Contacts of the helix formed by residues 316 - 341 (chain B) in PDB entry 4OIV
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 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR 3.9 1.4 + - - -
315B LEU* 1.3 74.4 - - - +
317B HIS* 1.3 59.2 + - - +
318B GLU* 3.0 21.2 + - - +
319B ASP* 3.0 27.2 + - - +
320B GLN* 2.9 25.3 + - - +
403B LYS* 2.9 36.9 + - - -
404B ASP* 5.9 2.5 - - + -
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Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 4.0 20.0 - - + -
470A GLU* 2.9 30.4 + - + -
315B LEU 3.4 2.0 + - - -
316B ASP* 1.3 70.6 + - - +
318B GLU* 1.3 68.9 + - + +
320B GLN* 3.4 22.3 + - - +
321B ILE* 3.1 33.7 + - + +
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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
----------------------------------------------------------
316B ASP* 3.0 8.7 + - - +
317B HIS* 1.3 84.2 - - + +
319B ASP* 1.3 61.5 + - - +
321B ILE* 3.4 13.0 + - + +
322B ALA* 3.1 23.0 + - - +
401B TYR 5.1 1.0 - - - +
403B LYS* 2.9 30.1 + - - +
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 5.1 8.5 - - + -
316B ASP* 3.0 30.9 + - + +
318B GLU* 1.3 74.3 - - - +
320B GLN* 1.3 62.3 + - - +
322B ALA* 3.2 4.4 + - - +
323B LEU* 2.8 34.3 + - - +
401B TYR 3.9 2.4 - - - +
402B ILE* 3.6 19.2 - - + +
403B LYS* 2.8 38.3 + - - +
404B ASP* 3.0 32.6 + - - +
408B VAL* 5.6 2.7 - - + -
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Residues in contact with GLN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 3.6 16.8 - - + +
312B PHE* 3.4 59.9 + - + +
313B GLN* 3.9 25.0 + - - +
315B LEU* 2.8 29.2 + - + +
316B ASP 2.9 12.9 + - - +
317B HIS* 3.6 23.3 + - - +
319B ASP* 1.3 76.8 - - - +
321B ILE* 1.3 63.1 + - - +
323B LEU* 3.7 0.6 - - - +
324B LEU* 3.1 25.1 + - - +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PRO* 3.7 31.2 - - + -
469A LEU* 3.9 28.8 + - + +
470A GLU* 3.7 22.9 - - - +
317B HIS* 3.1 25.4 + - + +
318B GLU* 3.6 14.1 - - + +
320B GLN* 1.3 80.7 - - - +
322B ALA* 1.4 58.6 + - - +
324B LEU* 3.4 1.7 + - - +
325B LYS* 2.9 35.9 + - + +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU 3.1 16.6 + - - +
319B ASP* 3.2 0.4 + - - -
321B ILE* 1.4 79.8 - - + +
323B LEU* 1.3 57.8 + - - +
325B LYS* 3.4 11.6 + - - +
326B GLY* 2.9 26.0 + - - -
399B ARG* 4.4 1.4 - - - +
400B GLN 3.9 13.5 - - - +
401B TYR* 3.6 24.5 - - + +
402B ILE* 3.6 20.9 - - + -
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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
----------------------------------------------------------
312B PHE* 3.9 14.8 - - + -
315B LEU* 3.8 28.5 - - + -
319B ASP 2.8 19.6 + - - +
320B GLN 3.7 4.3 - - - +
321B ILE 3.3 0.2 - - - -
322B ALA* 1.3 68.9 - - - +
324B LEU* 1.3 67.2 + - - +
326B GLY* 3.3 1.0 + - - -
327B SER* 3.0 30.9 + - - -
394B ILE* 3.5 19.5 - - + +
395B LEU* 3.9 18.4 - - + -
396B SER 3.2 29.8 - - - +
399B ARG* 3.8 12.7 - - + +
402B ILE* 3.8 13.4 - - + +
408B VAL* 4.1 15.3 - - + -
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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
----------------------------------------------------------
468A LEU* 3.9 22.9 - - + -
469A LEU* 3.6 47.6 - - + +
302B LEU* 4.6 13.0 - - + -
303B VAL* 4.1 15.7 - - + -
306B THR* 3.9 33.7 - - + +
320B GLN 3.1 14.0 + - - +
321B ILE* 4.0 2.7 - - - +
323B LEU* 1.3 77.2 - - - +
325B LYS* 1.3 67.1 + - - +
327B SER* 4.7 2.9 - - - -
328B ALA* 2.9 36.0 + - + +
394B ILE* 5.5 4.7 - - + -
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PRO* 6.5 0.7 - - + -
468A LEU* 5.4 5.8 - - - +
321B ILE* 2.9 25.5 + - + +
322B ALA* 3.6 11.0 - - - +
324B LEU* 1.3 79.9 - - - +
326B GLY* 1.3 61.7 + - - +
328B ALA* 3.8 10.4 + - - +
329B VAL 5.0 0.3 + - - -
401B TYR* 3.9 36.4 - - - -
453B GLU* 4.2 19.3 - - - +
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Residues in contact with GLY 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA 2.9 19.2 + - - -
323B LEU 3.8 1.6 - - - -
325B LYS* 1.3 75.0 - - - +
327B SER* 1.4 58.7 + - - +
328B ALA 3.6 0.2 - - - -
329B VAL* 5.2 1.4 + - - +
330B GLU* 4.6 4.5 + - - +
399B ARG* 3.4 35.1 + - - -
400B GLN 5.6 2.5 - - - -
449B HIS* 5.7 3.3 - - - -
453B GLU* 5.9 0.7 - - - -
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Residues in contact with SER 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU 3.0 14.9 + - - -
324B LEU* 4.2 2.5 - - - -
326B GLY* 1.4 76.4 - - - +
328B ALA* 1.3 66.1 + - - +
329B VAL 3.3 2.4 + - - -
330B GLU* 3.3 5.7 + - - +
331B ALA* 3.0 22.8 + - - +
393B VAL* 3.2 5.6 + - - +
394B ILE* 2.9 44.9 + - - -
399B ARG* 2.8 27.5 + - - +
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 3.7 26.0 - - + -
302B LEU* 3.8 17.3 - - + +
324B LEU* 2.9 19.8 + - + +
325B LYS* 3.8 6.4 + - - +
326B GLY 3.6 1.2 - - - -
327B SER* 1.3 76.7 - - - +
329B VAL* 1.3 65.2 + - + +
331B ALA 3.8 0.2 - - - -
332B MET* 2.8 28.1 + - - +
453B GLU* 6.0 1.1 - - - +
456B MET* 3.6 14.1 - - + -
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS 5.0 1.2 + - - -
326B GLY 5.2 1.7 + - - +
327B SER 3.4 0.8 - - - -
328B ALA* 1.3 76.0 - - - +
330B GLU* 1.3 59.5 + - - +
332B MET* 3.2 4.3 + - - +
333B PHE* 2.8 47.7 + - + -
449B HIS* 3.9 25.8 - - + +
452B ALA* 3.5 29.4 - - + -
453B GLU* 3.4 36.8 - - + +
456B MET* 3.4 22.4 - - + -
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLY 4.6 3.6 + - - +
327B SER 3.3 5.6 + - - +
329B VAL* 1.3 75.9 - - - +
331B ALA* 1.3 63.4 + - - +
333B PHE* 3.2 10.3 + - + +
334B LEU* 3.0 23.6 + - - +
393B VAL* 3.9 19.3 - - + +
399B ARG* 2.9 37.7 + - - +
441B LEU 4.9 1.6 - - - +
444B LEU* 4.0 23.8 - - + +
445B ARG* 3.6 27.2 + - - +
449B HIS* 2.7 34.7 + - + +
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 3.7 29.5 - - + +
327B SER 3.0 17.5 + - - +
328B ALA 3.8 2.0 - - - +
330B GLU* 1.3 78.4 - - - +
332B MET* 1.3 58.2 - - - +
334B LEU* 3.4 5.1 + - - +
335B ARG* 3.0 26.5 + - - +
390B THR* 4.7 8.2 - - + +
393B VAL* 4.2 14.2 - - + +
394B ILE* 4.0 17.9 - - + -
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Residues in contact with MET 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA* 3.5 14.4 - - + +
298B HIS* 3.8 19.3 - - + +
299B VAL* 3.5 43.5 - - + -
302B LEU* 4.0 12.8 - - + -
328B ALA 2.8 25.8 + - - +
329B VAL 3.5 4.7 - - - +
331B ALA* 1.3 70.1 - - - +
333B PHE* 1.3 60.0 + - - +
335B ARG* 3.2 7.0 + - - +
336B SER* 2.8 30.7 + - - -
456B MET* 3.8 13.2 - - + -
501B XX9 3.7 46.8 - - + -
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Residues in contact with PHE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 2.8 39.7 + - + -
330B GLU* 3.2 12.8 + - + +
332B MET* 1.3 74.2 - - + +
334B LEU* 1.3 63.7 + - - +
336B SER* 2.7 23.1 + - - -
337B ALA* 3.2 9.2 + - - +
369B MET* 4.0 18.1 - - + +
372B PHE* 4.6 2.4 - - - -
444B LEU* 3.9 31.0 - - + -
447B PHE* 4.1 28.5 - + + -
448B ASN 4.2 13.5 - - - -
449B HIS* 5.0 3.8 - + - -
452B ALA* 3.8 21.1 - - + -
501B XX9 3.6 33.0 - + + -
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU 3.0 11.2 + - - +
331B ALA* 3.5 9.4 - - - +
333B PHE* 1.3 74.4 - - - +
335B ARG* 1.3 64.3 + - - +
337B ALA* 3.1 19.1 + - - +
338B GLU 3.6 3.5 + - - -
372B PHE* 4.2 24.2 - - + -
376B ILE* 4.8 6.5 - - + -
381B MET* 5.7 0.4 - - - -
386B TYR* 3.6 30.0 - - + +
389B LEU* 4.1 20.0 - - + +
390B THR* 3.4 43.1 - - - +
393B VAL* 4.5 4.5 - - + -
440B ARG* 5.9 0.4 - - + -
441B LEU* 4.2 21.3 - - + -
444B LEU* 4.4 4.8 - - + +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 3.0 46.2 + - - +
267B GLN* 2.9 43.2 + - - +
298B HIS* 3.8 42.0 - - + +
301B VAL* 3.5 31.1 + - - +
302B LEU* 4.7 9.4 - - - +
305B PHE* 4.8 9.7 - - - +
331B ALA 3.0 15.1 + - - +
332B MET* 3.5 12.6 - - - +
334B LEU* 1.3 74.0 - - - +
336B SER* 1.3 67.2 + - - +
337B ALA 3.1 0.5 + - - -
338B GLU* 3.2 23.4 + - - +
339B ILE* 3.5 9.8 + - + +
386B TYR* 5.6 0.7 - - - -
390B THR* 5.2 6.4 + - - +
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B HIS* 4.8 0.4 - - - -
332B MET 2.8 13.8 + - - -
333B PHE* 2.7 21.2 + - - -
335B ARG* 1.3 78.4 - - - +
337B ALA* 1.3 61.0 + - - +
339B ILE* 3.2 14.4 + - - +
340B PHE* 3.3 19.2 - - - -
369B MET* 3.6 5.0 - - - +
373B TYR* 2.6 28.4 + - - -
501B XX9 3.5 39.9 - - - -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PHE 3.2 7.4 + - - +
334B LEU* 3.1 11.6 + - + +
335B ARG 3.0 0.8 - - - -
336B SER* 1.3 78.1 + - - +
338B GLU* 1.3 56.9 + - - +
340B PHE* 2.9 20.1 + - - +
341B ASN* 3.3 15.8 + - - -
372B PHE* 4.2 15.0 - - + -
373B TYR* 3.5 30.1 - - + -
376B ILE* 4.4 11.0 - - + -
386B TYR* 3.5 11.9 - - + +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 2.6 31.7 + - - -
267B GLN* 2.4 34.5 + - - -
334B LEU 3.6 0.8 + - - -
335B ARG* 3.2 17.5 + - - +
337B ALA* 1.3 78.7 - - - +
339B ILE* 1.3 66.5 + - + +
340B PHE 3.4 0.9 + - - -
341B ASN* 3.4 15.1 + - - +
383B GLN* 4.4 7.7 - - - +
386B TYR* 3.2 38.4 + - + -
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLN* 5.4 2.9 - - - +
269B MET* 5.2 3.4 - - + -
294B MET* 4.4 10.8 - - + -
298B HIS* 3.2 39.9 - - + +
335B ARG* 3.5 10.5 + - + +
336B SER* 3.2 9.9 + - - +
338B GLU* 1.3 88.6 - - + +
340B PHE* 1.3 68.3 + - + +
349B SER* 4.0 13.2 + - - -
352B LEU* 3.7 30.1 - - + -
501B XX9 4.7 2.5 - - + -
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Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER 3.3 18.2 - - - -
337B ALA 2.9 9.3 + - - +
339B ILE* 1.3 77.3 - - + +
341B ASN* 1.3 75.1 + - - +
349B SER* 4.0 36.5 + - - -
352B LEU* 3.7 15.5 - - + -
353B GLU* 4.1 6.5 - - + -
356B ILE* 3.3 27.6 - - + -
370B PHE* 3.6 24.5 - + + -
373B TYR* 3.3 32.5 - + + -
501B XX9 3.9 17.3 - - + -
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ALA 3.3 12.6 + - - +
338B GLU* 3.4 13.2 + - - +
339B ILE 3.5 0.2 - - - -
340B PHE* 1.3 104.5 + - - +
373B TYR* 2.8 33.2 + - - +
376B ILE* 3.4 18.0 - - + +
377B GLY* 3.6 13.3 + - - -
386B TYR* 4.5 9.6 - - + +
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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