Contacts of the helix formed by residues 313 - 344 (chain B) in PDB entry 1YAA
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 PRO 313 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLU 3.1 12.1 - - - +
312B THR* 1.3 84.9 - - + +
314B GLU* 1.3 64.4 + - + +
316B THR* 3.9 9.4 - - - +
317B GLU* 3.3 25.3 + - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR* 3.2 8.9 - - + +
313B PRO* 1.3 82.8 - - + +
315B LEU* 1.3 66.5 + - + +
317B GLU* 3.7 13.0 - - - +
318B GLN* 3.1 25.1 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B SER* 3.7 7.5 - - - +
55B ALA* 3.7 25.1 - - + -
56B ALA* 3.6 35.9 - - + -
59B LEU* 3.9 18.8 - - + -
308B LYS* 4.1 13.2 - - + +
309B LEU* 3.5 20.6 - - + +
312B THR* 3.0 19.3 + - + +
314B GLU* 1.3 81.5 - - + +
316B THR* 1.3 60.6 + - - +
317B GLU 3.2 0.4 - - - -
318B GLN* 4.2 5.2 - - + -
319B TRP* 2.9 29.3 + - - +
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 6.4 0.9 - - + -
309B LEU 2.5 22.1 + - - +
310B LEU* 3.3 22.2 + - + +
312B THR 2.9 16.0 + - - -
313B PRO* 4.0 8.9 - - - +
315B LEU* 1.3 77.6 - - - +
317B GLU* 1.3 60.6 + - - +
319B TRP* 3.5 12.6 + - + +
320B HIS* 3.0 52.8 + - + +
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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
----------------------------------------------------------
313B PRO 3.3 18.6 + - - +
314B GLU* 3.7 16.8 - - - +
315B LEU 3.2 0.2 - - - -
316B THR* 1.3 78.2 - - - +
318B GLN* 1.3 64.4 + - - +
320B HIS* 3.1 31.7 + - - +
321B LYS* 3.2 37.9 + - - +
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PRO* 4.1 12.7 - - + +
52B SER* 3.8 24.7 - - - +
55B ALA* 6.4 0.4 - - + -
314B GLU 3.1 17.0 + - - +
315B LEU* 3.9 8.7 - - + +
317B GLU* 1.3 78.5 - - - +
319B TRP* 1.3 57.4 - - - +
321B LYS* 3.2 26.3 + - - +
322B ASP* 2.8 56.0 + - - +
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Residues in contact with TRP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.7 19.7 - - + -
52B SER* 3.7 15.4 - - - +
86B ILE* 4.0 23.3 - - + -
233B LEU* 3.6 24.7 - - + -
256B PHE* 4.1 13.2 - + - -
259B ASN* 2.9 40.6 + - - -
260B ALA* 3.7 6.1 - - + +
306B VAL* 6.1 0.2 - - + -
309B LEU* 4.0 20.9 - - + -
310B LEU* 3.7 25.4 - - + -
315B LEU 2.9 20.2 + - - +
316B THR* 3.5 8.3 - - + +
317B GLU 3.2 0.2 - - - -
318B GLN* 1.3 72.7 - - - +
320B HIS* 1.3 77.2 + + - +
322B ASP* 3.1 1.9 + - - +
323B MET* 3.0 43.2 + - + +
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Residues in contact with HIS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLY 4.9 1.2 - - - +
233B LEU* 3.5 26.8 - - + +
316B THR* 3.0 38.2 + - + +
317B GLU* 3.1 26.2 + - - +
319B TRP* 1.3 80.2 - + - +
321B LYS* 1.3 64.0 + - + +
323B MET* 3.3 20.6 + - + +
324B VAL* 3.2 26.5 + - - +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLU* 3.2 36.8 + - - +
318B GLN* 3.4 30.4 + - - +
319B TRP 3.2 0.6 - - - -
320B HIS* 1.3 76.7 - - + +
322B ASP* 1.3 54.2 + - - +
324B VAL* 3.2 9.6 + - - +
325B THR* 2.7 36.9 + - - +
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 3.9 4.4 - - + -
50B LEU* 3.5 20.9 - - + +
51B PRO* 3.3 21.5 - - - +
52B SER* 2.7 40.7 + - - -
318B GLN* 2.8 36.3 + - - -
319B TRP 3.1 7.4 + - - +
321B LYS* 1.3 77.1 - - - +
323B MET* 1.3 57.9 + - - +
325B THR* 3.3 9.2 + - - -
326B MET* 3.1 33.4 + - - +
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Residues in contact with MET 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLN 4.3 2.5 - - - +
227B GLY* 4.3 17.6 - - - +
228B PHE* 5.2 3.2 - - + -
231B GLY 4.9 8.1 - - - +
233B LEU* 3.7 36.6 - - + -
259B ASN* 3.7 41.1 - - + +
319B TRP* 3.0 45.6 + - + +
320B HIS* 3.6 15.5 - - + +
321B LYS 3.2 0.2 - - - -
322B ASP* 1.3 78.0 - - - +
324B VAL* 1.3 54.1 + - - +
325B THR 3.2 0.2 - - - -
326B MET* 3.9 9.6 - - + +
327B SER* 2.7 37.7 + - - -
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLY* 4.0 19.5 - - - +
320B HIS 3.2 15.7 + - - +
321B LYS* 3.2 9.4 + - - +
323B MET* 1.3 74.4 - - - +
325B THR* 1.3 60.1 + - - +
327B SER* 3.4 6.9 + - - +
328B SER* 2.9 41.3 + - - -
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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
----------------------------------------------------------
40B TYR* 4.8 5.2 - - - +
48B TRP* 3.6 28.1 - - + -
321B LYS* 2.7 20.3 + - - +
322B ASP* 3.3 14.9 + - - -
324B VAL* 1.3 77.6 - - - +
326B MET* 1.3 58.6 - - - +
328B SER* 3.0 18.3 + - - -
329B ARG* 3.3 13.6 + - + +
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Residues in contact with MET 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.6 44.8 - - + -
48B TRP* 3.6 14.4 - - + -
50B LEU* 3.8 27.4 - - + -
228B PHE* 3.8 30.1 - - + -
258B LYS 4.0 5.6 - - - +
259B ASN 3.6 24.5 - - - +
261B GLY* 6.0 0.2 - - - -
322B ASP 3.1 17.8 + - - +
323B MET* 3.9 9.9 - - + +
324B VAL 3.3 0.2 - - - -
325B THR* 1.3 73.9 - - - +
327B SER* 1.3 65.9 + - - +
328B SER 3.1 1.2 + - - -
329B ARG 3.2 9.4 + - - -
330B ILE* 3.2 19.7 + - - +
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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
----------------------------------------------------------
227B GLY 4.3 12.6 - - - -
228B PHE* 4.4 23.5 - - - -
229B ALA 6.2 0.2 - - - -
230B THR 5.1 0.8 + - - -
231B GLY* 3.9 14.1 - - - -
323B MET 2.7 23.8 + - - -
324B VAL* 3.4 10.7 + - - +
326B MET* 1.3 76.4 - - - +
328B SER* 1.3 58.7 + - - +
330B ILE* 4.1 7.1 - - - +
331B THR* 3.0 25.5 + - - -
358B GLY 6.1 0.2 - - - -
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 2.9 29.7 + - - -
325B THR* 3.0 14.2 + - - -
327B SER* 1.3 77.7 + - - +
329B ARG* 1.3 59.5 + - - +
330B ILE 3.2 0.2 - - - -
331B THR* 3.3 7.5 + - - -
332B LYS* 3.1 26.9 + - - +
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Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.2 26.0 + - + +
41B ARG 3.0 20.6 + - - -
42B ASP* 3.6 13.6 + - - +
43B ASP* 3.9 21.3 - - + +
325B THR 3.3 6.9 + - - +
326B MET 3.2 3.6 + - - +
328B SER* 1.3 79.6 + - - +
330B ILE* 1.3 62.9 + - - +
332B LYS* 3.4 11.8 + - + +
333B MET* 3.2 36.3 + - + +
389B ILE 4.3 0.8 + - - -
390B ALA* 2.7 39.8 + - - +
392B LEU 2.8 21.8 + - - -
393B ASN* 3.8 11.9 - - - +
394B GLN 5.1 0.4 - - - +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 4.4 13.7 - - + -
228B PHE* 4.0 26.2 - - + -
326B MET 3.2 16.6 + - - +
327B SER* 4.1 7.0 - - - +
328B SER 3.2 0.2 - - - -
329B ARG* 1.3 77.9 - - - +
331B THR* 1.3 56.0 + - - +
333B MET* 3.4 1.0 + - - -
334B ARG* 3.1 41.7 + - - +
358B GLY 3.5 26.9 - - - +
359B MET* 4.1 20.2 - - + -
389B ILE* 3.3 30.2 - - + +
390B ALA* 4.6 11.9 - - + +
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Residues in contact with THR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B SER 3.0 14.8 + - - -
328B SER* 3.3 10.9 + - - -
329B ARG 3.3 0.2 - - - -
330B ILE* 1.3 77.2 - - - +
332B LYS* 1.3 63.2 + - - +
334B ARG* 3.1 21.5 + - - +
335B HIS* 2.9 44.0 - - + +
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Residues in contact with LYS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER 3.1 16.3 + - - +
329B ARG* 3.7 13.2 - - + +
330B ILE 3.4 0.2 - - - -
331B THR* 1.3 77.3 - - - +
333B MET* 1.3 68.3 + - + +
335B HIS* 3.5 7.8 + - - +
336B ALA* 2.9 25.9 + - + +
394B GLN* 4.5 18.8 - - - +
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Residues in contact with MET 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG* 3.2 28.5 + - + +
330B ILE* 4.7 0.4 - - - -
331B THR 3.2 0.2 - - - -
332B LYS* 1.3 92.5 - - + +
334B ARG* 1.3 58.6 + - - +
335B HIS 3.2 1.6 - - - -
336B ALA* 3.7 18.7 - - + +
337B LEU* 2.9 31.9 + - - +
389B ILE* 3.7 21.8 - - + +
392B LEU* 3.6 22.2 - - + +
393B ASN* 3.7 15.9 - - - -
394B GLN* 4.1 22.0 - - + +
397B VAL* 3.2 29.8 - - + -
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 3.1 31.7 + - - +
331B THR* 3.1 17.9 + - - +
333B MET* 1.3 76.2 - - - +
335B HIS* 1.3 59.4 + - + +
338B ARG* 3.2 21.8 + - - +
353B ILE* 3.0 42.2 + - + +
354B VAL* 3.2 23.4 - - + +
356B GLN* 3.3 23.6 + - - +
357B CYS* 3.4 8.5 - - - +
358B GLY 3.0 32.1 + - - +
359B MET 3.9 2.4 - - - -
360B PHE 2.8 34.5 + - - +
361B SER* 4.0 4.4 - - - -
389B ILE* 3.9 17.9 - - + +
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Residues in contact with HIS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B THR* 2.9 41.7 + - + +
332B LYS* 3.6 9.4 - - - +
334B ARG* 1.3 79.8 - - + +
336B ALA* 1.3 59.4 + - - +
338B ARG* 3.2 17.4 + - - +
339B ASP* 2.9 44.9 + - - +
354B VAL* 3.6 27.2 + - + +
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LYS* 2.9 19.2 + - + +
333B MET* 3.7 24.7 - - + +
335B HIS* 1.3 76.0 - - - +
337B LEU* 1.3 60.7 - - - +
339B ASP* 3.8 4.6 + - - +
340B HIS* 2.9 37.1 + - + -
394B GLN* 5.2 7.0 - - - +
397B VAL* 3.8 12.6 - - + -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 6.3 0.9 - - + -
333B MET 2.9 18.8 + - - +
334B ARG 4.0 3.1 - - - +
336B ALA* 1.3 74.7 - - - +
338B ARG* 1.3 65.6 + - - +
340B HIS* 3.6 0.9 + - - +
341B LEU* 3.3 36.0 + - + +
353B ILE* 4.3 22.9 - - + -
361B SER* 6.3 0.2 - - - -
363B THR* 6.3 3.4 - - + -
389B ILE* 5.0 5.8 - - + -
392B LEU* 3.6 24.2 - - + -
397B VAL* 3.8 14.3 - - + +
400B VAL* 4.5 6.3 - - + -
401B ALA* 4.0 28.7 - - + +
404B ILE* 4.3 16.6 - - + -
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ARG 3.2 19.8 + - - +
335B HIS* 3.2 23.5 + - - +
337B LEU* 1.3 78.2 - - - +
339B ASP* 1.3 83.5 + - - +
341B LEU* 3.3 6.8 + - - +
342B VAL* 3.0 48.3 + - - +
350B TRP* 3.4 30.1 - - + +
351B ASP* 2.9 30.1 + - - -
353B ILE* 4.5 10.0 - - + +
354B VAL* 3.7 21.8 - - + +
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Residues in contact with ASP 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B HIS* 2.9 29.5 + - - +
336B ALA* 4.2 5.5 + - - +
338B ARG* 1.3 104.4 + - - +
340B HIS* 1.3 60.8 + - + +
342B VAL* 3.7 7.9 - - - +
343B LYS* 2.9 29.1 + - - +
----------------------------------------------------------
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Residues in contact with HIS 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ALA* 2.9 33.2 + - + +
337B LEU* 3.9 2.7 - - - +
338B ARG 3.3 0.2 - - - -
339B ASP* 1.3 78.9 - - + +
341B LEU* 1.3 58.9 + - - +
343B LYS* 3.3 6.6 + - - +
344B LEU* 2.8 37.8 + - + +
394B GLN* 4.9 9.9 + - - -
397B VAL* 4.2 8.8 - - + +
398B GLU* 3.3 53.9 + - + +
401B ALA* 3.5 20.3 - - + +
----------------------------------------------------------
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.3 25.1 - - + +
338B ARG 3.3 7.1 + - - +
339B ASP 3.3 0.2 - - - -
340B HIS* 1.3 74.2 - - - +
342B VAL* 1.3 60.7 + - - +
344B LEU* 3.4 1.7 + - - -
345B GLY 2.9 21.5 + - - -
346B THR* 3.0 41.1 + - + +
350B TRP* 4.1 25.8 - - + -
353B ILE* 3.9 25.4 - - + -
401B ALA* 3.4 28.9 - - + +
404B ILE* 3.8 26.0 - - + -
405B ASP 4.4 0.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG* 3.0 42.6 + - + +
339B ASP* 3.7 8.1 - - - +
340B HIS 3.3 0.2 - - - -
341B LEU* 1.3 78.5 - - + +
343B LYS* 1.3 58.2 + - - +
345B GLY* 3.2 17.3 + - - -
346B THR 5.9 0.4 - - - -
350B TRP* 5.6 8.1 - - + +
351B ASP* 5.3 1.8 - - - +
----------------------------------------------------------
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASP 2.9 18.2 + - - +
340B HIS* 3.6 7.4 - - - +
342B VAL* 1.3 75.8 - - - +
344B LEU* 1.3 60.3 + - + +
345B GLY* 3.0 6.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B HIS* 2.8 27.6 + - + +
341B LEU* 3.7 8.3 - - - +
343B LYS* 1.3 77.6 - - + +
345B GLY* 1.3 61.1 + - - +
346B THR* 3.3 6.5 - - - +
398B GLU* 6.0 0.9 - - + -
401B ALA* 3.1 43.3 - - + +
402B LYS* 3.7 30.3 - - + +
405B ASP* 3.9 15.1 - - + +
409B ARG* 3.5 11.4 + - - -
----------------------------------------------------------
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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).
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