Contacts of the helix formed by residues 184 - 196 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182G ILE* 3.1 25.5 - - - +
183G ASN* 1.3 79.8 - - - +
185G THR* 1.3 63.4 + - - +
186G ALA* 3.6 10.2 + - - +
187G ASP* 2.6 35.3 + - - +
227G LEU* 3.8 8.3 - - - +
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Residues in contact with THR 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G SER* 1.3 72.7 - - - +
186G ALA* 1.3 61.9 + - - +
187G ASP 3.1 6.6 + - - -
188G LEU* 3.4 6.8 + - + +
189G ASP* 3.2 33.9 + - - +
226G HIS 3.7 19.2 + - - -
227G LEU* 3.8 24.8 - - - +
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Residues in contact with ALA 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G HIS* 4.1 8.4 + - - +
184G SER* 3.9 9.4 - - - +
185G THR* 1.3 81.0 - - - +
187G ASP* 1.3 62.9 + - - +
188G LEU 3.5 0.2 - - - -
189G ASP* 4.0 8.2 - - - +
190G PHE* 3.3 21.3 + - - +
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Residues in contact with ASP 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G HIS* 4.4 11.8 + - - -
154G ASN* 5.9 1.0 + - - -
156G TYR* 4.4 15.9 + - - +
180G LEU* 6.2 0.9 - - + -
181G LYS 5.2 3.5 - - - +
182G ILE* 4.2 15.0 - - + -
183G ASN* 3.6 10.6 + - - +
184G SER* 2.6 38.8 + - - +
185G THR 3.1 1.0 - - - -
186G ALA* 1.3 80.3 - - - +
188G LEU* 1.3 59.6 + - - +
189G ASP 3.2 0.2 - - - -
190G PHE* 3.2 6.5 + - - +
191G ILE* 2.9 36.8 + - + +
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Residues in contact with LEU 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ILE* 3.4 33.2 - - + +
184G SER 4.9 0.4 - - - +
185G THR* 3.4 11.6 + - + +
187G ASP* 1.3 79.9 - - - +
189G ASP* 1.3 55.2 + - - +
191G ILE* 4.3 6.7 - - + -
192G GLN* 2.7 54.8 + - + +
204G MET* 4.9 1.1 - - + -
227G LEU 4.3 5.6 - - - +
228G PHE* 3.4 41.3 - - + -
246G ILE* 3.8 15.3 - - + -
249G GLY 6.1 0.7 - - - +
251G VAL* 4.6 7.0 - - + -
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Residues in contact with ASP 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G THR* 3.2 30.0 + - - +
186G ALA* 4.3 6.9 - - - +
187G ASP 3.2 0.2 - - - -
188G LEU* 1.3 80.2 - - - +
190G PHE* 1.3 63.3 + - - +
192G GLN* 3.7 9.8 - - - +
193G GLN* 3.4 22.5 + - - +
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Residues in contact with PHE 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ILE* 4.0 25.4 - - + -
151G HIS* 3.3 60.1 - + + +
156G TYR* 3.7 21.5 - + + -
158G PHE* 6.1 0.4 - + - -
186G ALA 3.3 19.2 + - - +
187G ASP* 3.2 4.7 + - - +
188G LEU 3.2 0.2 - - - -
189G ASP* 1.3 78.4 - - - +
191G ILE* 1.3 85.2 + - + +
193G GLN* 3.6 3.7 + - - +
194G ALA* 3.1 32.9 + - + +
147H ASP* 3.5 21.3 - - + -
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Residues in contact with ILE 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G TYR* 3.7 24.5 - - + -
158G PHE* 5.3 1.6 - - + -
180G LEU* 3.7 27.4 - - + -
182G ILE* 5.0 1.1 - - + -
187G ASP* 2.9 28.3 + - + +
188G LEU* 3.8 11.4 - - + +
190G PHE* 1.3 102.9 - - + +
192G GLN* 1.3 63.8 + - - +
194G ALA* 3.1 7.1 + - + +
195G ILE* 3.1 25.3 + - + +
246G ILE* 4.7 10.3 - - + -
263G ILE* 3.4 31.9 - - + -
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Residues in contact with GLN 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G LEU* 2.7 33.6 + - + +
189G ASP* 3.9 14.8 - - - +
190G PHE 3.3 0.2 - - - -
191G ILE* 1.3 74.9 - - - +
193G GLN* 1.3 57.1 + - - +
195G ILE* 3.4 14.3 + - - +
196G SER* 2.9 28.0 + - - +
246G ILE* 2.7 38.9 - - - +
247G GLN 4.7 0.2 - - - +
248G ARG 4.7 0.2 - - - +
249G GLY* 2.9 44.6 - - - +
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Residues in contact with GLN 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G ASP 3.4 15.6 + - - +
190G PHE* 4.2 3.8 - - - +
192G GLN* 1.3 78.0 - - - +
194G ALA* 1.3 61.7 + - - +
195G ILE 3.1 1.3 - - - -
196G SER* 3.0 27.8 + - - +
197G TYR* 3.7 11.0 + - + -
147H ASP* 5.9 0.6 + - - -
158H PHE 4.9 8.1 + - - -
160H SER* 3.4 34.7 + - - +
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Residues in contact with ALA 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ILE* 4.9 5.6 - - + -
158G PHE* 3.0 36.5 - - + -
190G PHE* 3.1 34.5 + - + +
191G ILE* 3.1 11.2 + - + +
193G GLN* 1.3 79.2 - - - +
195G ILE* 1.3 58.1 + - - +
197G TYR* 3.1 26.6 + - - +
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Residues in contact with ILE 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G PHE* 3.1 30.3 - - + -
191G ILE* 3.2 17.9 - - + +
192G GLN* 3.4 16.6 - - - +
194G ALA* 1.3 75.7 - - - +
196G SER* 1.3 56.7 + - - +
197G TYR* 3.3 3.6 - - - -
198G SER* 2.6 45.1 + - - +
200G PHE 5.8 0.9 - - - +
202G PHE* 4.1 21.5 - - + -
246G ILE* 3.4 50.5 - - + +
247G GLN* 4.7 3.6 - - - +
248G ARG 5.6 0.4 - - - +
263G ILE* 4.1 5.6 - - + -
197H TYR* 6.2 0.2 - - - -
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Residues in contact with SER 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G GLN* 2.9 18.4 + - - +
193G GLN* 3.0 24.8 + - - +
195G ILE* 1.3 76.3 - - - +
197G TYR* 1.3 69.2 + - - +
198G SER 2.6 20.1 + - - +
248G ARG* 5.1 4.2 + - - -
160H SER* 6.1 0.5 - - - -
200H PHE* 4.0 7.1 - - - -
261H PHE* 5.8 3.6 - - - -
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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