Contacts of the helix formed by residues 166 - 178 (chain E) in PDB entry 2Q5E
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 LEU 166 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164E ALA 3.8 0.4 + - - -
165E SER* 1.3 78.6 - - - +
167E ALA* 1.3 66.5 + - - +
168E LYS* 3.1 38.5 + - + +
169E TYR* 3.4 6.2 + - + +
170E ALA* 2.9 19.3 + - - +
189E ARG* 3.9 44.6 - - + +
190E GLU* 5.7 2.7 - - - +
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Residues in contact with ALA 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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165E SER 3.8 1.0 + - - -
166E LEU* 1.3 76.7 - - - +
168E LYS* 1.3 62.7 + - - +
170E ALA 4.0 0.4 - - - +
171E ASP* 2.8 39.5 + - - +
188E PHE* 3.3 46.9 - - + +
190E GLU* 5.5 3.5 + - - +
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Residues in contact with LYS 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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129E ILE* 4.0 19.4 - - + +
130E GLU 3.5 25.4 + - - +
131E ILE* 4.2 20.6 - - - +
132E GLU 5.6 0.8 - - - +
166E LEU* 3.1 31.3 - - + +
167E ALA* 1.3 77.5 - - - +
169E TYR* 1.3 60.4 + - + +
171E ASP* 5.5 0.2 - - - -
172E PRO* 3.2 19.0 - - - +
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Residues in contact with TYR 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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108E LEU* 4.2 12.7 - - + +
109E ASP* 2.5 40.6 + - - -
113E VAL* 4.3 7.4 - - - +
115E SER* 2.7 30.5 + - - -
129E ILE* 3.7 31.4 - - + -
138E VAL* 3.8 14.4 - - + -
165E SER* 3.8 17.7 - - - -
166E LEU* 3.4 6.1 + - + +
167E ALA 3.0 0.2 - - - -
168E LYS* 1.3 86.4 - - + +
170E ALA* 1.3 67.9 + - - +
171E ASP 3.5 0.7 - - - -
172E PRO* 3.4 3.8 - - - +
173E VAL* 3.2 40.4 + - + +
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Residues in contact with ALA 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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108E LEU* 3.9 16.3 - - + +
161E LEU* 4.8 0.9 - - + -
163E THR* 3.9 13.7 - - + -
165E SER* 4.2 6.3 - - - -
166E LEU 2.9 17.9 + - - +
169E TYR* 1.3 78.3 - - - +
171E ASP* 1.3 63.7 + - - +
173E VAL* 3.3 1.6 + - - +
174E THR* 2.7 34.0 + - - -
188E PHE* 3.4 25.4 - - + -
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Residues in contact with ASP 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 ALA* 2.8 25.5 + - - +
168E LYS* 5.5 0.2 - - - -
170E ALA* 1.3 67.9 - - - +
172E PRO* 1.4 70.3 - - + +
174E THR* 2.8 13.5 + - - -
175E ASP* 2.9 20.2 + - - +
186E ARG* 2.2 46.8 + - - +
188E PHE* 3.7 21.1 - - - -
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Residues in contact with PRO 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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127E VAL* 4.2 21.5 - - + -
128E PRO 5.6 1.8 - - - +
129E ILE* 5.1 1.3 - - + -
167E ALA 3.5 0.9 - - - +
168E LYS* 3.2 28.9 - - - +
169E TYR* 3.4 12.1 - - - +
171E ASP* 1.4 93.1 - - + +
173E VAL* 1.3 62.5 + - - +
174E THR 3.3 0.2 + - - -
175E ASP* 3.5 13.1 - - + +
176E LEU* 3.4 24.8 + - + +
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Residues in contact with VAL 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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108E LEU* 4.2 22.2 - - + -
113E VAL* 4.5 11.9 - - + -
125E PHE* 5.0 4.7 - - + -
127E VAL* 4.0 24.9 - - + -
140E VAL* 4.1 28.3 - - + -
169E TYR* 3.2 41.0 + - + +
170E ALA 3.9 3.1 - - - +
171E ASP 3.1 1.4 - - - -
172E PRO* 1.3 77.6 - - - +
174E THR* 1.3 57.3 + - - +
176E LEU* 3.0 19.0 + - - +
177E LEU* 3.2 12.3 + - + +
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Residues in contact with THR 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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108E LEU* 4.1 7.7 - - + +
161E LEU* 3.4 23.7 - - + +
170E ALA 2.7 21.0 + - - -
171E ASP* 2.8 4.4 + - - -
173E VAL* 1.3 73.8 - - - +
175E ASP* 1.3 63.2 + - - +
176E LEU 3.0 1.8 - - - -
177E LEU* 4.1 9.6 - - + -
178E ASP* 2.7 37.0 + - + +
183E PHE* 3.5 36.6 - - + -
186E ARG* 4.0 21.9 - - - +
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Residues in contact with ASP 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 ASP* 2.9 18.2 + - - +
172E PRO* 3.5 17.6 - - + +
174E THR* 1.3 76.8 - - - +
176E LEU* 1.3 60.9 + - + +
178E ASP 3.9 10.0 - - - +
179E ARG* 4.0 15.9 + - - -
186E ARG* 3.0 30.5 + - - +
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Residues in contact with LEU 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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125E PHE* 3.6 40.6 - - + -
126E ILE 5.2 2.7 - - - +
127E VAL* 3.9 24.7 - - + -
172E PRO* 3.4 16.1 + - + +
173E VAL 3.0 8.0 + - - +
174E THR 3.0 0.8 - - - -
175E ASP* 1.3 79.3 - - + +
177E LEU* 1.3 63.5 + - - +
178E ASP 3.5 0.2 - - - -
179E ARG* 3.7 45.0 + - - +
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Residues in contact with LEU 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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108E LEU* 3.9 20.6 - - + -
112E LEU* 3.7 33.9 - - + -
113E VAL* 4.1 15.0 - - + -
125E PHE* 4.1 9.6 - - + -
142E LYS* 3.7 28.7 - - + +
146E VAL* 3.9 19.1 - - + -
147E ASP* 4.5 11.5 - - - +
150E LEU* 4.3 15.1 - - + +
173E VAL* 3.2 15.0 + - + +
174E THR* 3.1 6.0 + - + +
176E LEU* 1.3 79.0 - - - +
178E ASP* 1.3 59.1 + - - +
179E ARG* 3.7 5.2 + - - +
183E PHE* 4.9 5.4 - - + -
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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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150E LEU* 4.5 6.8 - - + +
174E THR* 2.7 25.0 + - + +
175E ASP* 3.9 7.9 - - - +
177E LEU* 1.3 69.7 - - - +
179E ARG* 1.3 63.3 + - - +
180E CYS* 4.6 0.3 + - - +
181E GLY* 3.2 12.9 + - - -
182E VAL* 2.7 32.8 + - - +
183E PHE* 2.8 56.1 + - + +
186E ARG* 5.0 6.8 + - - +
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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