Contacts of the helix formed by residues 158 - 172 (chain E) in PDB entry 6ACQ
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 158 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E ASP* 3.0 28.4 + - - +
153E ARG* 4.0 0.4 - - - -
156E ALA 3.2 3.3 + - - -
157E THR* 1.3 78.9 - - - +
159E GLN* 1.3 59.3 + - - +
160E GLU* 3.4 9.2 + - - +
161E THR* 2.7 32.4 + - - -
162E PHE* 3.0 24.4 + - - +
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Residues in contact with GLN 159 (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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153E ARG* 3.2 31.9 + - - +
158E SER* 1.3 70.4 - - - +
160E GLU* 1.3 66.6 + - + +
162E PHE* 3.7 16.5 - - - +
163E ASP* 2.8 52.7 + - - +
178E GLU* 4.9 1.0 + - - -
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Residues in contact with GLU 160 (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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133E LYS* 5.8 2.1 + - - -
158E SER* 3.3 9.5 + - - +
159E GLN* 1.3 77.4 - - + +
161E THR* 1.3 63.1 + - - +
163E ASP* 3.7 6.2 - - - +
164E ALA* 3.0 25.3 + - - +
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Residues in contact with THR 161 (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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111E ILE* 3.6 38.6 - - + +
132E ASP 2.6 28.2 + - - +
133E LYS* 3.6 21.0 + - - +
135E ILE* 4.3 8.7 - - + -
157E THR* 4.2 10.5 - - + -
158E SER* 2.7 18.6 + - - -
160E GLU* 1.3 74.6 - - - +
162E PHE* 1.3 67.4 + - - +
164E ALA* 3.3 2.3 + - - +
165E VAL* 3.1 27.2 + - - +
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Residues in contact with PHE 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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135E ILE* 4.0 9.6 - - + +
151E VAL* 3.7 32.3 - - + -
153E ARG* 4.0 32.3 - - + +
158E SER 3.0 11.1 + - - +
159E GLN* 3.3 19.0 + - - +
161E THR* 1.3 80.4 - - - +
163E ASP* 1.3 73.7 + - - +
165E VAL* 3.2 1.4 + - - +
166E LYS* 2.8 61.1 + - + +
176E PRO* 6.1 1.1 - - + -
177E VAL 4.9 1.1 - - - -
178E GLU* 3.5 44.9 - - + -
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Residues in contact with ASP 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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159E GLN* 2.8 44.2 + - - +
160E GLU* 3.7 6.4 - - - +
162E PHE* 1.3 91.2 - - - +
164E ALA* 1.3 56.7 + - - +
166E LYS* 3.4 9.8 + - - +
167E GLU* 3.0 40.0 + - - +
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Residues in contact with ALA 164 (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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1E MET* 3.4 23.4 - - + +
111E ILE* 4.3 6.1 - - + -
160E GLU 3.0 17.2 + - - +
161E THR 3.8 3.1 - - - +
163E ASP* 1.3 76.9 - - - +
165E VAL* 1.3 58.7 + - - +
167E GLU* 3.3 12.8 + - - +
168E THR* 2.8 32.4 + - - -
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Residues in contact with VAL 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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1E MET* 4.6 4.0 - - + -
83E LEU* 4.8 8.1 - - + -
111E ILE* 4.0 28.9 - - + -
135E ILE* 4.0 15.5 - - + -
137E MET* 3.6 33.4 - - + -
151E VAL* 4.0 22.2 - - + -
161E THR 3.1 18.1 + - - +
162E PHE 3.7 2.9 - - - +
164E ALA* 1.3 74.1 - - - +
166E LYS* 1.3 58.9 + - - +
168E THR* 3.8 6.4 - - - -
169E SER* 2.5 35.3 + - - +
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Residues in contact with LYS 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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151E VAL* 5.0 2.0 - - - -
162E PHE* 2.8 50.5 + - + +
163E ASP* 3.5 11.4 + - - +
165E VAL* 1.3 76.9 - - - +
167E GLU* 1.3 67.0 + - + +
169E SER* 3.3 7.1 + - - -
170E ILE* 3.3 35.8 + - + +
176E PRO* 3.8 24.4 - - + +
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Residues in contact with GLU 167 (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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163E ASP* 3.0 23.8 + - - +
164E ALA* 3.4 13.7 - - - +
166E LYS* 1.3 76.2 - - + +
168E THR* 1.3 61.8 + - - +
170E ILE* 2.9 13.5 + - + +
171E ALA* 2.9 25.7 + - - +
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Residues in contact with THR 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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1E MET* 3.5 28.0 - - + +
4E VAL* 5.8 0.2 - - + -
20E PHE* 3.8 31.4 - - + -
25E PHE* 4.4 15.5 - - + -
83E LEU* 4.4 11.9 - - + -
137E MET* 5.7 1.3 - - + -
164E ALA 2.8 15.8 + - - -
165E VAL* 3.8 7.4 - - - -
167E GLU* 1.3 79.9 - - - +
169E SER* 1.3 61.8 + - - +
170E ILE 3.1 0.7 + - - -
171E ALA* 3.2 8.9 + - - +
172E ILE* 3.1 21.8 + - - +
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Residues in contact with SER 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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137E MET* 3.8 18.5 - - - +
149E VAL* 4.4 16.8 - - - +
151E VAL* 4.4 0.2 - - - +
165E VAL* 2.5 26.6 + - - +
166E LYS* 3.5 7.4 - - - -
167E GLU 3.2 0.2 - - - -
168E THR* 1.3 76.8 - - - +
170E ILE* 1.3 52.1 + - - +
172E ILE* 3.5 12.3 - - - +
174E LYS* 2.7 40.3 + - - +
176E PRO* 3.9 23.1 - - - +
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Residues in contact with ILE 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 LYS* 3.3 35.6 + - + +
167E GLU* 2.9 10.8 + - - +
169E SER* 1.3 74.9 - - - +
171E ALA* 1.3 59.1 + - - +
172E ILE 3.0 1.8 - - - -
173E GLY* 2.7 26.7 + - - -
174E LYS 3.7 7.6 - - - +
175E ASP* 5.8 0.7 - - - +
176E PRO* 3.9 19.5 - - + -
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Residues in contact with ALA 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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23E LYS* 3.9 12.8 - - - +
25E PHE* 4.4 18.0 - - + -
167E GLU 2.9 11.1 + - - +
168E THR* 3.5 13.7 - - - +
170E ILE* 1.3 76.4 - - - +
172E ILE* 1.3 57.6 + - - +
173E GLY 3.2 1.8 + - - -
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Residues in contact with ILE 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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19E ALA* 4.3 10.2 - - + +
20E PHE* 3.8 41.5 - - + -
23E LYS* 3.6 33.6 + - + +
25E PHE* 3.2 37.0 - - + -
137E MET* 5.7 0.7 - - + -
139E PHE* 4.5 8.3 - - + -
168E THR 3.1 15.8 + - - +
169E SER* 3.5 13.9 - - - +
170E ILE 3.0 1.4 - - - -
171E ALA* 1.3 74.4 - - - +
173E GLY* 1.3 60.6 + - - +
174E LYS* 3.5 31.4 + - + +
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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