Contacts of the helix formed by residues 260 - 282 (chain A) in PDB entry 3S51
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 PRO 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A HIS* 3.3 33.2 - - + +
247A GLU* 5.0 9.4 - - + +
259A ALA* 1.4 94.1 - - + +
261A ALA* 1.3 69.9 + - + +
262A ASP 3.0 2.9 - - - -
263A GLU* 2.7 22.6 + - + +
264A LEU* 3.0 18.5 + - + -
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A HIS* 4.1 9.0 - - + +
258A THR* 2.9 26.2 - - - +
259A ALA 3.5 2.0 - - - -
260A PRO* 1.3 79.6 - - + +
262A ASP* 1.3 64.5 - - - +
264A LEU* 4.7 0.7 - - - +
265A TYR* 3.2 45.5 + - + +
373A HIS* 3.4 22.4 - - + +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A THR* 3.0 37.2 + - - +
259A ALA 3.7 7.5 - - - +
260A PRO 4.2 0.4 - - - +
261A ALA* 1.3 76.1 - - - +
263A GLU* 1.3 64.2 + - + +
266A HIS* 2.4 45.9 + - + +
373A HIS* 4.6 4.8 - - - -
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASN* 4.5 10.4 + - - -
207A LEU* 3.7 23.3 - - + +
208A GLN* 3.2 35.9 + - - +
259A ALA 5.5 0.2 + - - -
260A PRO* 2.7 13.6 + - + +
262A ASP* 1.3 76.7 - - + +
264A LEU* 1.3 66.7 + - - +
265A TYR 3.1 0.2 + - - -
266A HIS* 3.1 3.7 + - - -
267A VAL* 2.8 31.9 + - + +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU* 4.5 15.6 - - + +
237A PHE* 4.4 10.5 - - + -
240A LEU* 4.3 28.5 - - + +
241A ASP* 3.8 13.7 - - - +
244A HIS* 3.6 41.1 - - + +
260A PRO* 3.0 22.5 + - + +
263A GLU* 1.3 74.6 - - - +
265A TYR* 1.3 66.1 + - + +
267A VAL* 3.7 3.4 - - - +
268A GLU* 2.9 48.0 + - + +
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Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ASP* 4.0 13.1 + - - -
244A HIS* 3.0 42.6 + + - +
245A ARG* 4.8 4.5 - - - +
261A ALA* 3.2 28.8 + - + +
264A LEU* 1.3 78.2 - - + +
266A HIS* 1.3 60.9 + - - +
267A VAL 3.2 0.4 - - - -
268A GLU* 3.4 23.3 - - - -
269A GLY 2.9 12.6 + - - -
366A GLU* 4.4 1.7 + - - -
369A ARG* 3.8 8.1 + - - -
370A ASN* 3.3 47.6 + - + +
373A HIS* 3.6 31.4 - + + +
375A TRP* 2.8 34.8 + + + -
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Residues in contact with HIS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASP* 2.4 46.8 + - + +
263A GLU* 3.7 2.9 - - - +
265A TYR* 1.3 76.7 - - - +
267A VAL* 1.3 61.7 + - + +
269A GLY* 3.4 2.4 + - - -
270A THR* 2.9 27.0 + - - -
373A HIS* 3.5 25.4 - + + +
374A SER* 3.1 36.7 + - - -
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU* 4.0 25.1 - - + +
208A GLN* 3.8 27.8 - - + +
210A ILE* 5.0 0.4 - - + -
211A PRO* 4.0 19.5 - - + -
237A PHE* 4.2 14.8 - - + -
263A GLU* 2.8 23.3 + - - +
264A LEU 3.7 4.0 - - - +
266A HIS* 1.3 74.1 - - + +
268A GLU* 1.3 54.9 + - - +
270A THR* 2.9 9.8 + - - -
271A VAL* 2.7 48.7 + - + +
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE* 3.7 23.9 - - + +
241A ASP* 2.5 35.9 - - - +
264A LEU* 2.9 39.5 + - + +
265A TYR* 3.4 25.5 - - - +
266A HIS 3.4 0.2 - - - -
267A VAL* 1.3 75.3 - - - +
269A GLY* 1.3 52.5 + - - +
271A VAL* 3.7 7.8 - - - +
272A ILE* 2.8 41.1 + - - +
308A PHE* 3.7 20.8 - - + +
375A TRP* 3.8 13.0 - - + -
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Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A TYR 2.9 11.8 + - - -
266A HIS 3.7 2.2 - - - -
267A VAL 3.1 0.2 - - - -
268A GLU* 1.3 76.7 - - - +
270A THR* 1.3 50.7 + - - +
272A ILE* 3.3 3.9 + - - -
273A LEU* 2.6 38.4 + - - +
374A SER* 5.4 0.9 - - - -
375A TRP* 3.4 27.3 - - - +
377A HIS* 3.3 14.8 - - - -
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Residues in contact with THR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PRO* 3.9 15.3 - - + -
266A HIS 2.9 15.7 + - - -
267A VAL* 2.9 9.8 + - - -
269A GLY* 1.3 73.7 - - - +
271A VAL* 1.3 57.6 + - - +
273A LEU* 3.2 13.4 + - + +
274A HIS* 2.8 56.1 + - + -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PRO* 4.3 20.2 - - + -
214A VAL* 4.3 13.0 - - + -
233A ILE* 3.8 18.4 - - + -
237A PHE* 3.6 41.7 - - + -
267A VAL* 2.7 28.8 + - + +
268A GLU* 3.7 4.7 - - - +
270A THR* 1.3 69.6 - - - +
272A ILE* 1.3 63.9 + - - +
274A HIS* 3.0 15.7 + - - +
275A ILE* 2.8 28.3 + - + +
308A PHE* 4.1 8.7 - - + -
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLU 2.8 32.2 + - - +
269A GLY* 3.6 7.0 - - - +
271A VAL* 1.3 71.4 - - - +
273A LEU* 1.3 64.2 + - - +
274A HIS 3.2 0.3 + - - -
275A ILE* 3.2 7.2 + - - +
276A VAL* 3.0 24.7 + - + +
308A PHE* 3.6 28.3 - - + +
311A ALA* 3.8 16.8 - - + +
312A LEU* 3.6 45.1 - - + +
315A SER* 3.7 23.6 - - - +
375A TRP* 4.8 9.4 - - + -
377A HIS* 4.7 3.6 - - + -
378A VAL* 6.1 0.2 - - + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLY 2.6 18.6 + - - +
270A THR* 3.3 14.1 - - + +
272A ILE* 1.3 73.4 - - - +
274A HIS* 1.3 61.4 + - - +
276A VAL* 4.2 2.5 - - + +
277A PHE* 3.3 33.6 + - + +
318A ARG* 3.7 21.8 - - - +
376A ASP* 5.9 0.7 - - - +
377A HIS* 3.5 34.8 - - + +
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Residues in contact with HIS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PRO* 3.5 34.5 + - + +
212A PRO* 4.6 1.5 - - + +
214A VAL* 4.6 4.3 - - + -
215A TYR* 4.0 30.4 - + + +
218A LEU* 4.1 15.0 - - + +
270A THR* 2.8 41.1 + - + +
271A VAL* 3.0 10.5 + - - +
273A LEU* 1.3 77.5 - - - +
275A ILE* 1.3 59.4 + - - +
277A PHE* 3.2 10.6 - + + +
278A ALA* 3.1 21.8 + - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 4.6 2.5 - - + -
218A LEU* 3.8 26.7 - - + -
230A LEU* 4.0 23.8 - - + -
233A ILE* 4.8 9.2 - - + -
234A ILE* 6.0 0.9 - - + -
271A VAL* 2.8 30.2 + - + +
272A ILE* 3.2 3.6 + - - +
274A HIS* 1.3 71.4 - - - +
276A VAL* 1.3 67.7 + - - +
277A PHE 3.1 1.1 - - - -
278A ALA* 3.3 4.4 + - - +
279A ILE* 3.0 33.3 + - + +
285A LEU* 4.5 0.6 - - + +
289A LEU* 4.1 9.6 - - + -
308A PHE* 6.0 1.3 - - + -
312A LEU* 3.3 45.1 - - + -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE 3.0 19.0 + - - +
273A LEU* 4.2 3.6 - - + +
275A ILE* 1.3 77.7 - - - +
277A PHE* 1.3 66.6 + - + +
279A ILE* 3.2 9.5 + - - +
280A LYS* 3.0 19.5 + - + +
312A LEU* 4.0 14.6 - - + +
315A SER* 3.9 9.4 - - - +
316A LEU* 3.7 31.9 - - + +
318A ARG* 3.3 31.9 - - - +
319A ILE* 3.5 21.7 - - + +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A TYR* 6.5 0.9 - + - -
273A LEU* 3.3 25.3 + - + +
274A HIS* 3.2 16.2 - + + +
275A ILE 3.1 0.2 - - - -
276A VAL* 1.3 83.0 - - + +
278A ALA* 1.3 60.0 + - - +
280A LYS* 3.2 38.0 - - + +
281A LEU* 3.4 18.0 + - + +
318A ARG* 6.4 0.2 - - - -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A TYR* 6.6 0.2 - - + -
218A LEU* 4.4 17.9 - - + +
274A HIS 3.1 12.3 + - - +
275A ILE* 3.5 11.2 - - - +
277A PHE* 1.3 72.7 - - - +
279A ILE* 1.3 54.8 + - - +
280A LYS 3.0 1.6 - - - -
281A LEU* 2.9 10.3 + - - +
282A ASP* 2.7 36.4 + - - +
285A LEU* 3.6 24.0 - - + -
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ILE* 3.0 29.3 + - + +
276A VAL* 3.2 8.7 + - - +
278A ALA* 1.3 75.5 - - - +
280A LYS* 1.3 62.1 + - - +
282A ASP 3.0 19.9 - - - +
283A CYS* 3.9 4.9 + - - -
285A LEU* 3.7 18.2 - - + -
286A GLY* 3.4 27.6 - - - +
289A LEU* 3.6 31.4 - - + -
312A LEU* 4.8 0.4 - - + -
316A LEU* 3.8 25.8 - - + -
319A ILE* 4.1 1.5 - - + +
322A PHE* 3.6 23.0 - - + -
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A VAL* 3.0 12.3 + - + +
277A PHE* 3.2 33.0 - - + +
278A ALA 3.0 0.2 - - - -
279A ILE* 1.3 80.7 - - - +
281A LEU* 1.3 71.0 + - + +
282A ASP 4.9 0.3 - - - -
283A CYS* 5.0 5.7 - - - -
319A ILE* 3.7 22.0 - - + +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PHE* 3.4 16.3 + - + +
278A ALA* 2.9 9.4 + - - +
280A LYS* 1.3 92.2 - - + +
282A ASP* 1.3 61.2 + - + +
283A CYS* 4.2 2.2 + - - -
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A SER* 4.4 11.7 - - - +
226A ARG* 2.5 45.4 + - - +
278A ALA 2.7 14.0 + - - +
279A ILE* 3.0 14.9 - - - +
281A LEU* 1.3 76.0 - - + +
283A CYS* 1.3 62.3 + - - +
284A GLU* 3.2 8.6 + - - +
285A LEU* 3.0 40.3 + - + +
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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