Contacts of the helix formed by residues 261 - 280 (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 THR 261 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ARG* 3.6 10.0 + - - +
258C SER* 3.5 10.5 + - - -
259C SER 3.2 0.6 - - - -
260C ASP* 1.3 85.0 - - + +
262C TYR* 1.3 64.1 + - - +
263C GLU* 3.5 2.2 - - - -
264C GLU* 3.4 29.8 + - - +
265C ASP* 2.4 50.6 + - - +
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Residues in contact with TYR 262 (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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258C SER 3.6 5.6 + - - -
259C SER* 3.1 18.1 + - - +
260C ASP 3.4 1.8 + - - -
261C THR* 1.3 75.3 - - - +
263C GLU* 1.3 75.7 + - + +
266C SER* 2.5 62.1 + - - -
292C VAL* 3.3 32.4 + - + +
293C ARG* 3.6 25.1 - - + +
296C PHE* 3.4 25.6 - + - -
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C THR 3.5 0.4 - - - -
262C TYR* 1.3 98.4 - - + +
264C GLU* 1.3 65.8 + - - +
266C SER* 3.5 6.1 + - - -
267C GLU* 3.3 26.4 + - - +
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Residues in contact with GLU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LYS* 4.3 16.2 + - - +
255C ARG* 5.0 2.7 + - - -
261C THR* 3.4 32.0 + - - +
262C TYR 3.2 0.4 - - - -
263C GLU* 1.3 82.5 - - - +
265C ASP* 1.3 68.3 + - - +
267C GLU* 3.5 5.2 + - - +
268C LEU* 3.4 18.8 + - + +
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Residues in contact with ASP 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C PHE* 3.5 20.7 - - + -
253C LYS* 4.6 3.1 - - - -
255C ARG* 2.9 23.7 + - - -
257C PRO* 3.9 17.7 - - + -
258C SER 3.1 20.4 + - - +
261C THR* 2.4 39.3 + - - +
262C TYR 3.9 1.3 - - - +
264C GLU* 1.3 74.7 - - - +
266C SER* 1.3 65.7 + - - +
268C LEU* 3.3 4.3 + - - +
269C LEU* 2.9 29.3 + - - +
296C PHE* 4.1 4.3 - - + -
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Residues in contact with SER 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C TYR* 2.5 63.2 + - - -
263C GLU* 3.6 8.3 - - - -
265C ASP* 1.3 74.3 - - - +
267C GLU* 1.3 66.6 + - - +
269C LEU* 3.2 4.2 + - - +
270C LEU* 3.1 28.1 + - - +
292C VAL* 3.3 22.1 - - - +
296C PHE* 4.1 1.7 - - - -
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Residues in contact with GLU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C GLU* 3.3 14.2 + - - +
264C GLU* 4.0 7.5 - - - +
265C ASP 3.3 0.4 - - - -
266C SER* 1.3 80.0 - - - +
268C LEU* 1.3 64.0 + - - +
270C LEU* 3.0 18.0 + - + +
271C GLN* 2.9 35.2 + - - +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C PHE* 3.8 10.5 - - + -
252C ASP* 6.1 1.8 - - + -
253C LYS* 3.5 40.6 - - + +
264C GLU 3.4 10.6 + - - +
265C ASP* 3.3 9.6 + - - +
266C SER 3.3 0.4 - - - -
267C GLU* 1.3 77.3 - - - +
269C LEU* 1.3 53.7 + - - +
271C GLN* 2.9 26.6 + - + +
272C ILE* 2.7 58.6 + - + +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 3.8 25.2 - - + +
246C LEU* 4.0 12.3 - - + -
249C PHE* 3.5 32.8 - - + -
257C PRO* 4.1 9.6 - - + -
265C ASP 2.9 19.4 + - - +
266C SER 3.2 7.2 + - - +
268C LEU* 1.3 75.8 - - - +
270C LEU* 1.3 57.6 + - - +
272C ILE* 3.4 5.9 + - - +
273C ARG* 2.9 28.4 + - - +
291C PHE* 3.8 14.3 - - + -
292C VAL* 4.3 6.3 - - + -
295C CYS* 4.2 15.0 - - - -
296C PHE* 3.9 31.0 - - + -
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C SER* 3.1 21.2 + - - +
267C GLU* 3.0 19.2 + - + +
269C LEU* 1.3 72.5 - - - +
271C GLN* 1.3 64.9 + - + +
273C ARG* 3.3 24.1 + - - +
274C ASN* 2.9 22.5 + - - +
289C GLU* 3.8 36.3 - - + +
291C PHE* 4.2 4.5 - - + -
292C VAL* 3.7 21.5 - - + -
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Residues in contact with GLN 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLU* 2.9 31.9 + - - +
268C LEU* 3.2 24.9 - - + +
270C LEU* 1.3 78.9 - - + +
272C ILE* 1.3 63.9 + - + +
273C ARG 3.2 0.2 + - - -
274C ASN* 3.3 9.8 + - - +
275C ASP* 3.1 23.4 + - - +
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Residues in contact with ILE 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 3.7 25.6 - - + +
248C LYS* 3.8 24.0 - - + -
249C PHE* 3.7 35.7 - - + +
252C ASP* 4.7 9.0 - - + +
268C LEU* 2.7 49.8 + - + +
269C LEU* 3.6 6.1 - - - +
271C GLN* 1.3 72.7 - - + +
273C ARG* 1.3 63.6 + - - +
275C ASP* 4.2 5.8 - - - -
276C VAL* 2.9 28.8 + - + +
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Residues in contact with ARG 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 3.8 13.7 - - + -
269C LEU 2.9 15.3 + - - +
270C LEU* 3.3 17.9 + - - +
271C GLN 3.1 0.4 - - - -
272C ILE* 1.3 76.6 - - - +
274C ASN* 1.3 92.0 + - - +
276C VAL* 3.8 0.7 - - - +
277C LEU* 3.0 43.6 + - + +
284C PRO* 2.7 33.8 + - - +
285C ASP* 4.3 9.5 + - - +
287C LEU* 3.1 33.1 + - + -
289C GLU* 3.5 35.4 + - - +
291C PHE* 4.1 14.6 - - + -
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Residues in contact with ASN 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 2.9 23.7 + - - +
271C GLN* 3.8 8.3 - - - +
273C ARG* 1.3 106.1 + - - +
275C ASP* 1.3 63.4 + - - +
278C ASP* 2.8 37.6 + - - +
284C PRO* 3.1 25.2 - - + +
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Residues in contact with ASP 275 (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* 5.7 6.0 - - - -
271C GLN 3.1 17.6 + - - +
272C ILE* 3.6 7.9 - - - +
274C ASN* 1.3 79.2 - - - +
276C VAL* 1.3 65.3 + - + +
278C ASP* 3.9 4.7 - - - +
279C SER* 2.8 34.0 + - - -
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Residues in contact with VAL 276 (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* 4.1 30.1 - - + +
245C VAL* 4.9 7.4 - - + +
248C LYS* 4.2 21.5 - - + -
272C ILE* 2.9 40.6 + - + +
273C ARG 3.9 1.6 - - - +
275C ASP* 1.3 76.9 - - + +
277C LEU* 1.3 70.7 + - + +
279C SER* 2.9 22.5 + - - -
280C LEU* 3.3 19.9 + - + +
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Residues in contact with LEU 277 (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* 3.8 39.7 - - + +
244C GLN* 6.3 0.2 - - + -
245C VAL* 5.6 2.9 - - + -
273C ARG* 3.0 33.9 + - + +
274C ASN 4.3 0.9 - - - +
276C VAL* 1.3 80.9 - - + +
278C ASP* 1.3 64.1 + - - +
280C LEU* 3.0 14.4 + - + +
281C GLY 3.1 0.2 + - - -
282C ILE* 2.9 48.2 + - + +
283C SER 3.8 5.8 - - - +
284C PRO* 3.3 32.5 - - + +
286C LEU* 5.1 1.1 - - + -
287C LEU* 4.1 14.1 - - + +
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Residues in contact with ASP 278 (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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274C ASN* 2.8 34.4 + - - +
275C ASP* 3.9 5.2 - - - +
277C LEU* 1.3 76.0 - - - +
279C SER* 1.3 58.0 + - - +
280C LEU 3.0 0.2 - - - -
281C GLY* 2.9 20.2 + - - +
282C ILE 3.9 5.2 - - - +
284C PRO* 3.8 21.9 - - - +
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ASP* 2.8 24.8 + - - -
276C VAL* 2.9 12.6 + - - -
278C ASP* 1.3 77.6 - - - +
280C LEU* 1.3 64.1 + - - +
281C GLY 3.4 0.2 - - - -
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Residues in contact with LEU 280 (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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220C LEU 5.9 2.2 - - - +
221C GLU* 6.0 2.7 - - - -
222C VAL 4.3 18.4 - - - +
224C TRP* 4.2 25.2 + - + +
225C SER* 6.1 0.2 - - - -
240C TYR* 5.9 1.1 - - + -
241C PHE* 4.4 16.6 - - + -
244C GLN* 5.2 8.1 - - + -
276C VAL* 3.7 27.6 - - + +
277C LEU* 3.0 11.0 + - + +
279C SER* 1.3 84.1 - - - +
281C GLY* 1.3 64.2 + - - +
282C ILE* 3.8 25.6 - - + +
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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
------------------------------------------------------------
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