Contacts of the helix formed by residues 313 - 344 (chain B) in PDB entry 1AHF
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 313 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B SER 3.9 4.5 + - - +
312B ASN* 1.3 72.6 + - - +
314B ALA* 1.3 62.3 + - - +
316B ARG* 3.9 8.6 - - - +
317B ALA* 3.1 23.4 + - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 2.7 16.1 + - - +
313B ASP* 1.3 73.4 - - - +
315B LEU* 1.3 64.2 + - + +
317B ALA* 3.1 7.9 + - - +
318B ILE* 3.0 33.4 + - + +
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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* 3.9 15.4 - - - +
55B LYS* 3.9 33.2 - - + -
56B ALA* 4.3 12.8 - - + +
59B TYR* 6.2 1.1 - - + -
308B THR* 4.2 22.7 - - + +
309B ILE* 3.9 27.2 - - + +
312B ASN* 2.8 29.1 + - + +
314B ALA* 1.3 70.8 - - + +
316B ARG* 1.3 60.1 + - - +
318B ILE* 3.1 12.7 + - + +
319B TRP* 2.8 30.5 + - - +
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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
----------------------------------------------------------
82B CYS* 6.0 1.2 + - - +
86B LEU* 4.2 22.6 - - - +
233B LEU* 4.2 9.9 - - - +
234B GLU* 5.0 7.3 + - - -
309B ILE* 3.2 18.6 + - - +
310B LEU* 3.8 43.2 + - - +
312B ASN 2.9 21.9 + - - +
313B ASP* 3.9 10.1 - - - +
315B LEU* 1.3 76.8 - - - +
317B ALA* 1.3 59.0 + - - +
319B TRP* 3.8 7.3 - - + +
320B GLU* 2.8 54.3 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP 3.1 14.8 + - - +
314B ALA* 3.3 11.0 - - - +
316B ARG* 1.3 74.0 - - - +
318B ILE* 1.3 69.2 + - + +
320B GLU* 4.0 6.3 - - - +
321B GLN* 3.3 20.1 + - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 4.7 7.6 - - - +
52B SER* 4.2 10.5 - - - +
55B LYS* 5.5 9.2 - - + +
314B ALA* 3.0 26.6 + - + +
315B LEU* 3.1 14.5 + - + +
317B ALA* 1.3 84.4 - - + +
319B TRP* 1.4 63.3 + - - +
321B GLN* 3.0 7.3 + - - +
322B GLU* 3.0 38.7 + - + +
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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* 3.9 15.7 - - + -
52B SER* 3.5 19.5 - - - +
86B LEU* 4.9 7.9 - - + -
233B LEU* 3.7 24.9 - - + -
259B ASN* 2.9 32.1 + - + -
260B PHE* 3.4 43.0 - + - -
309B ILE* 3.5 17.7 - - + -
310B LEU* 3.3 32.8 - - + -
315B LEU 2.8 11.1 + - - +
316B ARG* 3.9 12.8 - - + -
318B ILE* 1.4 70.1 - - - +
320B GLU* 1.3 85.4 + - + +
322B GLU* 2.9 5.3 + - - -
323B LEU* 2.8 44.2 + - + +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 3.7 29.6 - - + +
316B ARG* 2.8 50.5 + - - +
317B ALA* 4.0 6.7 - - - +
319B TRP* 1.3 83.4 - - + +
321B GLN* 1.3 58.5 + - - +
323B LEU* 3.7 5.6 - - + +
324B THR* 2.8 37.7 + - + +
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Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA 3.3 13.3 + - - +
318B ILE* 3.0 6.7 + - - +
319B TRP 3.0 0.8 - - - -
320B GLU* 1.3 82.2 - - - +
322B GLU* 1.3 57.0 + - + +
324B THR* 3.2 18.6 + - - +
325B ASP* 2.8 54.6 + - - +
328B GLN* 5.4 2.4 - - - +
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Residues in contact with GLU 322 (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 22.3 - - + +
51B THR* 3.0 33.5 + - - +
52B SER* 2.9 41.0 + - - -
318B ILE* 3.0 20.6 + - + +
319B TRP* 2.9 4.6 + - - +
321B GLN* 1.3 74.1 - - + +
323B LEU* 1.3 59.0 + - - +
325B ASP* 3.0 13.2 + - + +
326B MET* 2.8 35.3 + - + +
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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
----------------------------------------------------------
226B GLN 4.1 3.6 - - - +
227B GLY* 3.8 21.3 - - - +
228B PHE* 4.1 17.5 - - + -
233B LEU* 3.1 37.7 - - + -
259B ASN* 4.0 16.6 - - + +
319B TRP* 2.8 34.2 + - + +
320B GLU* 3.7 6.3 - - - +
322B GLU* 1.3 75.6 - - - +
324B THR* 1.4 66.5 + - + +
326B MET* 2.9 38.0 + - + +
327B ARG* 3.0 14.5 + - - +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLU* 2.8 31.8 + - + +
321B GLN* 3.7 22.5 + - - +
323B LEU* 1.4 75.7 - - + +
325B ASP* 1.3 60.4 + - - +
327B ARG* 3.2 30.7 - - - +
328B GLN* 3.1 40.0 + - - +
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Residues in contact with ASP 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 4.4 1.3 + - - -
321B GLN* 2.8 45.1 + - - +
322B GLU* 3.5 13.8 - - - +
323B LEU 3.0 0.6 - - - -
324B THR* 1.3 75.7 + - - +
326B MET* 1.3 66.8 + - - +
328B GLN* 4.0 8.6 + - - +
329B ARG* 3.1 24.4 + - - +
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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 57.4 - - + +
50B LEU* 3.9 31.6 - - + -
228B PHE* 4.3 10.1 - - + -
258B LYS 4.4 8.3 - - - +
259B ASN 3.7 24.9 - - - +
261B GLY* 5.6 1.6 - - - -
322B GLU* 2.8 17.4 + - + +
323B LEU* 2.9 34.1 + - + +
325B ASP* 1.3 72.8 - - + +
327B ARG* 1.3 63.0 + - - +
329B ARG* 3.0 11.8 + - - +
330B ILE* 3.1 14.7 + - - +
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Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLY* 2.6 38.7 + - - +
228B PHE* 3.8 18.1 - - + +
229B ALA 3.4 23.3 - - - -
230B ARG 3.1 21.1 + - - -
231B GLY* 4.5 5.4 - - - -
233B LEU* 5.5 0.6 - - - +
323B LEU* 3.0 15.3 + - - +
324B THR* 3.2 38.7 - - - +
326B MET* 1.3 75.2 - - - +
328B GLN* 1.3 71.4 + - - +
330B ILE* 3.0 13.1 + - - +
331B GLN* 2.9 46.0 + - + +
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN* 5.4 2.0 - - - +
324B THR* 3.1 31.5 + - - +
325B ASP* 4.2 9.6 + - - +
327B ARG* 1.3 86.2 + - + +
329B ARG* 1.3 63.1 + - - +
331B GLN* 3.3 24.6 + - - +
332B ARG* 3.0 23.8 + - - +
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Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.0 18.1 + - - +
41B TYR 2.9 31.6 + - - -
42B ASP* 3.8 3.6 - - - +
43B GLU* 4.0 36.5 - - - +
325B ASP 3.1 17.9 + - - +
326B MET 3.0 5.3 + - - +
327B ARG 3.0 1.2 - - - -
328B GLN* 1.3 76.7 - - - +
330B ILE* 1.3 65.2 + - - +
332B ARG* 3.4 30.9 + - - +
333B MET* 3.0 51.9 + - - +
390B ALA* 3.2 19.1 + - - +
392B MET 2.9 22.8 + - - -
393B THR* 4.2 5.9 - - - +
394B PRO* 4.6 0.6 - - - +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 4.0 13.9 - - + -
228B PHE* 4.0 26.5 - - + +
326B MET 3.1 15.1 + - - +
327B ARG* 3.0 6.7 + - - +
329B ARG* 1.3 77.4 - - - +
331B GLN* 1.3 64.8 + - + +
333B MET* 3.0 7.3 + - - +
334B ARG* 2.9 26.7 + - - +
358B GLY 3.5 21.5 - - - +
359B MET* 4.1 11.0 - - + -
389B VAL* 3.5 24.7 - - + -
390B ALA* 3.6 32.1 - - + +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE 5.8 0.4 - - - +
229B ALA 3.8 17.8 - - - +
327B ARG* 2.9 40.3 + - + +
328B GLN* 3.7 27.2 - - - +
330B ILE* 1.3 75.3 - - + +
332B ARG* 1.3 59.7 + - - +
334B ARG* 3.6 16.0 + - + +
335B GLN* 3.2 31.6 + - - +
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 4.6 14.8 + - - +
328B GLN 3.0 14.1 + - - +
329B ARG* 3.7 40.2 - - - +
330B ILE 3.0 0.8 - - - -
331B GLN* 1.3 75.9 - - - +
333B MET* 1.3 90.6 + - + +
334B ARG 3.1 1.1 - - - -
335B GLN* 3.4 8.1 + - - +
336B LEU* 3.0 22.4 + - + +
394B PRO* 4.6 10.1 - - - +
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Residues in contact with MET 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG* 3.0 36.2 + - - +
330B ILE* 3.0 9.4 + - - +
332B ARG* 1.3 110.9 - - + +
334B ARG* 1.3 60.5 + - - +
336B LEU* 3.2 24.8 + - + +
337B PHE* 2.7 31.5 + - - +
389B VAL* 3.8 20.2 - - + +
390B ALA* 5.7 0.2 - - - -
392B MET* 3.3 34.2 - - + +
393B THR* 3.8 10.3 - - - -
394B PRO* 3.9 8.3 - - + -
397B MET* 4.6 3.2 - - - +
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 2.9 22.9 + - - +
331B GLN* 3.6 19.7 - - - +
332B ARG 3.1 0.4 - - - -
333B MET* 1.3 75.7 - - - +
335B GLN* 1.3 62.3 + - - +
337B PHE* 2.9 15.7 + - - +
338B VAL* 3.0 16.8 + - - +
353B ILE* 3.1 27.7 + - + +
354B ILE* 4.2 16.8 - - + +
356B GLN* 3.5 34.9 + - - +
358B GLY 2.6 33.5 + - - +
359B MET 4.4 0.8 - - - -
360B PHE 2.4 30.7 + - - -
361B SER* 3.4 16.0 - - - -
389B VAL* 3.9 14.6 - - + +
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Residues in contact with GLN 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLN* 3.2 20.5 + - - +
332B ARG* 3.4 7.6 + - - +
334B ARG* 1.3 74.6 - - - +
336B LEU* 1.3 63.0 + - - +
338B VAL* 3.7 0.9 + - - +
339B ASN* 3.1 38.0 + - - +
354B ILE* 3.6 37.6 - - + +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 3.0 18.1 + - + +
333B MET* 3.6 27.1 - - + +
334B ARG 3.1 0.2 - - - -
335B GLN* 1.3 79.7 - - - +
337B PHE* 1.3 57.5 + - - +
339B ASN* 4.0 6.0 - - + +
340B THR* 2.5 49.2 + - - +
394B PRO* 4.3 15.5 - - + -
397B MET* 4.0 24.0 - - + -
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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
----------------------------------------------------------
333B MET 2.7 16.6 + - - +
334B ARG* 2.9 10.5 + - - +
336B LEU* 1.3 70.2 - - - +
338B VAL* 1.3 68.6 + - + +
340B THR* 3.3 2.3 + - - -
341B LEU* 3.0 48.4 + - + +
350B PHE* 4.8 4.3 - + - -
353B ILE* 3.1 42.2 - - + -
361B SER* 4.8 5.2 - - - -
363B SER* 5.4 6.1 - - - -
387B VAL* 5.0 4.3 - - + -
389B VAL* 5.2 4.0 - - + -
392B MET* 3.8 30.7 - - + -
397B MET* 3.8 19.3 - - + -
400B LEU* 3.6 22.2 - - + -
401B CYS* 4.0 2.4 - - - -
404B ILE* 3.6 18.8 - - + -
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ARG 3.0 14.2 + - - +
335B GLN 4.3 0.9 - - - +
336B LEU 3.4 0.2 - - - -
337B PHE* 1.3 79.3 - - + +
339B ASN* 1.3 74.9 + - - +
341B LEU* 3.2 8.7 + - - +
342B GLN* 3.0 29.6 + - + +
350B PHE* 3.5 31.3 - - + +
351B SER* 4.8 9.0 - - - -
353B ILE* 3.7 14.6 - - + -
354B ILE* 3.4 28.7 - - + -
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Residues in contact with ASN 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLN* 3.1 25.2 + - - +
336B LEU* 4.2 7.7 - - + +
338B VAL* 1.3 89.0 - - - +
340B THR* 1.3 58.6 + - - +
342B GLN* 3.6 16.3 + - - +
343B GLU* 2.6 33.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 2.5 39.4 + - - +
339B ASN* 1.3 72.5 - - - +
341B LEU* 1.3 66.4 + - - +
343B GLU* 3.1 21.1 + - - +
344B LYS* 2.9 40.6 + - - +
397B MET* 3.6 20.1 - - + +
398B ALA* 4.6 2.2 - - + -
401B CYS* 3.7 26.0 - - + -
----------------------------------------------------------
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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 PHE* 3.0 41.7 + - + +
338B VAL 3.2 8.7 - - - +
340B THR* 1.3 74.8 - - - +
342B GLN* 1.3 56.8 + - - +
344B LYS* 2.7 24.6 + - - +
345B GLY 3.2 8.3 + - - -
346B ALA* 3.3 16.3 + - + +
350B PHE* 3.5 46.9 - - + -
401B CYS* 3.8 30.8 - - + +
404B ILE* 3.7 24.7 - - + -
405B VAL* 4.2 5.2 - - + +
----------------------------------------------------------
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B VAL* 3.0 14.2 + - + +
339B ASN* 3.6 16.3 + - - +
341B LEU* 1.3 81.3 - - - +
343B GLU* 1.3 67.7 + - + +
344B LYS 3.1 0.7 + - - -
345B GLY* 3.3 12.0 + - - -
346B ALA* 4.5 7.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASN* 2.6 23.5 + - - +
340B THR* 4.0 22.7 + - - +
341B LEU 3.1 0.4 - - - -
342B GLN* 1.3 78.6 - - + +
344B LYS* 1.3 72.0 + - + +
345B GLY 3.3 1.1 - - - -
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B THR* 2.9 30.6 + - - +
341B LEU 2.7 7.3 + - - +
343B GLU* 1.3 94.2 + - + +
345B GLY* 1.3 60.0 + - - +
398B ALA* 4.1 17.4 - - - +
401B CYS* 4.2 15.5 - - + +
402B GLU* 2.7 49.0 + - + +
405B VAL* 3.9 16.9 - - + +
----------------------------------------------------------
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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