Contacts of the helix formed by residues 315 - 340 (chain B) in PDB entry 4S15
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 GLN 315 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASN 3.6 10.3 + - - +
314B LYS* 1.3 74.2 - - - +
316B ARG* 1.3 66.8 + - - +
317B GLU* 3.7 22.2 - - - +
318B VAL* 3.1 19.3 + - + +
319B MET* 2.9 21.3 + - - +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LYS 3.7 0.8 + - - -
315B GLN* 1.3 75.2 + - - +
317B GLU* 1.3 60.3 + - - +
319B MET* 3.4 1.4 + - - +
320B TRP* 2.9 49.7 + - + +
393B SER* 3.3 26.4 + - - +
394B LEU 4.2 9.7 + - - +
395B GLY* 4.4 16.0 + - - -
491B PHE* 4.3 6.1 - - + -
494B ILE* 5.1 13.5 - - - +
495B TYR* 4.2 28.4 + - - +
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLN* 3.7 19.5 - - - +
316B ARG* 1.3 82.1 + - - +
318B VAL* 1.3 64.7 + - + +
320B TRP* 3.6 1.4 + - - +
321B GLN* 3.1 29.1 + - - +
491B PHE* 3.7 25.1 - - + -
495B TYR* 3.6 34.3 + - + -
498B ILE* 4.1 27.3 - - + +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A HIS* 3.4 33.1 - - + +
314B LYS* 4.2 22.9 - - + +
315B GLN* 3.1 27.1 + - + +
317B GLU* 1.3 82.0 - - + +
319B MET* 1.3 65.9 + - - +
321B GLN* 3.4 3.1 + - - +
322B LEU* 3.1 19.2 + - - +
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Residues in contact with MET 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B TYR* 4.3 22.4 - - + +
314B LYS* 4.4 8.5 - - + +
315B GLN 2.9 15.1 + - - +
316B ARG 3.9 3.1 - - - +
318B VAL* 1.3 77.1 - - - +
320B TRP* 1.3 64.0 + - - +
322B LEU* 3.4 22.6 + - - +
323B CYS* 3.0 40.6 + - - -
381B PHE* 4.3 8.1 - - + -
390B VAL* 3.4 25.4 - - + +
391B PHE* 3.9 16.2 - - + -
393B SER* 3.9 22.2 - - - -
394B LEU* 3.7 19.5 - - + +
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Residues in contact with TRP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 2.9 35.5 + - + +
317B GLU 3.8 0.4 - - - +
319B MET* 1.3 76.7 - - - +
321B GLN* 1.3 58.1 + - - +
323B CYS* 3.3 2.3 + - - +
324B ALA* 2.9 29.9 + - + +
394B LEU* 3.0 43.3 + - + +
396B CYS* 4.7 2.7 - - + -
484B HIS* 5.0 1.6 - - - -
487B LYS* 3.6 41.3 - - + -
488B LEU* 3.6 24.0 - - + -
491B PHE* 3.5 50.5 - + + -
503B PHE* 4.0 12.0 - + + -
507B TYR* 4.3 4.0 - - - -
601B 4D8 3.4 36.8 - - + -
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Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 3.0 26.5 - - - +
502A HIS* 2.7 37.5 + - - +
317B GLU 3.1 18.2 + - - +
318B VAL* 3.9 4.5 - - - +
319B MET 3.3 0.2 - - - -
320B TRP* 1.3 76.6 - - - +
322B LEU* 1.3 63.4 + - - +
324B ALA* 3.2 3.0 + - - +
325B ILE* 3.0 36.4 + - - +
498B ILE* 4.9 2.9 - - + -
502B HIS* 2.9 38.5 + - + +
503B PHE* 3.7 21.7 - - + -
504B PRO* 5.3 0.2 - - - +
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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
----------------------------------------------------------
501A LEU* 3.5 43.9 - - + +
502A HIS* 3.7 15.3 - - + -
311B TYR* 5.0 1.6 - - + -
314B LYS* 3.7 33.9 - - + -
318B VAL 3.1 14.9 + - - +
319B MET* 3.5 19.5 - - - +
321B GLN* 1.3 80.2 + - - +
323B CYS* 1.3 69.7 + - - +
325B ILE* 3.4 3.5 + - - +
326B LYS* 3.2 29.4 + - + +
381B PHE* 3.5 31.6 - - + -
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Residues in contact with CYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B MET* 3.0 45.5 + - - +
320B TRP 3.7 4.0 - - - +
322B LEU* 1.3 84.3 - - - +
324B ALA* 1.3 57.0 + - - +
326B LYS* 3.3 6.6 + - - +
327B ILE* 3.0 33.6 + - - +
381B PHE* 4.3 4.3 - - - -
391B PHE* 4.1 18.4 - - - -
394B LEU* 4.0 14.4 - - + -
601B 4D8 4.1 25.4 - - + +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TRP* 2.9 18.1 + - + +
321B GLN 3.2 5.1 + - - +
323B CYS* 1.3 75.9 - - - +
325B ILE* 1.3 54.8 + - - +
327B ILE* 3.8 2.6 - - - +
328B THR* 2.6 39.4 + - - -
503B PHE* 3.8 32.1 - - + -
504B PRO* 4.1 9.6 - - + -
507B TYR* 4.0 21.0 - - + +
601B 4D8 5.1 1.9 - - + +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 4.4 2.0 - - - +
500A ARG 5.7 1.1 - - - +
501A LEU 3.9 9.6 - - - +
502A HIS* 3.1 41.5 - - - +
503A PHE 4.0 11.0 - - - +
504A PRO* 4.6 3.1 - - + -
505A PRO* 4.2 25.5 - - + +
508A LYS* 6.2 1.3 - - - +
321B GLN* 3.0 29.5 + - - +
322B LEU 3.6 7.9 - - - +
323B CYS 3.3 0.2 - - - -
324B ALA* 1.3 76.2 - - - +
326B LYS* 1.3 63.4 + - + +
328B THR* 3.4 2.3 + - - -
329B GLU* 3.0 28.8 + - - +
502B HIS 5.3 0.2 - - - +
504B PRO* 4.0 19.7 - - + -
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ARG* 4.1 13.9 + - - +
501A LEU* 3.9 26.8 + - - +
508A LYS* 5.4 2.0 - - - +
322B LEU* 3.2 15.3 + - + +
323B CYS 3.7 7.0 - - - +
325B ILE* 1.3 80.8 - - + +
327B ILE* 1.3 65.3 + - - +
329B GLU* 3.3 16.5 + - - +
330B ALA* 3.2 21.0 + - - +
381B PHE* 4.2 17.0 - - + -
382B ASP* 4.0 37.1 + - - +
601B 4D8 3.9 32.7 + - + +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B CYS 3.0 17.2 + - - +
324B ALA* 3.9 4.0 - - - +
326B LYS* 1.3 74.6 - - - +
328B THR* 1.3 58.8 + - - +
330B ALA* 3.2 8.4 + - - +
331B ILE* 2.9 45.4 + - + +
361B LEU* 3.9 22.0 - - + -
364B VAL* 4.8 3.3 - - + +
365B PHE* 6.0 4.0 - - + -
484B HIS* 4.3 13.5 - - + +
507B TYR* 4.2 15.5 - - + -
511B PHE* 4.8 0.9 - - + -
601B 4D8 3.5 63.7 - - + -
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Residues in contact with THR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ALA 2.6 22.6 + - - -
325B ILE 3.7 4.3 - - - -
327B ILE* 1.3 78.2 - - - +
329B GLU* 1.3 62.7 + - - +
331B ILE* 3.2 9.5 + - + +
332B GLN* 3.0 37.5 + - - +
504B PRO* 3.4 23.8 - - + +
506B LEU* 4.1 26.5 - - + -
507B TYR* 3.2 26.2 - - - +
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A PRO* 3.7 33.8 - - + +
508A LYS* 5.7 2.1 + - - -
289B GLN* 4.3 13.2 - - - +
290B TYR* 5.7 2.9 + - - -
325B ILE* 3.0 16.2 + - - +
326B LYS* 3.5 22.3 + - - +
327B ILE 3.2 0.4 - - - -
328B THR* 1.3 76.3 - - - +
330B ALA* 1.3 62.1 + - - +
332B GLN* 3.2 22.4 + - - +
333B TYR* 3.1 34.6 + - + -
601B 4D8 5.3 0.7 - - - +
499C LEU* 5.1 6.3 - - + +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLN* 3.5 18.4 + - - +
326B LYS 3.2 6.2 + - - +
327B ILE* 3.2 10.0 + - - +
329B GLU* 1.3 78.0 - - - +
331B ILE* 1.3 62.0 + - - +
333B TYR* 3.2 7.6 + - - +
334B VAL* 3.2 21.9 + - + +
364B VAL* 4.0 25.4 - - + -
367B ARG* 4.9 1.0 + - - -
601B 4D8 3.2 24.8 + - + +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 2.9 28.6 + - + +
328B THR* 3.2 11.6 + - - +
330B ALA* 1.3 74.3 - - - +
332B GLN* 1.3 67.3 + - - +
334B VAL* 3.0 7.2 + - - +
335B VAL* 2.9 31.8 + - + +
360B SER* 4.1 15.5 - - - +
361B LEU* 4.5 3.1 - - + -
364B VAL* 3.8 16.2 - - + -
506B LEU* 4.3 6.7 - - + -
507B TYR* 5.3 1.6 - - + -
510B LEU* 3.5 25.4 - - + -
511B PHE* 3.5 40.2 - - + -
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Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN* 4.1 23.1 + - - +
505A PRO* 4.7 9.7 - - - +
506A LEU* 5.9 0.2 - - - +
328B THR* 3.0 26.7 + - + +
329B GLU* 3.2 22.1 + - - +
331B ILE* 1.3 75.9 - - - +
333B TYR* 1.3 61.5 + - - +
335B VAL* 3.5 7.0 + - - +
336B GLU* 3.3 26.7 + - - +
506B LEU* 4.1 19.7 - - + -
499C LEU* 3.8 40.6 - - + +
502C LEU* 3.8 3.5 - - + +
503C LEU* 4.8 6.9 - - + +
503D LEU* 5.8 5.8 - - + +
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU 5.8 0.7 - - - -
287B THR* 3.3 35.8 - - - +
288B CYS 4.6 2.2 - - - -
289B GLN* 3.5 42.2 - - + +
329B GLU* 3.1 36.1 + - + -
330B ALA 3.2 7.7 + - - +
331B ILE 3.1 0.4 - - - -
332B GLN* 1.3 75.8 - - + +
334B VAL* 1.3 59.5 + - - +
336B GLU* 3.2 2.3 + - - +
337B PHE* 2.9 23.0 + - - +
367B ARG* 3.8 7.6 - - - +
498C THR* 3.7 15.0 - - + +
499C LEU* 3.7 36.3 + - + +
502C LEU* 3.8 34.5 - - + -
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA* 3.2 14.5 + - + +
331B ILE* 3.0 9.5 + - - +
333B TYR* 1.3 75.2 - - - +
335B VAL* 1.3 60.8 + - - +
337B PHE* 3.1 9.8 + - + +
338B ALA* 2.9 27.5 + - - +
356B LEU* 5.1 2.5 - - + -
360B SER* 3.9 21.3 - - - +
363B VAL* 3.7 41.3 - - + -
364B VAL* 3.8 21.5 - - + -
367B ARG* 4.2 13.9 - - - +
428B LEU* 5.0 8.3 - - + -
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 2.9 32.3 + - + +
332B GLN* 3.7 10.8 - - - +
334B VAL* 1.3 75.0 - - - +
336B GLU* 1.3 64.3 + - - +
338B ALA* 3.3 7.4 + - - +
339B LYS* 3.1 42.5 + - + +
356B LEU* 4.5 20.6 - - + -
360B SER* 5.4 1.1 - - - -
506B LEU* 4.7 7.9 - - + -
510B LEU* 5.3 2.7 - - + -
500D LEU* 4.6 11.4 - - + -
503D LEU* 4.4 17.7 - - + -
504D LEU* 4.3 14.6 - - + -
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LYS* 5.8 0.3 + - - -
287B THR* 3.9 5.6 - - + -
332B GLN 3.3 14.0 + - - +
333B TYR 3.2 7.5 + - - +
334B VAL 3.2 0.2 - - - -
335B VAL* 1.3 80.6 - - - +
337B PHE* 1.3 64.9 + - - +
339B LYS* 3.1 40.3 + - - +
340B ARG* 3.3 41.4 + - - +
502C LEU* 3.6 42.8 - - + +
503C LEU* 4.3 16.8 - - + +
503D LEU* 4.6 8.8 - - - +
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Residues in contact with PHE 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.9 14.6 - - + -
283B SER* 3.8 7.6 - - - -
284B HIS* 3.7 37.2 - + + -
287B THR* 3.4 21.9 - - - +
333B TYR 2.9 10.4 + - - +
334B VAL* 3.2 11.9 - - + +
336B GLU* 1.3 76.3 - - - +
338B ALA* 1.3 65.4 + - - +
340B ARG* 3.1 14.2 + - - +
341B ILE* 3.4 34.3 + - + +
363B VAL* 4.6 9.9 - - + -
367B ARG* 3.7 12.1 - - - +
421B ALA 3.7 20.9 - - - -
424B SER* 3.8 23.1 - - - -
425B ALA 4.0 4.9 - - - -
428B LEU* 4.3 8.5 - - + -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B VAL 2.9 10.5 + - - +
335B VAL 3.5 9.2 - - - +
337B PHE* 1.3 75.5 - - - +
339B LYS* 1.3 63.1 + - - +
341B ILE* 3.0 17.3 + - - +
344B PHE* 3.3 33.5 - - + +
356B LEU* 3.8 18.8 - - + -
428B LEU* 3.6 29.8 - - + -
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Residues in contact with LYS 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLU* 5.5 1.2 + - - -
339A LYS* 4.9 12.3 - - - +
335B VAL* 3.1 27.8 + - + +
336B GLU* 3.1 39.4 + - - +
337B PHE 3.3 0.2 - - - -
338B ALA* 1.3 75.7 - - - +
340B ARG* 1.3 62.6 + - + +
341B ILE 3.7 1.9 + - - +
344B PHE* 4.2 1.5 - - + -
345B MET* 3.3 41.8 - - + +
503D LEU* 2.8 28.6 + - - +
504D LEU* 3.8 21.3 - - + +
----------------------------------------------------------
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Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASN* 5.1 2.8 - - - +
283B SER* 3.3 27.0 + - - +
286B GLU* 3.1 44.0 + - - +
287B THR* 4.0 16.8 - - - +
336B GLU* 3.3 25.6 + - - +
337B PHE 3.1 7.7 + - - +
338B ALA 3.1 1.0 - - - -
339B LYS* 1.3 79.2 - - + +
341B ILE* 1.3 63.2 + - - +
342B ASP* 3.5 9.5 + - - +
502C LEU* 3.7 32.3 + - - +
505C GLY* 3.8 22.0 + - - -
506C HIS 5.7 3.4 - - - -
----------------------------------------------------------
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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