Contacts of the helix formed by residues 167 - 184 (chain E) in PDB entry 3O2Q
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 167 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D VAL* 3.2 26.5 - - + +
124D ASN* 5.4 3.3 - - - +
127D LYS* 4.2 6.8 + - - -
176D ASN* 2.7 28.8 + - - +
165E THR* 3.2 2.9 - - - -
166E GLU* 1.3 82.1 - - + +
168E MET* 1.3 64.6 + - - +
169E GLU* 3.3 5.5 + - - -
170E ASN* 3.0 24.6 + - + +
171E GLU* 3.0 33.2 + - + +
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Residues in contact with MET 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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4E SER* 4.7 12.4 + - - +
6E LEU* 3.9 23.6 - - + -
106E ASP* 4.2 25.1 - - + +
107E LEU* 5.7 3.1 - - + -
135E HIS* 4.5 17.7 - - - +
162E ILE* 3.4 32.1 - - + +
165E THR* 3.6 12.2 + - - +
166E GLU 4.0 0.8 + - - -
167E ASP* 1.3 71.4 + - - +
169E GLU* 1.3 70.9 + - + +
171E GLU 3.1 0.7 + - - -
172E ILE* 2.9 45.6 + - + +
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Residues in contact with GLU 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LYS* 2.8 35.4 + - - +
177D ASP* 3.8 15.8 - - - +
178D GLY* 3.8 18.0 - - - -
181D THR* 4.6 7.6 + - - +
182D HIS* 3.0 24.6 + - - -
251D ILE* 5.5 1.7 - - - +
133E PRO* 3.6 17.4 - - - +
135E HIS* 3.0 33.8 + - + +
167E ASP* 3.3 2.6 + - - -
168E MET* 1.3 89.7 - - + +
170E ASN* 1.3 60.6 + - - +
171E GLU 3.5 0.3 + - - -
172E ILE* 4.0 15.3 - - - +
173E ASP* 4.9 2.4 - - - +
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Residues in contact with ASN 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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175D ASP 3.9 6.6 + - - +
176D ASN* 3.5 18.2 + - - +
177D ASP* 2.8 40.3 - - - +
178D GLY 4.7 0.4 - - - +
180D ARG* 5.0 1.2 - - - +
167E ASP* 3.0 29.6 + - + +
169E GLU* 1.3 79.7 - - - +
171E GLU* 1.3 64.8 + - + +
173E ASP* 5.4 0.9 + - - +
174E GLU* 5.6 1.6 + - - +
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Residues in contact with GLU 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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165E THR* 3.6 16.4 - - + +
166E GLU* 3.4 14.7 + - - +
167E ASP* 3.0 39.4 + - + +
168E MET 3.1 1.6 + - - -
170E ASN* 1.3 91.7 - - + +
172E ILE* 1.3 67.4 + - - +
173E ASP 3.3 2.5 - - - -
174E GLU* 2.9 23.8 + - + +
175E LEU* 3.1 19.5 + - + +
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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
----------------------------------------------------------
251D ILE* 5.7 0.2 - - + -
107E LEU* 4.4 10.3 - - + -
135E HIS* 4.1 15.9 - - + +
137E VAL* 4.3 13.9 - - + -
162E ILE* 4.0 28.7 - - + -
168E MET* 2.9 32.8 + - + +
169E GLU* 4.0 11.7 - - - +
170E ASN 3.8 0.2 - - - -
171E GLU* 1.3 75.8 - - - +
173E ASP* 1.3 61.6 + - - +
175E LEU* 3.1 12.1 + - - +
176E LEU* 2.8 37.7 + - + +
189E HIS* 3.6 32.3 - - + +
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Residues in contact with ASP 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ASP* 4.3 9.2 - - - +
249D SER* 5.9 1.4 - - - -
250D SER* 4.4 10.2 - - - -
251D ILE* 3.7 13.9 + - - +
293D GLN* 3.9 24.7 + - - +
169E GLU 4.9 2.3 + - - +
170E ASN 5.4 1.3 + - - +
171E GLU 3.3 0.8 - - - -
172E ILE* 1.3 81.5 - - - +
174E GLU* 1.3 57.6 + - - +
176E LEU* 3.2 8.0 + - - +
177E GLN* 2.9 33.6 + - - +
189E HIS* 2.6 39.5 + - - +
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Residues in contact with GLU 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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170E ASN 5.6 1.1 + - - +
171E GLU* 2.9 16.6 + - + +
173E ASP* 1.3 78.5 - - - +
175E LEU* 1.3 64.0 + - + +
177E GLN* 3.4 8.2 + - + +
178E GLU* 3.0 33.3 + - + +
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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
----------------------------------------------------------
158E LEU* 5.5 3.1 - - + -
161E CYS* 4.1 28.4 - - - +
162E ILE* 4.3 16.4 - - + -
165E THR* 2.9 38.6 - - + +
171E GLU* 3.1 24.8 + - + +
172E ILE* 3.6 7.6 - - - +
174E GLU* 1.3 82.8 - - + +
176E LEU* 1.3 66.3 + - + +
178E GLU* 3.4 22.5 + - - +
179E PHE* 3.0 27.3 + - - +
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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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137E VAL* 4.2 21.3 - - + -
158E LEU* 3.9 33.7 - - + -
162E ILE* 5.2 1.3 - - + -
172E ILE* 2.8 30.1 + - + +
173E ASP* 3.6 6.3 - - - +
175E LEU* 1.3 71.6 - - + +
177E GLN* 1.3 61.3 + - - +
179E PHE* 3.2 4.4 + - + +
180E GLU* 2.8 35.7 + - + +
187E PHE* 4.1 22.5 - - + +
189E HIS* 3.6 44.2 - - + -
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Residues in contact with GLN 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ALA* 3.1 35.1 - - + +
292D SER* 3.7 8.0 + - - -
293D GLN* 4.2 14.4 + - - +
173E ASP 2.9 21.6 + - - +
174E GLU* 3.6 8.7 - - + +
175E LEU 3.2 0.2 - - - -
176E LEU* 1.3 77.5 - - - +
178E GLU* 1.3 61.9 + - - +
180E GLU* 3.2 25.8 + - - +
181E GLU* 3.0 25.1 + - - +
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Residues in contact with GLU 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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161E CYS* 5.5 2.1 - - - -
174E GLU* 3.0 23.5 + - + +
175E LEU* 3.7 25.5 - - - +
177E GLN* 1.3 75.7 - - - +
179E PHE* 1.3 58.5 + - + +
181E GLU* 3.4 9.1 + - - +
182E LYS* 3.1 54.6 + - + +
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Residues in contact with PHE 179 (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* 3.8 33.7 - - + -
157E GLU* 3.7 42.6 - - + -
158E LEU* 3.8 30.1 - - + -
161E CYS* 4.9 11.9 - - + -
175E LEU 3.0 17.9 + - - +
176E LEU* 3.5 6.5 - - - +
178E GLU* 1.3 77.4 - - + +
180E GLU* 1.3 61.8 + - - +
182E LYS* 4.0 6.8 - - + +
183E SER* 2.8 37.1 + - - -
187E PHE* 3.5 31.6 - + + -
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Residues in contact with GLU 180 (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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290D ALA* 5.6 0.2 - - - +
291D LYS* 5.9 1.0 - - - +
292D SER* 2.6 35.1 + - - -
176E LEU* 2.8 16.7 + - - +
177E GLN* 3.4 24.7 + - - +
179E PHE* 1.3 71.8 - - - +
181E GLU* 1.3 58.6 + - - +
184E GLY* 2.8 33.4 + - - -
185E ARG 3.1 22.1 + - - +
186E THR* 3.8 7.0 - - - -
187E PHE* 2.7 42.3 + - + +
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Residues in contact with GLU 181 (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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177E GLN 3.0 12.9 + - - +
178E GLU* 3.7 13.1 - - - +
180E GLU* 1.3 78.9 - - - +
182E LYS* 1.3 79.5 + - - +
184E GLY* 4.1 4.4 + - - -
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Residues in contact with LYS 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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178E GLU* 3.1 44.8 + - + +
179E PHE* 4.0 9.2 - - + +
180E GLU 3.3 0.2 - - - -
181E GLU* 1.3 93.8 + - - +
183E SER* 1.3 61.4 + - - +
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Residues in contact with SER 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E LEU* 5.1 8.5 - - - -
179E PHE* 2.8 32.4 + - - -
182E LYS* 1.3 78.1 - - - +
184E GLY* 1.3 62.4 + - - +
185E ARG* 3.0 39.5 + - - +
187E PHE* 4.0 6.5 - - - -
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Residues in contact with GLY 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 GLU 2.8 12.9 + - - -
181E GLU 4.1 3.8 + - - -
182E LYS 3.5 2.4 - - - -
183E SER* 1.3 76.0 - - - +
185E ARG* 1.3 60.6 + - - +
186E THR* 5.1 3.3 - - - +
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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
------------------------------------------------------------
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