Contacts of the helix formed by residues 253 - 282 (chain A) in PDB entry 5J0Z
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 THR 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 3.8 19.5 + - - -
117A ARG* 3.9 5.6 - - - +
119A TYR* 4.3 6.6 - - - +
246A LEU* 4.4 19.5 - - + -
249A THR* 4.5 13.9 - - - +
251A TYR* 3.3 6.0 + - - -
252A MET* 1.3 83.8 - - - +
254A TYR* 1.3 61.5 + - - +
255A THR* 3.3 15.9 + - - -
256A GLY* 3.4 21.2 + - - +
257A ALA* 3.0 23.0 + - - +
314A PHE* 3.7 1.0 - - - -
200E ASN* 6.2 2.0 - - - +
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Residues in contact with TYR 254 (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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117A ARG 2.8 22.9 + - - +
118A ARG* 4.4 2.5 - - - -
119A TYR 3.7 13.4 + - - +
120A PRO* 5.3 0.4 - - + -
121A PHE* 4.0 26.7 - + - -
253A THR* 1.3 73.2 + - - +
255A THR* 1.3 66.7 + - - +
257A ALA* 3.3 3.3 + - - +
258A ILE* 3.1 47.6 + - + +
307A ASN* 5.2 2.4 + - - -
310A LEU* 4.6 4.9 - - + -
311A ALA* 4.3 23.6 - - - +
314A PHE* 3.7 37.4 - + + -
315A PHE* 4.1 20.9 - + - -
409A PLC 3.0 35.0 - - + +
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Residues in contact with THR 255 (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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119A TYR* 2.5 43.1 + - + -
120A PRO* 3.3 11.2 - - + +
201A ILE* 5.4 6.3 - - + -
202A ILE* 6.5 0.7 - - + -
242A VAL* 4.1 29.8 - - + -
246A LEU* 5.7 0.4 - - - -
253A THR* 3.3 5.8 + - - -
254A TYR* 1.3 81.4 - - - +
256A GLY* 1.3 57.0 + - - +
258A ILE* 3.5 9.9 + - + +
259A ILE* 2.9 36.5 + - + +
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Residues in contact with GLY 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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242A VAL* 5.7 2.7 - - - +
252A MET* 4.7 7.1 - - - +
253A THR* 3.4 25.6 + - - +
254A TYR 3.2 1.0 - - - -
255A THR* 1.3 76.5 - - - +
257A ALA* 1.3 56.4 + - - +
259A ILE* 3.7 9.0 - - - +
260A PHE* 2.8 35.6 + - - +
200E ASN* 5.5 5.4 - - - +
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Residues in contact with ALA 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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252A MET* 4.3 14.9 - - + +
253A THR 3.0 14.0 + - - +
254A TYR 3.5 9.0 - - - +
256A GLY* 1.3 72.5 - - - +
258A ILE* 1.3 56.9 + - - +
260A PHE* 3.0 8.0 + - - +
261A MET* 2.7 36.2 + - - +
310A LEU* 3.8 24.2 - - + -
314A PHE* 4.1 14.1 - - + -
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Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 6.4 0.9 - - + -
205A MET* 5.4 3.1 - - - -
206A LEU* 6.6 0.2 - - + -
254A TYR* 3.1 55.5 + - + +
255A THR* 3.6 12.6 - - + +
257A ALA* 1.3 78.3 - - - +
259A ILE* 1.3 62.0 + - + +
261A MET* 3.3 7.1 + - - +
262A ILE* 3.0 45.1 + - + +
303A PHE* 5.8 1.8 - - + -
307A ASN* 4.1 26.2 - - - +
310A LEU* 4.0 13.8 - - + +
409A PLC 4.2 13.2 - - + -
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Residues in contact with ILE 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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201A ILE* 5.7 0.4 - - + -
205A MET* 3.8 37.9 - - + -
235A HIS* 3.9 2.6 + - + +
238A PHE 4.3 3.6 - - - +
239A ASN* 3.7 31.2 - - + +
242A VAL* 3.6 37.7 - - + -
255A THR* 2.9 24.4 + - + +
256A GLY* 3.8 7.0 - - - +
258A ILE* 1.3 79.2 - - + +
260A PHE* 1.3 64.2 + - - +
262A ILE* 3.2 17.5 + - - +
263A TYR* 3.2 22.2 + - + -
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Residues in contact with PHE 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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252A MET* 5.7 5.4 - - + -
256A GLY 2.8 21.2 + - - +
257A ALA* 3.6 5.6 - - - +
259A ILE* 1.3 77.0 - - - +
261A MET* 1.3 68.6 + - + +
263A TYR* 3.3 23.0 + - + +
264A LEU* 3.9 19.7 + - + +
199E PRO* 3.5 42.0 - - + +
203E LEU* 3.7 43.5 - - + -
204E PRO* 5.0 4.7 - - + -
207E PHE* 4.2 15.7 - + - -
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Residues in contact with MET 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 ALA 2.7 21.9 + - - +
258A ILE* 3.7 8.3 - - - +
260A PHE* 1.3 78.2 - - + +
262A ILE* 1.3 66.0 + - - +
264A LEU* 3.0 31.4 + - + +
265A PHE* 3.5 23.3 - - + -
303A PHE* 3.3 29.6 - - + -
306A ALA* 4.0 29.8 - - + +
307A ASN* 3.3 26.2 - - - +
310A LEU* 4.4 13.2 - - + -
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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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205A MET* 4.1 18.8 - - + +
206A LEU* 5.3 4.5 - - + -
209A LEU* 4.5 13.5 - - + -
235A HIS* 3.2 37.7 - - + +
258A ILE* 3.0 36.7 + - + +
259A ILE* 3.2 8.5 + - - +
261A MET* 1.3 76.1 - - - +
263A TYR* 1.3 56.8 + - - +
264A LEU 2.8 7.3 + - - -
265A PHE* 2.9 17.8 + - - +
266A TYR* 3.2 31.1 + - + -
303A PHE* 4.2 26.7 - - + -
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Residues in contact with TYR 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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232A LEU* 4.6 12.8 - - + -
235A HIS* 3.4 25.1 - + - -
236A ILE* 3.5 20.1 - - + +
239A ASN* 2.8 44.4 + - - +
259A ILE* 3.2 24.0 - - + -
260A PHE* 3.3 15.3 + - + +
261A MET 3.2 1.0 - - - -
262A ILE* 1.3 74.9 - - - +
264A LEU* 1.3 57.4 + - - +
266A TYR* 4.2 8.3 - - - +
267A PHE* 3.4 20.9 + - - +
204E PRO* 3.6 37.9 - - + -
207E PHE* 3.7 23.6 - + + +
208E ILE* 5.2 4.3 - - + -
238E PHE* 3.5 16.5 - + - -
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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
----------------------------------------------------------
260A PHE* 4.0 24.0 - - + +
261A MET* 3.3 21.5 - - + +
262A ILE 2.8 2.4 + - - -
263A TYR* 1.3 73.1 - - - +
265A PHE* 1.3 64.8 + - + +
266A TYR 3.0 3.8 - - - -
267A PHE* 2.7 12.2 + - + -
268A VAL* 2.5 44.6 + - + +
207E PHE* 3.3 41.1 - - + -
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Residues in contact with PHE 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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209A LEU* 4.3 14.0 - - + +
212A SER* 4.2 8.8 + - - -
213A TRP* 3.9 21.9 + + - +
261A MET* 3.5 34.5 - - + +
262A ILE* 2.9 11.5 + - - +
264A LEU* 1.3 82.7 - - + +
266A TYR* 1.3 58.0 + - - +
268A VAL* 4.7 6.7 - - + -
269A ALA* 3.3 20.9 + - - +
299A PHE* 3.9 17.0 - + - -
302A VAL* 3.9 27.4 - - + -
303A PHE* 3.3 49.1 - + + -
306A ALA* 5.0 1.3 - - + -
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Residues in contact with TYR 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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208A ILE* 3.2 37.6 + - - +
209A LEU* 3.3 15.5 - - + +
212A SER* 3.8 16.4 - - - -
228A VAL* 3.9 19.0 - - + +
231A THR* 3.4 26.4 + - - -
232A LEU* 3.6 36.6 - - + -
235A HIS* 3.9 11.4 - + + -
262A ILE* 3.2 47.9 + - + +
263A TYR* 4.4 5.6 - - - +
264A LEU 3.0 0.8 - - - -
265A PHE* 1.3 78.8 - - - +
267A PHE* 1.3 64.7 - - - +
269A ALA* 3.3 4.8 + - - +
270A VAL* 3.0 28.0 + - - +
211E ILE* 5.0 1.3 - - + -
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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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263A TYR 3.4 15.2 + - - +
264A LEU* 2.7 17.9 + - + +
266A TYR* 1.3 76.0 - - - +
268A VAL* 1.3 64.0 + - + +
270A VAL* 3.3 5.6 + - + +
271A ILE* 3.1 50.2 + - + +
207E PHE* 3.9 31.6 - + + -
210E PHE* 3.5 40.2 - + + -
211E ILE* 3.6 29.1 - - + +
214E THR* 5.9 0.4 - - + -
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Residues in contact with VAL 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 LEU* 2.5 28.1 + - + +
265A PHE* 4.7 3.6 - - + -
267A PHE* 1.3 79.9 - - + +
269A ALA* 1.3 64.3 + - - +
271A ILE* 3.0 13.4 + - + +
272A GLU* 2.9 21.9 + - + +
299A PHE* 3.4 27.4 - - + -
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Residues in contact with ALA 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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212A SER* 4.5 6.5 - - - +
216A PHE* 4.5 9.2 - - + -
228A VAL* 4.3 18.8 - - + -
265A PHE 3.3 21.8 + - - +
266A TYR* 3.3 7.9 + - - +
268A VAL* 1.3 80.3 - - - +
270A VAL* 1.3 63.1 + - - +
272A GLU* 3.3 4.5 + - - +
273A VAL* 2.9 27.3 + - - +
299A PHE* 3.7 20.0 - - + -
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Residues in contact with VAL 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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228A VAL* 3.3 27.8 - - + +
229A VAL* 4.8 5.8 - - + -
232A LEU* 6.1 0.7 - - + -
266A TYR 3.0 13.4 + - - +
267A PHE 3.4 8.1 - - - +
269A ALA* 1.3 73.0 - - - +
271A ILE* 1.3 55.2 + - + +
273A VAL* 3.1 7.0 + - + +
274A THR* 2.7 43.3 + - - +
211E ILE* 3.9 38.6 - - + -
214E THR* 3.6 30.7 - - + +
227E LEU* 5.0 2.0 - - + -
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Residues in contact with ILE 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 PHE* 3.1 46.7 + - + +
268A VAL* 3.0 17.8 + - + +
270A VAL* 1.3 75.6 - - + +
272A GLU* 1.3 65.0 + - - +
274A THR* 3.1 6.3 + - + +
275A VAL* 2.8 34.8 + - + +
214E THR* 4.9 12.3 - - + -
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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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215A ALA 4.4 0.7 - - - +
216A PHE* 3.2 26.8 - - + -
268A VAL 2.9 12.1 + - - +
269A ALA 3.5 6.3 - - - +
271A ILE* 1.3 76.1 - - - +
273A VAL* 1.3 88.6 + - - +
275A VAL* 3.3 8.3 + - - +
276A GLN* 2.9 32.6 + - - +
291A ILE* 4.0 13.8 - - + +
292A THR* 2.6 35.2 + - - -
295A SER* 3.5 20.4 - - - +
299A PHE* 4.5 7.6 - - + -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ALA* 4.2 14.1 - - + +
216A PHE* 5.1 1.6 - - + -
221A TYR* 3.6 24.0 - - + -
224A ASN* 3.7 38.6 - - + +
225A VAL* 4.6 7.0 - - + +
228A VAL* 4.6 8.3 - - + -
269A ALA 2.9 19.4 + - - +
270A VAL* 3.7 6.3 - - + +
272A GLU* 1.3 92.9 + - - +
274A THR* 1.3 68.7 + - - +
275A VAL 3.2 0.2 + - - -
276A GLN* 3.4 6.2 + - - +
277A HIS* 3.0 23.2 + - - +
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.4 19.4 + - - +
225A VAL* 5.8 0.2 - - - +
270A VAL* 2.7 26.3 + - - +
271A ILE* 3.6 6.1 - - + +
273A VAL* 1.3 72.8 - - - +
275A VAL* 1.3 58.6 + - + +
277A HIS* 3.8 5.4 - - - +
278A TYR* 2.9 24.7 + - + +
214E THR* 3.2 49.6 + - + +
217E TRP* 4.3 19.8 - - + +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ILE* 2.8 26.8 + - + +
272A GLU* 3.4 10.3 - - - +
274A THR* 1.3 74.8 - - + +
276A GLN* 1.3 61.7 + - - +
277A HIS 3.2 1.3 - - - -
278A TYR* 2.7 26.2 + - + +
279A LEU* 2.8 26.7 + - + +
291A ILE* 3.8 31.2 - - + -
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ALA 4.3 0.7 - - - +
218A SER 3.0 19.5 + - - -
219A THR* 3.7 18.6 - - - +
224A ASN* 3.5 20.8 + - - -
272A GLU* 2.9 28.5 + - + +
273A VAL* 3.7 9.9 - - - +
275A VAL* 1.3 75.6 - - - +
277A HIS* 1.3 64.3 + - - +
279A LEU 3.6 0.2 + - - -
280A LYS* 3.2 31.4 + - - +
288A ALA* 3.7 26.8 - - + +
289A ALA* 5.3 0.4 - - - +
291A ILE* 5.7 1.1 - - + -
292A THR* 2.7 38.0 + - - +
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Residues in contact with HIS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.4 61.7 - + + +
222A GLU* 5.1 5.8 + - - -
273A VAL 3.0 10.3 + - - +
274A THR 3.8 3.8 - - - +
276A GLN* 1.3 78.6 + - - +
278A TYR* 1.3 74.5 + + - +
280A LYS* 3.2 15.4 + - - +
281A VAL* 3.3 31.7 + - + +
217E TRP 4.0 12.5 + - - -
218E SER* 4.0 17.7 + - - -
219E THR* 4.6 4.6 + - - -
220E SER* 4.9 9.6 - - - -
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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
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274A THR* 2.9 17.1 + - + +
275A VAL* 2.7 19.6 + - + +
277A HIS* 1.3 73.4 - - - +
279A LEU* 1.3 66.1 + - + +
281A VAL* 2.9 27.9 + - + +
282A GLU* 3.0 50.8 + - + +
217E TRP* 3.7 40.6 - + + +
293E ARG* 5.8 0.3 - - - -
296E ARG* 3.8 33.2 + - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 2.8 26.7 + - + +
278A TYR* 1.3 86.3 - - + +
280A LYS* 1.3 51.6 + - - +
282A GLU* 3.0 11.0 + - + -
283A SER 2.7 31.5 + - - -
284A GLN* 3.2 26.3 + - + +
287A ARG* 3.9 25.8 - - + +
288A ALA* 3.5 40.8 - - + +
291A ILE* 3.9 15.5 - - + -
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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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219A THR* 4.1 35.5 - - - +
276A GLN* 3.2 24.1 + - + +
277A HIS* 3.7 11.9 - - - +
278A TYR 3.2 0.2 - - - -
279A LEU* 1.3 78.0 - - - +
281A VAL* 1.3 61.7 + - + +
283A SER* 3.7 9.7 + - - +
285A PRO* 3.8 43.6 + - + +
288A ALA* 4.2 7.8 - - + +
289A ALA* 4.4 11.1 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A HIS* 3.3 35.8 + - + +
278A TYR* 2.9 14.3 + - + +
280A LYS* 1.3 78.1 - - + +
282A GLU* 1.3 70.5 + - - +
283A SER* 3.2 7.3 + - - -
219E THR* 4.9 15.0 - - + +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.0 55.3 + - + +
279A LEU* 3.0 13.2 + - + +
281A VAL* 1.3 93.5 - - - +
283A SER* 1.3 69.9 + - - +
284A GLN* 3.3 15.6 - - - +
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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).
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