Contacts of the helix formed by residues 186 - 196 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153H GLY* 4.1 0.2 - - - -
154H GLY 3.8 18.3 - - - +
155H HIS* 3.1 35.8 + + - -
157H ALA* 3.8 6.2 - - + +
158H LEU* 3.6 36.3 - - + +
185H CYS* 1.3 91.3 - - - +
187H GLY* 1.3 65.6 + - - +
188H PRO* 3.3 1.6 - - - -
189H ALA* 2.8 23.1 + - - +
209H PHE* 3.7 20.2 - + + -
214H ASP* 2.5 29.1 + - - -
227H LEU* 4.8 0.4 - - + +
231H PHE* 3.5 24.5 - + - -
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Residues in contact with GLY 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H VAL* 3.5 13.5 - - - +
152H PRO 3.8 9.9 - - - -
153H GLY* 3.6 4.2 - - - -
157H ALA* 4.1 5.2 - - - +
183H SER* 3.0 16.2 + - - -
184H LEU 2.8 11.9 + - - -
186H HIS* 1.3 77.9 - - - +
188H PRO* 1.3 61.7 - - - +
189H ALA 2.9 6.4 + - - -
190H ALA* 3.0 21.7 + - - +
191H PHE* 5.0 0.2 - - - -
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Residues in contact with PRO 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H SER* 3.1 15.9 - - - +
184H LEU 3.5 9.4 - - - +
185H CYS 3.4 14.8 - - - +
186H HIS 3.4 0.9 - - - -
187H GLY* 1.3 84.4 - - - +
189H ALA* 1.3 54.4 + - - +
190H ALA 2.9 6.3 - - - -
191H PHE* 2.9 53.3 + - + +
206H ILE* 3.8 7.2 - - + -
207H CYS 3.8 21.8 - - - +
208H ALA* 4.2 1.1 - - + -
231H PHE* 4.5 4.0 - - + -
235H LEU* 3.7 23.6 - - + +
259H THR* 4.7 2.5 - - + -
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Residues in contact with ALA 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H ALA 4.8 2.7 - - - +
158H LEU* 3.6 25.4 - - + -
162H PRO* 3.5 18.9 - - + +
186H HIS 2.8 18.2 + - - +
188H PRO* 1.3 76.2 - - - +
190H ALA* 1.3 60.0 + - - +
191H PHE 3.2 0.4 - - - -
192H LEU* 3.1 25.1 - - - +
229H TRP* 4.8 1.3 - - + -
231H PHE* 3.8 26.4 - - + -
235H LEU* 4.8 2.5 - - - -
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Residues in contact with ALA 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H VAL* 3.9 22.7 - - + -
157H ALA 5.2 0.8 + - - -
161H LEU* 3.8 26.4 - - + +
167H VAL* 3.6 16.6 - - + +
171H LEU* 5.0 0.9 - - + -
187H GLY 3.0 14.9 + - - +
188H PRO 2.9 0.2 - - - -
189H ALA* 1.3 75.1 - - - +
191H PHE* 1.3 64.4 + - + +
192H LEU 2.9 5.4 - - - -
193H ALA* 2.9 30.8 + - - +
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Residues in contact with PHE 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H VAL* 4.9 4.5 - - + -
171H LEU* 3.5 26.9 - - + -
181H VAL* 4.1 19.1 - - + -
183H SER* 4.0 20.0 - - - -
188H PRO* 2.9 43.2 + - + +
190H ALA* 1.3 76.2 - - + +
192H LEU* 1.3 57.0 + - - +
193H ALA 2.9 11.3 + - - -
194H LEU* 3.0 15.3 + - - +
201H LEU* 3.6 13.0 - - + -
206H ILE* 4.6 5.2 - - + -
235H LEU* 4.0 2.7 - - + -
238H MET* 3.2 14.8 - - + +
240H MET* 3.7 42.2 - - + -
257H LEU* 4.0 22.9 - - + -
259H THR* 4.8 0.4 - - + -
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Residues in contact with LEU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H PRO* 3.2 16.3 - - + +
163H GLU* 6.0 0.2 - - - +
189H ALA* 3.1 18.9 + - - +
190H ALA 2.9 0.2 + - - -
191H PHE* 1.3 77.8 - - - +
193H ALA* 1.3 55.9 + - - +
194H LEU 3.3 0.4 - - - -
195H ARG* 3.0 50.5 + - + +
229H TRP* 3.5 37.2 - - + -
231H PHE* 4.3 4.7 - - + +
234H GLU* 4.0 16.4 - - + +
235H LEU* 3.2 50.0 - - + +
238H MET* 3.9 8.3 - - + -
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Residues in contact with ALA 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H LEU 3.6 7.4 - - - +
162H PRO 3.2 14.7 + - - +
163H GLU* 5.1 0.9 - - - +
164H SER 3.4 25.7 - - - +
167H VAL* 3.8 1.1 - - + -
168H ALA* 3.7 26.2 - - + +
190H ALA 2.9 14.8 + - - +
191H PHE 2.9 1.2 - - - -
192H LEU* 1.3 75.1 - - - +
194H LEU* 1.3 56.7 + - + +
195H ARG* 3.0 9.7 + - - +
196H HIS* 4.2 11.3 + - - +
197H GLY 5.1 1.2 + - - -
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Residues in contact with LEU 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H ALA* 3.5 34.8 - - + +
171H LEU* 3.8 25.8 - - + -
172H GLN* 3.6 19.5 - - + +
191H PHE* 3.0 15.1 + - + +
193H ALA* 1.3 73.9 - - - +
195H ARG* 1.3 61.7 + - - +
196H HIS 3.1 4.4 + - - -
197H GLY* 3.6 11.2 + - - +
199H ASN* 3.3 49.1 - - - +
200H PRO* 3.8 13.7 - - + -
201H LEU* 3.9 20.6 - - + -
238H MET* 4.1 3.8 - - - -
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Residues in contact with ARG 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H PRO 3.9 5.1 + - - -
163H GLU* 2.9 36.0 + - - +
192H LEU* 3.0 51.8 + - + +
193H ALA* 3.0 2.4 - - - +
194H LEU* 1.3 77.7 - - - +
196H HIS* 1.3 92.2 + - + +
197H GLY 4.7 1.0 - - - +
199H ASN* 5.7 0.2 - - - -
234H GLU* 5.0 12.4 + - - +
238H MET* 3.8 25.4 - - + +
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Residues in contact with HIS 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H GLU* 6.2 0.7 - - - -
193H ALA 4.2 9.9 + - - +
194H LEU 3.1 0.4 - - - -
195H ARG* 1.3 123.5 + - + +
197H GLY* 1.3 69.8 + - - +
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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