Contacts of the helix formed by residues 155 - 170 (chain E) in PDB entry 4U0Z
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 155 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E SER* 3.2 21.6 + - - +
151E GLU* 4.4 2.4 + - - -
153E ASP* 3.4 6.0 - - + +
154E LYS* 1.4 72.6 - - - +
156E ILE* 1.3 61.3 + - - +
157E ILE* 3.6 8.5 + - - +
158E GLN* 3.0 51.0 + - + +
159E ALA* 3.4 17.2 + - - +
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Residues in contact with ILE 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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151E GLU* 4.2 15.7 - - + +
154E LYS 3.3 8.6 + - - +
155E ASP* 1.3 72.5 - - - +
157E ILE* 1.3 63.2 + - + +
159E ALA* 3.1 7.3 + - - +
160E ASP* 2.9 27.5 + - + -
183E THR* 3.8 24.9 - - + -
186E LEU* 3.6 32.8 - - + -
187E VAL* 3.8 29.8 - - + +
190E ILE* 3.8 19.5 - - + -
313G GLN* 5.5 5.8 - - + -
323G HIS* 6.5 0.7 - - + -
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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
----------------------------------------------------------
155E ASP* 3.4 6.9 + - - +
156E ILE* 1.3 81.2 - - + +
158E GLN* 1.4 61.8 + - - +
160E ASP* 3.4 3.8 + - - +
161E TYR* 3.2 20.9 + - + +
187E VAL* 3.9 19.9 - - + +
190E ILE* 3.8 26.5 - - + -
191E ASP* 4.5 3.1 - - - +
416E ARG* 3.5 50.6 + - - +
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Residues in contact with GLN 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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130E MET* 4.6 8.3 - - - +
146E PHE* 3.8 31.1 - - - -
150E SER* 4.1 14.4 - - - -
155E ASP* 3.0 36.6 + - + +
157E ILE* 1.4 72.6 - - - +
159E ALA* 1.3 65.0 + - - +
161E TYR* 3.2 15.3 + - + +
162E LEU* 3.1 39.9 + - + +
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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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147E GLY* 3.3 27.1 - - - +
150E SER* 3.6 11.8 + - - +
151E GLU* 3.7 17.7 - - + -
155E ASP 3.4 9.4 + - - +
156E ILE* 3.1 10.0 + - + +
158E GLN* 1.3 77.3 - - - +
160E ASP* 1.3 52.9 + - - +
162E LEU* 3.1 6.8 + - - +
163E TYR* 2.8 46.3 + - + -
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Residues in contact with ASP 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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156E ILE* 2.9 15.2 + - + +
157E ILE 3.6 5.2 - - - +
159E ALA* 1.3 74.7 - - - +
161E TYR* 1.4 51.7 + - - +
163E TYR* 3.2 10.6 + - - +
164E THR* 2.6 42.2 + - - -
180E ARG* 3.3 17.0 + - - -
183E THR* 2.9 28.8 + - - +
184E LEU 3.5 5.9 + - - -
187E VAL* 3.3 20.5 - - + +
412E ARG* 2.8 38.7 + - - -
416E ARG* 4.9 0.5 + - - -
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Residues in contact with TYR 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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157E ILE 3.2 13.4 + - - +
158E GLN* 3.2 16.8 - - + +
160E ASP* 1.4 75.8 + - - +
162E LEU* 1.4 66.8 + - + +
164E THR* 3.5 3.9 - - - -
165E ARG* 2.8 78.6 + - + +
401E HIS* 5.9 3.9 - + - -
405E ALA* 4.2 21.1 + - + +
408E GLU* 4.8 6.8 - - - +
410E ASP* 3.4 38.8 - - + +
412E ARG* 4.7 0.9 - - - +
413E PRO* 4.2 21.3 - - + -
416E ARG* 5.8 3.8 - - - +
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Residues in contact with LEU 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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133E LEU* 6.0 0.7 - - + -
143E LEU* 3.4 44.6 - - + +
146E PHE* 4.1 18.8 - - + +
147E GLY* 3.8 22.0 - - - +
150E SER* 4.2 1.8 - - - +
158E GLN* 3.1 44.3 + - + +
159E ALA* 3.1 7.0 + - - +
161E TYR* 1.4 94.8 - - + +
163E TYR* 1.4 60.4 + - - +
165E ARG* 3.2 7.4 + - - +
166E ALA* 2.8 30.6 + - - +
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Residues in contact with TYR 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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144E THR* 3.7 37.5 - - + -
147E GLY* 3.2 9.8 - - - -
148E ILE* 3.2 26.7 + - + +
151E GLU* 2.7 29.4 + - - -
159E ALA* 2.8 34.2 + - + -
160E ASP* 3.2 3.6 + - - +
162E LEU* 1.4 72.1 - - - +
164E THR* 1.3 56.5 + - - +
166E ALA* 3.3 8.8 + - - +
167E LEU* 3.0 31.9 + - - +
176E ALA* 4.1 14.4 - - - +
179E ASN* 3.5 34.9 + - + -
180E ARG* 4.1 10.3 - - + -
183E THR* 3.8 24.9 - - + -
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Residues in contact with THR 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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160E ASP* 2.6 20.9 + - - -
161E TYR 3.5 5.4 - - - -
163E TYR* 1.3 72.7 - - - +
165E ARG* 1.4 65.1 + - - +
167E LEU* 3.1 13.9 + - - +
168E THR* 3.2 27.6 + - + +
180E ARG* 3.2 39.5 + - - +
410E ASP* 4.5 9.4 - - + +
412E ARG* 3.3 24.0 + - - +
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Residues in contact with ARG 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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133E LEU* 4.4 7.5 - - - +
137E PRO* 3.4 38.8 + - - +
138E ASP* 5.4 2.5 - - - -
143E LEU* 3.4 27.8 - - + +
161E TYR* 2.8 65.0 + - + +
162E LEU* 3.2 10.5 + - - +
164E THR* 1.4 72.0 - - - +
166E ALA* 1.3 60.4 + - - +
168E THR* 2.7 26.8 + - - +
169E ILE* 3.2 18.8 - - + +
408E GLU* 5.3 15.6 - - + +
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Residues in contact with ALA 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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140E VAL* 3.8 26.9 - - + +
143E LEU* 3.9 23.0 - - + +
144E THR* 4.3 4.9 - - + -
162E LEU 2.8 13.6 + - - +
163E TYR 3.3 10.3 - - - +
164E THR 3.2 0.2 - - - -
165E ARG* 1.3 75.7 - - - +
167E LEU* 1.3 57.5 + - - +
169E ILE* 3.3 7.3 + - - +
170E SER 2.9 25.4 + - - +
176E ALA* 4.1 13.0 - - + -
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Residues in contact with LEU 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 TYR 3.0 14.9 + - - +
164E THR* 3.1 6.6 + - - +
166E ALA* 1.3 73.2 - - - +
168E THR* 1.3 64.2 + - + +
170E SER 3.6 9.4 - - - +
171E PRO* 3.1 51.3 - - + +
173E HIS 3.9 9.2 - - - +
176E ALA* 3.7 22.7 - - + +
177E LEU* 4.0 17.0 - - + +
180E ARG* 3.6 41.5 - - + +
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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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164E THR* 3.2 22.8 + - + +
165E ARG* 2.7 25.3 + - - +
167E LEU* 1.3 75.9 - - + +
169E ILE* 1.3 71.0 + - - +
171E PRO* 4.7 2.9 - - - +
409E GLY* 6.2 3.1 - - - +
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Residues in contact with ILE 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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138E ASP* 3.4 60.8 - - + +
140E VAL* 5.0 7.6 - - + -
143E LEU* 4.8 4.7 - - + -
165E ARG* 3.2 22.7 - - + +
166E ALA* 3.5 7.4 - - - +
167E LEU 3.2 0.2 - - - -
168E THR* 1.3 90.0 - - - +
170E SER* 1.4 62.2 + - - +
171E PRO* 3.7 6.3 - - - +
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Residues in contact with SER 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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140E VAL* 3.9 28.0 - - - -
166E ALA 2.9 6.3 + - - +
167E LEU* 3.3 17.3 - - - +
169E ILE* 1.4 77.9 - - - +
171E PRO* 1.4 65.1 - - - +
172E TYR 3.3 2.8 + - - -
173E HIS* 3.4 24.3 + - - +
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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