Contacts of the helix formed by residues 186 - 196 (chain E) in PDB entry 1PV2
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 186 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153E GLY* 4.2 0.8 - - - -
154E GLY 3.9 18.4 - - - +
155E HIS* 3.3 28.0 + + - -
157E ALA* 3.6 9.1 - - + +
158E LEU* 3.9 29.2 - - + -
185E CYS* 1.3 90.3 - - - +
187E GLY* 1.3 64.5 + - - +
188E PRO* 3.3 2.2 - - - -
189E ALA* 3.1 21.5 + - - +
209E PHE* 3.4 28.1 - + - -
214E ASP* 2.4 30.7 + - - -
227E LEU* 5.2 0.2 - - + -
231E PHE* 3.4 30.4 - + - -
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Residues in contact with GLY 187 (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 VAL* 3.5 14.3 - - - +
152E PRO 3.7 10.3 - - - -
153E GLY* 3.9 2.6 - - - -
157E ALA* 4.1 3.1 - - - +
183E SER* 3.0 15.3 - - - -
184E LEU 3.0 9.9 + - - -
186E HIS* 1.3 78.0 - - - +
188E PRO* 1.3 63.8 - - - +
190E ALA* 2.8 32.1 + - - +
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Residues in contact with PRO 188 (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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183E SER* 3.1 18.1 - - - +
184E LEU 3.9 7.4 - - - +
185E CYS 3.5 13.0 - - - +
186E HIS 3.4 3.6 - - - -
187E GLY* 1.3 87.5 - - - +
189E ALA* 1.3 63.1 + - - +
190E ALA 3.0 0.7 - - - -
191E PHE* 3.0 48.6 + - + +
206E ILE* 3.8 15.5 - - + -
207E CYS 4.0 20.4 - - - +
208E ALA* 4.3 1.3 - - + -
231E PHE* 4.6 3.1 - - + -
235E LEU* 3.5 15.8 - - + +
259E THR* 5.0 2.0 - - + -
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Residues in contact with ALA 189 (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 ALA 4.4 2.9 - - - +
158E LEU* 3.7 25.6 - - + -
162E PRO* 3.6 17.0 - - + +
186E HIS 3.1 18.1 + - - +
187E GLY 2.8 0.8 + - - -
188E PRO* 1.3 75.3 - - - +
190E ALA* 1.3 65.4 + - - +
192E LEU* 2.8 34.3 + - + +
229E TRP* 4.7 0.2 - - + -
231E PHE* 3.9 18.8 - - + -
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Residues in contact with ALA 190 (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 VAL* 3.7 25.6 - - + -
157E ALA 4.8 0.6 + - - -
161E LEU* 4.1 29.1 - - + +
162E PRO* 4.4 1.5 - - - +
167E VAL* 3.9 13.1 - - + +
171E LEU* 4.1 2.9 - - + +
187E GLY 2.8 16.4 + - - +
189E ALA* 1.3 77.3 - - - +
191E PHE* 1.3 61.5 + - + +
193E ALA* 2.8 31.7 + - - +
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Residues in contact with PHE 191 (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 VAL* 5.0 4.0 - - + -
171E LEU* 3.8 21.1 - - + -
181E VAL* 3.8 18.4 - - + -
183E SER* 3.8 23.8 - - - -
188E PRO* 3.0 37.1 + - + +
190E ALA* 1.3 79.0 - - + +
192E LEU* 1.3 56.1 + - - +
193E ALA 2.9 6.7 + - - -
194E LEU* 3.0 17.4 + - - +
201E LEU* 3.5 26.0 - - + -
206E ILE* 4.5 9.6 - - + -
235E LEU* 3.9 9.9 - - + -
238E MET* 3.3 12.6 - - + +
240E MET* 4.0 16.2 - - + -
257E LEU* 3.8 30.1 - - + -
259E THR* 5.0 0.2 - - + -
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162E PRO* 3.6 16.7 - - + +
188E PRO 4.0 0.2 + - - -
189E ALA* 2.8 31.1 + - + +
190E ALA 2.8 0.6 + - - -
191E PHE* 1.3 76.5 - - - +
193E ALA* 1.3 61.0 + - - +
194E LEU 3.1 0.4 - - - -
195E ARG* 3.1 43.7 + - - +
229E TRP* 3.9 29.4 - - + -
231E PHE* 4.0 11.0 - - + +
234E GLU* 4.0 18.6 - - + +
235E LEU* 3.5 37.5 - - + +
238E MET* 4.1 10.1 - - + -
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Residues in contact with ALA 193 (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 LEU 3.7 13.0 - - - +
162E PRO 3.5 9.9 + - - +
163E GLU* 5.2 0.7 - - - +
164E SER 3.4 26.0 - - - +
165E GLN* 5.7 0.2 - - - -
167E VAL* 3.9 3.6 - - + -
168E ALA* 3.4 25.8 - - - +
190E ALA 2.8 15.3 + - - +
192E LEU* 1.3 78.8 - - - +
194E LEU* 1.3 57.2 + - + +
195E ARG* 3.1 4.9 + - - +
196E HIS* 4.2 12.7 + - - +
197E GLY 5.4 0.7 + - - -
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Residues in contact with LEU 194 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168E ALA* 3.5 32.3 - - + +
171E LEU* 4.0 22.9 - - + -
172E GLN* 3.8 20.9 - - + +
175E ILE* 4.7 2.0 - - + -
191E PHE 3.0 13.3 + - - +
193E ALA* 1.3 75.4 - - - +
195E ARG* 1.3 63.0 + - - +
196E HIS 3.2 4.1 + - - -
197E GLY* 3.6 11.3 + - - +
199E ASN* 3.6 40.0 + - - +
200E PRO* 3.9 12.1 - - + -
201E LEU* 3.8 31.6 - - + -
238E MET* 4.1 3.1 - - - -
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Residues in contact with ARG 195 (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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162E PRO* 4.1 7.5 + - - +
163E GLU* 3.3 36.8 + - - +
192E LEU* 3.1 38.8 + - + +
193E ALA 3.1 1.4 - - - -
194E LEU* 1.3 78.4 - - - +
196E HIS* 1.3 94.7 + - + +
197E GLY 4.7 1.7 - - - +
229E TRP* 6.3 0.8 - - - -
234E GLU* 5.7 10.9 - - - +
238E MET* 3.9 27.3 - - + +
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Residues in contact with HIS 196 (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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162E PRO 5.8 0.2 - - - -
163E GLU* 6.2 2.0 - - - -
192E LEU 5.2 0.4 - - - -
193E ALA* 4.2 11.6 + - - +
194E LEU 3.2 0.6 - - - -
195E ARG* 1.3 118.3 + - + +
197E GLY* 1.3 69.0 + - - +
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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
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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