Contacts of the helix formed by residues 312 - 338 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TYR* 5.1 0.5 + - - -
310B ARG 3.7 1.0 + - - -
311B LYS* 1.3 77.7 - - - +
313B MET* 1.3 65.2 + - - +
314B TRP* 3.0 42.4 + - - -
315B GLU* 3.3 15.1 + - - +
316B MET* 3.1 22.7 + - - +
390B ALA* 4.6 0.2 - - - -
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LYS 3.8 1.2 + - - -
312B SER* 1.3 73.3 - - - +
314B TRP* 1.3 57.9 + - - +
316B MET* 4.0 0.7 - - - +
317B TRP* 3.0 48.4 + - + -
390B ALA* 3.2 27.7 + - - +
391B LEU 3.7 12.6 - - - +
392B GLY* 4.7 8.5 - - - -
485B ILE* 6.4 0.2 - - - -
486B PHE* 3.8 18.2 - - + -
489B LEU* 3.7 32.5 - - + -
490B HIS* 4.0 12.3 - - + -
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Residues in contact with TRP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU* 4.9 3.1 - - + -
329A GLN* 3.7 29.8 - - + -
330A TYR* 4.0 38.6 - + - -
312B SER* 3.0 29.0 + - - -
313B MET* 1.3 80.6 - - - +
315B GLU* 1.3 82.0 + - + +
317B TRP* 3.8 1.6 - - - +
318B GLU* 2.9 54.8 + - - +
486B PHE* 3.7 17.3 - - + -
490B HIS* 4.4 19.2 - + + -
493B VAL* 3.8 27.1 - - + +
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN* 4.3 13.2 + - - +
326A GLU* 4.2 16.4 - - - +
330A TYR* 2.5 33.0 + - - -
311B LYS* 3.0 35.6 + - + +
312B SER* 3.3 20.5 + - - +
314B TRP* 1.3 96.5 - - + +
316B MET* 1.3 57.2 + - - +
318B GLU* 3.2 5.1 + - - +
319B ARG* 2.9 43.1 + - - +
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Residues in contact with MET 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B TYR* 4.0 21.8 - - + +
311B LYS* 4.0 15.6 - - + +
312B SER 3.1 17.0 + - - +
313B MET 4.0 2.7 - - - +
315B GLU* 1.3 74.4 - - - +
317B TRP* 1.3 64.8 + - - +
319B ARG* 3.4 7.9 + - - +
320B CYS* 3.0 38.2 + - - -
378B PHE* 4.1 5.2 - - + -
387B LEU* 3.7 40.8 - - + +
388B PHE* 3.8 20.6 - - + -
390B ALA* 4.0 20.4 - - + +
391B LEU* 3.7 19.3 - - + +
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Residues in contact with TRP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B MET* 3.0 29.5 + - + +
316B MET* 1.3 76.3 - - - +
318B GLU* 1.3 57.7 + - - +
320B CYS* 3.8 1.5 - - - +
321B ALA* 2.8 32.9 + - - +
391B LEU* 2.7 42.6 + - + +
393B CYS* 4.2 13.5 - - - -
479B HIS* 4.7 4.0 - + - -
482B ARG* 3.6 39.7 - - + -
483B LEU* 3.6 17.3 - - + -
486B PHE* 3.4 45.9 - + + +
498B PHE* 3.8 10.0 - + + -
502B TYR* 3.5 25.1 - + - -
601B C3S 3.6 30.1 - - + -
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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
----------------------------------------------------------
322A HIS* 3.6 24.5 + - + +
325A THR* 5.2 1.4 - - - +
326A GLU* 4.0 15.5 + - - +
329A GLN* 2.7 38.3 + - - +
314B TRP* 2.9 31.0 + - - +
315B GLU 3.3 6.1 - - - +
317B TRP* 1.3 75.2 - - - +
319B ARG* 1.3 65.5 + - - +
321B ALA* 3.5 2.1 + - - +
322B HIS 3.1 16.8 + - - -
493B VAL* 3.5 6.2 - - - +
497B ALA* 3.3 28.0 - - + +
498B PHE* 3.7 19.3 - - + -
499B PRO* 5.1 2.0 - - + +
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN* 4.3 7.3 - - - +
287A LEU* 6.2 2.4 - - - +
322A HIS* 4.0 12.3 - - + +
323A HIS* 5.8 9.3 + - + -
326A GLU* 3.8 25.6 + - - +
308B TYR* 4.3 2.3 + - - -
311B LYS* 3.3 38.5 - - - +
315B GLU* 2.9 35.0 + - - +
316B MET* 3.7 11.4 - - - +
318B GLU* 1.3 74.9 - - - +
320B CYS* 1.3 65.4 - - - +
322B HIS* 3.1 5.5 + - - +
323B HIS* 3.0 30.7 + - + +
378B PHE* 5.1 2.0 - - + -
379B GLU* 2.9 42.3 + - - +
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Residues in contact with CYS 320 (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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316B MET* 3.0 45.5 + - - +
317B TRP 4.0 2.5 - - - +
319B ARG* 1.3 77.4 - - - +
321B ALA* 1.3 56.5 + - - +
323B HIS* 3.3 5.6 + - - +
324B LEU* 2.8 32.6 + - - +
378B PHE* 4.0 15.0 - - - -
388B PHE* 4.2 11.4 - - - -
391B LEU* 4.2 12.8 - - + -
601B C3S 3.4 34.9 - - + +
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TRP* 2.8 23.0 + - + +
318B GLU 3.8 4.5 - - - +
320B CYS* 1.3 73.2 - - - +
322B HIS* 1.3 54.4 + - - +
324B LEU* 3.9 1.3 - - - +
325B THR* 2.7 37.8 + - - -
498B PHE* 3.7 30.1 - - + -
499B PRO* 4.1 8.5 - - + -
502B TYR* 4.0 24.5 - - + -
601B C3S 4.2 2.1 - - + +
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Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 3.7 47.0 + - + +
319A ARG* 3.9 23.2 - - + +
322A HIS* 3.7 37.0 - + + +
323A HIS* 5.5 2.8 + + - -
497A ALA 5.4 2.4 + - - -
318B GLU 3.1 13.8 + - - +
319B ARG 3.1 7.2 + - - +
321B ALA* 1.3 74.5 - - - +
323B HIS* 1.3 84.4 + + - +
325B THR* 3.4 2.9 + - - -
326B GLU* 3.0 33.5 + - - +
499B PRO* 3.8 17.8 - - + +
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Residues in contact with HIS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 5.8 7.5 + - + -
322A HIS* 6.1 0.4 + + - -
323A HIS* 5.5 6.9 - + - -
379A GLU* 5.5 6.7 - - - -
319B ARG* 3.0 26.3 + - - +
320B CYS 3.9 0.2 - - - +
322B HIS* 1.3 89.3 + + - +
324B LEU* 1.3 60.3 + - - +
326B GLU* 3.4 17.6 + - - +
327B ALA* 3.0 22.3 + - - +
378B PHE* 3.7 21.8 - + + -
379B GLU* 2.8 41.8 + - + +
601B C3S 3.5 33.5 - - + +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B CYS 2.8 18.4 + - - +
321B ALA 3.9 3.1 - - - +
323B HIS* 1.3 74.8 - - - +
325B THR* 1.3 59.6 + - - +
327B ALA* 3.2 5.6 + - - +
328B ILE* 2.9 38.6 + - + +
358B MET* 3.8 39.3 - - + -
361B VAL* 3.8 25.1 - - + -
362B LEU* 6.0 0.4 - - + -
479B HIS* 3.8 11.9 - - + +
502B TYR* 3.8 26.0 - - + -
506B PHE* 4.6 1.6 - - + -
601B C3S 4.0 33.3 - - + +
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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
----------------------------------------------------------
318A GLU* 4.8 1.8 - - - +
497A ALA* 4.7 7.0 - - + -
321B ALA 2.7 23.1 + - - -
322B HIS 3.6 4.3 - - - -
324B LEU* 1.3 75.4 - - - +
326B GLU* 1.3 58.1 + - - +
328B ILE* 3.1 11.6 + - - +
329B GLN* 2.8 41.6 + - - +
499B PRO* 3.3 31.5 - - + +
501B LEU* 4.2 24.0 - - + -
502B TYR* 3.3 15.8 + - - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TRP* 4.9 3.8 - - + -
315A GLU* 3.1 34.0 - - + +
318A GLU* 4.4 10.4 + - - +
319A ARG* 3.5 25.2 + - - +
286B GLN* 2.7 31.2 + - - +
322B HIS* 3.0 22.3 + - - +
323B HIS* 3.4 21.7 + - - +
325B THR* 1.3 77.6 - - - +
327B ALA* 1.3 58.9 + - - +
329B GLN* 3.4 18.5 + - - +
330B TYR* 3.0 28.4 + - + -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLN* 3.8 9.1 + - - +
323B HIS 3.0 13.2 + - - +
324B LEU 3.2 8.7 + - - +
326B GLU* 1.3 72.8 - - - +
328B ILE* 1.3 65.0 + - - +
330B TYR* 3.3 8.9 + - - +
331B VAL* 3.2 23.6 + - - +
361B VAL* 4.1 21.1 - - + -
364B ARG* 4.7 1.4 + - - -
601B C3S 3.7 31.6 - - + +
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 2.9 30.0 + - + +
325B THR* 3.1 11.6 + - - +
327B ALA* 1.3 75.0 - - - +
329B GLN* 1.3 59.3 + - - +
331B VAL* 3.0 8.8 + - - +
332B VAL* 2.9 32.8 + - + +
357B ALA* 4.1 19.7 - - + +
358B MET* 5.0 2.2 - - - -
361B VAL* 4.0 15.9 - - + -
501B LEU* 4.0 16.2 - - + -
502B TYR* 5.5 1.8 - - + -
505B LEU* 3.9 23.6 - - + -
506B PHE* 3.7 35.9 - - + -
501Q LEU* 6.1 0.2 - - + -
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TRP* 3.5 27.7 - - + -
318A GLU* 2.7 41.8 + - - +
493A VAL* 4.7 11.7 - - - +
496A ALA* 5.9 1.7 - - + +
497A ALA* 3.7 11.5 - - - +
325B THR* 2.8 25.9 + - - +
326B GLU* 3.5 11.9 - - - +
327B ALA 3.3 0.4 - - - -
328B ILE* 1.3 76.1 - - - +
330B TYR* 1.3 60.6 + - - +
332B VAL* 3.6 9.7 + - - +
333B GLU* 3.3 19.4 + - - +
501B LEU* 4.5 13.7 - - + -
504Q LEU* 5.2 15.7 - - + +
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Residues in contact with TYR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER* 4.9 0.7 + - - -
314A TRP* 3.9 27.2 - + - -
315A GLU* 2.6 27.7 + - - -
283B GLU 5.4 2.0 - - - -
284B THR* 3.3 41.4 - - + +
285B CYS 4.4 4.0 - - - -
286B GLN* 3.5 43.5 + - + +
326B GLU* 3.0 28.0 + - + -
327B ALA* 3.3 9.3 + - - +
328B ILE 3.2 0.8 - - - -
329B GLN* 1.3 75.0 - - - +
331B VAL* 1.3 60.1 + - - +
333B GLU* 3.3 9.1 + - + +
334B PHE* 2.9 23.2 + - - +
364B ARG* 3.8 7.4 - - - +
601B C3S 5.0 1.3 - - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA 3.2 14.1 + - - +
328B ILE* 3.0 11.5 + - - +
330B TYR* 1.3 74.5 - - - +
332B VAL* 1.3 60.2 + - - +
334B PHE* 3.1 12.7 + - + +
335B ALA* 2.8 27.6 + - - +
353B LEU* 4.2 8.7 - - + -
357B ALA* 3.9 28.0 - - + +
360B VAL* 3.8 35.7 - - + -
361B VAL* 3.8 19.3 - - + -
364B ARG* 4.3 12.1 - - - +
425B LEU* 5.3 2.2 - - + -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE* 2.9 30.3 + - + +
329B GLN* 3.8 9.9 - - - +
330B TYR 3.4 0.2 - - - -
331B VAL* 1.3 75.3 - - + +
333B GLU* 1.3 58.1 + - - +
335B ALA* 3.2 4.7 + - - +
336B LYS* 2.9 34.7 + - + +
353B LEU* 4.2 25.6 - - + -
357B ALA* 5.7 0.7 - - + -
501B LEU* 5.1 0.7 - - + -
501Q LEU* 4.2 21.1 - - + -
504Q LEU* 4.3 29.8 - - + +
505Q LEU* 4.2 13.5 - - + -
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B THR* 3.7 9.2 - - + -
329B GLN 3.3 11.4 + - - +
330B TYR* 3.3 14.3 + - + +
331B VAL 3.2 0.6 - - - -
332B VAL* 1.3 76.4 - - - +
334B PHE* 1.3 63.1 + - - +
336B LYS* 3.3 27.1 + - - +
337B ARG* 2.9 70.1 + - - +
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Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.9 7.6 - - + -
280B SER* 3.8 7.5 - - - -
281B TYR* 3.6 36.8 - + + -
284B THR* 3.4 26.4 - - - +
330B TYR 2.9 11.4 + - - +
331B VAL* 3.1 11.4 + - + +
333B GLU* 1.3 75.7 - - - +
335B ALA* 1.3 64.8 + - - +
337B ARG* 3.4 4.4 + - - +
338B LEU* 3.0 48.5 + - + +
360B VAL* 5.2 9.6 - - + -
364B ARG* 3.6 12.6 - - - +
418B ALA 3.9 19.1 - - - -
421B THR* 3.9 13.0 - - - -
422B ALA* 4.1 19.3 - - + -
425B LEU* 4.6 8.1 - - + -
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B VAL 2.8 15.4 + - - +
332B VAL 3.3 8.7 - - - +
334B PHE* 1.3 73.5 - - - +
336B LYS* 1.3 62.2 + - - +
338B LEU* 3.2 10.7 + - - +
341B PHE* 3.2 45.2 - - + +
353B LEU* 3.9 15.7 - - + -
425B LEU* 3.8 27.1 - - + -
505Q LEU* 5.3 0.2 - - + -
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 2.9 24.6 + - + +
333B GLU* 3.7 30.0 + - - +
334B PHE 3.3 0.4 - - - -
335B ALA* 1.3 76.3 - - - +
337B ARG* 1.3 60.5 + - + +
338B LEU 3.6 1.6 + - - +
342B MET* 3.4 33.6 - - + +
504Q LEU 3.2 27.3 + - - +
505Q LEU* 3.7 36.1 + - + -
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER* 4.8 3.8 + - - -
280B SER* 3.0 27.4 + - - +
283B GLU* 3.3 37.4 + - - +
284B THR* 3.8 14.8 - - - +
333B GLU* 2.9 55.4 + - - +
335B ALA 3.3 0.4 - - - -
336B LYS* 1.3 76.5 - - + +
338B LEU* 1.3 62.1 + - - +
339B SER* 3.5 2.3 + - - -
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER 5.8 0.2 - - - -
277B VAL* 3.8 34.3 - - + -
280B SER* 4.1 3.6 - - - +
334B PHE* 3.0 45.2 + - + +
335B ALA 3.2 10.2 + - - +
336B LYS 4.4 2.3 - - - +
337B ARG* 1.3 77.8 - - - +
339B SER* 1.3 69.4 - - - +
340B GLY 3.2 3.1 + - - -
341B PHE* 3.3 17.1 + - + +
342B MET* 4.4 3.3 + - - +
422B ALA* 4.2 9.4 - - + -
425B LEU* 3.9 26.7 - - + -
426B ILE* 4.1 22.4 - - + -
442B LEU* 5.9 0.2 - - + -
446B LEU* 4.8 3.8 - - + -
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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