Contacts of the helix formed by residues 312 - 338 (chain A) in PDB entry 5NTI
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 SER 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ARG 3.8 2.0 + - - -
311A LYS* 1.3 78.1 - - - +
313A MET* 1.3 65.2 + - - +
314A TRP* 2.9 43.0 + - - -
315A GLU* 3.4 13.8 + - - +
316A MET* 3.2 20.3 + - - +
330B TYR* 4.9 0.9 + - - -
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS 3.7 1.2 + - - -
312A SER* 1.3 73.5 - - - +
314A TRP* 1.3 63.8 + - - +
316A MET* 3.3 1.2 + - - +
317A TRP* 3.0 39.6 + - + +
390A ALA 3.4 25.5 + - - +
391A LEU 3.7 13.7 - - - +
392A GLY* 4.4 10.3 - - - +
486A PHE* 3.8 21.8 - - + -
489A LEU* 4.5 12.3 - - + -
490A HIS* 4.0 18.6 - - + -
374C ARG* 6.1 3.6 - - - +
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Residues in contact with TRP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER* 2.9 30.8 + - - -
313A MET* 1.3 78.7 - - - +
315A GLU* 1.3 81.4 + - + +
317A TRP* 3.6 1.6 + - - +
318A GLU* 3.0 48.6 + - - +
486A PHE* 3.7 15.4 - - + -
490A HIS* 4.7 14.9 - + + -
493A VAL* 3.8 30.8 - - + +
326B GLU* 4.9 3.1 - - + -
329B GLN* 3.5 38.4 - - + -
330B TYR* 3.9 39.9 - + - -
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 3.7 38.5 + - + +
312A SER* 3.2 22.1 + - - +
314A TRP* 1.3 94.5 - - + +
316A MET* 1.3 60.9 + - - +
318A GLU* 3.3 3.8 + - - +
319A ARG* 2.9 39.8 + - - +
286B GLN* 3.8 7.2 + - - +
326B GLU* 3.1 33.9 - - - +
330B TYR* 2.6 28.1 + - - -
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Residues in contact with MET 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 4.0 22.2 - - + +
311A LYS* 4.6 12.3 - - + +
312A SER 3.2 13.3 + - - +
313A MET 3.9 2.7 - - - +
315A GLU* 1.3 80.4 - - - +
317A TRP* 1.3 57.0 + - - +
319A ARG* 3.3 9.1 + - - +
320A CYS* 2.9 52.9 + - - -
378A PHE* 3.9 22.2 - - + -
387A LEU* 3.7 22.7 - - + +
388A PHE* 3.9 13.2 - - + -
390A ALA* 4.1 21.3 - - + -
391A LEU* 3.7 20.2 - - + +
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Residues in contact with TRP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 3.0 24.6 + - + +
316A MET* 1.3 75.9 - - - +
318A GLU* 1.3 58.5 + - - +
320A CYS* 3.9 0.6 - - - +
321A ALA* 2.8 33.8 + - - +
391A LEU* 2.8 43.7 + - + +
393A CYS* 4.3 6.7 - - + -
479A HIS* 4.9 2.5 - + - -
482A ARG* 3.4 43.5 - - + -
483A LEU* 3.7 14.1 - - + -
486A PHE* 3.4 45.9 - + + +
498A PHE* 3.9 20.9 - + + -
502A TYR* 3.4 24.5 - + - -
601A C3S 3.5 30.5 - - + -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TRP* 3.0 29.4 + - - +
315A GLU 3.4 5.6 - - - +
317A TRP* 1.3 75.0 - - - +
319A ARG* 1.3 65.6 + - - +
321A ALA* 3.8 1.7 - - - +
322A HIS* 3.0 23.2 + - - +
493A VAL* 3.9 5.2 - - - +
497A ALA* 3.3 29.8 - - + +
498A PHE* 3.7 17.2 - - + -
499A PRO* 5.2 1.7 - - - +
322B HIS* 3.7 21.3 + - + +
325B THR* 4.8 2.1 - - - +
326B GLU* 4.3 13.9 + - - +
329B GLN* 2.7 40.0 + - - +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 3.8 7.1 + - - -
311A LYS* 3.6 31.2 - - - +
315A GLU* 2.9 35.7 + - - +
316A MET* 3.6 14.4 - - - +
318A GLU* 1.3 76.1 - - - +
320A CYS* 1.3 64.0 + - - +
322A HIS* 3.2 4.9 + - - +
323A HIS* 3.0 30.5 + - + +
378A PHE* 5.2 0.7 - - + -
379A GLU* 2.8 46.8 + - - +
286B GLN* 4.1 6.7 - - - +
287B LEU* 6.0 3.2 - - - +
322B HIS* 3.9 16.2 - - - +
323B HIS* 5.8 7.7 + - + -
326B GLU* 3.5 29.4 + - - +
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Residues in contact with CYS 320 (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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316A MET* 2.9 44.4 + - - +
317A TRP 3.9 1.8 - - - +
319A ARG* 1.3 76.6 - - - +
321A ALA* 1.3 52.2 + - - +
323A HIS* 3.3 4.9 + - - +
324A LEU* 2.8 36.6 + - - +
378A PHE* 4.1 13.7 - - - -
388A PHE* 4.1 12.1 - - - -
391A LEU* 4.0 15.3 - - + -
601A C3S 3.6 35.9 - - + +
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Residues in contact with ALA 321 (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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317A TRP* 2.8 22.6 + - + +
318A GLU 3.8 3.6 - - - +
320A CYS* 1.3 73.0 - - - +
322A HIS* 1.3 53.5 + - - +
324A LEU* 3.9 1.6 - - - +
325A THR* 2.6 39.4 + - - -
498A PHE* 3.9 28.0 - - + -
499A PRO* 4.2 6.7 - - + -
502A TYR* 4.0 27.2 - - + -
601A C3S 4.3 1.7 - - + +
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Residues in contact with HIS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU 3.0 15.2 + - - +
319A ARG 3.5 7.0 - - - +
321A ALA* 1.3 76.8 - - - +
323A HIS* 1.3 82.2 + + - +
325A THR* 3.3 4.4 + - - -
326A GLU* 2.9 51.3 + - - +
499A PRO* 3.9 18.4 - - + +
318B GLU* 3.6 41.8 + - + +
319B ARG* 4.0 12.5 - - - +
322B HIS* 3.7 33.5 - + + +
323B HIS* 6.2 0.4 - + - -
497B ALA 4.9 3.8 + - - -
499B PRO* 5.9 1.2 - - - +
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Residues in contact with HIS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN* 5.4 0.2 + - - -
319A ARG* 3.0 21.9 + - - +
322A HIS* 1.3 95.7 + + - +
324A LEU* 1.3 62.1 + - - +
326A GLU* 3.4 14.8 + - - +
327A ALA 3.2 16.8 + - - -
378A PHE* 3.8 21.8 - + + -
379A GLU* 2.6 39.8 + - + +
601A C3S 3.4 34.4 - - + +
319B ARG* 5.8 9.6 + - + -
322B HIS* 5.5 4.0 + + - -
323B HIS* 5.5 7.2 - + - -
379B GLU* 5.8 2.9 - - - -
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Residues in contact with LEU 324 (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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320A CYS 2.8 18.6 + - - +
321A ALA 3.9 3.6 - - - +
323A HIS* 1.3 75.1 - - - +
325A THR* 1.3 64.8 + - - +
327A ALA* 3.3 4.0 + - - +
328A ILE* 3.0 34.5 + - + +
358A MET* 3.8 40.8 - - + -
361A VAL* 3.8 24.5 - - + -
362A LEU* 6.3 0.4 - - + -
479A HIS* 4.0 7.6 - - + +
502A TYR* 3.7 26.7 - - + -
506A PHE* 4.4 2.9 - - + -
601A C3S 4.0 35.6 - - + +
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Residues in contact with THR 325 (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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321A ALA 2.6 23.6 + - - -
322A HIS 3.3 4.7 + - - -
324A LEU* 1.3 74.8 - - - +
326A GLU* 1.3 57.6 + - - +
328A ILE* 3.2 11.7 + - + +
329A GLN* 2.9 38.2 + - - +
499A PRO* 3.4 24.5 - - + +
501A LEU* 4.1 27.8 - - + -
502A TYR* 3.3 23.7 - - - +
318B GLU* 5.2 0.7 - - - +
497B ALA* 4.8 5.8 - - + -
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN* 3.0 27.6 + - - +
322A HIS* 2.9 41.2 + - - +
323A HIS* 3.4 19.7 + - - +
324A LEU 3.2 0.2 - - - -
325A THR* 1.3 75.6 - - - +
327A ALA* 1.3 62.4 + - - +
329A GLN* 3.1 23.5 + - - +
330A TYR* 3.2 21.1 - - + -
314B TRP* 4.9 4.5 - - + -
315B GLU* 4.2 21.6 - - + +
318B GLU* 4.0 14.2 + - - +
319B ARG* 3.8 24.0 + - - +
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Residues in contact with ALA 327 (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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286A GLN* 3.7 10.7 + - - +
323A HIS 3.2 3.5 + - - +
324A LEU 3.3 7.4 + - - +
326A GLU* 1.3 79.4 - - - +
328A ILE* 1.3 62.0 + - - +
330A TYR* 3.2 11.7 + - - +
331A VAL* 3.1 21.5 + - - +
361A VAL* 4.1 23.6 - - + -
364A ARG* 4.6 2.2 + - - +
601A C3S 3.8 36.1 - - + +
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.0 31.5 + - + +
325A THR* 3.2 12.8 + - + +
327A ALA* 1.3 74.7 - - - +
329A GLN* 1.3 59.4 + - - +
331A VAL* 2.9 9.0 + - - +
332A VAL* 2.8 33.3 + - + +
357A ALA* 3.9 18.8 - - + +
358A MET* 5.1 1.8 - - - +
361A VAL* 3.9 17.3 - - + -
501A LEU* 4.1 13.0 - - + -
502A TYR* 5.4 0.9 - - + -
505A LEU* 3.8 23.6 - - + -
506A PHE* 3.6 37.7 - - + -
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A THR* 2.9 22.7 + - - +
326A GLU* 3.3 14.4 - - - +
328A ILE* 1.3 75.2 - - - +
330A TYR* 1.3 57.3 + - - +
332A VAL* 3.6 10.0 + - - +
333A GLU* 3.2 25.1 + - - +
501A LEU* 4.5 14.1 - - + -
314B TRP* 3.7 25.7 - - + -
318B GLU* 2.7 40.9 + - - +
493B VAL* 4.6 9.5 - - - +
496B ALA* 5.8 1.9 - - + +
497B ALA* 3.5 17.0 - - - +
504P LEU* 5.3 14.2 - - + +
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Residues in contact with TYR 330 (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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283A GLU 5.6 1.8 - - - -
284A THR* 3.3 36.4 - - - +
285A CYS 4.3 4.0 - - - -
286A GLN* 3.6 49.5 + - + +
326A GLU* 3.2 25.7 + - + -
327A ALA* 3.2 8.7 + - - +
328A ILE 3.1 0.4 - - - -
329A GLN* 1.3 78.4 - - - +
331A VAL* 1.3 58.7 + - - +
333A GLU* 3.3 8.8 + - + +
334A PHE* 2.9 27.2 + - - +
364A ARG* 3.8 7.0 - - - +
601A C3S 4.9 0.7 - - - +
312B SER* 5.1 0.9 + - - -
314B TRP* 4.0 26.3 - + - -
315B GLU* 2.5 26.8 + - - -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA 3.1 13.6 + - - +
328A ILE* 2.9 10.1 + - - +
330A TYR* 1.3 74.3 - - - +
332A VAL* 1.3 59.8 + - - +
334A PHE* 3.2 12.1 + - + +
335A ALA* 3.0 27.2 + - - +
353A LEU* 4.5 8.5 - - + -
356A GLY 5.3 0.2 - - - -
357A ALA* 4.0 19.7 - - + +
360A VAL* 3.7 41.1 - - + -
361A VAL* 3.7 22.0 - - + -
364A ARG* 4.3 11.9 - - - +
425A LEU* 5.3 2.5 - - + -
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 2.8 32.6 + - + +
329A GLN* 3.7 10.1 - - - +
331A VAL* 1.3 75.0 - - + +
333A GLU* 1.3 57.9 + - - +
335A ALA* 3.3 3.6 + - - +
336A LYS* 3.0 30.4 + - + +
353A LEU* 4.0 28.0 - - + -
357A ALA* 5.8 0.4 - - + -
501A LEU* 5.0 1.1 - - + -
501P LEU* 4.3 18.2 - - + -
504P LEU* 4.1 37.5 - - + +
505P LEU* 4.3 10.1 - - + -
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A THR* 3.8 12.6 - - + -
329A GLN 3.2 12.7 + - - +
330A TYR* 3.5 13.7 - - + +
331A VAL 3.2 0.6 - - - -
332A VAL* 1.3 76.2 - - - +
334A PHE* 1.3 64.7 + - - +
336A LYS* 3.3 27.1 + - - +
337A ARG* 3.2 65.2 + - - +
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Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL 4.0 7.0 - - - -
280A SER* 3.8 7.3 - - - -
281A TYR* 3.6 36.8 - + + -
284A THR* 3.4 26.8 - - - +
330A TYR 2.9 10.9 + - - +
331A VAL* 3.3 12.6 - - + +
333A GLU* 1.3 75.3 - - - +
335A ALA* 1.3 63.5 + - - +
337A ARG* 3.3 4.8 + - - +
338A LEU* 3.0 46.2 + - + +
360A VAL* 5.1 10.1 - - + -
364A ARG* 3.7 13.0 - - - +
418A ALA 3.8 20.0 - - - -
421A THR* 3.8 18.2 - - - -
422A ALA* 4.1 15.0 - - - -
425A LEU* 4.6 9.0 - - + -
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL 3.0 11.9 + - - +
332A VAL 3.4 8.7 - - - +
333A GLU 3.3 0.2 - - - -
334A PHE* 1.3 76.6 - - - +
336A LYS* 1.3 63.5 + - + +
338A LEU* 3.1 11.5 + - - -
341A PHE* 3.2 38.4 - - + +
353A LEU* 3.8 17.7 - - + -
425A LEU* 3.6 29.8 - - + -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL* 3.0 21.1 + - + +
333A GLU* 3.3 33.5 + - - +
335A ALA* 1.3 76.0 - - - +
337A ARG* 1.3 61.7 + - + +
338A LEU 3.8 0.7 + - - +
342A MET* 3.3 33.3 - - - +
504P LEU 3.0 29.2 + - - +
505P LEU* 3.7 33.6 - - + +
506P GLY* 5.2 0.4 - - - +
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 4.6 4.0 + - - -
279A LYS* 6.4 0.2 - - - +
280A SER* 2.9 27.8 + - - +
283A GLU* 2.9 43.7 + - - +
284A THR* 4.1 13.4 - - - +
333A GLU* 3.2 49.3 + - - +
334A PHE* 4.0 2.7 - - - +
335A ALA 3.2 0.2 - - - -
336A LYS* 1.3 78.1 - - + +
338A LEU* 1.3 63.7 + - - +
339A SER* 3.4 3.1 + - - -
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 3.7 34.1 - - + -
280A SER* 4.0 2.7 - - - -
334A PHE* 3.0 36.3 + - + +
335A ALA 3.1 13.6 + - - +
336A LYS 4.7 1.7 - - - +
337A ARG* 1.3 76.4 - - - +
339A SER* 1.3 70.8 + - - +
340A GLY 3.1 3.8 + - - -
341A PHE* 3.1 16.8 + - + +
342A MET* 4.3 3.1 + - - +
422A ALA* 4.0 15.7 - - + -
425A LEU* 3.8 27.6 - - + -
426A ILE* 4.1 23.3 - - + -
442A LEU* 6.4 0.2 - - + -
446A LEU* 5.0 3.6 - - + -
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il