Contacts of the helix formed by residues 149 - 164 (chain F) in PDB entry 3E5Q
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 PRO 149 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142F ALA 4.9 4.7 - - - +
143F GLU 3.9 16.4 - - - +
150F THR* 1.3 70.2 - - - +
151F ILE* 3.2 7.6 - - + +
152F ARG* 3.0 72.9 - - + +
153F ILE 3.9 0.3 + - - -
189F VAL* 3.5 17.3 - - + +
193F THR* 5.7 2.5 - - + -
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Residues in contact with THR 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F PRO* 1.3 75.6 - - - +
151F ILE* 1.3 58.9 + - - +
153F ILE* 3.0 32.9 + - - +
154F LEU* 3.5 13.1 + - + -
193F THR* 4.5 10.6 - - - +
197F VAL* 3.2 42.3 - - + +
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Residues in contact with ILE 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E GLU* 5.1 13.7 - - + -
149F PRO* 4.9 4.7 - - + -
150F THR* 1.3 76.4 - - + +
152F ARG* 1.3 64.0 + - + +
153F ILE 3.3 0.2 - - - -
154F LEU* 3.1 7.8 + - - -
155F ARG* 2.7 38.7 + - + +
225F LEU 3.4 25.6 - - - +
226F SER* 4.0 14.8 - - - +
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Residues in contact with ARG 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ARG* 4.8 0.6 - - - +
185E GLU* 3.1 23.6 - - - +
186E ILE* 3.1 25.2 - - - +
188E GLY* 2.8 40.5 + - - -
143F GLU* 4.1 19.2 + - - +
149F PRO* 3.0 47.8 - - + +
151F ILE* 1.3 82.3 - - + +
153F ILE* 1.3 65.9 + - - +
155F ARG 3.0 7.1 + - - -
156F LEU* 3.1 10.7 + - - +
187F THR* 3.4 12.8 - - - +
188F GLY 3.1 29.3 + - - -
189F VAL* 3.5 6.5 - - + +
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Residues in contact with ILE 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F PRO 3.9 0.4 + - - -
150F THR* 3.0 10.8 + - - +
152F ARG* 1.3 76.8 - - - +
154F LEU* 1.3 66.6 + - + +
156F LEU* 3.1 8.2 - - - +
157F PHE* 3.0 46.6 + - + -
183F ILE* 3.5 12.6 - - + -
187F THR* 3.3 26.3 - - + +
189F VAL* 4.8 8.7 - - + -
193F THR* 5.2 0.4 - - + -
194F VAL* 3.6 45.3 - - + +
197F VAL* 3.6 33.4 - - + -
198F LEU* 4.6 2.2 - - + -
201F LEU* 4.4 2.7 - - + -
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F THR* 3.5 15.3 + - + -
151F ILE* 3.1 11.9 + - - +
153F ILE* 1.3 90.5 - - + +
155F ARG* 1.3 57.5 + - - +
157F PHE* 3.5 5.2 - - + -
158F TYR* 2.7 30.3 + - - +
197F VAL* 4.0 13.5 - - + -
201F LEU* 3.8 34.8 - - + -
222F LEU* 3.4 23.5 - - + +
225F LEU* 3.5 48.2 - - + +
226F SER* 4.7 1.2 - - - -
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Residues in contact with ARG 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E SER* 2.9 27.9 + - - -
185E GLU* 3.4 33.8 + - + -
186E ILE* 3.2 21.9 - - + +
151F ILE* 2.7 18.2 + - + +
152F ARG 3.5 6.3 - - - +
154F LEU* 1.3 67.7 - - - +
156F LEU* 1.3 66.2 + - - +
157F PHE 2.7 5.0 + - - -
158F TYR* 2.7 24.4 + - - -
159F GLU* 2.4 57.7 + - - +
226F SER* 3.2 41.3 - - - +
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E LEU* 3.8 19.7 - - + -
159E GLU* 6.2 1.8 - - + -
160E LEU* 5.4 1.3 - - + -
186E ILE* 3.2 28.4 - - + +
152F ARG 3.1 5.3 + - - +
153F ILE* 3.1 13.5 - - - +
155F ARG* 1.3 77.7 - - - +
157F PHE* 1.3 56.9 + - + +
159F GLU* 3.8 2.0 - - + +
160F LEU* 3.3 43.8 + - + +
178F LEU* 5.3 8.3 - - + -
183F ILE* 4.5 28.0 - - + -
186F ILE* 3.5 35.9 - - + -
187F THR* 4.5 6.1 - - + -
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Residues in contact with PHE 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ILE* 3.0 34.9 + - + +
154F LEU* 3.5 9.0 - - + +
155F ARG 2.7 4.9 + - - -
156F LEU* 1.3 77.5 - - + +
158F TYR* 1.3 63.4 + - - +
160F LEU* 4.5 8.7 - - + -
161F CYS* 3.9 11.4 + - - +
174F ILE* 4.9 6.4 - - + +
178F LEU* 6.1 1.8 - - + -
183F ILE* 3.9 29.8 - - + -
198F LEU* 3.3 35.9 - - + -
201F LEU* 4.4 0.9 - - + -
207F LEU* 3.0 42.5 - - + +
209F LYS* 5.1 3.4 - - + -
214F ILE* 4.0 22.2 - - + -
216F VAL* 5.1 0.6 - - + +
222F LEU* 3.4 16.3 - - + +
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Residues in contact with TYR 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F LEU 2.7 14.8 + - - +
155F ARG* 2.7 23.8 + - - +
157F PHE* 1.3 70.6 - - - +
159F GLU* 1.3 78.1 + - - +
161F CYS* 3.0 5.4 + - - +
162F SER* 2.8 51.8 + - - -
219F LEU* 3.6 22.7 - - + +
222F LEU* 3.6 12.1 - - + +
223F LYS* 3.3 59.5 + - + +
226F SER* 4.4 9.0 - - - +
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Residues in contact with GLU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E MET* 5.9 2.5 - - + -
177E PRO* 3.9 19.4 - - - +
178E LEU* 4.1 10.1 - - + +
179E SER 5.7 0.2 + - - -
182E SER* 4.0 5.2 + - - -
186E ILE* 3.3 22.2 - - + -
155F ARG* 2.4 64.5 + - - +
156F LEU* 3.8 5.6 - - + +
158F TYR* 1.3 91.3 - - - +
160F LEU* 1.3 63.7 + - + +
162F SER* 2.6 22.0 + - - -
163F SER* 2.7 21.3 + - - -
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E LEU* 5.9 0.2 - - + -
160E LEU* 3.9 28.7 - - + -
176E MET* 5.7 1.8 - - + -
156F LEU* 3.3 30.0 + - + +
157F PHE* 4.9 8.7 - - + +
159F GLU* 1.3 79.5 - - + +
161F CYS* 1.3 59.9 + - - +
163F SER 3.2 1.4 + - - -
164F GLN* 2.9 50.0 + - - +
174F ILE* 4.4 17.9 - - + -
176F MET* 3.3 40.6 - - + -
178F LEU* 4.4 13.5 - - + -
214F ILE* 6.0 2.9 - - + -
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Residues in contact with CYS 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F PHE 3.9 9.5 + - - +
158F TYR 3.0 8.5 + - - +
160F LEU* 1.3 78.5 - - - +
162F SER* 1.3 59.4 + - - +
163F SER 3.3 0.2 - - - -
165F GLY* 3.3 21.0 - - - +
172F TYR* 3.2 52.3 - - - -
174F ILE* 3.7 25.0 - - + +
216F VAL* 4.2 15.5 - - + -
219F LEU* 5.3 6.7 - - + +
222F LEU* 4.5 9.6 - - + -
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Residues in contact with SER 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E PRO* 6.1 1.4 - - - +
158F TYR* 2.8 37.0 + - - -
159F GLU* 2.6 31.4 + - - -
161F CYS* 1.3 76.6 - - - +
163F SER* 1.3 60.8 + - - +
165F GLY 5.7 0.9 - - - -
172F TYR* 5.6 0.4 - - - -
219F LEU* 5.9 7.1 - - - +
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Residues in contact with SER 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E THR 5.0 2.5 - - - -
176E MET* 3.8 25.7 - - - +
177E PRO* 4.8 9.4 - - - +
159F GLU* 2.7 18.5 + - - -
160F LEU 3.2 1.2 + - - -
162F SER* 1.3 82.2 + - - +
164F GLN* 1.3 79.6 + - - +
165F GLY 3.6 2.2 - - - -
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Residues in contact with GLN 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E SER* 5.7 0.7 - - - -
164E GLN* 2.8 54.9 + - + +
175E THR 4.8 1.6 - - - +
176E MET* 3.3 16.3 - - - +
160F LEU* 2.9 41.3 + - - +
161F CYS* 4.9 0.7 - - - -
163F SER* 1.3 96.7 - - - +
165F GLY* 1.3 58.4 + - - +
166F LYS* 4.0 12.9 + - - -
173F GLU 4.0 8.1 - - - +
174F ILE* 4.3 16.6 - - + +
175F THR 4.9 1.6 + - - -
176F MET* 5.6 4.6 - - + -
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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