Contacts of the helix formed by residues 312 - 346 (chain B) in PDB entry 5TIN
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 THR 312 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ALA* 2.7 21.9 + - + +
311B GLY* 1.3 76.5 - - - +
313B LYS* 1.3 67.4 + - - +
314B VAL* 3.9 7.3 - - - +
315B PHE* 3.0 32.1 + - - -
316B ILE* 3.0 22.0 + - - +
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Residues in contact with LYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLY 4.2 0.6 + - - -
312B THR* 1.3 72.3 - - - +
314B VAL* 1.3 58.6 + - - +
316B ILE* 3.8 6.0 - - - +
317B ASP* 2.9 44.2 + - - +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR* 3.9 7.2 - - - +
313B LYS* 1.3 77.3 - - - +
315B PHE* 1.3 86.3 + - + +
317B ASP* 3.7 7.0 + - - +
318B ARG* 3.2 24.1 + - - +
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 3.4 34.5 - - + +
308B SER* 4.2 1.9 - - - -
310B ALA* 3.9 22.9 - - + +
312B THR* 3.0 24.9 + - - +
314B VAL* 1.3 93.7 - - + +
316B ILE* 1.3 66.0 + - - +
317B ASP 3.3 1.1 - - - -
318B ARG* 3.4 9.5 + - + +
319B ALA* 3.1 23.6 + - - +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET* 4.0 18.5 - - + +
247B ASP* 6.0 1.8 - - - +
308B SER* 4.1 26.7 - - - +
311B GLY* 4.0 17.7 - - - +
312B THR 3.0 24.8 + - - +
313B LYS* 3.8 7.4 - - - +
315B PHE* 1.3 74.6 - - - +
317B ASP* 1.3 62.5 + - - +
319B ALA* 3.4 6.7 + - - +
320B LYS* 2.9 28.9 + - + +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LYS* 2.9 29.4 + - - +
314B VAL* 3.8 8.5 - - - +
316B ILE* 1.3 78.4 - - - +
318B ARG* 1.3 57.7 + - - +
320B LYS* 3.3 8.7 + - - +
321B LYS* 3.0 28.6 + - - +
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 4.5 9.2 - - + -
314B VAL 3.2 15.3 + - - +
315B PHE* 3.7 13.9 - - + +
316B ILE 3.3 0.4 - - - -
317B ASP* 1.3 77.5 - - - +
319B ALA* 1.3 62.2 + - - +
321B LYS* 3.3 7.8 + - - +
322B ILE* 3.2 27.8 + - + +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET* 3.8 12.8 - - + +
304B VAL* 3.7 25.1 - - + +
307B VAL* 3.6 25.9 - - + +
308B SER* 3.8 9.9 - - - -
315B PHE 3.1 14.3 + - - +
316B ILE 3.6 4.9 - - - +
318B ARG* 1.3 77.6 - - - +
320B LYS* 1.3 59.8 + - - +
322B ILE* 3.3 9.0 + - - +
323B ASP* 3.3 18.4 + - - +
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET* 3.6 13.6 - - + +
316B ILE* 2.9 20.0 + - + +
317B ASP* 3.3 10.7 + - - +
319B ALA* 1.3 76.3 - - - +
321B LYS* 1.3 57.6 + - - +
323B ASP* 3.4 7.4 + - - +
324B THR* 3.1 33.5 + - + +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ASP 3.0 17.0 + - - +
318B ARG* 3.6 9.0 - - - +
319B ALA 3.2 0.2 - - - -
320B LYS* 1.3 73.6 - - - +
322B ILE* 1.3 65.7 + - - +
324B THR* 3.0 9.5 + - - +
325B ILE* 3.0 37.9 + - + +
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Residues in contact with ILE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLU* 3.5 28.0 - - + +
303B ALA* 4.6 15.3 - - + -
304B VAL* 3.7 11.4 - - + -
307B VAL* 4.2 28.5 - - + -
318B ARG* 3.2 17.0 + - + +
319B ALA* 3.3 8.7 + - - +
321B LYS* 1.3 76.6 - - - +
323B ASP* 1.3 56.7 + - - +
325B ILE* 3.9 7.3 - - + +
326B SER* 2.8 33.8 + - - +
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.0 9.2 - - - +
244B ILE 4.6 2.9 - - - +
246B MET* 4.5 12.1 - - - +
252B ARG* 2.6 35.7 + - - -
300B GLU* 2.8 25.3 - - - +
304B VAL* 3.7 16.3 - - - +
319B ALA 3.3 6.7 + - - +
320B LYS* 3.6 10.3 - - - +
321B LYS 3.2 0.4 - - - -
322B ILE* 1.3 80.3 - - - +
324B THR* 1.3 62.6 + - - +
326B SER* 3.2 3.1 + - - -
327B ARG* 3.0 43.2 + - - +
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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 LYS* 3.1 19.6 + - + +
321B LYS* 3.0 17.9 + - - -
323B ASP* 1.3 77.3 - - - +
325B ILE* 1.3 63.3 + - - +
327B ARG* 3.6 39.2 + - - +
328B ALA* 3.8 6.8 + - - +
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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
----------------------------------------------------------
321B LYS* 3.0 30.0 + - + +
322B ILE* 3.9 6.7 - - + +
324B THR* 1.3 77.2 + - - +
326B SER* 1.3 55.8 + - - +
328B ALA* 3.0 6.7 + - - +
329B CYS* 2.8 55.3 + - + +
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Residues in contact with SER 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 3.8 22.1 - - - -
300B GLU* 3.0 30.8 + - - +
322B ILE* 2.8 23.7 + - - +
323B ASP 3.5 3.8 - - - -
325B ILE* 1.3 78.6 - - - +
327B ARG* 1.3 60.9 + - - +
329B CYS* 4.4 2.0 - - - +
330B PHE* 3.2 43.5 + - - +
331B PRO* 3.6 0.5 - - - +
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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
----------------------------------------------------------
306A PHE* 3.8 33.1 - - - -
309A ARG* 4.9 8.7 - - - +
242B PHE* 2.9 40.4 + - + -
243B TRP* 3.6 49.9 - - + +
244B ILE 5.6 0.8 + - - -
323B ASP* 3.0 29.1 + - - +
324B THR* 3.6 35.4 - - - +
325B ILE 3.2 0.4 - - - -
326B SER* 1.3 76.2 - - - +
328B ALA* 1.3 58.9 + - - +
331B PRO* 3.4 20.7 - - - +
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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
----------------------------------------------------------
324B THR 3.8 7.1 + - - +
325B ILE* 3.0 9.2 + - - +
327B ARG* 1.3 80.1 - - - +
329B CYS* 1.3 64.2 + - - +
330B PHE 3.5 0.7 - - - -
331B PRO* 3.5 4.3 - - - +
332B LEU* 3.1 31.6 + - + +
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Residues in contact with CYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 2.8 42.2 + - + +
326B SER* 4.7 2.2 - - - +
328B ALA* 1.3 76.8 - - - +
330B PHE* 1.3 60.1 + - + +
332B LEU* 3.7 11.3 - - - +
333B ALA* 2.7 38.3 + - + +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.7 22.2 - + - +
242B PHE* 3.7 22.9 - + + -
293B PHE* 3.5 43.2 - + - -
296B SER* 3.7 29.2 - - - -
297B ALA* 3.6 13.9 - - + -
300B GLU* 4.4 5.8 - - + -
326B SER* 3.2 32.1 + - - +
329B CYS* 1.3 80.6 - - + +
331B PRO* 1.3 71.0 - - + +
333B ALA* 3.4 0.8 + - - -
334B PHE* 3.0 25.8 + - - +
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Residues in contact with PRO 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.6 42.1 - - + -
242B PHE* 5.3 0.7 - - + -
243B TRP* 5.4 5.4 - - + -
326B SER 3.6 2.5 - - - +
327B ARG* 3.4 27.1 - - - +
328B ALA 3.5 5.4 - - - +
330B PHE* 1.3 95.3 - - + +
332B LEU* 1.3 55.8 + - - +
334B PHE* 3.8 1.6 - - - +
335B LEU* 3.0 28.9 + - - +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ALA* 3.1 23.1 + - + +
329B CYS* 3.7 12.3 - - - +
330B PHE 3.2 0.2 - - - -
331B PRO* 1.3 76.4 - - - +
333B ALA* 1.3 57.8 + - - +
335B LEU* 3.3 19.4 + - + +
336B ILE* 3.0 47.8 + - + +
----------------------------------------------------------
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PHE* 3.7 19.0 - - + -
329B CYS* 2.7 22.4 + - + +
330B PHE* 4.0 2.0 - - - +
332B LEU* 1.3 73.3 - - - +
334B PHE* 1.3 57.8 + - - +
336B ILE* 3.4 13.3 + - - +
337B PHE* 3.0 27.7 + - - +
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Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 3.5 28.0 - - + -
235B VAL* 4.1 20.6 - - + -
236B ILE* 6.1 0.2 - - + -
239B TRP* 3.7 25.4 - + + -
286B TRP* 4.3 5.2 - + - -
289B VAL* 5.1 0.2 - - + -
290B CYS* 4.1 28.7 - - - -
293B PHE* 3.5 34.2 - + + -
330B PHE 3.0 18.4 + - - +
331B PRO 3.8 2.7 - - - +
333B ALA* 1.3 76.7 - - - +
335B LEU* 1.3 59.5 + - - +
337B PHE* 3.5 16.1 + + - +
338B ASN* 3.0 52.8 + - - -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B PRO 3.0 18.0 + - - +
332B LEU* 3.5 18.8 - - + +
334B PHE* 1.3 75.4 - - - +
336B ILE* 1.3 67.1 + - + +
338B ASN* 3.3 11.4 + - + +
339B ILE* 3.0 44.2 + - + +
----------------------------------------------------------
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.0 40.7 + - + +
333B ALA* 3.6 10.8 - - - +
335B LEU* 1.3 77.7 - - + +
337B PHE* 1.3 63.2 + - - +
339B ILE* 3.2 10.7 + - + +
340B PHE* 3.1 43.2 + - + -
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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
----------------------------------------------------------
285B ILE* 4.7 5.6 - - + -
286B TRP* 3.7 33.2 - + - -
289B VAL* 3.5 51.4 - - + -
293B PHE* 4.7 4.7 - - + -
333B ALA 3.0 17.3 + - - +
334B PHE* 3.7 22.9 - + - +
335B LEU 3.3 0.2 - - - -
336B ILE* 1.3 78.1 - - - +
338B ASN* 1.3 60.1 + - - +
340B PHE* 3.2 8.7 + - + +
341B TYR* 2.8 55.4 + + + +
----------------------------------------------------------
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Residues in contact with ASN 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 4.8 4.7 - - - +
286B TRP* 3.7 17.5 - - - -
334B PHE* 3.0 53.2 + - - +
335B LEU* 3.3 16.8 + - + +
337B PHE* 1.3 76.8 - - - +
339B ILE* 1.3 69.2 + - + +
341B TYR* 4.4 2.5 - - - -
342B TRP* 2.9 56.8 + - + +
----------------------------------------------------------
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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
----------------------------------------------------------
335B LEU* 3.0 39.2 + - + +
336B ILE* 3.2 10.3 + - - +
338B ASN* 1.3 78.2 - - + +
340B PHE* 1.3 71.7 + - + +
342B TRP* 4.4 0.8 - - - +
343B VAL* 3.1 40.7 + - + +
----------------------------------------------------------
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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 ILE* 3.1 38.0 + - + +
337B PHE* 3.6 11.4 - - + +
339B ILE* 1.3 86.5 - - + +
341B TYR* 1.3 61.4 + - - +
343B VAL* 4.0 3.0 - - - +
344B ILE* 2.9 42.3 + - + +
----------------------------------------------------------
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Residues in contact with TYR 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B MET* 3.6 14.4 - - + +
228B TYR* 2.7 40.2 + + - -
282B ALA 2.8 30.3 + - - -
285B ILE* 4.3 7.6 - - + -
286B TRP* 3.7 27.3 - + + +
337B PHE* 2.8 45.0 + + + +
338B ASN* 3.4 6.5 + - - +
340B PHE* 1.3 75.7 - - - +
342B TRP* 1.3 83.2 - + - +
344B ILE* 3.3 2.5 + - - +
345B TYR* 3.2 52.8 + + - -
----------------------------------------------------------
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Residues in contact with TRP 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B MET* 3.8 18.4 - - + -
220B MET* 3.5 34.3 - - + -
224B LEU* 4.5 9.4 - - + -
228B TYR* 3.8 35.9 - + + -
286B TRP* 4.1 7.5 - + - -
338B ASN* 2.9 49.9 + - + +
339B ILE* 4.4 1.1 - - - +
341B TYR* 1.3 86.7 - + - +
343B VAL* 1.3 62.9 + - + +
346B LYS* 2.8 44.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 3.1 35.9 + - + +
340B PHE* 4.0 3.1 - - - +
342B TRP* 1.3 78.4 - - + +
344B ILE* 1.3 66.5 + - + +
346B LYS 5.0 1.8 - - - -
347B ILE* 3.2 30.5 + - + +
----------------------------------------------------------
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PHE* 2.9 40.1 + - + +
341B TYR* 3.7 5.2 - - - +
343B VAL* 1.3 80.2 - - + +
345B TYR* 1.3 76.4 + - + +
348B LEU* 3.0 42.0 + - + +
----------------------------------------------------------
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Residues in contact with TYR 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LYS 4.8 1.6 + - - -
144B ASN* 3.6 32.1 - - + -
147B MET* 3.6 33.5 - - + +
281B LYS 4.9 0.7 - - - -
282B ALA* 3.4 32.1 + - + -
285B ILE* 4.0 15.7 - - + +
341B TYR* 3.2 56.8 + + - +
342B TRP* 4.6 0.7 - - - +
344B ILE* 1.3 89.9 - - + +
346B LYS* 1.3 58.1 + - - +
347B ILE 3.1 9.5 + - - +
348B LEU 3.6 15.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B MET* 4.9 4.0 - - + -
342B TRP* 2.8 30.8 + - + +
343B VAL* 3.7 5.4 - - - +
345B TYR* 1.3 71.9 - - - +
347B ILE* 1.3 58.0 + - - +
----------------------------------------------------------
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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