Contacts of the helix formed by residues 184 - 195 (chain H) in PDB entry 1YPO
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 SER 184 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182H ILE* 3.6 9.1 - - - +
183H ASN* 1.3 82.3 - - - +
185H THR* 1.3 63.6 + - - +
186H ALA* 3.3 12.4 + - - +
187H ASP* 2.7 32.5 + - - -
188H LEU* 3.1 19.1 + - - +
227H LEU* 3.6 12.1 - - - +
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Residues in contact with THR 185 (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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184H SER* 1.3 76.0 - - - +
186H ALA* 1.3 59.8 + - - +
188H LEU* 3.5 11.9 + - + +
189H ASP* 2.8 38.7 + - - +
226H HIS 4.7 10.3 - - - +
227H LEU* 3.8 17.2 - - + +
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Residues in contact with ALA 186 (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 HIS* 4.6 5.8 + - - +
184H SER* 3.1 11.1 + - - +
185H THR* 1.3 81.1 + - - +
187H ASP* 1.3 61.7 + - - +
189H ASP* 3.4 9.7 + - - +
190H PHE* 3.1 25.8 + - - +
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Residues in contact with ASP 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 HIS* 4.9 7.4 + - - -
154H ASN* 5.5 1.7 + - - -
156H TYR* 4.2 16.4 + - + +
180H LEU* 6.0 1.3 - - + -
181H LYS 5.0 3.6 - - - +
182H ILE* 4.2 16.6 - - + -
183H ASN* 3.3 11.8 + - - +
184H SER* 2.7 37.7 + - - +
186H ALA* 1.3 72.9 - - - +
188H LEU* 1.3 67.8 + - - +
189H ASP 3.0 2.1 + - - -
190H PHE* 3.1 9.0 + - + +
191H ILE* 2.9 33.5 + - + +
265H GLN* 6.3 0.7 - - - -
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Residues in contact with LEU 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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182H ILE* 3.9 29.3 - - + +
184H SER 3.1 10.7 + - - +
185H THR* 3.6 14.6 - - + +
186H ALA 3.3 0.2 - - - -
187H ASP* 1.3 79.4 - - - +
189H ASP* 1.3 64.7 + - - +
191H ILE* 4.3 1.3 - - + +
192H GLN* 3.1 26.1 + - + +
227H LEU* 3.5 26.0 - - - +
228H PHE* 4.2 20.4 - - + -
246H ILE* 4.1 19.5 - - + -
249H GLY 4.2 13.0 - - - +
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Residues in contact with ASP 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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185H THR* 2.8 28.0 + - - +
186H ALA* 3.6 9.2 - - - +
187H ASP 3.0 0.8 - - - -
188H LEU* 1.3 78.8 - - - +
190H PHE* 1.3 66.9 + - - +
192H GLN* 3.1 11.8 + - - +
193H GLN* 2.9 24.6 + - - +
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Residues in contact with PHE 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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147G ASP* 3.4 21.1 - - - -
149H ILE* 4.3 19.1 - - + -
151H HIS* 3.4 48.2 - + + +
156H TYR* 3.5 46.4 - + + -
158H PHE* 5.8 0.7 - + - -
186H ALA 3.1 7.7 + - - +
187H ASP* 3.6 8.1 - - + +
189H ASP* 1.3 80.8 - - - +
191H ILE* 1.3 86.3 + - + +
193H GLN* 3.1 21.5 - - - +
194H ALA* 2.9 34.6 + - + +
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Residues in contact with ILE 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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156H TYR* 4.5 3.4 - - + -
158H PHE* 5.2 7.2 - - + -
180H LEU* 3.7 47.3 - - + -
182H ILE* 4.8 5.4 - - + -
187H ASP* 2.9 23.8 + - + +
188H LEU* 4.3 4.0 - - + +
190H PHE* 1.3 91.9 - - + +
192H GLN* 1.3 67.9 + - - +
194H ALA* 3.1 6.4 + - - +
195H ILE* 3.1 29.2 + - + +
246H ILE* 4.2 23.1 - - + -
263H ILE* 4.2 21.5 - - + -
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Residues in contact with GLN 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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188H LEU* 3.1 19.0 + - + +
189H ASP* 3.1 13.6 + - - +
191H ILE* 1.3 81.7 - - - +
193H GLN* 1.3 73.5 + - + +
195H ILE* 3.3 12.0 + - - +
196H SER* 3.0 29.2 + - - +
246H ILE* 5.7 0.9 - - + -
248H ARG 4.6 3.8 - - - +
249H GLY* 4.0 29.4 + - - +
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Residues in contact with GLN 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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147G ASP* 4.3 11.4 - - - +
157G LEU* 6.2 2.4 - - - +
158G PHE* 5.2 7.3 + - - +
160G SER* 5.9 8.7 - - - +
189H ASP 2.9 12.6 + - - +
190H PHE* 3.1 33.6 - - - +
192H GLN* 1.3 88.1 - - + +
194H ALA* 1.3 72.4 + - - +
195H ILE 2.8 11.8 + - - -
196H SER* 2.8 26.3 + - - +
197H TYR* 4.8 8.9 + - - -
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Residues in contact with ALA 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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197G TYR* 5.7 1.0 - - - -
149H ILE* 5.2 5.4 - - + -
158H PHE* 3.6 30.8 - - + -
190H PHE* 2.9 25.3 + - + +
191H ILE* 3.1 11.9 + - - +
193H GLN* 1.3 90.5 - - - +
195H ILE* 1.3 60.1 + - - +
197H TYR* 3.5 24.7 + - - -
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Residues in contact with ILE 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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158H PHE* 3.1 35.0 - - + -
191H ILE* 3.1 18.6 + - + +
192H GLN* 3.4 10.8 - - - +
193H GLN 2.8 2.8 + - - -
194H ALA* 1.3 74.3 - - - +
196H SER* 1.3 67.3 + - - +
197H TYR* 3.1 4.9 - - - +
198H SER* 3.0 27.2 + - - +
200H PHE 5.6 0.2 - - - +
202H PHE* 4.1 25.1 - - + -
246H ILE* 4.0 39.3 - - + +
247H GLN* 4.8 7.0 - - - -
248H ARG* 4.8 6.3 - - - +
249H GLY 4.9 2.9 - - - +
263H ILE* 4.4 7.0 - - + -
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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