Contacts of the helix formed by residues 169 - 186 (chain E) in PDB entry 4O46
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 HIS 169 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLU* 3.8 21.4 + - + +
165E MET* 3.4 25.3 - - + +
166E GLN* 3.0 22.9 + - + +
168E THR* 1.4 78.2 + - - +
170E PRO* 1.4 78.0 - - + +
171E ILE* 3.1 50.1 + - + -
172E ARG* 3.0 12.4 + - + +
173E LEU* 2.9 20.8 + - - +
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Residues in contact with PRO 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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168E THR 3.4 1.1 - - - +
169E HIS* 1.4 96.6 - - + +
171E ILE* 1.4 52.8 + - + +
173E LEU* 4.5 2.7 - - + -
174E GLY* 2.8 31.4 + - - -
215E SER* 4.1 19.5 - - - +
218E ASP* 4.0 23.3 - - + -
219E SER* 3.5 20.6 - - - +
222E ILE* 3.3 24.2 - - + +
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Residues in contact with ILE 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ARG* 3.6 27.4 - - - +
118E GLU* 4.1 20.9 - - + +
121E VAL* 3.8 24.0 - - + -
122E PHE* 4.0 28.5 - - + +
125E LYS* 4.9 6.3 - - + +
165E MET* 3.7 7.2 - - + -
169E HIS* 3.1 27.3 + - + +
170E PRO* 1.4 77.5 - - + +
172E ARG* 1.4 56.9 + - - +
174E GLY* 3.8 1.1 - - - -
175E LEU* 3.0 28.4 + - - +
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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
----------------------------------------------------------
158E HIS* 6.0 2.9 + - + -
161E SER* 3.6 40.9 + - - +
162E LYS* 4.0 31.9 + - - +
165E MET* 2.8 32.2 + - + +
166E GLN 3.4 18.2 - - - +
167E PRO* 3.3 33.3 + - + +
169E HIS* 3.0 16.2 + - + +
171E ILE* 1.4 77.9 - - - +
173E LEU* 1.3 60.4 + - - +
175E LEU* 3.4 6.9 + - - +
176E ALA* 3.1 22.4 + - + +
200E ALA* 6.2 1.6 - - - +
203E ASP* 4.0 19.2 + - - +
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Residues in contact with LEU 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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167E PRO 3.5 19.5 - - - +
168E THR* 3.4 29.2 - - - +
169E HIS 2.9 10.5 + - - +
170E PRO* 3.8 3.4 - - + +
172E ARG* 1.3 72.1 - - - +
174E GLY* 1.3 58.5 + - - +
176E ALA* 3.2 8.5 + - - +
177E LEU* 2.9 24.9 + - - +
200E ALA* 3.9 10.8 - - + +
204E ALA* 3.8 15.3 - - + -
219E SER* 3.7 31.2 - - - +
222E ILE* 3.6 20.1 - - + +
223E MET* 4.0 10.5 - - + -
226E LEU* 3.8 22.3 - - + +
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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
----------------------------------------------------------
125E LYS* 3.8 15.5 - - - -
170E PRO 2.8 21.3 + - - -
171E ILE* 3.8 1.8 - - - -
173E LEU* 1.3 72.4 - - - +
175E LEU* 1.3 60.3 + - - +
177E LEU* 3.5 5.3 + - - +
178E ASN* 3.2 24.9 + - - +
222E ILE* 3.8 16.9 - - - +
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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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121E VAL* 3.9 8.1 - - + -
125E LYS* 3.9 23.9 - - + +
154E TYR* 3.7 32.1 - - + +
157E ALA* 3.5 49.6 - - + +
158E HIS* 3.5 14.1 - - + +
161E SER* 3.6 15.0 - - - +
171E ILE 3.0 17.9 + - - +
172E ARG 3.6 4.9 - - - +
173E LEU 3.2 0.2 - - - -
174E GLY* 1.3 73.3 - - - +
176E ALA* 1.3 55.8 + - - +
178E ASN* 3.3 1.4 + - - +
179E TYR* 2.8 40.1 + - + +
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Residues in contact with ALA 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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158E HIS* 5.4 6.1 - - + +
172E ARG* 3.1 12.9 + - + +
173E LEU* 3.2 9.8 + - - +
175E LEU* 1.3 77.2 - - - +
177E LEU* 1.4 56.1 + - - +
179E TYR* 4.5 4.0 - - - -
180E SER* 3.0 31.9 + - - -
196E LEU* 3.9 18.1 - - + +
197E ALA* 5.1 0.2 - - - -
200E ALA* 3.5 32.1 - - + -
226E LEU* 4.3 5.4 - - + +
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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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173E LEU 2.9 12.4 + - - +
174E GLY* 3.5 9.9 - - - +
176E ALA* 1.4 75.5 - - - +
178E ASN* 1.3 67.1 + - - +
180E SER* 2.7 20.6 + - - +
181E VAL* 3.1 20.3 + - + +
222E ILE* 3.9 20.0 - - + -
225E LEU* 3.8 47.6 - - + -
226E LEU* 3.9 15.0 - - + +
229E ASN* 3.4 29.2 - - - +
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Residues in contact with ASN 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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50E LYS* 6.3 0.4 - - - +
125E LYS* 3.5 13.3 - - - +
129E ASP* 2.7 39.6 + - - +
132E ARG* 3.4 17.3 + - - +
133E TYR* 4.9 2.6 + - - -
154E TYR* 3.9 9.4 - - + +
174E GLY 3.2 16.0 + - - +
175E LEU 4.1 2.2 - - - +
177E LEU* 1.3 86.2 - - - +
179E TYR* 1.3 59.5 + - - +
181E VAL* 3.3 10.2 + - - +
182E PHE* 2.9 27.4 + - - +
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Residues in contact with TYR 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E GLU* 2.7 27.4 + - - -
154E TYR* 3.5 56.0 - + + -
155E SER* 3.7 11.6 + - - -
158E HIS* 4.0 26.7 - + + -
175E LEU* 2.8 25.5 + - + +
176E ALA* 4.5 0.2 - - - -
178E ASN* 1.3 71.6 - - - +
180E SER* 1.4 56.9 + - - +
182E PHE* 3.2 18.9 + + - +
183E TYR* 2.9 55.4 + + - -
196E LEU* 3.6 18.6 - - + -
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Residues in contact with SER 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E ALA 3.0 16.8 + - - -
177E LEU* 2.7 25.6 + - - +
179E TYR* 1.4 71.3 - - - +
181E VAL* 1.4 58.6 + - - +
183E TYR* 3.2 5.1 + - - -
184E TYR 3.0 23.7 + - - -
193E ALA* 3.3 33.2 - - - +
196E LEU* 3.5 11.3 - - - +
197E ALA* 4.1 12.0 - - - +
226E LEU* 4.6 0.7 - - - +
229E ASN* 5.0 0.3 + - - -
233E TRP* 3.6 16.3 - - - -
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Residues in contact with VAL 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ARG* 3.8 24.2 - - - +
177E LEU* 3.1 17.8 + - + +
178E ASN* 3.3 11.9 + - - +
180E SER* 1.4 79.5 + - - +
182E PHE* 1.4 54.9 + - - +
185E GLU* 2.8 49.3 + - + +
229E ASN* 3.6 24.5 - - - +
233E TRP* 4.2 12.1 - - + -
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Residues in contact with PHE 182 (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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132E ARG* 3.8 13.4 - - + +
147E VAL* 3.5 23.3 - - + -
150E SER* 3.4 27.1 - - - -
151E GLU* 3.7 30.7 - - + -
154E TYR* 3.8 15.0 - + + -
178E ASN 2.9 13.2 + - - +
179E TYR* 3.2 25.8 + + - +
181E VAL* 1.4 76.1 - - - +
183E TYR* 1.3 60.3 + + - +
186E ILE* 2.9 57.1 + - + +
187E GLN* 3.0 36.8 + - + -
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Residues in contact with TYR 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E GLU* 3.8 20.3 + - - -
179E TYR* 2.9 56.5 + + - -
180E SER* 3.2 6.9 + - - +
182E PHE* 1.3 77.9 - + - +
184E TYR* 1.3 53.5 + - - +
187E GLN* 3.5 18.7 - - + +
188E ASN 3.0 10.2 + - - -
189E ALA* 2.8 32.6 + - + +
192E GLN* 3.5 53.2 + - + -
193E ALA* 3.7 14.8 - - + +
196E LEU* 3.7 23.1 - - + -
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Residues in contact with TYR 184 (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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180E SER 3.0 6.9 + - - +
181E VAL 3.9 0.9 - - - +
183E TYR* 1.3 75.3 - - - +
185E GLU* 1.3 86.9 + - + +
188E ASN* 3.4 22.9 - - - +
189E ALA 4.3 2.7 - - - +
190E PRO* 3.6 35.2 - - + +
193E ALA* 3.6 13.4 - - + +
232E LEU* 5.9 1.3 - - + -
233E TRP* 3.4 62.8 + + + -
236E ASP* 3.8 25.3 + - - +
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Residues in contact with GLU 185 (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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136E GLU* 6.0 1.3 - - - +
143E ARG* 4.8 1.9 + - - -
181E VAL* 2.8 35.5 + - + +
184E TYR* 1.3 99.6 - - + +
186E ILE* 1.3 70.4 + - + +
188E ASN* 4.6 3.3 + - - +
232E LEU* 5.9 2.1 - - - +
233E TRP* 4.6 5.5 + - + -
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Residues in contact with ILE 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ARG* 3.7 32.3 - - + +
135E ALA* 4.1 6.5 - - + -
136E GLU* 3.9 37.2 - - + +
143E ARG* 2.8 37.3 + - - +
147E VAL* 3.6 25.4 - - + -
182E PHE* 2.9 36.3 + - + +
185E GLU* 1.3 85.1 - - + +
187E GLN* 1.3 63.2 + - - +
188E ASN* 3.3 2.0 + - - +
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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
------------------------------------------------------------
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