Contacts of the helix formed by residues 305 - 338 (chain B) in PDB entry 4TNV
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 305 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA* 3.7 9.4 - - + +
304B GLY* 1.3 78.7 - - - +
306B THR* 1.3 67.8 + - - +
307B GLU* 3.3 13.8 + - + +
308B TRP* 3.4 42.9 + - + +
309B ASN* 3.4 10.9 + - - -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLY 4.8 4.5 - - - +
305B THR* 1.3 77.4 + - - +
307B GLU* 1.3 66.3 + - - +
309B ASN* 3.1 16.2 - - - +
310B ASP* 3.1 25.7 + - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 3.2 9.9 + - + +
306B THR* 1.3 80.7 + - - +
308B TRP* 1.3 64.2 + - - +
310B ASP* 3.1 22.8 + - + +
311B ILE* 3.2 23.9 + - + +
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Residues in contact with TRP 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ILE* 3.4 43.7 - - + +
303B ALA* 3.4 26.4 - - + +
305B THR* 3.4 27.2 + - + +
307B GLU* 1.3 77.3 - - - +
309B ASN* 1.3 52.9 + - - +
311B ILE* 3.0 45.6 + - + +
312B SER* 2.7 35.9 + - - -
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Residues in contact with ASN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ARG* 3.3 40.1 + - - +
300B ILE 5.5 0.4 - - - -
301B ALA* 4.2 12.9 + - - +
303B ALA 4.6 6.8 + - - -
304B GLY 4.8 4.8 + - - -
305B THR 3.4 14.6 + - - -
306B THR* 3.1 21.6 + - - +
307B GLU 3.1 0.4 - - - -
308B TRP* 1.3 80.0 - - - +
310B ASP* 1.3 56.3 + - - +
312B SER* 3.7 4.4 - - - -
313B LYS* 2.9 33.0 + - - +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B THR* 3.1 18.2 + - - +
307B GLU* 3.1 18.3 + - + +
309B ASN* 1.3 78.3 - - - +
311B ILE* 1.3 58.7 + - + +
313B LYS* 4.2 4.5 - - - +
314B ARG* 3.1 27.9 + - - +
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ILE* 3.9 16.4 - - + -
307B GLU* 3.2 23.3 + - + +
308B TRP* 3.0 42.1 + - + +
310B ASP* 1.3 78.6 - - + +
312B SER* 1.3 64.6 + - - +
314B ARG* 3.1 11.3 + - + +
315B VAL* 3.0 29.5 + - + +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ARG* 3.8 9.4 - - - -
297B VAL* 3.3 34.0 + - - +
300B ILE* 3.6 23.8 - - - +
301B ALA* 3.4 17.8 - - - +
308B TRP 2.7 19.9 + - - -
309B ASN* 3.7 7.0 - - - -
311B ILE* 1.3 75.4 - - - +
313B LYS* 1.3 60.3 + - - +
315B VAL* 3.6 8.8 + - - +
316B ASP* 3.7 9.9 + - - +
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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
----------------------------------------------------------
238B ASP* 5.7 8.7 - - - +
239B ARG* 5.3 14.8 - - - +
309B ASN 2.9 16.6 + - - +
310B ASP* 4.2 5.2 - - - +
312B SER* 1.3 74.8 + - - +
314B ARG* 1.3 64.2 + - - +
316B ASP* 3.5 10.8 + - + +
317B LEU* 3.3 43.3 + - + +
320B ARG* 3.7 25.7 - - - +
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Residues in contact with ARG 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP 3.1 21.4 + - - +
311B ILE* 3.1 12.0 + - - +
313B LYS* 1.3 76.2 - - - +
315B VAL* 1.3 65.6 + - - +
317B LEU* 3.2 9.8 + - + +
318B ILE* 3.0 47.0 + - + +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU* 3.6 24.0 - - + +
296B LEU* 4.3 21.1 - - + -
297B VAL* 3.8 12.8 - - + -
300B ILE* 4.2 16.8 - - + -
311B ILE* 3.0 21.6 + - + +
312B SER 3.9 6.1 - - - +
313B LYS 3.4 0.2 - - - -
314B ARG* 1.3 77.2 - - + +
316B ASP* 1.3 60.9 + - - +
318B ILE* 3.4 12.4 + - + +
319B SER* 3.1 24.5 + - - +
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 3.4 22.8 - - - +
237B PHE 3.4 7.6 - - - +
238B ASP* 4.8 1.0 - - - -
239B ARG* 4.8 4.3 + - - +
245B ARG* 3.2 24.9 + - - -
293B GLU* 3.0 18.9 - - - +
297B VAL* 3.2 19.9 - - - +
312B SER 3.7 5.9 + - - +
313B LYS* 3.5 15.9 + - + +
314B ARG 3.2 0.4 - - - -
315B VAL* 1.3 79.2 - - - +
317B LEU* 1.3 62.9 + - + +
318B ILE 3.2 0.2 + - - -
319B SER* 3.2 3.5 + - - -
320B ARG* 2.9 36.3 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LYS* 3.3 41.5 + - + +
314B ARG* 3.2 11.5 + - + +
316B ASP* 1.3 80.1 - - + +
318B ILE* 1.3 63.4 + - + +
320B ARG* 3.5 47.2 - - - +
321B ALA* 4.0 5.7 + - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ARG* 3.0 46.0 + - + +
315B VAL* 3.6 11.9 - - + +
317B LEU* 1.3 76.6 - - + +
319B SER* 1.3 55.1 + - - +
321B ALA* 3.0 8.0 + - - +
322B LEU* 2.6 59.1 + - + +
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 3.2 31.5 - - - -
293B GLU* 3.4 26.7 - - - +
315B VAL* 3.1 17.2 + - - +
316B ASP 3.8 2.0 - - - -
318B ILE* 1.3 71.7 - - - +
320B ARG* 1.3 61.8 + - - +
321B ALA 3.0 6.3 + - - -
322B LEU* 3.5 19.6 + - - +
323B PHE* 3.6 23.3 + - - -
324B PRO* 3.7 3.1 - - - +
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A HIS* 5.9 2.8 + - - -
232B TRP* 6.1 0.3 - - - +
235B PHE* 3.2 30.9 + - + -
236B TRP* 3.5 90.0 + - + +
237B PHE 5.2 2.2 + - - -
238B ASP* 5.7 0.6 - - - +
313B LYS* 3.7 19.4 - - - +
316B ASP* 2.9 23.8 + - - +
317B LEU* 3.5 40.4 - - - +
318B ILE 3.1 0.4 - - - -
319B SER* 1.3 75.5 - - - +
321B ALA* 1.3 60.5 + - + +
324B PRO* 3.8 12.5 - - - +
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU 4.7 4.9 - - - +
318B ILE 3.0 5.3 + - - +
320B ARG* 1.3 81.3 - - + +
322B LEU* 1.3 59.7 + - - +
324B PRO* 3.6 10.2 - - - +
325B VAL* 3.2 30.2 + - + +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 2.6 43.1 + - + +
319B SER* 3.5 5.6 + - - +
321B ALA* 1.3 71.0 - - - +
323B PHE* 1.3 74.3 + - + +
325B VAL* 3.0 9.0 + - + +
326B LEU* 2.9 64.3 + - + +
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Residues in contact with PHE 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 3.3 29.1 - + + +
235B PHE* 3.5 25.6 - + - -
286B PHE* 3.8 24.7 - + - -
289B CYS* 3.8 27.8 - - + -
290B ALA* 3.7 21.8 - - - -
293B GLU* 4.3 5.6 - - + -
319B SER* 3.6 29.4 + - - +
322B LEU* 1.3 91.4 - - + +
324B PRO* 1.4 68.0 - - + +
326B LEU* 3.4 8.8 + - + +
327B PHE* 3.0 27.5 + - - +
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Residues in contact with PRO 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 3.5 41.2 - - + -
319B SER 3.7 7.6 - - - +
320B ARG 3.8 13.9 - - - +
321B ALA* 3.6 17.5 - - - +
323B PHE* 1.4 95.2 - - + +
325B VAL* 1.3 59.1 + - + +
327B PHE* 4.1 1.6 - - - +
328B PHE* 3.2 23.6 + - - +
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ALA* 3.2 16.5 + - + +
322B LEU* 3.0 12.5 + - + +
324B PRO* 1.3 77.5 - - + +
326B LEU* 1.3 69.2 + - + +
328B PHE* 3.1 9.5 + - + +
329B VAL* 2.8 43.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 3.8 16.7 - - + -
322B LEU* 2.9 57.9 + - + +
323B PHE* 4.0 8.5 - - + +
325B VAL* 1.3 80.7 - - + +
327B PHE* 1.3 57.1 + - - +
329B VAL* 3.3 11.5 + - + +
330B PHE* 3.0 27.0 + - - +
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B CYS* 4.4 23.3 - - - -
228B VAL* 3.8 35.4 - - + -
232B TRP* 3.7 23.6 - + + -
279B TRP* 4.4 9.6 - + - -
283B CYS* 4.5 10.1 - - - -
286B PHE* 3.5 29.5 - + + -
323B PHE 3.0 17.7 + - - +
324B PRO 4.1 0.4 - - - +
326B LEU* 1.3 75.4 - - - +
328B PHE* 1.3 55.9 + - - +
330B PHE* 3.3 13.5 + + - +
331B ASN* 2.6 63.0 + - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B PRO 3.2 16.8 + - - +
325B VAL* 3.1 9.5 + - + +
327B PHE* 1.3 78.7 - - + +
329B VAL* 1.3 62.8 + - + +
331B ASN* 3.4 16.8 - - + +
332B ILE* 3.0 63.9 + - + +
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 2.8 33.6 + - + +
326B LEU* 3.4 15.3 - - + +
328B PHE* 1.3 76.8 - - + +
330B PHE* 1.3 60.4 + - - +
332B ILE* 3.1 10.2 + - + +
333B LEU* 2.9 51.6 + - + +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 4.6 10.1 - - + -
279B TRP* 3.7 25.8 - + - -
282B ALA* 3.4 32.8 - - + -
283B CYS* 5.9 0.4 - - - -
286B PHE* 4.6 15.7 - + + -
326B LEU 3.0 14.7 + - - +
327B PHE* 3.6 20.4 - + - +
329B VAL* 1.3 76.2 - - - +
331B ASN* 1.3 56.7 + - - +
333B LEU* 4.2 10.3 - - + -
334B TYR* 2.6 70.4 + + + +
----------------------------------------------------------
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B CYS* 5.6 3.2 - - - -
279B TRP* 4.2 12.1 + - - -
327B PHE* 2.6 46.1 + - - +
328B PHE* 3.4 21.9 - - + +
329B VAL 3.2 0.2 - - - -
330B PHE* 1.3 76.3 - - - +
332B ILE* 1.3 62.5 + - + +
334B TYR* 3.9 2.1 - - - +
335B TRP* 2.9 54.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 3.0 53.3 + - + +
329B VAL* 3.1 10.5 + - + +
331B ASN* 1.3 76.9 - - + +
333B LEU* 1.3 68.1 + - + +
335B TRP* 4.2 2.2 - - - +
336B SER* 2.9 31.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 2.9 44.1 + - + +
330B PHE* 3.6 12.3 - - + +
332B ILE* 1.3 83.4 - - + +
334B TYR* 1.3 61.3 + - - +
336B SER* 2.8 19.0 + - - -
337B ARG* 3.1 15.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 5.0 0.8 - - - +
221B TYR* 2.6 32.0 + + - -
275B ALA* 2.8 35.2 + - - +
278B VAL* 4.2 4.9 - - + -
279B TRP* 3.5 35.6 - + + +
330B PHE* 2.6 51.1 + + + +
331B ASN* 3.9 4.5 - - - +
333B LEU* 1.3 73.1 - - - +
335B TRP* 1.3 88.6 + + - +
337B ARG* 3.1 7.5 + - - +
338B PHE* 3.0 51.1 + + + +
----------------------------------------------------------
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Residues in contact with TRP 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET* 3.5 32.8 - - + -
213B PHE* 3.7 27.8 - + - -
217B LEU* 4.9 5.4 - - + -
221B TYR* 3.5 37.9 - + + -
279B TRP* 4.9 3.8 - + - -
331B ASN* 2.9 50.4 + - - +
332B ILE* 4.4 2.0 - - - +
334B TYR* 1.3 94.6 - + - +
336B SER* 1.3 56.7 + - - +
338B PHE* 3.5 2.9 - - + +
339B GLY* 2.8 32.6 + - - -
----------------------------------------------------------
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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
----------------------------------------------------------
332B ILE* 2.9 22.0 + - - +
333B LEU* 2.8 25.6 + - - -
335B TRP* 1.3 77.2 - - - +
337B ARG* 1.3 59.2 + - - +
338B PHE 3.6 0.2 + - - -
339B GLY* 3.9 5.6 + - - -
340B HIS* 5.0 1.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLN* 6.1 3.0 - - - +
136B TYR* 3.5 24.8 + - - -
333B LEU 3.4 13.9 - - - +
334B TYR* 3.1 7.3 + - - +
336B SER* 1.3 81.1 + - - +
338B PHE* 1.3 93.8 + - + +
339B GLY 3.5 0.6 + - - -
340B HIS* 4.8 2.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLN* 4.3 9.2 - - + -
136B TYR* 3.5 26.5 - + + -
139B MET* 3.8 34.3 - - + +
275B ALA* 3.4 33.0 - - + -
278B VAL* 4.5 16.2 - - + -
334B TYR* 3.0 55.4 + + + +
335B TRP* 3.5 4.3 - - - +
337B ARG* 1.3 115.3 - - + +
339B GLY* 1.3 54.3 - - - +
340B HIS 3.4 5.7 + - - -
----------------------------------------------------------
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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