Contacts of the helix formed by residues 235 - 249 (chain B) in PDB entry 1YCH
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 ASP 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B ASP* 3.2 15.6 + - - +
232B TRP* 4.5 7.8 - - - -
234B LYS* 1.3 87.5 - - + +
236B PRO* 1.3 63.8 - - - +
237B GLY* 3.3 12.5 + - - -
238B ARG* 3.3 37.6 + - + +
239B ILE 4.2 1.7 + - - -
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Residues in contact with PRO 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ILE* 4.4 14.8 - - + +
222B LYS 3.4 27.8 - - - +
223B THR* 3.8 1.3 - - - -
224B ILE* 3.8 22.0 - - + -
232B TRP* 3.3 30.5 - - + +
233B ARG 4.5 0.2 - - - +
234B LYS 3.8 5.4 - - - +
235B ASP* 1.3 87.4 - - - +
237B GLY* 1.3 65.9 + - - +
239B ILE* 3.3 5.8 + - - +
240B ILE* 3.0 27.3 + - + +
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ASP* 3.1 9.1 + - - -
236B PRO* 1.3 80.7 - - - +
238B ARG* 1.3 52.1 + - - +
240B ILE* 3.1 8.2 + - - +
241B GLU* 2.8 49.4 + - - +
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ALA* 3.3 36.5 + - - +
186B GLY* 6.3 0.2 - - - -
189B MET* 3.6 31.2 - - + +
232B TRP* 5.9 1.8 - - + -
235B ASP* 3.3 32.7 + - + +
236B PRO 3.3 0.2 - - - -
237B GLY* 1.3 75.7 - - - +
239B ILE* 1.3 57.7 + - - +
241B GLU* 3.3 13.9 + - - +
242B ALA* 2.9 29.2 + - + +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PHE* 3.4 25.4 - - + +
189B MET* 4.2 11.6 - - + +
192B ALA* 4.2 10.1 - - + -
224B ILE* 4.2 5.2 - - + -
232B TRP* 3.0 59.9 - - + +
235B ASP 4.2 0.6 + - - -
236B PRO 3.3 10.6 + - - +
238B ARG* 1.3 76.2 - - - +
240B ILE* 1.3 67.6 + - - +
242B ALA* 4.1 11.9 - - + -
243B TYR* 3.1 50.3 + - + -
246B TRP* 4.4 1.6 - - + -
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU* 5.7 0.2 - - + -
169B PHE* 4.3 12.8 - - + -
211B LEU* 3.9 23.4 - - + +
221B ILE* 3.8 34.5 - - + -
224B ILE* 3.9 22.2 - - + -
236B PRO* 3.0 19.2 + - + +
237B GLY* 3.7 6.3 - - - +
239B ILE* 1.3 77.7 - - + +
241B GLU* 1.3 65.8 + - + +
243B TYR* 3.2 4.3 + - - +
244B ALA* 3.0 21.1 + - + +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLY* 2.8 35.4 + - - +
238B ARG* 3.6 15.3 + - - +
240B ILE* 1.3 73.4 - - + +
242B ALA* 1.3 57.2 + - - +
244B ALA* 3.2 8.6 + - - +
245B ARG* 2.9 56.5 + - - +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B MET* 4.1 19.7 - - - -
238B ARG* 2.9 17.5 + - + +
239B ILE* 3.6 15.3 - - + +
241B GLU* 1.3 75.8 - - - +
243B TYR* 1.3 56.9 + - - +
245B ARG* 3.1 12.1 + - - +
246B TRP* 2.8 49.4 + - + -
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Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ALA* 4.1 3.3 - - + -
169B PHE* 2.6 64.4 + + + -
170B GLY 3.9 2.6 + - - -
192B ALA* 5.1 3.4 + - + -
195B TYR* 4.3 9.4 - - - -
196B TYR* 3.5 22.6 - + + +
200B LEU* 3.4 31.5 - - + +
207B ILE* 4.1 15.8 - - + +
211B LEU* 4.2 9.9 - - + -
239B ILE* 3.1 38.2 + - + +
240B ILE 3.2 7.6 + - - +
242B ALA* 1.3 78.9 - - - +
244B ALA* 1.3 57.8 + - - +
246B TRP* 3.9 17.7 - + - +
247B ALA* 2.8 33.5 + - - +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B THR* 4.6 4.7 - - - +
211B LEU* 3.7 17.4 - - + +
240B ILE* 3.0 14.2 + - + +
241B GLU* 3.3 12.6 - - - +
242B ALA 3.2 0.2 - - - -
243B TYR* 1.3 76.5 - - - +
245B ARG* 1.3 58.0 + - + +
247B ALA* 3.8 2.2 - - - +
248B GLU* 2.9 31.2 + - - +
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B GLU* 2.9 46.0 + - - +
242B ALA* 3.6 8.2 - - - +
244B ALA* 1.3 74.0 - - + +
246B TRP* 1.3 68.9 + - + +
248B GLU* 3.3 10.0 + - - +
249B GLY* 3.1 18.9 + - - -
250B GLN* 4.3 4.0 + - - +
251B GLY 5.4 1.2 + - - -
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Residues in contact with TRP 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B MET* 4.2 19.1 - - + -
192B ALA* 4.0 15.5 - - + -
193B ALA* 3.4 34.5 - - + +
196B TYR* 3.7 41.6 + + + -
204B SER* 4.4 4.0 + - - -
239B ILE* 4.4 1.8 - - + -
242B ALA* 2.8 43.9 + - + +
243B TYR* 3.9 16.4 - + - +
245B ARG* 1.3 82.8 - - + +
247B ALA* 1.3 63.6 + - - +
249B GLY* 3.4 13.0 + - - -
302B LEU* 3.8 29.4 - - + +
303B ASP* 3.5 26.2 + - - -
335B LYS* 5.6 0.3 - - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B TYR* 3.5 16.3 + - - +
204B SER* 3.4 30.5 - - - +
207B ILE* 3.8 11.7 - - + -
208B THR* 3.5 15.0 - - + -
243B TYR 2.8 22.0 + - - +
244B ALA* 3.9 1.3 - - - +
246B TRP* 1.3 71.3 - - - +
248B GLU* 1.3 57.1 + - - +
249B GLY 3.4 0.2 + - - -
335B LYS* 2.7 31.7 + - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B THR* 4.1 7.5 - - + +
244B ALA 2.9 19.2 + - - +
245B ARG* 3.6 9.7 - - - +
246B TRP 3.3 0.2 - - - -
247B ALA* 1.3 75.6 - - - +
249B GLY* 1.3 60.5 + - - +
250B GLN* 3.2 35.7 - - - +
335B LYS* 3.4 21.2 + - - +
336B ASN* 5.7 0.7 - - - +
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ARG 3.1 7.9 + - - -
246B TRP* 3.4 10.5 + - - -
247B ALA 3.2 2.9 - - - -
248B GLU* 1.3 79.3 - - - +
250B GLN* 1.3 66.6 + - - +
251B GLY* 3.2 5.0 + - - -
302B LEU 5.7 2.5 - - - -
335B LYS* 4.2 17.0 - - - +
336B ASN* 2.9 24.9 + - - +
337B LYS* 4.6 7.8 + - - -
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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