Contacts of the helix formed by residues 256 - 279 (chain A) in PDB entry 4R8U
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ILE* 4.8 0.2 - - - +
255A HIS* 1.3 97.4 + - + +
257A TRP* 1.3 67.2 + - - +
258A SER* 3.9 16.4 - - - +
259A GLU* 2.8 42.3 + - - +
260A CYS 3.3 3.6 + - - -
321A TRP* 3.6 8.4 - - - -
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Residues in contact with TRP 257 (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 HIS* 1.3 69.7 - - - +
258A SER* 1.3 71.3 + - - +
260A CYS* 2.9 40.1 + - + -
261A GLU* 3.0 47.8 + - + -
264A ILE* 4.4 2.5 - - + -
314A ILE* 3.7 32.8 - - + -
317A ALA* 4.0 9.6 - - + -
318A ARG* 3.5 56.9 - - + +
321A TRP* 3.6 37.3 - + + +
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 3.9 13.7 - - - +
257A TRP* 1.3 83.8 - - - +
259A GLU* 1.3 66.2 + - - +
261A GLU* 3.5 5.1 + - - +
262A ALA* 3.1 24.8 + - - +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 3.2 24.6 - - + +
255A HIS 2.8 31.4 + - - -
256A HIS* 2.8 35.5 + - + +
258A SER* 1.3 80.5 - - - +
260A CYS* 1.3 62.0 + - - +
262A ALA* 3.5 6.6 + - - +
263A ILE* 3.1 27.6 + - + +
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Residues in contact with CYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 3.8 8.7 - - + +
256A HIS 3.3 1.6 + - - -
257A TRP* 2.9 35.1 + - + +
259A GLU* 1.3 80.0 - - - +
261A GLU* 1.3 57.4 + - - +
263A ILE* 3.2 6.9 + - - +
264A ILE* 3.0 35.1 + - - +
291A LEU* 4.4 8.1 - - - -
317A ALA* 5.0 1.3 - - - -
321A TRP* 3.9 30.3 - - + -
333A VAL* 4.2 26.2 - - - -
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TRP* 3.0 45.4 + - + +
258A SER* 4.1 5.5 - - - +
260A CYS* 1.3 73.6 - - - +
262A ALA* 1.3 67.9 + - - +
264A ILE* 3.2 7.2 + - - +
265A GLU* 3.0 43.6 + - + +
314A ILE* 3.9 27.6 - - + +
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Residues in contact with ALA 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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258A SER 3.1 18.3 + - - +
259A GLU* 3.7 7.2 - - - +
260A CYS 3.3 0.2 - - - -
261A GLU* 1.3 79.3 - - - +
263A ILE* 1.3 61.1 + - - +
265A GLU* 3.5 8.8 + - - +
266A ARG* 3.3 37.5 + - - +
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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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248A ARG* 4.2 19.3 - - + -
250A MET* 3.5 38.1 - - + -
254A ILE* 3.6 28.3 - - + -
259A GLU 3.1 21.3 + - - +
260A CYS 3.2 5.8 + - - +
262A ALA* 1.3 75.0 - - - +
264A ILE* 1.3 65.4 + - - +
266A ARG* 3.0 29.3 + - - +
267A LEU* 3.0 21.3 + - + +
333A VAL* 3.9 25.4 - - + -
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Residues in contact with ILE 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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257A TRP* 4.4 9.4 - - + -
260A CYS* 3.0 25.4 + - - +
261A GLU* 3.2 8.3 + - - +
263A ILE* 1.3 75.4 - - - +
265A GLU* 1.3 60.2 + - - +
267A LEU* 3.0 7.3 + - - +
268A TYR* 2.8 32.9 + - + +
310A LYS* 5.3 2.7 - - + +
313A LEU* 4.7 3.4 - - + +
314A ILE* 3.9 29.6 - - + +
317A ALA* 3.4 33.0 - - + -
333A VAL* 3.9 19.5 - - + -
335A LEU* 4.2 25.4 - - + -
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Residues in contact with GLU 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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261A GLU* 3.0 36.8 + - + +
262A ALA* 3.8 8.5 - - - +
263A ILE 3.2 0.2 - - - -
264A ILE* 1.3 76.5 - - - +
266A ARG* 1.3 59.7 + - + +
268A TYR* 4.7 4.3 - - - +
269A PRO* 3.1 24.1 - - - +
310A LYS* 2.6 42.0 + - - +
314A ILE* 3.9 7.7 - - + +
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Residues in contact with ARG 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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248A ARG* 3.9 27.5 - - - +
250A MET* 5.0 3.6 - - - +
262A ALA* 3.3 25.9 + - - +
263A ILE* 3.0 25.5 + - + +
265A GLU* 1.3 78.3 - - + +
267A LEU* 1.3 65.8 + - + +
269A PRO* 3.4 10.4 - - - +
270A GLU* 4.0 12.1 - - - +
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Residues in contact with LEU 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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246A VAL* 4.1 25.4 - - + +
247A GLU 4.2 1.8 - - - -
248A ARG* 4.2 30.1 - - + +
263A ILE* 3.0 26.5 + - + +
264A ILE* 3.0 8.3 + - - +
266A ARG* 1.3 77.7 - - + +
268A TYR* 1.3 65.8 + - - +
270A GLU* 2.9 20.6 + - + +
271A LEU* 3.2 9.9 + - - +
333A VAL* 3.4 33.4 - - + +
334A GLY* 4.1 2.9 - - - -
335A LEU* 3.8 26.0 - - + -
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Residues in contact with TYR 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 ILE* 2.8 20.5 + - + +
265A GLU 4.5 0.7 - - - +
267A LEU* 1.3 71.9 - - - +
269A PRO* 1.4 75.3 - - + +
270A GLU 3.1 0.2 + - - -
271A LEU* 3.2 4.7 + - + +
272A GLU* 2.9 47.8 + - - +
282A LEU* 5.4 0.5 - - - +
308A LEU* 3.5 47.4 + - + +
309A ASN* 4.0 0.6 - - - -
310A LYS* 3.5 66.3 + - + -
313A LEU* 4.0 13.5 - - + -
335A LEU* 3.8 11.0 - - + -
295B ASP* 6.1 0.5 - - - +
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Residues in contact with PRO 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 GLU 3.1 22.0 - - - +
266A ARG* 3.4 12.1 - - - +
268A TYR* 1.4 98.5 - - + +
270A GLU* 1.3 63.4 + - - +
272A GLU* 3.3 10.4 + - + +
273A ARG* 2.9 30.0 + - - +
310A LYS* 6.0 0.4 - - + -
18C C 6.3 0.9 - - - +
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Residues in contact with GLU 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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246A VAL* 4.5 16.4 - - + -
266A ARG 4.0 12.3 - - - +
267A LEU* 2.9 13.7 + - + +
269A PRO* 1.3 80.2 - - - +
271A LEU* 1.3 66.9 + - - +
273A ARG* 2.9 36.0 + - - +
274A ARG* 3.1 32.5 + - + +
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Residues in contact with LEU 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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244A VAL* 3.9 36.1 - - + +
245A GLY* 5.0 0.7 - - - -
246A VAL* 3.9 22.6 - - + +
267A LEU 3.2 4.0 + - - +
268A TYR* 3.2 8.9 + - + +
270A GLU* 1.3 79.3 - - - +
272A GLU* 1.3 57.3 + - - +
274A ARG* 3.5 4.3 + - - +
275A LEU* 3.0 32.4 + - + +
308A LEU* 3.8 29.6 - - + -
313A LEU* 4.1 5.2 - - + -
335A LEU* 3.6 35.0 - - + +
336A HIS 4.4 4.9 - - - +
337A VAL* 4.4 13.9 - - + -
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Residues in contact with GLU 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 TYR* 2.9 39.4 + - + +
269A PRO* 3.5 12.9 - - - +
270A GLU 3.2 0.2 - - - -
271A LEU* 1.3 74.3 - - - +
273A ARG* 1.3 65.7 + - - +
276A ALA* 3.0 28.4 + - + +
282A LEU* 3.9 23.0 - - + +
308A LEU* 3.7 22.6 - - + +
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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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269A PRO 2.9 16.3 + - - +
270A GLU* 2.9 38.6 + - - +
272A GLU* 1.3 75.6 - - - +
274A ARG* 1.3 82.7 + - - +
276A ALA* 3.6 5.3 + - - +
277A LYS* 3.3 50.2 + - - +
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Residues in contact with ARG 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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241A ARG* 5.3 7.5 + - - +
244A VAL* 4.2 19.8 - - + +
245A GLY 3.1 18.7 + - - -
246A VAL* 3.6 18.1 - - - +
270A GLU* 3.1 20.5 + - - +
271A LEU* 3.9 3.8 - - - +
273A ARG* 1.3 95.4 - - - +
275A LEU* 1.3 66.5 + - - +
277A LYS* 3.0 33.8 + - - +
278A VAL* 3.9 6.2 + - - +
22V G 2.5 43.3 + - - -
23V G 3.5 20.9 + - - -
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Residues in contact with LEU 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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244A VAL* 4.6 7.8 - - + +
271A LEU* 3.0 23.5 + - + +
272A GLU 4.0 2.9 - - - +
274A ARG* 1.3 76.1 - - - +
276A ALA* 1.3 58.8 + - - +
278A VAL* 3.1 10.7 + - + +
279A LYS* 2.8 36.0 + - + -
282A LEU* 3.8 24.7 - - + -
284A ILE* 3.6 24.0 - - + -
308A LEU* 3.9 21.8 - - + -
337A VAL* 4.4 11.4 - - + -
339A LEU* 3.6 31.0 - - + -
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Residues in contact with ALA 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 GLU* 3.0 21.1 + - + +
273A ARG* 3.9 6.1 - - - +
275A LEU* 1.3 76.6 - - - +
277A LYS* 1.3 63.2 - - - +
278A VAL 3.1 0.7 + - - -
279A LYS 3.5 12.1 - - - +
280A PRO* 3.3 30.4 - - + +
282A LEU* 3.9 11.2 - - + +
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Residues in contact with LYS 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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273A ARG* 3.3 43.3 + - - +
274A ARG* 3.0 28.5 + - - +
276A ALA* 1.3 80.2 - - - +
278A VAL* 1.3 63.5 + - + +
280A PRO* 5.0 2.1 - - - +
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Residues in contact with VAL 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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241A ARG* 3.1 34.5 - - - +
244A VAL* 5.1 1.8 - - + -
274A ARG 4.6 3.4 - - - +
275A LEU* 3.1 14.8 + - + +
277A LYS* 1.3 86.8 - - + +
279A LYS* 1.3 73.0 + - + +
280A PRO* 3.8 5.6 - - - +
339A LEU* 4.6 20.2 - - + -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 2.8 25.7 + - + +
276A ALA* 3.5 11.9 - - - -
278A VAL* 1.3 87.4 - - + +
280A PRO* 1.3 61.6 - - + +
281A ASP* 3.1 32.3 + - - +
282A LEU* 2.7 28.8 + - - +
283A LEU* 3.8 23.7 - - - +
339A LEU* 4.9 6.1 - - + -
340A LEU* 4.4 20.0 - - - +
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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