Contacts of the helix formed by residues 296 - 319 (chain B) in PDB entry 1PTH
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 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 1.3 83.1 - - - +
297B GLY* 1.3 50.2 + - - +
299B MET* 4.1 9.1 - - + +
300B LEU* 2.7 38.1 + - - +
407B PHE* 3.2 61.0 - - + +
409B PHE 5.6 0.2 - - - -
410B ASN* 4.4 13.9 - - + +
413B MET* 4.3 23.8 - - + -
414B LEU* 4.6 13.2 - - + +
422B LEU* 4.7 8.1 - - + -
426B PHE* 4.9 1.8 - - - -
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 3.8 39.3 - - - -
295B LEU 2.7 6.3 + - - -
296B PRO* 1.3 80.6 - - - +
298B LEU* 1.3 62.9 + - - +
300B LEU* 3.1 13.7 - - - +
301B TYR* 3.3 12.1 + - - -
407B PHE* 4.1 4.9 - - - -
426B PHE* 4.1 9.0 - - - -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 4.3 4.7 - - + +
203B GLN* 3.2 39.9 - - + +
204B HIS* 3.7 23.4 + - + +
207B HIS* 5.9 2.0 - - + -
291B VAL* 5.1 5.6 - - + +
292B PHE* 3.5 46.7 - - + +
294B LEU* 5.1 2.9 - - + +
295B LEU* 2.7 39.5 + - + +
297B GLY* 1.3 70.1 - - - -
299B MET* 1.3 65.8 + - - +
300B LEU 2.9 1.2 + - - -
301B TYR* 3.0 6.6 + - - +
302B ALA* 2.9 22.1 + - - +
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Residues in contact with MET 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B PRO* 4.5 2.0 - - - -
275B TYR* 4.7 2.5 - - - +
285B MET* 3.9 36.3 - - - +
287B VAL* 3.7 30.7 - - + -
292B PHE* 2.8 39.3 - - + +
293B GLY* 3.5 15.3 - - - +
295B LEU 3.3 7.3 + - - +
296B PRO* 4.1 9.6 - - + +
298B LEU* 1.3 79.3 - - - +
300B LEU* 1.3 56.2 + - - +
302B ALA* 3.6 4.5 - - + +
303B THR* 2.9 31.4 + - - +
414B LEU* 4.0 14.1 - - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET* 4.6 5.6 - - - -
200B PHE* 6.4 0.2 - - + -
296B PRO 2.7 23.7 + - - +
297B GLY* 3.1 9.0 - - - +
298B LEU 2.9 0.2 + - - -
299B MET* 1.3 74.6 - - - +
301B TYR* 1.3 74.3 + - + +
303B THR* 3.1 10.4 + - - -
304B ILE* 3.1 24.0 + - + +
414B LEU* 3.8 19.5 - - + +
419B VAL* 3.7 45.1 - - + +
422B LEU* 4.4 6.5 - - + -
423B VAL* 3.7 20.2 - - + -
426B PHE* 4.3 23.6 - - + -
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Residues in contact with TYR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET* 2.8 51.5 + - + +
200B PHE* 3.8 11.7 - - + -
201B PHE* 3.2 59.5 - + - +
204B HIS* 4.0 23.1 - + + +
297B GLY 3.3 11.1 + - - -
298B LEU 3.0 6.9 + - - +
300B LEU* 1.3 84.3 - - + +
302B ALA* 1.3 64.0 + - - +
304B ILE* 2.9 22.3 + - + +
305B TRP* 2.9 36.4 + + - -
426B PHE* 6.5 0.4 - + - -
564B LEU* 4.4 10.7 - - + +
567B LEU* 5.4 3.8 - - + -
580B PHE* 3.6 3.5 - - - -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B HIS* 3.9 16.9 - - + -
232B HIS 6.0 1.1 - - - +
233B ILE* 5.8 3.8 - - - +
263B PRO* 4.8 3.5 - - + +
287B VAL* 4.6 21.9 - - + +
292B PHE* 4.6 9.4 - - + -
298B LEU 2.9 13.0 + - - +
299B MET* 3.6 15.7 - - + +
300B LEU 3.2 0.2 - - - -
301B TYR* 1.3 77.0 - - - +
303B THR* 1.3 56.9 + - - +
305B TRP* 3.9 4.1 + - - +
306B LEU* 3.1 27.2 + - - +
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL 3.8 5.2 - - - +
262B TYR* 3.8 10.2 - - + -
263B PRO* 2.9 30.2 - - - +
299B MET 2.9 13.1 + - - -
300B LEU* 3.5 7.6 - - - -
301B TYR 3.1 0.2 - - - -
302B ALA* 1.3 75.0 - - - +
304B ILE* 1.3 67.3 + - - +
306B LEU* 3.1 6.2 + - - +
307B ARG* 2.8 54.8 + - - +
414B LEU* 3.9 6.4 - - - +
419B VAL* 3.7 16.8 - - + -
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.1 35.3 + - + +
301B TYR* 2.9 22.6 + - + +
303B THR* 1.3 75.7 - - + +
305B TRP* 1.3 58.6 + - + +
307B ARG* 3.0 12.2 + - - +
308B GLU* 2.8 26.3 + - - +
419B VAL* 4.1 16.8 - - + -
423B VAL* 4.1 8.5 - - + -
567B LEU* 3.5 46.0 - - + +
568B VAL* 4.1 24.0 - - + +
571B ASN* 3.9 4.2 + - + +
572B THR* 6.1 0.2 - - + -
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 4.7 16.0 - + - -
204B HIS* 3.7 29.7 + + - -
232B HIS* 5.9 1.0 - + - -
233B ILE* 3.4 28.5 - - + +
301B TYR* 2.9 25.0 + + + +
302B ALA* 4.3 2.7 - - - +
304B ILE* 1.3 77.5 - - + +
306B LEU* 1.3 62.3 + - - +
308B GLU* 3.4 5.0 + - + +
309B HIS* 3.1 22.2 + - - +
336B LEU* 3.6 37.7 - - + +
339B GLU* 3.9 17.3 - - + -
340B THR* 3.4 43.5 - - + -
343B ILE* 4.3 6.5 - - + -
567B LEU* 3.3 45.1 - - + +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ILE* 5.3 4.7 - - + +
252B LEU* 4.3 24.2 - - + -
253B LYS 3.4 24.9 - - - +
254B TYR* 4.1 17.5 - - + -
261B VAL* 4.9 4.7 - - + -
262B TYR* 4.8 5.8 - - - +
263B PRO* 4.1 23.8 - - + -
264B PRO* 4.7 2.0 - - + -
302B ALA 3.1 18.7 + - - +
303B THR* 3.1 7.6 + - - +
305B TRP* 1.3 72.5 - - - +
307B ARG* 1.3 83.4 + - + +
308B GLU 3.1 0.3 + - - -
309B HIS* 3.1 7.0 + - - +
310B ASN* 3.0 29.6 + - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU* 4.3 20.5 + - - +
261B VAL* 2.7 66.6 + - + +
262B TYR* 4.2 6.3 + - - -
303B THR* 2.8 28.1 + - - +
304B ILE* 3.3 9.5 - - - +
306B LEU* 1.3 85.0 - - + +
308B GLU* 1.3 63.0 + - - +
310B ASN* 3.2 5.8 + - - +
311B ARG* 3.0 21.1 + - - +
419B VAL* 3.6 25.2 - - - +
420B GLU* 4.6 1.2 + - - -
571B ASN* 2.9 44.7 + - + +
572B THR* 3.5 20.8 - - - +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE 2.8 9.8 + - - +
305B TRP* 3.5 17.7 - - + +
307B ARG* 1.3 72.6 - - - +
309B HIS* 1.3 67.2 + - - +
311B ARG* 2.6 51.9 + - - +
312B VAL* 3.0 17.6 + - - +
336B LEU* 4.0 10.8 - - + -
339B GLU* 2.7 38.5 - - - +
567B LEU* 4.1 14.8 - - + -
570B LEU* 5.4 0.9 - - - +
571B ASN* 3.1 25.1 + - - +
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ILE* 5.5 0.4 - - + -
234B TYR* 2.5 42.5 + + - +
250B GLY 2.8 27.2 + - - -
252B LEU* 3.5 25.3 + - + +
305B TRP 3.1 10.7 + - - +
306B LEU 3.1 6.3 + - - +
308B GLU* 1.3 77.1 - - - +
310B ASN* 1.3 79.8 + - - +
312B VAL* 3.5 2.5 + - - +
313B CYS* 3.1 22.6 + - - -
329B PHE* 3.8 18.1 - + - -
332B ALA* 3.6 24.1 - - + +
336B LEU* 3.8 15.5 - - + +
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Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LYS* 3.3 20.7 - - + +
252B LEU* 2.7 35.9 + - - +
254B TYR* 2.8 44.2 - - + -
261B VAL* 5.5 0.4 - - - +
306B LEU* 3.0 19.2 + - - +
307B ARG* 3.6 9.6 - - - +
309B HIS* 1.3 81.6 - - - +
311B ARG* 1.3 64.2 + - - +
313B CYS* 3.1 17.5 + - - +
314B ASP* 3.3 11.6 + - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG 3.0 13.2 + - - +
308B GLU* 2.6 50.1 + - - +
310B ASN* 1.3 73.5 - - - +
312B VAL* 1.3 71.9 + - - +
314B ASP* 3.1 21.2 + - - +
315B LEU* 3.3 30.6 + - + +
339B GLU* 4.7 1.2 + - - -
558B LEU* 4.6 11.9 - - - +
566B LYS* 5.8 2.8 - - - +
570B LEU* 3.4 40.7 - - - +
571B ASN* 3.5 20.2 - - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 3.0 35.7 + - - +
309B HIS 4.0 3.8 - - - +
311B ARG* 1.3 77.2 - - - +
313B CYS* 1.3 65.5 + - - +
315B LEU* 2.9 20.2 + - + +
316B LEU* 3.0 35.3 + - + +
332B ALA* 4.6 5.8 - - + -
335B ILE* 3.6 22.7 - - + -
336B LEU* 4.0 15.9 - - + -
339B GLU* 4.3 0.9 - - - +
558B LEU* 3.6 23.1 - - + -
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Residues in contact with CYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ASP* 3.2 17.5 - - - +
250B GLY* 3.0 35.2 - - - -
251B LYS* 4.0 9.2 - - + -
309B HIS* 3.1 26.9 + - - -
310B ASN 3.1 9.7 + - - +
312B VAL* 1.3 75.1 - - - +
314B ASP* 1.3 64.4 + - - +
316B LEU* 3.2 9.0 + - - +
317B LYS* 2.9 24.4 + - - +
328B LEU* 3.9 7.6 - - - +
332B ALA* 3.9 13.0 - - - -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ASP* 5.2 2.6 - - - +
251B LYS* 3.2 34.7 + - - -
310B ASN 3.3 5.3 + - - +
311B ARG* 3.1 14.8 + - - +
313B CYS* 1.3 80.0 - - - +
315B LEU* 1.3 62.4 + - + +
317B LYS* 3.4 7.7 + - - +
318B ALA* 3.2 19.1 + - - +
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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
----------------------------------------------------------
311B ARG* 3.3 27.3 + - + +
312B VAL* 2.9 22.6 + - - +
314B ASP* 1.3 74.4 - - + +
316B LEU* 1.3 72.0 + - + +
318B ALA* 2.9 23.4 + - + +
319B GLU* 3.3 8.8 + - - +
554B VAL* 4.7 16.8 - - + -
558B LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 3.0 46.8 + - + +
313B CYS* 3.5 4.9 - - - +
315B LEU* 1.3 83.8 - - + +
317B LYS* 1.3 50.6 + - - +
319B GLU* 3.2 5.3 + - + -
320B HIS* 2.6 54.2 + - + +
323B TRP* 4.1 4.7 - - + -
328B LEU* 3.4 22.9 - - + +
331B THR* 3.9 19.1 - - + -
332B ALA* 4.7 6.3 - - + +
335B ILE* 3.8 10.3 - - + -
550B PHE 4.1 17.7 - - - +
551B GLY* 4.6 2.5 - - - +
554B VAL* 5.4 4.9 - - + -
555B GLY* 5.1 7.0 - - - +
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASP* 3.7 28.4 + - + +
313B CYS 2.9 15.5 + - - +
314B ASP* 3.6 11.2 - - - +
315B LEU 3.1 0.4 - - - -
316B LEU* 1.3 73.2 - - - +
318B ALA* 1.3 68.9 + - - +
320B HIS 3.3 6.0 - - - +
321B PRO* 3.2 39.8 + - + +
323B TRP 2.9 27.5 + - - -
328B LEU* 3.5 22.9 - - + +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ASP 3.2 9.9 + - - +
315B LEU* 2.9 14.6 + - + +
317B LYS* 1.3 79.1 - - - +
319B GLU* 1.3 71.3 + - - +
321B PRO* 3.7 8.5 - - - +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 4.1 20.7 - - + +
51A GLY* 3.3 14.2 + - - -
315B LEU 3.3 7.6 + - - +
316B LEU* 3.2 9.3 + - + +
318B ALA* 1.3 85.5 - - - +
320B HIS* 1.3 83.4 + - + +
321B PRO* 2.8 12.5 - - - +
551B GLY 5.0 1.6 - - - +
554B VAL* 3.8 33.6 - - + +
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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