Contacts of the helix formed by residues 186 - 194 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLY* 4.1 0.2 - - - -
154A GLY 3.8 17.7 - - - +
155A HIS* 3.2 39.5 + + - -
157A ALA* 3.9 6.5 - - + +
158A LEU* 4.1 22.0 - - + -
185A CYS* 1.3 93.7 - - - +
187A GLY* 1.3 55.5 + - - +
188A PRO* 3.2 3.6 - - - -
189A ALA* 2.8 36.1 + - - +
209A PHE* 3.6 26.9 - + - -
214A ASP* 2.7 23.9 + - - -
227A LEU* 5.3 0.4 - - + -
231A PHE* 3.4 31.2 - + - -
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Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 3.6 13.3 - - - +
152A PRO 3.8 10.5 - - - -
153A GLY* 3.8 3.6 - - - -
157A ALA* 4.0 7.3 - - - +
183A SER* 3.1 15.0 + - - -
184A LEU 2.8 11.9 + - - -
186A HIS* 1.3 78.1 - - - +
188A PRO* 1.3 58.8 - - - +
189A ALA 2.8 6.8 + - - -
190A ALA* 2.9 24.8 + - - +
191A PHE* 5.2 0.2 - - - -
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Residues in contact with PRO 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 3.1 17.0 - - - +
184A LEU* 3.5 14.1 - - - +
185A CYS 3.5 10.5 - - - +
186A HIS 3.3 3.6 - - - -
187A GLY* 1.3 84.4 - - - +
189A ALA* 1.3 60.2 + - - +
190A ALA 2.9 7.3 + - - -
191A PHE* 3.0 46.3 + - + +
206A ILE* 3.8 15.7 - - + -
207A CYS 4.0 19.3 - - - +
208A ALA* 4.3 1.6 - - + -
231A PHE* 4.5 2.7 - - + -
235A LEU* 3.6 15.3 - - + +
259A THR* 4.9 2.2 - - + -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ALA 4.6 2.7 - - - +
158A LEU* 3.5 26.9 - - + -
162A PRO* 3.4 18.5 - - + +
186A HIS 2.8 18.2 + - - +
188A PRO* 1.3 77.1 - - - +
190A ALA* 1.3 57.1 + - - +
191A PHE 3.2 0.2 - - - -
192A LEU* 3.1 30.3 - - + +
229A TRP* 4.8 0.2 - - + -
231A PHE* 3.8 26.0 - - + -
235A LEU* 4.8 0.4 - - - -
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 3.9 23.1 - - + -
157A ALA 5.1 0.8 + - - +
161A LEU* 3.9 27.6 - - + +
162A PRO* 4.2 1.8 - - - +
167A VAL* 3.7 16.3 - - + +
171A LEU* 3.9 2.7 - - + +
187A GLY 2.9 14.3 + - - +
189A ALA* 1.3 74.8 - - - +
191A PHE* 1.3 66.6 + - + +
192A LEU 3.0 4.9 - - - -
193A ALA* 3.0 24.3 + - - +
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 5.3 4.5 - - + -
171A LEU* 3.5 27.1 - - + -
181A VAL* 3.9 18.8 - - + -
183A SER* 4.0 24.5 - - - -
188A PRO* 3.0 35.6 + - + +
190A ALA* 1.3 75.1 - - + +
192A LEU* 1.3 54.0 + - - +
193A ALA 2.8 15.7 + - - -
194A LEU* 3.0 21.7 + - + +
201A LEU* 3.5 20.6 - - + -
206A ILE* 4.8 4.7 - - + -
235A LEU* 4.0 8.7 - - + -
238A MET* 3.4 8.4 - - - +
240A MET* 3.8 29.4 - - + -
257A LEU* 4.0 24.2 - - + -
259A THR* 4.9 0.9 - - + -
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO* 3.2 7.1 - - + +
189A ALA* 3.1 20.0 + - - +
190A ALA 3.0 0.4 - - - -
191A PHE* 1.3 75.9 - - - +
193A ALA* 1.3 57.1 + - - +
194A LEU 3.3 0.9 - - - -
195A ARG* 3.0 64.2 + - - +
229A TRP* 3.4 36.1 - - + -
231A PHE* 4.0 10.3 - - + -
234A GLU* 3.8 18.6 - - + +
235A LEU* 3.4 42.0 - - + +
238A MET* 4.2 7.2 - - - -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU 3.7 11.9 - - - +
162A PRO 3.3 7.7 + - - +
163A GLU* 5.0 1.1 - - - +
164A SER 3.4 26.7 - - - +
165A GLN* 5.8 0.3 - - - -
167A VAL* 4.0 1.8 - - + -
168A ALA* 3.6 24.6 - - + +
190A ALA 3.0 16.2 + - - +
191A PHE 2.8 0.6 + - - -
192A LEU* 1.3 75.3 - - - +
194A LEU* 1.3 60.4 + - + +
195A ARG* 3.1 5.9 + - - +
196A HIS* 4.4 3.8 + - - +
197A GLY 5.3 0.3 + - - -
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ALA* 3.8 17.0 - - - +
171A LEU* 3.7 32.1 - - + -
172A GLN* 4.0 19.5 - - + +
175A ILE* 5.1 1.3 - - + -
191A PHE* 3.0 18.8 + - - +
193A ALA* 1.3 76.2 - - - +
195A ARG* 1.3 66.0 + - - +
196A HIS 3.3 0.4 - - - -
197A GLY* 2.8 22.7 + - - -
199A ASN* 4.2 11.5 + - - +
200A PRO* 4.2 15.9 - - + -
201A LEU* 3.8 34.3 - - + -
238A MET* 3.3 17.5 - - + +
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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