Contacts of the helix formed by residues 161 - 178 (chain E) in PDB entry 3MQ6
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 VAL 161 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E LEU 3.8 0.2 + - - -
160E LEU* 1.3 74.8 - - - +
162E PRO* 1.3 69.0 - - + +
163E GLU* 3.4 21.5 - - + +
164E SER* 2.9 39.4 + - - +
165E GLN 3.1 6.2 + - - -
228E GLY 3.6 3.6 - - - +
229E ARG* 3.5 25.6 - - - +
230E VAL 2.9 22.8 + - - +
231E GLN* 3.8 30.3 - - - +
232E PRO* 4.7 0.4 - - + -
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Residues in contact with PRO 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E LEU 3.5 2.7 - - - +
161E VAL* 1.3 84.1 - - + +
163E GLU* 1.3 70.6 - - - +
165E GLN* 3.3 13.4 + - + +
166E GLU* 2.8 47.8 + - - +
228E GLY* 3.5 18.2 - - - +
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Residues in contact with GLU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E VAL* 3.4 23.1 - - + +
162E PRO* 1.3 92.3 - - + +
164E SER* 1.3 57.2 + - - +
166E GLU* 3.5 14.5 + - - +
167E VAL* 3.1 30.3 + - - +
231E GLN* 4.7 4.7 + - - -
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Residues in contact with SER 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E LEU* 3.9 17.7 - - - -
161E VAL* 2.9 17.1 + - - +
163E GLU* 1.3 76.0 - - - +
165E GLN* 1.3 66.9 + - - +
166E GLU 3.1 1.3 - - - -
167E VAL* 3.1 13.1 + - - +
168E ILE* 3.2 16.8 + - - +
231E GLN* 5.0 0.2 + - - -
232E PRO* 3.0 36.1 - - - +
268E LEU* 3.7 16.4 - - - +
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Residues in contact with GLN 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E VAL* 3.2 38.9 + - + +
158E SER* 3.6 22.5 + - - +
160E LEU* 2.9 29.1 + - + +
161E VAL 3.1 6.2 + - - +
162E PRO* 3.6 14.4 - - + +
164E SER* 1.3 75.3 - - - +
166E GLU* 1.3 58.4 + - + +
168E ILE* 3.0 6.8 + - - +
169E GLU* 2.8 29.9 + - - +
228E GLY* 4.2 6.7 - - - +
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Residues in contact with GLU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E PRO* 2.8 39.0 + - + +
163E GLU* 3.6 12.3 - - - +
165E GLN* 1.3 76.9 - - + +
167E VAL* 1.3 63.3 + - - +
169E GLU* 3.8 6.0 - - - +
170E GLU* 3.0 38.6 + - + +
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Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E GLU 3.1 16.0 + - - +
164E SER* 3.1 9.6 + - - +
166E GLU* 1.3 76.6 - - - +
168E ILE* 1.3 64.3 + - + +
170E GLU* 3.5 14.2 + - - +
171E PHE* 3.3 22.3 + - + +
267E LYS* 4.3 18.6 - - + +
268E LEU* 3.8 26.2 - - + -
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E TRP* 4.5 2.0 - - + -
157E VAL* 4.0 20.6 - - + -
160E LEU* 3.7 30.5 - - + -
164E SER 3.2 5.6 + - - +
165E GLN* 3.0 9.2 + - - +
167E VAL* 1.3 80.0 - - + +
169E GLU* 1.3 58.9 + - - +
171E PHE* 3.3 7.7 + - - +
172E ARG* 3.0 62.6 + - + +
263E LEU* 4.2 32.3 - - + +
267E LYS* 5.8 1.8 - - + -
268E LEU* 3.9 19.1 - - + -
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Residues in contact with GLU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E GLN 2.8 15.5 + - - +
166E GLU* 4.0 6.5 - - - +
168E ILE* 1.3 74.9 - - - +
170E GLU* 1.3 62.0 + - + +
172E ARG* 3.8 22.8 + - - -
173E ALA* 3.0 28.9 + - + +
176E ARG* 2.6 39.1 + - - -
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Residues in contact with GLU 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLU* 3.0 28.7 + - + +
167E VAL* 3.8 14.0 - - - +
169E GLU* 1.3 74.5 - - - +
171E PHE* 1.3 65.5 + - - +
173E ALA* 3.1 7.1 + - - +
174E GLY* 3.1 19.8 + - - -
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Residues in contact with PHE 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E VAL* 3.3 12.3 + - + +
168E ILE* 3.4 11.0 - - - +
170E GLU* 1.3 78.5 - - - +
172E ARG* 1.3 65.1 + - + +
174E GLY* 3.6 2.3 + - - -
175E LEU* 3.3 43.1 + - + +
182E LEU* 4.2 10.3 - - + -
262E LEU* 4.4 0.9 - - + -
263E LEU* 3.9 30.3 - - + -
267E LYS* 3.4 41.7 - - + -
299F LEU* 3.9 26.7 - - + -
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Residues in contact with ARG 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ASP* 4.3 9.9 + - - -
157E VAL* 4.3 10.1 - - - +
168E ILE* 3.0 44.7 + - + +
169E GLU* 3.8 20.1 + - - +
171E PHE* 1.3 81.3 - - + +
173E ALA* 1.3 67.9 + - - +
174E GLY 3.1 1.8 - - - -
175E LEU* 3.3 8.2 + - - +
176E ARG* 2.9 46.7 + - + +
182E LEU* 3.0 42.8 + - + +
183E PRO* 3.6 2.4 - - - +
184E THR* 2.5 44.7 + - - +
263E LEU* 4.9 2.3 - - + +
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Residues in contact with ALA 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E GLU* 3.0 22.1 + - + +
170E GLU* 3.1 7.8 + - - +
172E ARG* 1.3 77.0 - - - +
174E GLY* 1.3 65.6 + - - +
176E ARG* 3.4 22.3 + - - +
177E LYS* 3.3 16.6 + - - +
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Residues in contact with GLY 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLU 3.1 11.9 + - - -
171E PHE 3.9 3.4 - - - -
172E ARG 3.1 0.4 - - - -
173E ALA* 1.3 72.1 - - - +
175E LEU* 1.3 68.1 + - - +
177E LYS* 2.8 22.8 + - - +
178E ASP* 3.4 10.7 + - - -
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Residues in contact with LEU 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E PHE* 3.3 45.8 + - + +
172E ARG* 3.6 9.0 - - - +
174E GLY* 1.3 71.3 - - - +
176E ARG* 1.3 56.8 + - - +
178E ASP* 2.8 28.0 + - - +
180E LEU* 3.1 45.1 + - + +
181E GLY* 4.0 9.4 - - - +
182E LEU* 4.0 22.0 - - + +
294F ALA* 4.7 0.9 - - + -
299F LEU* 3.8 26.7 - - + -
306F VAL* 5.9 0.4 - - + -
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Residues in contact with ARG 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E GLU* 2.6 31.9 + - - -
172E ARG* 2.9 44.9 + - - +
173E ALA* 3.7 19.3 - - - +
174E GLY 3.1 0.2 - - - -
175E LEU* 1.3 73.8 - - - +
177E LYS* 1.3 61.1 + - - +
179E GLY* 3.4 11.0 + - - -
180E LEU 3.0 16.8 - - - +
181E GLY* 4.3 9.0 - - - -
182E LEU 6.1 0.4 - - - +
292F GLU* 5.6 5.8 - - - +
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Residues in contact with LYS 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ALA 3.3 9.7 + - - +
174E GLY* 2.8 14.1 + - - +
176E ARG* 1.3 78.8 - - - +
178E ASP* 1.3 64.8 + - - +
179E GLY 3.2 2.9 + - - -
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Residues in contact with ASP 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E GLY 3.9 12.6 - - - +
175E LEU* 2.8 11.6 + - - +
177E LYS* 1.3 83.4 - - - +
179E GLY* 1.3 57.2 + - - +
180E LEU* 3.2 23.6 + - + +
306F VAL 5.6 0.3 - - - +
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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