Contacts of the helix formed by residues 335 - 367 (chain A) in PDB entry 3DBL
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 335 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ASP* 4.9 7.1 - - - +
211A HIS* 3.0 35.0 + - + +
334A ALA* 1.3 71.3 - - - +
336A SER* 1.3 67.5 + - - +
337A GLY* 3.0 18.7 + - - -
338A LYS* 3.0 37.5 + - + +
339A TYR* 3.0 10.4 + - - +
221B MET* 4.3 10.8 - - - +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA 3.5 4.2 + - - -
335A ASP* 1.3 71.7 + - - +
337A GLY* 1.3 57.4 + - - +
339A TYR* 3.6 0.9 + - - +
340A ILE* 3.0 36.7 + - - +
220B SER 4.2 0.2 + - - -
221B MET* 3.1 22.5 - - - +
222B PRO* 2.5 34.8 + - - +
223B ARG* 4.3 6.5 - - - -
271B TYR* 3.8 24.2 - - - -
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Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASP* 3.0 10.8 + - - -
336A SER* 1.3 78.8 - - - +
338A LYS* 1.3 53.1 + - - +
340A ILE* 3.5 4.3 + - - +
341A LYS* 2.8 35.0 + - - +
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS* 4.9 0.9 + - - -
199A TYR* 3.6 33.0 + - + +
204A MET* 4.3 11.8 - - - +
208A ASP* 2.9 55.5 + - - +
211A HIS 3.7 15.5 + - - +
212A THR* 3.8 4.2 + - - -
213A PRO* 4.0 15.2 - - + +
335A ASP* 3.0 23.3 + - + +
337A GLY* 1.3 73.1 - - - +
339A TYR* 1.3 61.5 + - - +
341A LYS* 3.8 5.1 - - - +
342A LEU* 2.8 32.1 + - - +
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Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PRO* 4.4 6.1 - - + +
329A ILE* 3.4 28.1 + - + +
330A PRO 2.9 33.4 + - - -
331A ASP* 3.7 7.4 - - - -
332A MET* 3.7 35.4 - - + -
334A ALA* 4.2 5.6 - - + -
335A ASP 3.0 15.1 + - - +
336A SER 3.9 1.1 - - - +
338A LYS* 1.3 75.6 - - - +
340A ILE* 1.3 56.3 + - + +
342A LEU* 3.5 6.1 - - + +
343A GLN* 2.7 65.4 + - - +
223B ARG* 3.5 43.7 - - + -
224B LEU* 4.2 9.4 - - + +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER* 3.0 26.4 + - - +
337A GLY* 3.8 5.2 - - - +
339A TYR* 1.3 77.2 - - + +
341A LYS* 1.3 63.6 + - - +
343A GLN* 3.3 22.6 + - - +
344A ASN* 2.7 49.1 + - - +
223B ARG* 4.0 17.9 - - - +
271B TYR 4.2 9.6 - - - +
272B ASN* 3.9 33.4 - - + +
273B ILE* 4.2 10.5 - - + -
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Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS* 3.8 28.5 - - + +
198A SER* 5.0 10.3 + - - -
337A GLY 2.8 22.5 + - - +
338A LYS* 3.8 7.2 - - - +
340A ILE* 1.3 74.2 - - - +
342A LEU* 1.3 63.4 + - - +
344A ASN* 3.1 15.7 + - - +
345A VAL* 3.3 16.8 + - + +
114E ASP* 3.5 42.0 + - + +
138E ARG* 4.7 4.2 - - - +
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 4.8 2.5 - - + -
195A HIS* 3.6 33.5 + - + +
196A PHE* 4.7 9.4 - - + -
213A PRO* 4.0 24.7 - - + -
215A ILE* 4.3 9.9 - - + -
216A VAL* 4.6 7.9 - - + -
329A ILE* 3.9 6.7 - - + -
332A MET* 3.9 28.3 - - + -
338A LYS 2.8 21.9 + - - +
339A TYR* 3.5 4.9 - - + +
341A LYS* 1.3 71.7 - - - +
343A GLN* 1.3 54.0 + - - +
345A VAL* 2.8 33.1 + - + +
346A TYR* 3.5 31.9 + - + +
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Residues in contact with GLN 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLY 4.5 2.4 - - - +
328A THR* 6.4 0.4 - - - +
329A ILE* 3.8 25.0 + - + +
339A TYR* 2.7 43.0 + - + +
340A ILE* 3.3 31.1 - - - +
341A LYS 3.4 0.2 - - - -
342A LEU* 1.3 74.2 - - - +
344A ASN* 1.3 58.5 + - - +
346A TYR* 3.6 5.7 + - - +
347A ARG* 3.2 41.5 + - + +
223B ARG 4.3 3.4 + - - +
224B LEU* 5.4 4.8 - - - +
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Residues in contact with ASN 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ILE* 2.7 45.4 + - - +
341A LYS* 3.7 7.0 - - - +
342A LEU 2.9 1.8 + - - -
343A GLN* 1.3 77.7 - - - +
345A VAL* 1.3 60.6 + - - +
346A TYR 3.3 0.7 - - - -
347A ARG* 2.9 37.1 + - - +
348A GLU* 3.1 31.5 + - - +
274B ARG* 4.9 0.3 + - - -
107E GLU* 4.5 0.3 - - - +
108E SER* 5.9 0.2 + - - -
111E ASN* 2.9 34.9 + - - +
114E ASP* 6.0 2.5 - - + +
115E ASN* 3.9 4.7 + - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 4.0 4.2 - - + -
191A GLU* 3.7 39.2 - - + +
192A LEU* 4.0 11.0 - - + +
195A HIS* 4.0 28.0 - - + +
341A LYS* 3.3 19.1 - - + +
342A LEU* 2.8 15.1 + - + +
344A ASN* 1.3 74.5 - - - +
346A TYR* 1.3 62.8 + - + +
348A GLU* 4.0 0.9 - - - +
349A LYS* 3.1 26.3 + - - +
114E ASP* 6.5 0.9 - - + -
115E ASN* 4.5 10.8 - - - +
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Residues in contact with TYR 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ASP 4.1 11.2 - - - -
183A LEU* 2.8 38.4 + - + +
184A ARG* 5.1 0.2 - - + -
189A PHE* 3.8 22.0 - + - -
192A LEU* 3.7 19.3 - - + +
215A ILE* 4.2 16.9 - - + +
325A VAL* 4.4 8.9 - - + +
327A GLY* 3.8 20.5 - - - +
328A THR 5.1 0.9 - - - -
329A ILE* 3.5 29.6 - - + -
342A LEU* 3.5 39.0 + - + -
343A GLN 3.6 4.0 + - - +
345A VAL* 1.3 77.2 - - + +
347A ARG* 1.3 60.8 + - - +
349A LYS* 3.0 5.1 + - - +
350A ALA* 2.7 32.4 + - - +
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLY* 3.7 18.6 + - - +
343A GLN* 3.2 30.9 + - + +
344A ASN* 2.9 29.0 + - - +
346A TYR* 1.3 78.7 - - - +
348A GLU* 1.3 66.0 + - - +
350A ALA* 3.4 2.9 + - - +
351A LYS* 3.0 28.5 + - - +
274B ARG* 3.0 37.5 - - - +
107E GLU* 2.7 34.2 + - - -
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASN 3.1 17.4 + - - +
345A VAL 4.3 2.0 - - - +
347A ARG* 1.3 85.8 + - + +
349A LYS* 1.3 58.7 - - - +
351A LYS* 3.6 32.7 + - - +
352A LYS* 3.2 42.9 + - - +
107E GLU* 3.8 18.8 - - - +
111E ASN* 3.8 14.2 + - - +
112E LEU* 6.3 0.7 - - - -
115E ASN* 3.1 42.4 - - + +
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Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.6 44.6 - - + +
190A PRO* 5.3 1.8 - - - +
191A GLU* 3.8 23.7 + - + +
318A GLU 5.6 3.6 + - - -
325A VAL* 3.6 23.1 - - + -
345A VAL 3.1 19.0 + - - +
346A TYR 3.0 4.6 + - - +
348A GLU* 1.3 75.2 - - - +
350A ALA* 1.3 64.9 + - - +
351A LYS 3.2 0.4 - - - -
352A LYS* 3.6 10.5 + - + +
353A ASP* 3.2 46.5 + - - -
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 3.1 30.3 - - - +
326A ARG 3.7 3.8 - - - +
327A GLY* 3.4 19.1 - - - -
346A TYR 2.7 16.0 + - - +
347A ARG* 3.8 4.0 - - - +
349A LYS* 1.3 76.6 - - - +
351A LYS* 1.3 59.1 + - - +
353A ASP* 3.5 5.0 + - - +
354A ALA* 3.1 26.7 + - - +
384A CYS* 5.2 4.0 - - - +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ARG 3.0 16.5 + - - +
348A GLU* 3.6 36.1 + - - +
350A ALA* 1.3 75.5 - - - +
352A LYS* 1.3 64.6 + - + +
354A ALA* 3.4 9.2 + - - +
355A ALA* 3.3 18.0 + - - +
381A LYS* 4.4 24.5 - - - +
105E VAL* 5.9 3.4 - - - +
107E GLU* 4.7 16.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 3.6 28.5 - - - +
348A GLU* 3.2 35.0 + - - +
349A LYS* 4.0 9.4 - - + +
350A ALA 3.4 0.2 - - - -
351A LYS* 1.3 73.9 - - + +
353A ASP* 1.3 70.0 + - - +
355A ALA* 3.0 10.2 + - - +
356A ALA* 3.0 21.0 + - - +
115E ASN* 5.1 14.0 + - - +
116E ASP* 6.3 0.8 - - - +
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Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.6 27.7 - - + -
318A GLU 5.1 1.2 - - - +
323A LEU 4.5 0.3 - - - +
324A PRO* 3.3 19.0 - - + +
325A VAL* 2.6 36.7 + - - +
349A LYS* 3.2 35.3 + - - +
350A ALA 3.6 10.1 - - - +
351A LYS 3.3 0.2 - - - -
352A LYS* 1.3 79.3 - - - +
354A ALA* 1.3 63.0 + - - +
356A ALA* 3.0 6.3 + - - +
357A VAL* 2.9 22.5 + - - +
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA 3.1 10.8 + - - +
351A LYS* 3.5 10.3 - - - +
352A LYS 3.2 0.2 - - - -
353A ASP* 1.3 79.3 - - - +
355A ALA* 1.3 50.0 + - - +
357A VAL* 3.2 3.6 + - - +
358A GLY* 2.6 32.1 + - - -
380A LEU* 3.7 12.5 - - + +
381A LYS* 4.2 26.9 - - + -
384A CYS* 3.7 28.9 - - + -
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS 3.3 9.4 + - - +
352A LYS* 3.0 13.8 + - - +
354A ALA* 1.3 79.8 - - - +
356A ALA* 1.3 51.3 + - - +
358A GLY* 2.9 4.1 + - - +
359A ASN* 2.8 40.2 + - - +
380A LEU* 5.3 1.8 - - - -
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.4 22.7 - - + -
318A GLU* 3.5 23.2 - - + +
352A LYS 3.0 11.4 + - - +
353A ASP* 3.3 9.4 - - - +
355A ALA* 1.3 75.3 - - - +
357A VAL* 1.3 61.2 + - - +
359A ASN* 3.5 12.7 + - - +
360A HIS* 3.3 25.8 + - - -
----------------------------------------------------------
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA* 4.1 17.3 - - + +
311A LEU* 3.7 22.9 - - + -
314A PHE* 3.6 34.1 - - + -
324A PRO* 3.8 11.0 - - + -
353A ASP 2.9 9.5 + - - +
354A ALA 3.5 6.3 - - - +
356A ALA* 1.3 74.1 - - - +
358A GLY* 1.3 66.1 + - - +
360A HIS* 3.0 10.5 + - - +
361A VAL* 2.9 20.4 + - + +
380A LEU* 3.7 20.4 - - + -
383A LEU* 4.8 3.8 - - + -
384A CYS* 4.1 10.8 - - - -
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Residues in contact with GLY 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ALA 2.6 16.0 + - - -
355A ALA* 2.9 6.5 + - - -
357A VAL* 1.3 77.3 - - - +
359A ASN* 1.3 63.1 + - - +
361A VAL* 3.0 14.9 + - - +
362A ALA* 3.0 13.4 + - - +
380A LEU* 3.6 23.1 - - - -
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Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 5.6 2.4 - - - +
355A ALA* 2.8 19.8 + - - +
356A ALA* 3.6 14.0 - - - +
357A VAL 3.2 0.2 - - - -
358A GLY* 1.3 72.0 - - - +
360A HIS* 1.3 63.8 + - + +
362A ALA* 3.3 8.8 + - - +
363A LYS* 3.1 39.5 + - - +
----------------------------------------------------------
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Residues in contact with HIS 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA* 3.8 19.1 - - - +
313A GLU* 3.6 29.4 + - + +
314A PHE* 3.8 24.0 - - + -
317A LYS* 4.6 11.4 - - + -
318A GLU* 3.1 27.4 + - - -
356A ALA 3.3 18.3 + - - -
357A VAL* 3.0 8.3 + - - +
359A ASN* 1.3 76.9 - - + +
361A VAL* 1.3 65.8 + - - +
363A LYS* 3.4 27.5 + - - +
364A LEU* 3.1 33.7 + - + +
----------------------------------------------------------
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 4.7 4.7 - - + -
307A LEU* 3.8 22.9 - - + -
310A ALA* 3.4 24.9 - - + -
357A VAL 2.9 14.2 + - - +
358A GLY* 3.0 9.4 + - - +
360A HIS* 1.3 77.5 - - - +
362A ALA* 1.3 53.2 + - - +
364A LEU* 3.1 4.4 + - - +
365A LEU* 2.7 61.7 + - + +
375A ILE* 4.3 18.8 - - + +
380A LEU* 3.9 13.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLY 3.0 11.0 + - - +
359A ASN* 3.6 11.4 - - - +
360A HIS 3.3 0.2 - - - -
361A VAL* 1.3 77.9 - - - +
363A LYS* 1.3 64.0 + - + +
365A LEU* 3.1 10.1 + - - +
366A GLN* 3.0 32.7 + - + +
372A PRO* 4.7 15.0 - - + +
----------------------------------------------------------
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LYS* 5.1 9.9 - - - +
359A ASN* 3.1 25.9 + - - +
360A HIS* 3.7 32.6 + - - +
361A VAL 3.3 0.2 - - - -
362A ALA* 1.3 75.0 - - + +
364A LEU* 1.3 67.3 - - + +
366A GLN* 3.1 14.0 + - - +
367A SER* 3.0 23.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 4.2 18.6 - - + -
306A ILE* 4.3 16.8 - - + -
309A ARG* 3.9 42.8 - - + +
310A ALA* 4.5 6.3 - - - -
313A GLU* 4.4 14.1 - - + -
360A HIS* 3.1 28.2 + - + +
361A VAL 3.7 5.2 - - - +
363A LYS* 1.3 82.0 - - + +
365A LEU* 1.3 62.4 + - - +
367A SER* 2.9 24.4 + - - +
368A ILE* 3.3 19.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 3.8 14.8 - - + -
361A VAL* 2.7 44.6 + - + +
362A ALA* 3.6 6.1 - - - +
364A LEU* 1.3 72.8 - - - +
366A GLN* 1.3 57.8 + - - +
368A ILE* 4.0 3.6 - - - -
369A GLY 3.4 1.2 + - - -
370A GLN* 2.8 73.7 + - + +
371A ALA 4.7 0.4 - - - +
372A PRO* 4.0 32.5 - - + +
374A SER* 3.9 4.3 - - - +
375A ILE* 3.3 29.6 - - + +
----------------------------------------------------------
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Residues in contact with GLN 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA* 3.0 20.0 + - - +
363A LYS* 3.5 14.9 - - - +
364A LEU 3.1 0.2 - - - -
365A LEU* 1.3 76.2 - - - +
367A SER* 1.3 55.0 + - - +
368A ILE 2.5 17.4 + - - -
369A GLY* 2.9 14.6 + - - +
370A GLN 4.8 0.7 - - - -
372A PRO* 3.6 23.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 5.9 0.2 - - - +
363A LYS 3.0 11.5 + - - -
364A LEU* 2.9 31.0 + - - +
366A GLN* 1.3 76.2 - - - +
368A ILE* 1.3 64.5 + - - +
----------------------------------------------------------
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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