Contacts of the helix formed by residues 149 - 161 (chain E) in PDB entry 3CQ6
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 ASP 149 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E SER 4.8 2.0 + - - +
142E ARG* 4.5 2.4 - - - +
143E GLY* 4.3 20.5 - - - +
147E ARG 3.3 3.4 + - - -
148E ILE* 1.3 71.6 - - - +
150E MET* 1.3 52.7 + - - +
151E ASP* 3.1 12.6 + - - +
152E VAL* 2.9 36.9 + - + +
153E ALA* 2.8 33.4 + - - +
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Residues in contact with MET 150 (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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148E ILE* 3.3 24.5 + - - +
149E ASP* 1.3 72.4 + - - +
151E ASP* 1.3 59.6 - - - +
153E ALA* 3.9 2.2 - - - -
154E LEU* 2.9 44.9 + - + +
178E THR* 5.4 1.8 - - - -
182E ASP* 3.3 62.1 - - + +
185E ARG* 3.6 39.3 - - + +
186E ILE* 4.0 15.9 - - + -
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Residues in contact with ASP 151 (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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149E ASP* 3.1 9.2 + - - +
150E MET* 1.3 79.8 - - - +
152E VAL* 1.3 60.1 + - - +
154E LEU* 4.3 3.9 - - - +
155E GLU* 3.3 24.7 + - - +
185E ARG* 4.4 10.9 + - - -
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Residues in contact with VAL 152 (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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140E VAL* 4.4 13.0 - - + -
141E SER 4.2 15.0 - - - +
149E ASP* 2.9 45.3 + - + +
151E ASP* 1.3 71.3 - - - +
153E ALA* 1.3 67.2 + - - +
155E GLU* 3.6 15.2 - - - +
156E GLU* 2.9 35.9 + - - +
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Residues in contact with ALA 153 (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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119E PHE* 4.0 21.4 - - + -
140E VAL* 4.5 5.4 - - + -
148E ILE* 3.7 22.2 - - + -
149E ASP 2.8 22.5 + - - +
150E MET* 3.5 11.0 - - - +
152E VAL* 1.3 76.2 - - + +
154E LEU* 1.3 62.9 + - - +
156E GLU* 3.1 1.9 + - - +
157E ILE* 3.0 29.7 + - - +
186E ILE* 4.9 5.8 - - + -
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Residues in contact with LEU 154 (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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150E MET* 2.9 26.1 + - + +
151E ASP* 4.3 4.3 - - - +
153E ALA* 1.3 73.0 - - - +
155E GLU* 1.3 61.6 + - - +
157E ILE* 3.4 5.8 + - - +
158E ARG* 3.0 49.6 + - - +
185E ARG* 3.2 71.1 - - + +
186E ILE* 3.9 7.2 - - + +
189E VAL* 3.3 19.2 - - + +
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Residues in contact with GLU 155 (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 ASP 3.3 20.6 + - - +
152E VAL* 3.6 15.9 - - - +
154E LEU* 1.3 80.5 - - - +
156E GLU* 1.3 67.3 + - - +
158E ARG* 3.5 11.8 + - - +
159E ALA* 3.0 30.2 + - + +
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Residues in contact with GLU 156 (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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117E LEU* 4.4 4.4 - - + +
138E ILE* 5.2 1.6 - - + -
140E VAL* 3.7 32.5 - - + -
152E VAL* 2.9 30.2 + - - +
153E ALA 3.8 2.5 - - - +
155E GLU* 1.3 84.0 - - - +
157E ILE* 1.3 66.4 + - - +
159E ALA* 4.3 6.2 - - - +
160E LYS* 3.0 56.4 + - + +
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Residues in contact with ILE 157 (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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117E LEU* 4.6 12.1 - - + -
119E PHE* 4.5 7.2 - - + -
153E ALA 3.0 25.0 + - - +
154E LEU* 3.7 5.6 - - - +
156E GLU* 1.3 75.0 - - - +
158E ARG* 1.3 59.8 - - - +
161E GLN* 2.9 31.5 + - - -
162E PRO* 3.3 22.6 - - + +
165E VAL* 4.5 10.8 - - + -
186E ILE* 3.6 30.3 - - + +
189E VAL* 3.6 25.8 - - + +
190E ALA* 3.7 33.2 - - + +
191E PRO* 4.3 0.2 - - + -
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Residues in contact with ARG 158 (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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154E LEU* 3.0 42.7 + - - +
155E GLU* 3.6 8.8 - - - +
157E ILE* 1.3 77.0 - - - +
159E ALA* 1.3 61.8 + - - +
161E GLN* 2.9 25.8 + - - +
189E VAL* 3.7 30.9 - - + +
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Residues in contact with ALA 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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155E GLU* 3.0 19.7 + - + +
156E GLU* 3.7 13.2 - - - +
157E ILE 3.2 0.4 - - - -
158E ARG* 1.3 79.7 - - - +
160E LYS* 1.3 69.4 + - + +
161E GLN* 4.6 3.1 - - - +
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Residues in contact with LYS 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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115E THR* 5.0 2.3 + - - -
117E LEU* 4.9 2.5 - - + -
138E ILE* 3.9 46.0 - - + +
156E GLU* 3.0 39.0 + - + +
159E ALA* 1.3 82.7 - - + +
161E GLN* 1.3 74.0 + - - +
162E PRO* 4.4 6.9 - - + +
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Residues in contact with GLN 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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115E THR* 4.2 3.8 + - - -
157E ILE 2.9 20.1 + - - -
158E ARG* 2.9 31.0 + - - +
159E ALA 4.6 2.5 - - - +
160E LYS* 1.3 80.9 - - - +
162E PRO* 1.4 66.7 - - - +
163E ASP* 3.7 6.1 + - - +
189E VAL 4.7 8.5 + - - +
191E PRO* 3.4 29.3 - - + +
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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