Contacts of the helix formed by residues 258 - 293 (chain A) in PDB entry 3GIA
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 ASN 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY 3.4 12.3 - - - +
111A TYR* 3.6 28.7 + - + -
114A PRO* 3.4 31.2 - - - +
255A ALA* 3.5 13.2 - - - +
256A SER 3.2 0.2 - - - -
257A GLU* 1.3 76.9 + - - +
259A ALA* 1.3 66.6 + - - +
260A LEU 3.3 2.2 - - - -
261A ALA* 3.1 15.8 + - + +
262A VAL* 3.5 18.8 + - - +
273A PHE* 3.8 21.2 - - - -
277A SER* 5.4 0.4 + - - -
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Residues in contact with ALA 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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30A PHE* 4.1 24.0 - - + -
31A GLY* 4.5 7.4 - - - +
34A ALA* 6.0 0.2 - - + -
111A TYR* 3.7 3.2 + - - +
247A LEU* 4.9 0.3 - - - +
252A LEU* 4.1 22.5 - - + +
255A ALA* 2.8 23.6 + - - +
256A SER 3.6 9.9 + - - +
258A ASN* 1.3 72.2 - - - +
260A LEU* 1.3 58.4 + - + +
262A VAL* 3.5 4.2 + - - +
263A ALA* 2.9 28.7 + - - +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.3 43.5 - - + +
27A PHE* 4.5 4.0 - - + -
30A PHE* 3.7 22.2 - - + -
111A TYR* 3.0 16.4 + - - +
162A LEU* 4.6 6.3 - - + -
165A PHE* 3.5 15.0 - - + -
239A VAL* 3.5 22.0 - - + -
243A ALA* 3.7 30.1 - - + -
259A ALA* 1.3 74.6 - - + +
261A ALA* 1.3 60.8 + - - +
263A ALA* 3.7 2.9 - - - -
264A ALA* 3.0 27.0 + - - +
276A ILE* 3.6 13.6 - - + +
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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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111A TYR* 3.8 12.2 - - + -
258A ASN* 3.1 11.6 + - - +
260A LEU* 1.3 75.7 - - - +
262A VAL* 1.3 64.7 + - - +
264A ALA* 3.4 7.4 + - - +
265A LYS* 3.5 8.8 + - - +
273A PHE* 3.5 38.7 - - + +
276A ILE* 3.6 12.6 - - + +
277A SER* 3.3 26.2 - - - +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.1 20.3 - - + +
251A GLU* 4.7 4.7 - - + +
255A ALA* 3.6 34.1 - - + -
258A ASN* 3.5 22.6 + - - +
259A ALA 3.8 3.8 - - - +
261A ALA* 1.3 77.3 - - - +
263A ALA* 1.3 60.5 + - - +
265A LYS* 3.4 20.1 + - + +
266A PRO* 3.3 16.6 - - - +
273A PHE* 4.5 6.7 - - + -
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 4.1 3.6 - - + -
243A ALA* 4.0 26.7 - - + -
246A ASN* 4.6 3.5 - - - +
247A LEU* 3.9 14.1 - - + +
252A LEU* 4.0 11.4 - - + -
259A ALA 2.9 19.5 + - - +
260A LEU* 3.6 9.8 + - - +
261A ALA 3.3 0.2 - - - -
262A VAL* 1.3 76.1 - - - +
264A ALA* 1.3 60.1 + - - +
266A PRO* 3.4 9.8 - - - +
267A PHE* 3.0 21.3 - - - -
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Residues in contact with ALA 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 3.8 13.0 - - + -
260A LEU 3.0 17.8 + - - +
261A ALA 3.7 6.5 - - - +
262A VAL 3.2 0.6 - - - -
263A ALA* 1.3 77.3 - - - +
265A LYS* 1.3 56.7 + - - +
266A PRO 3.5 0.2 - - - -
267A PHE* 3.2 8.4 + - - -
268A LEU* 2.8 41.4 + - + +
269A GLY 4.6 0.7 - - - -
272A GLY 3.9 12.8 - - - +
276A ILE* 3.8 21.5 - - + -
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Residues in contact with LYS 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ALA 3.5 11.8 + - - +
262A VAL* 3.4 16.8 + - + +
264A ALA* 1.3 77.6 - - - +
266A PRO* 1.4 71.0 - - + +
269A GLY* 2.9 34.3 + - - +
270A ASN* 3.9 18.0 + - - +
273A PHE* 3.7 34.3 - - + -
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Residues in contact with PRO 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ASN* 3.6 27.1 - - + +
247A LEU* 4.1 16.4 - - + -
262A VAL 3.3 14.4 - - - +
263A ALA 3.4 11.4 - - - +
265A LYS* 1.4 91.2 - - + +
267A PHE* 1.3 62.8 + - + +
269A GLY 4.8 0.2 - - - -
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Residues in contact with PHE 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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165A PHE* 3.6 42.8 - + - -
168A ALA* 4.1 6.6 - - + +
169A GLY* 3.6 29.4 - - - -
172A THR* 3.8 21.1 - - + +
242A SER* 3.9 4.3 - - - -
246A ASN* 3.7 30.5 - - + +
263A ALA 3.0 25.8 - - - -
264A ALA* 3.2 4.7 + - - -
266A PRO* 1.3 78.8 - - + +
268A LEU* 1.3 92.3 + - + +
269A GLY 3.7 0.9 - - - -
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Residues in contact with LEU 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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164A LEU* 4.4 31.4 - - + -
165A PHE* 4.7 10.1 - - + -
168A ALA* 4.3 15.0 - - + -
264A ALA* 2.8 23.5 + - + +
267A PHE* 1.3 106.5 - - + +
269A GLY* 1.3 66.0 + - - +
270A ASN 3.9 0.2 + - - -
271A LEU* 4.0 6.4 + - - +
272A GLY* 3.2 28.2 + - - -
275A LEU* 5.4 2.9 - - + -
276A ILE* 5.3 4.0 - - + -
810A BCN 5.7 2.8 + - - -
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Residues in contact with GLY 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 2.9 30.5 + - - +
266A PRO 5.2 0.2 + - - -
267A PHE 3.7 0.8 - - - -
268A LEU* 1.3 83.2 - - - +
270A ASN* 1.3 59.8 + - - -
272A GLY* 3.1 10.9 + - - -
273A PHE 3.2 9.4 + - - -
810A BCN 5.5 6.3 - - - -
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Residues in contact with ASN 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 3.9 21.3 + - - -
269A GLY* 1.3 72.1 - - - -
271A LEU* 1.3 58.6 + - + +
272A GLY 3.3 0.2 - - - -
273A PHE* 3.5 12.0 + - + +
274A LEU* 3.1 27.3 + - - +
810A BCN 5.8 0.6 + - - -
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Residues in contact with LEU 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU 4.0 6.0 + - - +
269A GLY 3.2 0.4 - - - -
270A ASN* 1.3 77.2 - - + +
272A GLY* 1.3 61.1 + - - +
274A LEU* 3.4 19.1 + - + +
275A LEU* 2.9 30.2 + - - +
810A BCN 3.7 48.7 - - - +
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Residues in contact with GLY 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ALA* 4.0 6.5 - - - -
268A LEU* 3.2 36.3 + - - -
269A GLY 3.1 8.4 + - - -
271A LEU* 1.3 73.4 - - - +
273A PHE* 1.3 64.1 + - - +
275A LEU* 4.4 5.8 - - - -
276A ILE* 2.9 31.1 + - - +
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Residues in contact with PHE 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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114A PRO* 4.2 20.9 - - + -
115A LEU* 4.5 19.5 - - + -
258A ASN* 3.8 25.6 - - - -
261A ALA* 3.5 38.1 + - + +
262A VAL* 4.1 6.1 - - + -
264A ALA* 4.3 0.8 - - - +
265A LYS* 3.7 28.7 - - + -
269A GLY 3.2 6.6 + - - +
270A ASN* 3.5 14.4 - - + +
271A LEU 3.4 0.2 - - - -
272A GLY* 1.3 75.8 - - - +
274A LEU* 1.3 64.0 + - + +
277A SER* 2.7 49.4 + - - -
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Residues in contact with LEU 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.6 26.5 - - + -
270A ASN 3.1 11.0 + - - +
271A LEU* 3.5 24.7 - - + +
272A GLY 3.2 0.2 - - - -
273A PHE* 1.3 84.4 - - + +
275A LEU* 1.3 59.0 - - - +
277A SER* 3.4 2.5 + - - -
278A ILE* 2.9 44.5 + - + +
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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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161A ILE* 3.9 42.6 - - + +
164A LEU* 3.9 27.8 - - + -
268A LEU* 5.4 2.0 - - + -
271A LEU 2.9 17.7 + - - +
272A GLY* 3.4 7.2 + - - +
274A LEU* 1.3 76.0 - - - +
276A ILE* 1.3 59.8 + - + +
278A ILE* 3.4 5.4 + - + +
279A GLY* 2.8 28.8 + - - -
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Residues in contact with ILE 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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27A PHE* 4.1 10.4 - - + -
111A TYR* 4.3 5.4 - - + -
161A ILE* 3.7 25.6 - - + +
162A LEU* 4.8 9.0 - - + -
165A PHE* 3.8 27.8 - - + -
260A LEU* 3.6 35.4 - - + +
261A ALA* 3.6 9.9 - - + +
264A ALA* 3.8 16.2 - - + -
268A LEU* 5.3 3.8 - - + -
272A GLY* 2.9 21.9 + - - +
275A LEU* 1.3 77.9 - - + +
277A SER* 1.3 57.4 + - - +
279A GLY* 3.8 1.2 - - - +
280A ALA* 2.8 28.5 + - - +
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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
----------------------------------------------------------
111A TYR* 4.0 18.6 + - - +
115A LEU* 3.8 27.1 - - - -
258A ASN* 5.4 0.5 + - - -
261A ALA* 3.3 15.2 - - - +
273A PHE* 2.7 35.3 + - - -
274A LEU 3.7 4.5 - - - -
275A LEU 3.3 0.2 - - - -
276A ILE* 1.3 76.6 - - - +
278A ILE* 1.3 60.5 + - - +
280A ALA* 3.4 2.8 + - - +
281A LEU* 3.2 28.5 + - - +
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Residues in contact with ILE 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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115A LEU* 3.6 31.0 - - + -
274A LEU* 2.9 37.6 + - + +
275A LEU* 3.9 5.2 - - + +
277A SER* 1.3 72.8 - - - +
279A GLY* 1.3 65.6 + - - +
281A LEU* 3.2 6.5 + - + +
282A PHE* 3.1 53.6 + - + -
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Residues in contact with GLY 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.4 6.5 - - - -
158A LYS* 4.6 7.8 - - - +
161A ILE* 4.1 21.5 - - - +
275A LEU 2.8 17.0 + - - -
276A ILE* 3.8 2.0 - - - -
278A ILE* 1.3 78.8 - - - +
280A ALA* 1.3 54.7 + - - +
282A PHE* 3.5 5.8 + - - +
283A SER* 2.8 32.2 + - - -
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Residues in contact with ALA 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.3 33.1 - - + -
111A TYR* 3.6 27.6 - - + -
276A ILE 2.8 18.8 + - - +
277A SER 3.5 6.5 - - - +
278A ILE 3.2 0.2 - - - -
279A GLY* 1.3 77.5 - - - +
281A LEU* 1.3 57.6 + - - +
283A SER* 3.3 0.7 + - - -
284A ILE* 3.0 37.1 + - + +
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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
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108A PHE* 3.6 54.0 - - + +
111A TYR* 4.0 9.0 - - + +
112A PHE* 3.9 30.3 - - + +
115A LEU* 3.6 29.8 - - + -
277A SER 3.2 11.3 + - - +
278A ILE* 3.2 10.5 + - + +
280A ALA* 1.3 75.7 - - - +
282A PHE* 1.3 55.7 + - + +
284A ILE* 5.4 0.2 - - + -
285A SER* 2.8 38.5 + - - -
802A D10 4.0 16.6 - - + -
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Residues in contact with PHE 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.4 45.0 - - + +
158A LYS* 6.5 0.2 - - + -
278A ILE* 3.1 48.4 + - + +
279A GLY* 3.9 5.6 - - - +
281A LEU* 1.3 75.9 - - + +
283A SER* 1.3 59.1 + - - +
285A SER* 3.7 5.5 - - - -
286A SER* 2.9 24.8 + - - -
802A D10 4.5 26.2 - - + -
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Residues in contact with SER 283 (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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23A GLY* 3.5 8.5 + - - -
27A PHE* 3.3 34.6 - - - -
154A ILE* 4.2 0.6 - - - +
158A LYS* 2.9 36.7 + - - +
279A GLY 2.8 22.5 + - - -
280A ALA 3.3 0.9 + - - -
282A PHE* 1.3 73.8 - - - +
284A ILE* 1.3 56.6 + - - +
286A SER* 2.9 18.8 + - - -
287A ALA* 3.0 16.2 + - - +
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Residues in contact with ILE 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY* 3.8 18.8 - - - +
27A PHE* 3.7 24.5 - - + +
28A SER* 4.1 2.2 - - - +
104A PHE* 3.2 35.3 - - + +
107A GLY* 3.5 31.2 - - - +
108A PHE* 3.6 18.2 - - + +
111A TYR* 4.8 2.7 - - + -
280A ALA* 3.0 23.3 + - + +
281A LEU* 4.2 2.2 - - + +
283A SER* 1.3 73.7 - - - +
285A SER* 1.3 55.7 + - - +
287A ALA* 3.1 8.4 + - - +
288A MET* 2.8 38.3 + - + +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.7 17.2 - - - -
136A PHE* 3.1 34.0 - - - -
147A VAL* 5.6 3.4 - - - -
154A ILE* 6.0 1.8 - - - -
281A LEU 2.8 22.6 + - - -
282A PHE* 3.7 9.4 - - - -
283A SER 3.4 0.2 - - - -
284A ILE* 1.3 76.7 - - - +
286A SER* 1.3 56.4 + - - +
288A MET* 3.2 2.6 + - - -
289A ASN* 3.0 24.3 + - - +
802A D10 3.7 17.7 - - - +
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY* 5.0 2.0 + - - -
147A VAL* 5.3 2.4 - - - +
151A GLU* 3.9 23.9 - - - -
154A ILE* 3.7 32.8 - - - +
155A VAL* 4.6 5.8 - - - +
158A LYS* 4.0 8.3 + - - -
282A PHE 2.9 15.8 + - - -
283A SER* 2.9 15.4 + - - -
285A SER* 1.3 75.4 - - - +
287A ALA* 1.3 58.0 + - - +
289A ASN* 4.5 2.9 - - - +
290A ALA* 3.2 27.7 + - - +
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Residues in contact with ALA 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 3.9 5.6 - - - +
20A VAL* 3.9 24.4 - - - +
23A GLY* 4.2 2.0 - - - -
104A PHE* 3.8 30.3 - - + -
283A SER 3.0 18.3 + - - +
284A ILE* 3.1 6.5 + - - +
286A SER* 1.3 76.2 + - - +
288A MET* 1.3 59.0 + - - +
290A ALA* 3.6 1.9 + - - +
291A THR* 2.9 33.3 + - - -
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Residues in contact with MET 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 4.3 23.8 - - + +
104A PHE* 3.9 36.8 - - + +
105A ALA* 4.1 2.9 - - - +
108A PHE* 5.0 0.2 - - + -
132A ILE* 3.9 25.6 - - + +
133A VAL* 4.6 11.7 - - - -
136A PHE* 4.1 23.1 - - + -
284A ILE* 2.8 25.3 + - + +
285A SER* 3.2 4.7 + - - +
287A ALA* 1.3 75.2 - - - +
289A ASN* 1.3 58.9 + - - +
291A THR* 4.3 3.4 - - - -
292A ILE* 2.9 53.9 + - + +
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Residues in contact with ASN 289 (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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136A PHE* 3.8 8.3 - - + -
139A LEU* 3.4 21.1 - - - +
144A SER 3.2 23.1 + - - +
147A VAL* 3.7 14.9 - - + +
148A GLY* 3.4 10.7 - - - +
151A GLU* 2.8 23.1 + - - +
285A SER 3.0 16.2 + - - +
286A SER 3.9 3.4 - - - +
287A ALA 3.4 0.2 - - - -
288A MET* 1.3 76.6 - - - +
290A ALA* 1.3 56.8 + - - +
293A TYR* 2.8 55.9 + - - +
315A LYS* 3.6 5.3 + - - +
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Residues in contact with ALA 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 4.7 15.9 - - + +
20A VAL* 3.7 23.1 - - + -
151A GLU* 3.6 14.2 + - - +
206A VAL* 3.8 8.5 - - + +
286A SER 3.2 16.1 + - - +
287A ALA 3.9 0.2 - - - +
289A ASN* 1.3 78.6 - - - +
291A THR* 1.3 60.5 - - - +
293A TYR 3.5 6.1 - - - +
294A GLY* 3.6 3.6 - - - -
295A GLY 3.4 15.8 + - - -
314A ARG* 5.4 1.2 + - - +
315A LYS* 3.8 10.3 - - - +
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Residues in contact with THR 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.2 11.1 - - - +
97A TYR* 3.7 38.4 - - + +
100A SER* 4.3 10.4 - - - -
101A ILE* 3.8 14.8 - - + -
104A PHE* 3.3 18.0 - - + -
202A MET* 5.1 1.4 - - - +
206A VAL* 4.7 6.6 - - - +
287A ALA 2.9 21.3 + - - -
288A MET* 3.8 5.2 - - - -
289A ASN 3.3 0.2 - - - -
290A ALA* 1.3 74.6 - - - +
292A ILE* 1.3 54.6 + - - +
295A GLY* 3.4 3.4 - - - +
296A ALA* 2.7 32.2 + - - +
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.8 28.7 - - + -
133A VAL* 5.6 2.9 - - + +
136A PHE* 3.8 32.8 - - + +
137A THR* 5.3 0.4 - - - +
288A MET* 2.9 33.0 + - + +
291A THR* 1.3 78.0 - - - +
293A TYR* 1.3 89.3 + - + +
296A ALA* 4.1 4.7 - - + -
297A ASN* 3.1 32.1 + - - +
317A TRP* 4.1 7.9 - - + -
324A LEU* 4.1 17.0 - - + -
327A THR* 5.5 2.2 - - + -
328A SER* 5.6 5.8 - - - +
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Residues in contact with TYR 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 2.5 32.0 + + - -
137A THR 3.5 2.4 + - - -
139A LEU* 4.6 1.8 - - + -
140A ASN* 3.2 43.5 + - + +
144A SER* 3.8 8.5 - - - -
289A ASN* 2.8 42.9 + - - +
290A ALA 3.5 2.6 - - - +
292A ILE* 1.3 94.0 - - + +
294A GLY* 1.3 57.0 + - - +
297A ASN* 3.8 2.0 - - - +
314A ARG 3.2 7.9 - - - +
315A LYS* 2.7 58.4 + - - +
316A VAL* 3.7 21.3 - - - -
317A TRP* 3.8 5.6 - + + -
324A LEU* 3.9 10.1 - - + +
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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