Contacts of the helix formed by residues 238 - 254 (chain C) in PDB entry 1Y8Q
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 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236C THR 3.4 2.6 + - - -
237C THR* 1.3 70.8 + - - +
239C ASP* 1.3 65.7 + - - +
240C TYR 3.1 0.4 - - - -
241C PHE* 2.8 31.9 + - - +
242C LEU* 2.8 12.7 + - - +
286C LEU* 3.4 27.6 - - - +
287C LEU* 3.9 17.5 - - - +
288C PRO* 4.5 6.7 - - - +
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Residues in contact with ASP 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C PHE* 5.9 0.9 - - - -
162C HIS* 3.2 37.2 + - - +
163C GLY 5.0 0.9 - - - +
237C THR* 3.0 16.6 + - - +
238C SER* 1.3 84.8 + - - +
240C TYR* 1.3 56.9 + - - +
242C LEU* 3.1 12.9 + - + +
243C LEU* 2.9 29.1 + - - +
330C PHE* 3.6 31.2 - - + +
331C PHE 3.5 14.7 - - - +
332C ASP* 4.2 9.2 - - - +
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Residues in contact with TYR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ALA 2.6 29.0 + - - -
220C LEU* 3.6 8.1 + - + -
222C VAL* 3.6 13.5 + - + +
224C TRP* 3.7 23.1 + + - -
236C THR* 4.3 3.4 - - + -
237C THR* 3.3 14.9 + - + +
238C SER 3.1 0.4 - - - -
239C ASP* 1.3 78.2 - - - +
241C PHE* 1.3 86.8 + + - +
243C LEU* 3.5 5.5 - - + +
244C GLN* 3.3 46.3 + - + +
280C LEU* 5.9 1.1 - - + -
328C PHE* 4.1 13.7 - + - -
330C PHE* 3.5 29.6 - + + -
343C LEU* 3.4 31.2 - - + -
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Residues in contact with PHE 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C TRP* 4.1 12.6 - + - -
233C LEU* 3.4 28.5 - - + -
236C THR* 4.4 13.2 - - + -
237C THR 4.4 1.1 - - - -
238C SER* 2.8 14.3 + - - +
240C TYR* 1.3 101.0 - + - +
242C LEU* 1.3 66.6 + - - +
243C LEU 3.1 1.8 - - - -
244C GLN* 3.2 8.7 + - + +
245C VAL* 3.0 27.4 + - - +
277C LEU* 3.8 28.6 - - + +
280C LEU* 4.4 8.3 - - + -
282C ILE* 3.6 18.6 - - + -
286C LEU* 3.7 34.8 - - + -
287C LEU* 4.3 12.8 - - + -
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C PHE* 4.2 9.0 - - + -
162C HIS* 3.6 48.0 - - + +
238C SER 2.8 11.5 + - - +
239C ASP* 3.1 15.9 + - + +
241C PHE* 1.3 76.4 - - - +
243C LEU* 1.3 62.3 + - - +
245C VAL* 3.3 3.5 + - - +
246C LEU* 3.0 45.5 + - + +
287C LEU* 4.1 14.3 - - + +
291C PHE* 3.4 42.4 - - + -
295C CYS* 4.4 7.0 - - + -
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C PHE* 4.5 14.1 - - + -
164C TYR* 3.6 42.6 - - + -
220C LEU* 4.3 14.4 - - + -
239C ASP 2.9 11.7 + - - +
240C TYR* 3.5 11.9 - - + +
241C PHE 3.1 0.2 - - - -
242C LEU* 1.3 75.7 - - - +
244C GLN* 1.3 60.4 + - + +
246C LEU* 3.2 5.7 + - + +
247C LEU* 2.8 53.5 + - + +
328C PHE* 3.8 29.6 - - + -
330C PHE* 4.3 9.2 - - + -
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Residues in contact with GLN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ARG* 4.1 16.4 - - - +
220C LEU* 3.1 40.9 + - - +
240C TYR* 3.3 38.7 + - + +
241C PHE* 3.2 17.9 + - + +
243C LEU* 1.3 76.9 - - - +
245C VAL* 1.3 57.5 + - - +
247C LEU* 3.8 6.3 - - - +
248C LYS* 3.1 28.1 + - - +
276C VAL* 4.1 24.9 - - + +
277C LEU* 6.3 0.2 - - + -
280C LEU* 5.2 7.2 - - + -
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C PHE 3.0 13.8 + - - +
242C LEU* 3.6 8.1 - - - +
244C GLN* 1.3 75.9 - - + +
246C LEU* 1.3 60.9 - - + +
248C LYS* 3.4 2.6 + - - +
249C PHE* 2.9 26.0 + - - +
269C LEU* 3.8 30.7 - - + +
272C ILE* 3.7 23.3 - - + +
273C ARG* 3.8 25.4 - - + +
276C VAL* 4.9 7.4 - - + -
277C LEU* 5.6 3.4 - - + -
287C LEU* 3.9 15.3 - - + -
291C PHE* 4.4 10.8 - - + -
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C PHE* 3.3 55.6 - - + -
242C LEU* 3.0 31.4 + - + +
243C LEU* 3.9 4.9 - - + +
245C VAL* 1.3 74.1 - - + +
247C LEU* 1.3 61.3 + - - +
249C PHE* 3.5 4.4 - - - +
250C ARG* 2.9 32.3 + - - +
257C PRO* 4.2 22.8 - - + +
269C LEU* 4.0 21.8 - - + -
291C PHE* 5.5 0.2 - - + -
295C CYS* 4.3 16.6 - - + +
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C CYS 4.6 5.8 - - - +
135C SER* 5.5 0.2 - - - -
136C ARG* 4.2 40.2 + - + +
139C ILE* 4.3 16.2 - - + -
157C ASP* 5.7 1.3 - - - +
164C TYR* 5.2 2.0 - - + +
220C LEU* 4.0 37.2 - - + -
243C LEU* 2.8 40.8 + - + +
244C GLN* 3.8 9.2 - - - +
246C LEU* 1.3 77.4 - - - +
248C LYS* 1.3 61.7 + - - +
250C ARG* 3.2 15.0 + - - +
251C THR* 3.0 25.9 + - - -
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Residues in contact with LYS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C GLN 3.1 16.0 + - - +
245C VAL 3.6 4.5 - - - +
247C LEU* 1.3 76.6 - - - +
249C PHE* 1.3 65.0 + - - +
251C THR* 3.0 12.6 + - - +
252C ASP* 3.0 51.7 + - - +
272C ILE* 3.8 20.9 - - + -
275C ASP* 5.7 6.5 - - - -
276C VAL* 4.2 14.1 - - + -
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Residues in contact with PHE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C VAL 2.9 18.7 + - - +
246C LEU* 3.5 6.5 - - - +
248C LYS* 1.3 75.4 - - - +
250C ARG* 1.3 63.1 + - - +
252C ASP* 5.1 0.4 - - - -
253C LYS* 2.9 39.7 + - + +
255C ARG* 3.2 22.0 - - - -
256C ASP* 3.4 2.9 - - - -
257C PRO* 3.1 39.9 - - + -
265C ASP* 3.5 33.9 - - + -
268C LEU* 3.8 22.2 - - + -
269C LEU* 3.5 27.4 - - + -
272C ILE* 3.7 23.3 - - + +
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Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C CYS* 3.3 12.3 - - - +
134C CYS 2.6 52.8 + - - +
135C SER* 4.0 11.4 - - - +
157C ASP* 3.0 37.8 + - - +
158C VAL 5.5 0.4 + - - -
159C PHE* 5.3 5.3 - - - -
246C LEU* 2.9 15.4 + - - +
247C LEU* 3.5 18.8 - - - +
249C PHE* 1.3 76.4 - - - +
251C THR* 1.3 56.1 + - - +
254C GLY* 2.7 33.7 + - - -
255C ARG* 3.2 18.8 - - - +
256C ASP* 2.7 43.2 + - - +
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C SER* 5.1 7.8 - - - -
136C ARG* 4.2 21.5 + - - +
137C ASP* 5.3 10.9 + - - +
247C LEU 3.0 15.5 + - - -
248C LYS* 3.0 17.7 + - + +
250C ARG* 1.3 79.9 - - - +
252C ASP* 1.3 73.4 + - - +
254C GLY* 3.7 4.3 + - - -
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Residues in contact with ASP 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C LYS* 3.0 47.2 + - - +
249C PHE* 4.2 2.2 - - - +
251C THR* 1.3 87.4 - - - +
253C LYS* 1.3 68.3 + - + +
254C GLY* 3.3 0.5 + - - -
268C LEU* 6.1 1.6 - - + -
272C ILE* 4.7 9.3 - - + +
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C PHE* 2.9 40.8 + - + +
252C ASP* 1.3 78.0 - - + +
254C GLY* 1.3 61.4 + - - +
255C ARG* 3.4 39.3 + - + +
264C GLU* 4.3 15.9 + - - +
265C ASP* 4.6 2.5 - - - -
268C LEU* 3.5 33.8 - - + +
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Residues in contact with GLY 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ARG* 2.7 22.4 + - - -
251C THR 4.3 4.0 - - - -
252C ASP 3.2 3.6 - - - -
253C LYS* 1.3 72.1 - - - +
255C ARG* 1.3 63.5 + - - +
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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