Contacts of the helix formed by residues 186 - 195 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C GLY* 4.2 0.4 - - - -
154C GLY 3.7 19.0 - - - +
155C HIS* 3.2 31.1 + + - -
157C ALA* 3.8 8.8 - - + +
158C LEU* 3.8 31.1 - - + +
185C CYS* 1.3 92.3 - - - +
187C GLY* 1.3 64.7 + - - +
188C PRO* 3.3 2.5 - - - -
189C ALA* 3.1 22.2 + - - +
209C PHE* 3.3 25.3 - + - -
214C ASP* 2.4 28.4 + - - -
231C PHE* 3.3 29.4 - + - -
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Residues in contact with GLY 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL* 3.8 4.6 - - - +
152C PRO 3.4 22.1 + - - -
153C GLY* 4.0 0.8 - - - -
157C ALA* 4.1 5.4 - - - +
183C SER* 3.1 15.9 + - - -
184C LEU 3.0 5.9 + - - -
186C HIS* 1.3 77.7 - - - +
188C PRO* 1.3 56.6 - - - +
190C ALA* 2.8 37.6 + - - +
191C PHE* 4.8 0.4 - - - -
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Residues in contact with PRO 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C SER* 3.1 14.1 - - - +
184C LEU 3.7 7.4 - - - +
185C CYS 3.5 9.4 - - - +
186C HIS 3.4 3.4 - - - -
187C GLY* 1.3 88.3 - - - +
189C ALA* 1.3 60.1 + - - +
190C ALA 3.0 0.7 - - - -
191C PHE* 3.0 49.1 + - + +
206C ILE* 3.8 17.9 - - + -
207C CYS 3.9 10.5 - - - +
208C ALA* 3.9 19.1 - - + -
231C PHE* 4.9 1.1 - - + -
235C LEU* 3.5 15.5 - - + +
259C THR* 5.4 1.3 - - - -
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA 4.6 2.2 - - - +
158C LEU* 3.7 25.4 - - + -
162C PRO* 3.5 17.2 - - + +
186C HIS 3.1 17.7 + - - +
187C GLY 2.8 4.2 + - - -
188C PRO* 1.3 74.9 - - - +
190C ALA* 1.3 55.8 + - - +
191C PHE 3.0 0.4 - - - -
192C LEU* 2.9 46.0 + - + +
231C PHE* 3.9 14.2 - - + -
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 6.4 0.4 - - + -
151C VAL* 3.7 26.0 - - + -
157C ALA 5.1 0.8 + - - -
161C LEU* 4.0 26.0 - - + +
162C PRO* 4.5 2.2 - - - +
167C VAL* 3.4 17.5 - - + +
171C LEU* 3.7 2.9 - - + +
187C GLY 2.8 15.4 + - - +
189C ALA* 1.3 78.3 - - - +
191C PHE* 1.3 65.1 + - + +
192C LEU 3.2 0.2 - - - -
193C ALA* 3.3 21.3 + - - +
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Residues in contact with PHE 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL* 4.8 8.5 - - + -
171C LEU* 3.4 24.9 - - + -
181C VAL* 4.1 18.2 - - + -
183C SER* 3.8 27.1 - - - -
187C GLY 4.8 0.4 - - - -
188C PRO* 3.0 36.7 + - + +
190C ALA* 1.3 75.0 - - - +
192C LEU* 1.3 53.9 + - - +
193C ALA 2.8 15.2 + - - -
194C LEU* 2.8 17.8 + - + +
201C LEU* 3.8 11.2 - - + -
206C ILE* 4.5 11.4 - - + -
235C LEU* 4.0 7.9 - - + -
238C MET* 3.4 12.0 - - + +
240C MET* 3.9 26.7 - - + -
257C LEU* 4.1 24.0 - - + -
259C THR* 5.1 2.0 - - + -
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C PRO* 3.6 13.0 - - + +
188C PRO 4.0 1.0 + - - -
189C ALA* 2.9 33.6 + - + +
191C PHE* 1.3 77.2 - - - +
193C ALA* 1.3 54.4 + - - +
194C LEU 3.0 0.9 - - - -
195C ARG* 3.0 53.2 + - - +
229C TRP* 3.7 33.0 - - + -
231C PHE* 4.0 9.2 - - + +
234C GLU* 4.0 14.4 - - + +
235C LEU* 3.9 36.1 - - + +
238C MET* 4.1 9.4 - - + -
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C LEU 3.5 16.8 - - - +
162C PRO 3.4 10.7 + - - +
163C GLU* 5.1 1.1 - - - +
164C SER 3.4 24.2 - - - +
167C VAL* 3.9 7.4 - - + -
168C ALA* 3.2 19.3 - - + +
190C ALA 3.3 17.8 + - - +
191C PHE 2.8 1.0 + - - -
192C LEU* 1.3 77.2 - - - +
194C LEU* 1.3 55.8 + - + +
195C ARG* 3.3 2.6 + - - +
196C HIS* 4.8 8.7 + - - -
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Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ALA* 3.6 32.3 - - + +
171C LEU* 3.8 27.6 - - + -
172C GLN* 3.8 23.3 - - + +
175C ILE* 5.3 0.2 - - + -
191C PHE* 2.8 16.9 + - - +
193C ALA* 1.3 77.7 - - - +
195C ARG* 1.3 65.5 + - - +
196C HIS 2.9 9.6 + - - -
198C ASP 4.1 1.7 + - - +
199C ASN* 3.6 45.9 + - - +
200C PRO* 4.0 10.8 - - + -
201C LEU* 3.9 20.4 - - + -
238C MET* 4.1 3.1 - - - -
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Residues in contact with ARG 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C PRO* 3.4 12.6 + - - -
163C GLU* 2.8 41.0 + - - +
192C LEU* 3.0 34.8 + - + +
193C ALA* 3.3 1.2 - - - +
194C LEU* 1.3 76.6 - - - +
196C HIS* 1.3 89.5 + - + +
199C ASN* 5.6 1.1 - - - +
229C TRP* 5.9 3.6 - - - -
234C GLU* 5.4 10.8 + - - +
238C MET* 3.8 25.6 - - + +
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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