LYS* 1.3 88.3 - - + +
170B ASP* 1.3 64.5 + - - +
171B PRO* 4.5 1.8 - - - +
173B TYR* 4.2 8.5 - - + -
213B ARG* 3.6 60.4 + - + +
214B VAL* 3.8 21.8 - - + +
217B GLN* 3.5 37.9 - - + +
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Residues in contact with ASP 170 (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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166B VAL 3.1 3.8 + - - +
167B LYS* 3.6 4.6 - - - -
169B LEU* 1.3 82.7 - - - +
171B PRO* 1.3 75.2 - - - +
172B GLU* 3.1 20.0 + - - +
173B TYR* 3.0 41.4 + - + +
197B HIS* 3.5 20.8 + - - -
213B ARG* 6.2 1.1 - - - +
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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