Contacts of the helix formed by residues 295 - 329 (chain B) in PDB entry 3X0Y
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 ASP 295 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TRP* 4.8 10.1 + - - +
289B ILE* 3.6 30.6 - - + +
291B GLN 3.5 2.2 + - - -
292B ALA* 3.4 13.7 + - - +
293B THR 3.5 0.4 - - - -
294B GLU* 1.3 76.2 - - - +
296B PRO* 1.3 72.6 - - - +
297B TYR* 3.1 18.7 + - - +
298B THR* 2.9 41.4 + - - +
299B ILE* 3.0 25.1 + - - +
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Residues in contact with PRO 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 4.2 13.7 - - + -
294B GLU 3.4 8.2 - - - +
295B ASP* 1.3 91.5 - - - +
297B TYR* 1.3 81.1 + - + +
299B ILE* 3.6 9.8 + - + +
300B ARG* 3.0 26.5 + - - +
399C ALA* 5.7 1.9 - - - +
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Residues in contact with TYR 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP* 3.1 12.4 + - - +
296B PRO* 1.3 92.9 - - + +
298B THR* 1.3 61.3 + - - +
300B ARG* 3.4 18.2 + - - +
301B SER* 2.9 34.3 + - - +
365B GLU* 5.8 4.7 - - - +
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Residues in contact with THR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR* 4.2 11.0 - - + -
292B ALA 4.0 12.7 + - - +
295B ASP* 2.9 33.2 + - - +
297B TYR* 1.3 75.7 - - - +
299B ILE* 1.3 62.9 + - - +
301B SER* 3.2 3.5 + - - -
302B TYR* 3.0 51.2 + - + -
366B VAL* 3.8 25.0 - - + +
406C LEU* 4.2 4.9 - - + -
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B THR 3.6 24.0 - - - +
294B GLU* 3.7 17.0 - - - +
295B ASP 3.0 22.8 + - - +
296B PRO* 3.8 7.4 - - + +
298B THR* 1.3 76.7 - - - +
300B ARG* 1.3 58.5 + - - +
302B TYR* 3.5 3.9 + - - -
303B GLY* 3.0 23.2 + - - -
398C ILE 4.5 0.5 - - - +
399C ALA* 3.2 37.0 - - + +
402C GLY* 3.2 9.8 - - - -
403C LYS* 3.6 37.2 - - + +
406C LEU* 4.5 7.9 - - + -
407C ASN* 4.7 3.1 - - - +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO 3.0 18.4 + - - +
297B TYR* 3.5 20.4 - - - +
299B ILE* 1.3 78.2 - - - +
301B SER* 1.3 59.4 + - - +
303B GLY* 3.0 16.3 + - - +
304B GLU* 3.0 40.3 + - - +
394C VAL* 6.1 0.4 - - - +
395C SER* 4.2 25.7 + - - +
398C ILE* 3.6 33.5 - - + +
399C ALA* 5.0 6.9 - - + +
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TYR* 2.9 22.2 + - - +
298B THR 3.2 4.5 + - - -
300B ARG* 1.3 74.7 - - - +
302B TYR* 1.3 63.0 + - - +
304B GLU* 3.2 14.5 + - - +
305B PHE* 3.1 43.7 + - - -
365B GLU* 4.6 15.7 + - - -
366B VAL* 3.8 19.6 - - - +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.9 26.0 - - + -
273B ALA* 2.9 20.4 + - + -
274B ARG* 4.0 17.9 - - + -
277B THR* 2.5 24.3 + - - -
298B THR* 3.0 45.1 + - + +
299B ILE 3.8 4.7 - - - +
301B SER* 1.3 71.7 - - - +
303B GLY* 1.3 64.7 + - - +
305B PHE* 3.9 7.2 - + - +
306B THR* 2.8 31.8 + - - -
366B VAL* 3.5 22.6 - - + +
402C GLY* 4.0 15.7 - - - +
405C THR* 3.9 14.3 - - + +
406C LEU* 3.6 30.7 - - + -
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE 3.0 11.3 + - - -
300B ARG 3.0 5.8 + - - -
302B TYR* 1.3 78.2 - - - +
304B GLU* 1.3 56.5 + - - +
306B THR* 3.5 1.9 - - - -
307B ILE* 2.9 38.6 + - - +
398C ILE* 3.5 24.9 - - - -
401C VAL* 4.2 3.4 - - - -
402C GLY* 3.5 9.5 - - - -
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ARG* 3.0 46.0 + - - +
301B SER* 3.2 16.9 + - - +
303B GLY* 1.3 72.3 - - - +
305B PHE* 1.3 73.1 + - + +
307B ILE* 4.0 6.2 - - + +
308B ALA* 2.9 26.7 + - - +
358B ASN* 5.9 0.4 - - - -
398C ILE* 4.1 18.6 - - + +
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Residues in contact with PHE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.8 32.3 - - + -
301B SER* 3.1 39.5 + - - +
302B TYR* 3.9 8.3 - + - +
304B GLU* 1.3 81.2 - - + +
306B THR* 1.3 63.5 + - - +
308B ALA* 4.6 0.2 - - - -
309B LEU* 3.1 19.4 + - - +
358B ASN* 4.0 16.2 - - - -
359B ILE* 3.3 38.9 - - + +
362B GLY* 3.6 35.2 - - - -
363B VAL* 3.8 18.6 - - + -
365B GLU* 6.1 0.4 - - - -
366B VAL* 4.5 10.3 - - + -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 4.2 11.3 - - + +
302B TYR 2.8 16.1 + - - -
303B GLY 3.5 3.8 - - - -
305B PHE* 1.3 78.1 - - - +
307B ILE* 1.3 56.4 + - - +
309B LEU* 3.3 6.0 + - - +
310B GLN* 2.8 33.1 + - + +
343C VAL* 6.0 1.8 - - + -
401C VAL* 3.5 20.4 - - + -
405C THR* 2.6 34.7 + - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLY 2.9 24.8 + - - +
304B GLU* 4.0 5.8 - - - +
305B PHE 3.3 0.2 - - - -
306B THR* 1.3 71.4 - - - +
308B ALA* 1.3 66.6 + - - +
310B GLN* 3.2 18.1 + - - +
311B GLY 3.2 9.9 + - - -
347C GLY* 3.8 23.6 - - - +
350C ALA* 3.8 22.2 - - + -
351C LEU* 3.5 39.0 - - + +
398C ILE* 3.8 26.7 - - + -
401C VAL* 4.2 11.9 - - + -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU 2.9 19.7 + - - +
305B PHE* 3.6 5.4 - - - +
307B ILE* 1.3 79.2 - - - +
309B LEU* 1.3 60.3 + - - +
311B GLY* 3.5 1.9 + - - -
312B ALA* 3.3 20.3 + - - +
355B ALA* 4.3 16.3 - - + +
358B ASN* 5.5 5.4 - - - +
359B ILE* 4.4 10.8 - - + -
351C LEU* 5.1 5.1 - - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU* 3.7 28.5 - - + -
266B ALA* 3.8 17.0 - - + -
267B HIS* 3.8 43.1 - - + +
270B LEU* 4.0 21.1 - - + -
305B PHE 3.1 5.0 + - - +
306B THR* 3.6 7.6 - - - +
308B ALA* 1.3 77.2 - - - +
310B GLN* 1.3 66.4 + - - +
312B ALA* 4.5 1.6 - - - +
313B ASP* 2.9 42.6 + - - +
355B ALA* 4.6 3.6 - - + -
359B ILE* 3.5 23.1 - - + -
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B THR* 2.8 23.0 + - + +
307B ILE* 3.2 16.1 + - - +
309B LEU* 1.3 72.4 - - - +
311B GLY* 1.3 60.8 + - - +
313B ASP* 4.3 3.2 - - - +
314B ALA* 3.3 24.8 + - - +
317B ARG* 4.9 2.4 + - - +
315C ALA* 4.1 13.6 + - + +
318C GLU* 5.2 0.4 - - - +
343C VAL 4.9 0.9 - - - +
344C LYS* 3.0 59.5 + - + +
347C GLY* 3.4 26.1 - - - -
348C VAL* 4.0 10.9 - - - +
351C LEU* 4.7 0.9 - - + -
401C VAL* 5.5 1.0 - - - +
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE 3.2 8.8 + - - -
308B ALA 4.0 2.7 - - - -
310B GLN* 1.3 78.4 - - - +
312B ALA* 1.3 62.8 + - - +
314B ALA* 3.5 0.5 + - - +
315B ALA* 3.1 17.8 + - - +
351B LEU* 5.0 1.1 - - - -
311C GLY* 3.4 37.8 - - - +
315C ALA* 4.4 0.9 - - - -
351C LEU* 4.0 14.3 - - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.5 27.3 - - + +
308B ALA 3.3 15.6 + - - +
309B LEU 3.3 3.4 + - - +
311B GLY* 1.3 72.3 - - - +
313B ASP* 1.3 55.6 + - - +
315B ALA* 3.2 4.0 + - - +
316B ALA* 2.7 36.1 + - - +
348B VAL* 4.9 2.8 - - + +
351B LEU* 4.0 37.7 - - + +
352B ALA 4.4 0.4 - - - +
355B ALA* 4.5 2.7 - - + -
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 2.7 36.0 + - - +
263B LEU* 3.5 13.2 - - - +
267B HIS* 2.7 26.8 + - - -
309B LEU* 2.9 26.3 + - - +
310B GLN* 4.3 2.3 - - - +
312B ALA* 1.3 74.4 - - - +
314B ALA* 1.3 54.3 + - - +
316B ALA* 3.1 7.1 + - - +
317B ARG* 2.8 60.7 + - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B GLN 3.3 20.4 + - - +
311B GLY 3.7 2.2 - - - +
312B ALA 3.3 0.2 - - - -
313B ASP* 1.3 78.7 - - - +
315B ALA* 1.3 61.2 + - - +
317B ARG* 3.6 3.1 + - - +
318B GLU* 3.2 23.4 + - - +
314C ALA* 3.4 25.6 - - + +
315C ALA* 3.5 17.0 - - - +
318C GLU* 3.6 25.0 - - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLY 3.1 17.6 + - - +
312B ALA 3.6 3.8 - - - +
314B ALA* 1.3 72.7 - - - +
316B ALA* 1.3 65.7 + - - +
318B GLU* 3.4 6.5 + - - +
319B ALA* 3.0 18.7 + - - +
348B VAL* 3.4 18.4 - - + +
351B LEU* 3.8 22.7 - - + -
310C GLN* 4.1 18.3 + - + +
311C GLY* 4.1 5.2 - - - -
314C ALA* 3.4 7.6 - - - +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 4.8 0.9 - - - +
256B LEU* 4.3 3.9 - - - +
260B ASN* 3.6 26.4 + - - +
263B LEU* 3.8 14.4 - - + -
312B ALA 2.7 17.4 + - - +
313B ASP* 3.1 9.4 + - - +
315B ALA* 1.3 73.6 - - - +
317B ARG* 1.3 62.4 + - + +
319B ALA* 3.2 4.9 + - - +
320B ALA* 3.0 22.1 + - - +
348B VAL* 3.8 20.1 - - + +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 4.0 26.0 + - - +
81B ARG* 4.7 9.4 - - - +
310B GLN* 4.9 2.0 + - - +
313B ASP* 2.8 36.8 + - - +
314B ALA* 3.7 16.8 - - - +
316B ALA* 1.3 72.6 - - + +
318B GLU* 1.3 61.2 + - - +
320B ALA* 3.3 8.8 + - - +
321B HIS* 3.1 39.0 + - + +
318C GLU* 2.7 43.5 + - - +
344C LYS* 5.1 0.8 - - - +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ALA 3.2 13.8 + - - +
315B ALA* 3.5 7.2 - - - +
317B ARG* 1.3 79.7 - - - +
319B ALA* 1.3 59.6 + - - +
321B HIS* 3.4 12.6 + - - +
322B LEU* 3.2 21.0 + - - +
344B LYS* 4.0 25.2 + - + +
310C GLN* 5.5 4.2 - - - +
314C ALA* 3.9 13.4 - - - +
317C ARG* 3.0 41.5 + - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 3.9 14.7 - - + +
315B ALA 3.0 16.5 + - - +
316B ALA 3.2 4.7 + - - +
318B GLU* 1.3 75.1 - - - +
320B ALA* 1.3 60.6 + - - +
322B LEU* 3.4 8.8 + - - +
323B LEU* 2.9 27.7 + - - +
341B LEU* 4.0 3.6 - - + +
344B LYS* 4.6 15.9 - - + +
345B VAL* 4.4 13.0 - - + -
348B VAL* 4.0 16.4 - - + -
310C GLN* 5.5 0.4 - - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 4.4 1.2 - - - +
74B PRO* 4.1 24.0 - - + +
77B ILE* 3.8 28.9 - - + -
256B LEU* 3.9 10.4 - - + +
316B ALA 3.0 11.9 + - - +
317B ARG* 3.5 12.6 - - - +
318B GLU 3.3 0.2 - - - -
319B ALA* 1.3 73.7 - - - +
321B HIS* 1.3 59.7 + - - +
323B LEU* 3.3 4.7 + - - +
324B GLN* 3.0 26.5 + - - +
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Residues in contact with HIS 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PRO* 3.8 24.0 - - + +
317B ARG* 3.1 30.5 + - + +
318B GLU* 3.6 10.1 - - - +
319B ALA 3.4 0.2 - - - -
320B ALA* 1.3 77.4 - - - +
322B LEU* 1.3 57.9 + - - +
324B GLN* 3.2 9.4 + - - +
325B THR* 3.0 30.3 + - - -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU 3.2 11.2 + - - +
319B ALA* 3.6 9.6 - - - +
320B ALA 3.3 0.2 - - - -
321B HIS* 1.3 76.0 - - - +
323B LEU* 1.3 59.3 + - - +
325B THR* 3.2 15.2 + - + -
326B VAL* 2.8 40.0 + - + +
340B GLU* 4.6 3.8 - - + +
341B LEU* 4.0 25.1 - - + +
344B LYS* 3.8 34.8 - - + -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 4.0 38.1 - - + +
77B ILE* 5.0 1.1 - - + -
249B LEU* 5.1 5.8 - - + -
252B PRO* 4.9 1.6 - - + +
253B ILE* 4.0 37.2 - - + +
256B LEU* 3.8 21.5 - - + -
319B ALA 2.9 15.5 + - - +
320B ALA 3.3 8.9 + - - +
322B LEU* 1.3 75.0 - - - +
324B GLN* 1.3 52.7 + - - +
326B VAL* 3.7 0.3 - - - -
327B TRP* 2.7 44.7 + - + +
341B LEU* 3.9 30.0 - - + +
345B VAL* 6.1 0.2 - - + -
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 3.3 19.0 - - + +
73B TRP* 2.8 41.1 + - - -
74B PRO* 4.4 5.8 - - + -
320B ALA 3.0 13.1 + - - +
321B HIS* 3.2 13.6 + - - +
323B LEU* 1.3 76.1 - - - +
325B THR* 1.3 56.9 + - - +
327B TRP* 3.2 13.1 + - - +
328B ASP* 2.8 69.7 + - - +
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B HIS 3.0 14.8 + - - -
322B LEU* 3.2 20.6 + - + -
324B GLN* 1.3 78.1 - - - +
326B VAL* 1.3 64.5 + - + +
328B ASP* 3.4 13.7 + - - +
329B LYS* 3.4 29.3 + - + +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 3.7 32.3 - - + +
322B LEU* 2.8 32.4 + - + +
323B LEU* 3.8 2.9 - - + +
325B THR* 1.3 74.3 - - + +
327B TRP* 1.3 64.1 + - - +
329B LYS* 3.2 24.1 + - + +
330B GLY 3.9 2.3 + - - +
333B LEU* 4.2 20.0 - - + +
337B ASP* 4.0 35.2 - - + +
341B LEU* 4.1 17.0 - - + -
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Residues in contact with TRP 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 3.5 34.4 - + - +
102B PRO* 4.0 20.6 - - + -
105B GLU* 3.6 29.0 + - - -
106B LEU* 3.7 30.1 - - + -
246B ARG* 3.0 36.8 + - - +
249B LEU* 4.1 17.0 - - + -
253B ILE* 3.8 22.4 - - + -
323B LEU* 2.7 24.9 + - + +
324B GLN* 3.5 10.5 - - - +
326B VAL* 1.3 75.5 - - - +
328B ASP* 1.3 69.7 + - - +
330B GLY* 3.0 19.2 + - - -
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLN* 2.8 53.3 + - - +
325B THR* 3.8 7.3 - - - +
326B VAL 3.3 0.2 - - - -
327B TRP* 1.3 77.9 - - - +
329B LYS* 1.3 59.9 + - - +
330B GLY 3.2 0.6 + - - -
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B THR* 3.4 28.9 + - - +
326B VAL* 3.4 12.1 - - - +
327B TRP 3.1 1.2 + - - -
328B ASP* 1.3 77.7 - - - +
330B GLY* 1.3 62.6 + - - +
331B ASP 3.6 0.2 + - - -
332B ALA* 3.3 23.2 + - + +
333B LEU* 4.1 14.6 - - - +
334B THR* 5.7 0.8 - - - +
337B ASP* 2.8 44.0 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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