Contacts of the helix formed by residues 258 - 284 (chain A) in PDB entry 6V01
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 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A VAL* 3.1 39.0 + - + +
255A VAL 3.3 4.3 - - - +
256A PHE 3.3 0.2 - - - -
257A ILE* 1.3 91.8 + - + +
259A ARG* 1.3 62.1 + - - +
260A GLN 3.2 3.1 - - - -
261A GLU* 2.8 29.2 + - - +
262A LEU* 3.3 27.5 + - + +
346A ILE* 3.9 21.1 - - + +
347A LEU* 5.0 0.9 - - + -
349A SER* 4.3 10.8 - - - -
350A GLY* 3.8 17.6 - - - -
353A LEU* 6.2 2.8 - - - +
352J ALA* 4.2 19.5 - - + +
356J GLN* 5.4 7.0 - - - -
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 3.1 10.6 + - - +
256A PHE* 3.0 65.8 + - + +
257A ILE* 3.3 7.3 + - - +
258A HIS* 1.3 77.8 - - - +
260A GLN* 1.3 68.0 + - + +
262A LEU* 4.1 3.1 - - - +
263A ILE* 3.0 40.7 + - + +
83L ARG* 5.5 9.3 - - - +
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Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE 5.0 1.3 + - - +
258A HIS 3.2 0.6 - - - -
259A ARG* 1.3 89.3 - - + +
261A GLU* 1.3 59.1 + - - +
263A ILE* 3.9 3.1 - - - +
264A THR* 2.9 42.5 + - - +
246J GLY 5.4 4.2 - - - +
250J LEU* 4.7 6.9 - - + +
355J VAL* 4.0 38.5 - - + +
75L LEU* 4.7 14.2 - - - +
78L GLY* 5.9 1.4 + - - -
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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 ILE 5.1 1.6 - - - +
258A HIS* 2.8 46.4 + - - +
259A ARG 3.5 0.4 - - - -
260A GLN* 1.3 74.3 - - - +
262A LEU* 1.3 59.8 + - - +
264A THR* 3.4 7.0 + - - +
265A THR* 2.9 33.3 + - - +
346A ILE* 3.7 22.6 - - + +
250J LEU* 5.4 1.3 - - + -
351J PHE* 3.5 34.8 - - + +
352J ALA* 3.7 15.1 - - - +
355J VAL* 3.5 29.8 - - + +
356J GLN* 6.0 0.3 - - - +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 4.1 31.2 - - + +
258A HIS* 3.3 22.0 + - + +
259A ARG* 4.1 3.6 - - - +
260A GLN 3.3 0.4 - - - -
261A GLU* 1.3 78.0 - - - +
263A ILE* 1.3 60.5 + - + +
265A THR* 3.6 1.7 - - - +
266A LEU* 3.0 44.3 + - + +
343A PRO* 3.7 33.2 - - + -
346A ILE* 4.3 17.0 - - + -
347A LEU* 4.1 23.6 - - + -
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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
----------------------------------------------------------
259A ARG* 3.0 28.5 + - + +
260A GLN* 4.0 4.0 - - - +
262A LEU* 1.3 75.6 - - + +
264A THR* 1.3 57.9 + - - +
266A LEU* 3.9 3.8 - - + +
267A TYR* 2.9 32.2 + - - +
70L VAL* 4.9 2.2 - - + +
71L THR* 3.7 39.2 - - + +
74L SER* 3.8 29.6 - - - +
75L LEU* 3.8 32.8 - - + +
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Residues in contact with THR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLN* 2.9 31.5 + - - -
261A GLU* 3.6 6.7 - - - -
263A ILE* 1.3 77.9 - - - +
265A THR* 1.3 60.7 + - - +
267A TYR* 3.3 3.6 + - - +
268A ILE* 3.0 36.8 + - + +
246J GLY 5.4 0.3 + - - -
247J THR* 3.7 35.9 + - + +
250J LEU* 3.9 20.8 - - + +
251J LEU* 5.7 1.1 - - + -
351J PHE* 3.8 24.5 - - + -
75L LEU* 5.3 1.1 - - - +
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Residues in contact with THR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLU 2.9 20.8 + - - +
262A LEU* 3.6 10.5 - - + +
264A THR* 1.3 76.2 - - - +
266A LEU* 1.3 67.1 + - + +
268A ILE* 4.1 5.7 - - - +
269A GLY* 2.9 25.6 + - - -
339A PHE* 2.4 43.1 + - - +
340A PHE* 5.6 0.3 - - - -
342A LEU* 3.6 26.7 - - + +
343A PRO* 4.1 18.8 - - + -
346A ILE* 5.1 0.7 - - + -
351J PHE* 4.7 4.3 - - - -
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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
----------------------------------------------------------
262A LEU* 3.0 29.3 + - + +
263A ILE* 4.2 2.5 - - + +
265A THR* 1.3 81.7 - - + +
267A TYR* 1.3 61.5 + - - +
269A GLY* 5.1 0.4 - - - -
270A PHE* 2.9 48.1 + - + +
339A PHE 5.6 0.9 - - - +
340A PHE* 4.3 26.0 - - + -
343A PRO* 4.9 11.7 - - + -
335D PHE* 5.6 11.0 - - + -
71L THR* 3.7 28.7 - - + -
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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
----------------------------------------------------------
263A ILE 2.9 20.1 + - - +
264A THR* 3.6 2.0 - - - +
266A LEU* 1.3 76.6 - - - +
268A ILE* 1.3 69.6 + - + +
270A PHE* 3.9 1.9 - - - +
271A LEU* 2.9 39.0 + - + +
238J MET 4.8 2.6 + - - -
239J LEU* 3.3 30.1 - - - +
242J ASP* 3.6 30.8 + - + +
247J THR* 3.7 26.0 - - + -
248J TRP* 4.2 8.3 - + - -
68L PHE* 4.0 27.5 - + - -
71L THR* 4.4 15.4 - - - +
72L VAL* 4.1 16.2 - - + -
75L LEU* 4.1 17.7 - - + -
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A THR* 3.0 20.8 + - + +
265A THR* 4.1 5.6 - - - +
266A LEU 3.4 0.2 - - - -
267A TYR* 1.3 84.0 - - + +
269A GLY* 1.3 57.8 + - - +
271A LEU* 3.3 3.3 + - - +
272A GLY* 2.9 25.6 + - - -
339A PHE* 3.8 34.8 - - + -
247J THR* 3.7 25.4 - - + +
248J TRP* 3.5 42.2 - - + -
251J LEU* 4.7 12.3 - - + -
801J PT5 6.0 1.0 - - + +
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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
----------------------------------------------------------
265A THR 2.9 16.9 + - - -
268A ILE* 1.3 78.5 - - - +
270A PHE* 1.3 56.8 + - - +
272A GLY* 3.4 1.9 + - - -
273A LEU* 2.9 27.7 + - - +
336A ALA* 5.0 7.2 - - - +
339A PHE* 4.6 9.3 - - - +
340A PHE* 3.4 31.0 - - - -
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 2.9 43.9 + - + +
267A TYR 4.2 0.7 - - - +
269A GLY* 1.3 73.3 - - - +
271A LEU* 1.3 61.0 + - - +
273A LEU* 3.6 25.0 - - + +
274A ILE* 2.9 35.7 + - + +
307A VAL* 5.5 4.5 - - + -
340A PHE* 3.9 22.2 - + - -
334D VAL* 5.4 10.1 - - + -
335D PHE* 6.4 0.9 - + - -
64L VAL* 4.9 11.9 - - + -
67L LEU* 3.5 48.5 - - + -
68L PHE* 4.1 23.3 - - + -
71L THR* 4.0 8.7 - - + -
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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
----------------------------------------------------------
267A TYR* 2.9 29.9 + - + +
268A ILE* 3.7 5.2 - - - +
269A GLY 3.3 0.2 - - - -
270A PHE* 1.3 74.2 - - - +
272A GLY* 1.3 60.0 + - - +
274A ILE* 4.6 7.2 - - + -
275A PHE* 2.9 57.5 + - + +
235J ILE* 6.3 0.2 - - + -
238J MET* 4.7 11.9 - - + -
239J LEU* 3.9 17.7 - - + +
248J TRP* 3.6 35.7 - - + -
801J PT5 4.3 9.4 - - + -
68L PHE* 4.4 22.4 - - + -
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE 2.9 15.8 + - - -
269A GLY* 3.4 3.3 + - - -
271A LEU* 1.3 76.3 - - - +
273A LEU* 1.3 56.6 + - - +
275A PHE* 4.7 3.4 - - - -
276A SER* 2.9 34.7 + - - -
332A PHE* 3.6 11.8 - - - -
336A ALA* 5.4 4.7 - - - -
801J PT5 5.0 12.0 - - - +
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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
----------------------------------------------------------
269A GLY 2.9 18.1 + - - +
270A PHE* 3.6 30.5 - - + +
272A GLY* 1.3 74.6 - - - +
274A ILE* 1.3 65.3 + - + +
277A SER* 3.2 27.0 + - - -
303A LEU* 4.0 15.2 - - + +
306A GLY* 3.2 43.3 - - - +
307A VAL* 3.5 22.4 - - + +
310A VAL* 4.8 5.4 - - + -
332A PHE* 3.8 12.5 - - + -
340A PHE* 5.0 4.0 - - + -
64L VAL* 4.0 14.4 - - + -
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 2.9 23.4 + - + +
271A LEU* 4.0 11.7 - - + +
273A LEU* 1.3 76.8 - - + +
275A PHE* 1.3 64.6 + - - +
278A TYR* 3.8 6.1 + - - +
299A TYR* 3.0 25.6 + - - +
303A LEU* 4.2 19.3 - - + -
137J LEU* 5.0 10.1 - - + -
235J ILE* 4.2 25.5 - - + +
238J MET* 5.6 5.8 - - + -
64L VAL* 4.4 17.5 - - + +
65L MET* 4.3 27.4 - - + -
68L PHE* 5.1 17.9 - - + -
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 2.9 51.3 + - + +
272A GLY 4.2 1.6 - - - +
274A ILE* 1.3 78.1 - - + +
276A SER* 1.3 61.7 + - - +
278A TYR* 3.0 25.2 + + - +
279A PHE* 3.6 21.2 + + + -
232J PHE* 3.7 18.4 - + - -
235J ILE* 3.9 25.1 - - + -
236J LEU* 3.6 45.1 - - + -
239J LEU* 4.9 12.3 - - + -
801J PT5 4.3 28.3 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLY* 2.9 21.4 + - - -
275A PHE* 1.3 74.6 - - - +
277A SER* 1.3 56.8 + - - +
278A TYR 3.2 1.9 + - - -
279A PHE* 3.8 13.4 + - - -
280A VAL* 3.4 23.6 + - - +
305A TRP* 4.5 0.7 - - - -
328A ILE* 3.3 18.7 + - - +
332A PHE* 3.2 34.7 - - - +
801J PT5 6.3 1.6 - - - -
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLY 4.2 0.4 + - - -
273A LEU* 3.2 21.1 + - - -
274A ILE 4.5 0.2 - - - -
275A PHE 3.3 0.6 - - - -
276A SER* 1.3 75.9 - - - +
278A TYR* 1.3 57.6 + - - +
280A VAL* 4.3 4.3 - - - -
281A TYR 4.2 1.3 + - - -
299A TYR* 3.7 10.1 - - - -
302A ALA* 2.3 52.1 + - - +
303A LEU* 3.5 9.4 - - - +
305A TRP* 4.0 18.1 - - - -
306A GLY* 4.3 8.7 - - - -
332A PHE* 5.1 1.9 - - - -
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Residues in contact with TYR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE 3.8 8.0 + - - +
275A PHE* 3.0 11.9 + + - +
277A SER* 1.3 78.2 - - - +
279A PHE* 1.3 74.2 + + - +
280A VAL 3.2 1.6 - - - -
281A TYR* 3.3 7.7 + + - +
282A LEU* 3.0 68.1 + - + +
299A TYR* 3.6 30.5 - + + +
141J VAL* 5.8 0.9 - - + -
228J ARG* 3.7 15.6 + - - -
231J ARG* 3.5 39.1 - - + +
232J PHE* 3.9 28.1 + + + -
235J ILE* 3.8 17.7 - - + -
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.6 27.1 + + + -
276A SER* 3.8 11.4 + - - +
278A TYR* 1.3 89.5 - + - +
280A VAL* 1.3 61.6 + - - +
282A LEU* 3.4 13.4 + - + +
283A ALA* 2.9 28.2 + - - +
328A ILE* 3.9 28.9 - - + +
232J PHE* 3.5 42.2 - + - -
801J PT5 6.3 1.6 - - + -
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 3.4 18.7 + - - +
277A SER* 4.7 3.8 - - - +
278A TYR 3.2 0.2 - - - -
279A PHE* 1.3 77.0 - - - +
281A TYR* 1.3 58.3 + - - +
283A ALA* 3.1 6.2 + - - +
284A GLU* 2.8 37.9 + - + +
296A PHE* 4.0 31.2 - - + -
302A ALA* 5.4 0.4 - - + -
305A TRP* 3.8 29.4 - - + -
320A PRO* 4.5 10.1 - - + -
325A GLY* 4.4 8.7 - - - +
328A ILE* 4.2 20.9 - - + -
329A ALA 4.7 0.4 - - - +
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER 4.2 5.4 + - - +
278A TYR* 3.3 22.6 + + - +
280A VAL* 1.3 79.6 - - - +
282A LEU* 1.3 75.8 + - + +
284A GLU* 4.3 3.8 - - - +
285A LYS* 3.0 46.1 + - + +
296A PHE* 4.1 12.1 - - - -
297A GLY 3.8 15.7 + - - -
298A SER 3.4 26.2 - - - -
299A TYR* 4.4 9.4 - + + -
302A ALA* 3.8 21.2 - - + +
144J THR* 2.5 32.5 + - + -
228J ARG* 6.4 0.7 - - + -
231J ARG* 5.4 9.2 - - - -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.0 63.7 + - + +
279A PHE* 3.7 15.3 - - + +
281A TYR* 1.3 90.0 - - + +
283A ALA* 1.3 59.3 + - - +
284A GLU 3.7 0.2 + - - -
285A LYS* 4.2 22.0 - - + +
228J ARG* 4.0 31.9 - - + +
231J ARG* 6.1 0.2 - - - -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE 2.9 17.5 + - - +
280A VAL 3.1 4.7 + - - +
282A LEU* 1.3 76.4 - - - +
284A GLU* 1.3 58.3 + - - +
285A LYS 3.8 0.9 - - - -
322A THR* 3.0 22.2 + - - +
324A VAL* 4.3 18.1 - - + +
325A GLY* 4.1 28.0 - - - +
328A ILE* 4.5 2.5 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 2.8 18.1 + - + +
281A TYR 3.5 2.7 - - - -
283A ALA* 1.3 79.5 - - + +
285A LYS* 1.3 62.5 + - - +
286A ASP 3.4 4.9 + - - +
287A ALA* 3.9 22.0 + - - +
294A VAL* 5.1 1.2 - - - +
295A GLU* 4.0 5.5 - - - +
296A PHE* 3.3 41.9 + - + +
320A PRO* 3.2 19.2 - - + +
321A GLN* 2.5 20.4 + - - +
322A THR* 2.4 48.7 + - - +
325A GLY* 4.9 1.1 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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