Contacts of the helix formed by residues 255 - 278 (chain A) in PDB entry 5YUS
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 HIS 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A HIS* 1.3 91.5 - - + +
256A TRP* 1.3 65.9 + - - +
257A SER* 3.2 15.5 - - - +
258A GLU* 3.0 41.3 + - + +
259A CYS 3.4 4.0 + - - -
320A TRP* 3.4 9.6 - - - -
293F ASP 5.3 0.7 - - - -
294F ASP* 2.7 42.9 + - + +
295F PHE* 5.0 0.8 - - - +
839G T 4.5 13.5 - - - -
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Residues in contact with TRP 256 (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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255A HIS* 1.3 71.1 - - - +
257A SER* 1.3 67.8 + - - +
259A CYS* 2.9 31.1 + - + +
260A GLU* 2.9 46.7 + - + +
263A ILE* 4.7 1.1 - - + -
313A ILE* 3.7 12.1 - - + -
316A ALA* 3.8 9.4 - - + -
317A ARG* 3.5 59.9 - - + +
320A TRP* 3.5 32.8 - + + +
294F ASP* 5.4 1.8 + - - -
296F GLN* 3.6 45.1 - - + +
869H G 2.7 30.6 + - - -
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Residues in contact with SER 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 3.9 13.2 - - - +
256A TRP* 1.3 85.0 - - - +
258A GLU* 1.3 61.7 + - - +
260A GLU* 3.9 7.2 - - - +
261A ALA* 3.0 28.4 + - - +
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 3.3 26.3 - - + +
254A HIS 3.0 28.4 + - - -
255A HIS* 3.0 31.5 + - + +
257A SER* 1.3 77.8 + - - +
259A CYS* 1.3 65.4 + - - +
261A ALA* 3.4 5.9 + - - +
262A ILE* 3.1 29.5 + - + +
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Residues in contact with CYS 259 (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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253A ILE* 3.7 9.3 - - + +
255A HIS 3.4 2.2 + - - -
256A TRP* 2.9 33.3 + - + +
258A GLU* 1.3 79.1 - - - +
260A GLU* 1.3 62.3 + - - +
262A ILE* 3.1 6.6 + - - +
263A ILE* 3.0 36.7 + - - +
290A LEU* 4.2 10.5 - - - -
316A ALA* 4.7 2.7 - - - -
320A TRP* 3.8 29.4 - - + -
332A VAL* 4.0 18.8 - - - -
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Residues in contact with GLU 260 (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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256A TRP* 2.9 33.3 + - + +
257A SER* 3.9 7.6 - - - +
259A CYS* 1.3 76.4 - - - +
261A ALA* 1.3 62.2 + - - +
263A ILE* 3.2 12.0 + - - +
264A GLU* 3.0 29.3 + - + +
313A ILE* 3.3 34.8 - - + +
317A ARG* 4.2 2.6 + - - -
869H G 2.9 37.7 + - - +
870H A 5.6 1.7 + - - -
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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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257A SER 3.0 18.9 + - - +
258A GLU* 3.7 7.4 - - - +
259A CYS 3.2 0.2 - - - -
260A GLU* 1.3 76.3 - - - +
262A ILE* 1.3 63.8 + - + +
264A GLU* 3.3 10.6 + - - +
265A ARG* 3.3 24.7 + - - +
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Residues in contact with ILE 262 (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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247A ARG* 5.2 5.4 - - + -
249A MET* 3.6 44.0 - - + -
253A ILE* 4.0 18.2 - - + -
258A GLU* 3.1 21.0 + - + +
259A CYS* 3.1 6.5 + - - +
261A ALA* 1.3 76.6 - - + +
263A ILE* 1.3 65.5 + - - +
265A ARG* 3.0 15.9 + - + +
266A LEU* 2.9 35.3 + - + +
332A VAL* 3.9 24.2 - - + +
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Residues in contact with ILE 263 (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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256A TRP* 4.7 1.8 - - + -
259A CYS* 3.0 25.9 + - - +
260A GLU* 3.6 12.8 - - - +
262A ILE* 1.3 76.4 - - - +
264A GLU* 1.3 57.3 + - - +
266A LEU* 3.1 7.5 + - - +
267A TYR* 2.8 34.0 + - + +
288A VAL* 5.3 0.2 - - + -
309A LYS* 5.1 2.5 - - + -
312A LEU* 4.8 3.8 - - + +
313A ILE* 3.6 33.9 - - + +
316A ALA* 3.4 33.7 - - + -
332A VAL* 3.9 18.2 - - + -
334A LEU* 4.1 23.8 - - + -
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Residues in contact with GLU 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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260A GLU* 3.0 26.2 + - + +
261A ALA* 3.6 12.1 - - - +
262A ILE 3.2 0.2 - - - -
263A ILE* 1.3 76.1 - - - +
265A ARG* 1.3 58.8 + - + +
267A TYR* 4.5 3.0 - - - +
268A PRO* 3.1 24.1 - - - +
309A LYS* 2.6 34.2 + - - -
313A ILE* 3.1 25.8 - - + +
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Residues in contact with ARG 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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247A ARG* 3.6 33.8 - - - +
261A ALA* 3.3 13.4 + - - +
262A ILE* 3.0 16.9 + - + +
264A GLU* 1.3 78.1 - - + +
266A LEU* 1.3 65.7 + - + +
268A PRO* 3.3 11.5 - - - +
269A GLU* 4.5 5.5 + - - +
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Residues in contact with LEU 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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245A VAL* 3.9 28.0 - - + +
246A GLU 4.4 0.4 - - - -
247A ARG* 4.0 24.9 - - + +
262A ILE* 2.9 32.3 + - + +
263A ILE* 3.8 2.2 - - - +
265A ARG* 1.3 79.1 - - + +
267A TYR* 1.3 64.9 + - - +
269A GLU* 3.1 16.6 + - - +
270A LEU* 3.2 12.3 + - - +
332A VAL* 3.4 35.4 - - + +
333A GLY* 4.2 8.5 - - - -
334A LEU* 3.7 18.6 - - + -
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Residues in contact with TYR 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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263A ILE 2.8 15.8 + - - +
264A GLU 4.5 1.8 - - - +
266A LEU* 1.3 76.9 - - - +
268A PRO* 1.3 72.0 - - + +
269A GLU 3.2 0.3 + - - -
270A LEU* 3.2 4.2 + - + +
271A GLU* 3.0 45.6 + - - -
281A LEU* 5.4 0.5 - - - +
307A LEU* 3.3 50.2 + - + +
308A ASN* 4.0 0.2 - - - -
309A LYS* 3.4 64.9 + - + -
312A LEU* 3.7 16.8 - - + -
334A LEU* 3.7 10.3 - - + -
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Residues in contact with PRO 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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264A GLU 3.1 21.8 - - - +
265A ARG* 3.3 13.2 - - - +
267A TYR* 1.3 96.9 - - + +
269A GLU* 1.3 54.9 + - - +
271A GLU* 3.3 7.4 + - + +
272A ARG* 3.0 50.0 + - - +
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Residues in contact with GLU 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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245A VAL* 4.2 13.5 - - + -
265A ARG 4.5 4.6 + - - +
266A LEU* 3.1 10.5 + - - +
268A PRO* 1.3 76.1 - - - +
270A LEU* 1.3 66.6 + - - +
272A ARG* 2.7 45.5 + - - +
273A ARG* 3.0 56.9 + - - +
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Residues in contact with LEU 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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243A VAL* 3.7 39.5 - - + +
244A GLY* 4.3 2.9 - - - -
245A VAL* 3.7 22.2 - - + +
266A LEU 3.2 7.5 + - - +
267A TYR* 3.2 10.6 + - + +
269A GLU* 1.3 77.7 - - - +
271A GLU* 1.3 57.4 + - - +
273A ARG* 3.3 1.2 + - - -
274A LEU* 2.9 34.4 + - + +
307A LEU* 3.8 28.3 - - + -
312A LEU* 4.5 4.3 - - + -
334A LEU* 3.7 29.8 - - + -
335A HIS 4.3 4.5 - - - +
336A VAL* 4.1 12.8 - - + -
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Residues in contact with GLU 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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267A TYR* 3.0 38.3 + - + +
268A PRO* 3.6 10.3 - - + +
270A LEU* 1.3 76.3 - - - +
272A ARG* 1.3 57.8 + - - +
274A LEU* 3.8 1.4 - - - +
275A ALA* 2.9 35.0 + - + +
281A LEU* 3.2 29.3 - - + +
306A ARG* 5.3 1.2 + - - -
307A LEU* 3.7 19.9 - - + +
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Residues in contact with ARG 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 PRO* 3.0 38.3 + - - +
269A GLU* 2.7 43.6 + - - +
271A GLU* 1.3 78.5 - - - +
273A ARG* 1.3 65.2 + - + +
275A ALA* 3.3 5.7 + - - -
276A LYS* 3.0 47.8 + - - +
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Residues in contact with ARG 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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240A ARG* 6.1 0.7 - - - -
243A VAL* 4.0 19.9 - - + +
244A GLY 3.7 8.3 + - - -
245A VAL* 3.9 16.0 - - - +
269A GLU* 3.0 40.6 + - + +
270A LEU 4.0 2.7 - - - +
272A ARG* 1.3 76.9 - - + +
274A LEU* 1.3 63.7 + - - +
276A LYS* 3.4 17.6 + - - +
277A VAL* 3.8 9.2 + - - +
842B G 3.1 42.7 + - - -
843B G 4.7 7.3 + - - -
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Residues in contact with LEU 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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243A VAL* 4.5 10.4 - - + +
270A LEU* 2.9 20.9 + - + +
271A GLU 3.9 2.5 - - - +
273A ARG* 1.3 73.8 - - - +
275A ALA* 1.3 55.6 + - - +
277A VAL* 3.1 10.8 + - + +
278A LYS* 2.7 43.0 + - + +
281A LEU* 3.7 26.0 - - + -
283A ILE* 3.8 19.5 - - + -
307A LEU* 3.8 26.2 - - + -
336A VAL* 4.3 10.1 - - + -
338A LEU* 3.6 30.7 - - + -
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Residues in contact with ALA 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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271A GLU* 2.9 22.1 + - + +
272A ARG* 3.6 5.8 - - - +
273A ARG 3.3 0.4 - - - -
274A LEU* 1.3 77.9 - - - +
276A LYS* 1.3 76.0 + - + +
277A VAL 3.2 0.9 + - - -
278A LYS 3.6 9.9 - - - -
279A PRO* 3.3 31.6 - - + +
281A LEU* 4.0 9.6 - - + -
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Residues in contact with LYS 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 ARG* 3.0 47.2 + - - +
273A ARG* 3.7 11.2 - - - +
274A LEU 3.2 0.6 - - - -
275A ALA* 1.3 86.3 - - + +
277A VAL* 1.3 58.0 + - + +
279A PRO* 5.3 1.8 - - - +
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Residues in contact with VAL 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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240A ARG* 4.6 25.6 - - + +
243A VAL* 4.6 2.9 - - + -
273A ARG 3.9 10.1 - - - +
274A LEU* 3.4 24.7 - - + +
276A LYS* 1.3 80.0 - - + +
278A LYS* 1.3 65.6 + - + +
279A PRO* 4.2 4.7 - - - +
338A LEU* 4.5 18.6 - - + -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 2.7 34.1 + - + +
275A ALA* 3.4 6.7 - - - -
277A VAL* 1.3 83.1 - - + +
279A PRO* 1.3 71.4 - - - +
280A ASP* 3.1 35.8 + - - +
281A LEU* 3.0 14.3 + - - +
282A LEU* 3.4 34.5 - - - +
338A LEU* 5.5 8.7 - - + -
339A LEU* 4.1 16.0 - - + +
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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