Contacts of the helix formed by residues 325 - 346 (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 ASP 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B ARG* 3.1 14.2 + - - +
247B PHE* 3.1 46.9 + - + +
248B LYS* 2.9 16.0 + - - -
249B ASP 5.0 2.7 - - - +
250B GLY* 2.8 36.5 + - - +
324B GLY* 1.3 67.5 - - - +
326B GLU* 1.3 56.5 + - + +
328B LEU* 2.6 28.6 + - - +
329B PHE* 2.8 11.7 + - - -
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A HIS* 2.8 29.9 + - + +
136A TYR* 3.3 10.3 - - - +
140A GLU* 5.9 0.7 - - - +
238B LEU* 6.0 0.2 - - - +
241B GLN* 4.7 0.7 + - - -
242B TYR* 4.2 17.8 + - - -
245B ARG* 3.2 31.9 + - - +
247B PHE* 5.6 0.9 - - + -
324B GLY 3.6 0.4 - - - -
325B ASP* 1.3 77.4 - - + +
327B GLN* 1.3 66.0 + - - +
329B PHE* 2.9 2.4 + - - -
330B GLN* 2.7 52.4 + - - +
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP 5.3 1.2 + - - -
136A TYR* 2.9 65.5 + - + +
323B TRP* 3.0 57.9 - - + +
324B GLY* 3.4 17.4 + - - +
325B ASP 3.3 0.6 - - - -
326B GLU* 1.3 72.7 - - - +
328B LEU* 1.3 63.1 + - - +
330B GLN* 4.1 0.3 - - - +
331B THR* 3.0 32.7 + - - -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASP* 3.8 29.8 - - - +
250B GLY* 3.9 1.3 - - - -
313B CYS* 3.9 8.5 - - - +
316B LEU* 3.4 33.5 - - + +
317B LYS* 3.5 39.5 - - + +
323B TRP* 3.5 27.1 - - + +
324B GLY 2.9 24.0 + - - +
325B ASP 2.6 11.8 + - - +
327B GLN* 1.3 70.8 - - - +
329B PHE* 1.3 63.7 + - - +
331B THR* 3.1 4.2 + - - +
332B ALA* 2.8 24.9 + - - +
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Residues in contact with PHE 329 (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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234B TYR* 3.8 34.1 - + - -
241B GLN* 3.3 34.8 - - + -
245B ARG* 2.9 56.5 - - + +
250B GLY* 3.7 22.0 - - - +
251B LYS 5.2 0.2 - - - -
252B LEU* 4.2 3.1 - - + -
309B HIS* 3.8 14.9 - + - -
325B ASP 2.8 13.4 + - - +
326B GLU 2.9 4.9 + - - +
328B LEU* 1.3 71.5 - - - +
330B GLN* 1.3 94.7 + - + +
332B ALA* 2.9 14.6 + - - +
333B ARG* 3.0 22.3 + - - +
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A HIS* 4.1 1.3 - - - +
136A TYR* 3.6 21.1 - - + -
137A ILE 5.5 0.4 - - - -
138A SER* 3.2 31.6 + - - -
139A TRP* 3.7 11.3 + - - +
140A GLU* 3.8 19.9 + - - +
241B GLN* 4.6 3.6 + - - +
245B ARG* 4.1 1.0 - - - +
326B GLU* 2.7 50.3 + - - +
329B PHE* 1.3 99.2 - - - +
331B THR* 1.3 62.0 + - - +
333B ARG* 3.4 7.9 + - - +
334B LEU* 3.2 29.1 + - - +
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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
----------------------------------------------------------
136A TYR* 5.1 4.0 - - - +
137A ILE 5.2 3.4 + - - -
316B LEU* 3.9 13.2 - - + -
323B TRP* 3.4 30.4 - - + -
327B GLN* 3.0 27.5 + - - -
328B LEU 3.5 2.5 - - - -
330B GLN* 1.3 73.4 - - - +
332B ALA* 1.3 66.4 + - - +
334B LEU* 3.1 9.2 + - - +
335B ILE* 3.1 22.1 + - + +
549B THR 4.4 7.0 + - - +
550B PHE* 3.7 28.7 - - - +
551B GLY 5.0 0.3 + - - -
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Residues in contact with ALA 332 (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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309B HIS* 3.6 28.5 - - + +
312B VAL* 4.6 10.5 - - + -
313B CYS* 3.9 15.0 - - - +
316B LEU* 4.7 2.0 - - + -
328B LEU 2.8 15.4 + - - +
329B PHE 2.9 7.8 + - - +
331B THR* 1.3 72.8 - - - +
333B ARG* 1.3 64.5 + - - +
335B ILE* 2.9 22.9 + - - +
336B LEU* 2.9 19.0 + - + +
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Residues in contact with ARG 333 (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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139A TRP* 4.0 34.5 - - + +
140A GLU* 5.8 3.0 - - - +
229B ASP* 2.9 31.5 + - - +
230B LEU* 4.5 0.2 - - - +
231B GLY* 4.1 10.5 - - - -
234B TYR* 3.3 56.2 + - + +
235B GLY 4.5 5.7 + - - -
241B GLN* 3.4 24.4 + - - +
329B PHE* 3.0 20.4 + - + +
330B GLN* 3.5 14.4 + - - +
332B ALA* 1.3 76.8 - - - +
334B LEU* 1.3 62.6 + - + +
336B LEU* 4.0 1.8 - - - +
337B ILE* 3.1 33.8 + - + +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 4.3 6.7 - - + +
138A SER* 3.7 8.3 - - - -
139A TRP* 3.3 39.0 - - + +
330B GLN 3.2 20.8 + - - +
331B THR* 3.1 10.8 + - - +
333B ARG* 1.3 79.5 - - - +
335B ILE* 1.3 63.5 + - - +
337B ILE* 3.4 11.0 + - + +
338B GLY 3.1 15.6 + - - -
539B ILE* 3.4 33.4 - - + +
544B TYR* 5.1 5.6 - - + -
549B THR* 4.2 29.2 - - + +
550B PHE* 3.2 18.9 - - + -
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Residues in contact with ILE 335 (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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312B VAL* 3.6 26.7 - - + -
316B LEU* 3.8 13.0 - - + -
331B THR* 3.3 12.8 - - + +
332B ALA 2.9 7.2 + - - +
334B LEU* 1.3 76.6 - - - +
336B LEU* 1.3 58.4 + - - +
338B GLY* 2.8 5.7 + - - -
339B GLU* 2.8 31.0 + - + +
550B PHE* 3.5 43.5 - - + +
555B GLY* 3.6 13.0 - - - +
558B LEU* 3.8 34.1 - - + -
559B VAL* 3.3 7.2 - - + +
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Residues in contact with LEU 336 (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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230B LEU* 3.4 18.6 - - + -
233B ILE* 4.6 5.4 - - + -
234B TYR* 3.7 17.3 - - - +
305B TRP* 3.6 43.5 - - + +
308B GLU* 4.0 1.3 - - + -
309B HIS* 3.8 21.5 - - + +
312B VAL* 4.0 13.9 - - + -
332B ALA 2.9 22.7 + - - +
333B ARG 4.1 2.2 - - - +
335B ILE* 1.3 73.1 - - + +
337B ILE* 1.3 58.2 + - - +
339B GLU* 2.9 24.3 + - - +
340B THR* 2.7 37.4 + - - -
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Residues in contact with ILE 337 (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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139A TRP* 3.8 32.5 - - + -
228B VAL* 3.6 26.2 - - + +
229B ASP 4.2 5.2 - - - +
230B LEU* 3.8 24.2 - - + -
333B ARG* 3.1 36.4 + - + +
334B LEU* 3.6 11.7 - - + +
335B ILE 3.2 0.2 - - - -
336B LEU* 1.3 74.7 - - - +
338B GLY* 1.3 64.0 + - - +
340B THR* 3.4 1.7 + - - -
341B ILE* 3.0 29.3 + - + +
537B ASN* 3.9 12.8 - - - +
539B ILE* 3.8 18.4 - - + -
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Residues in contact with GLY 338 (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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334B LEU 3.1 8.5 + - - -
335B ILE 2.8 10.1 + - - -
337B ILE* 1.3 79.0 - - - +
339B GLU* 1.3 64.1 + - - +
341B ILE* 3.2 4.8 + - - +
342B LYS* 3.1 19.4 + - - +
361B PHE* 4.3 2.9 - - - -
539B ILE* 4.0 12.3 - - - +
559B VAL* 3.6 29.0 - - - +
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Residues in contact with GLU 339 (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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305B TRP* 3.9 14.8 - - + -
308B GLU* 2.7 41.3 - - - +
311B ARG* 4.7 1.2 + - - -
312B VAL* 4.3 1.9 - - - +
335B ILE* 2.8 28.7 + - + +
336B LEU* 3.4 19.4 - - - +
338B GLY* 1.3 69.3 - - - +
340B THR* 1.3 66.7 + - - +
342B LYS* 2.9 14.5 + - - +
343B ILE* 3.0 17.4 + - + +
558B LEU* 4.1 25.5 - - - +
559B VAL* 4.2 1.7 - - - +
562B ALA* 4.0 21.0 - - + +
567B LEU* 5.7 3.3 - - - +
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Residues in contact with THR 340 (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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201B PHE* 5.3 3.1 - - + -
205B PHE* 3.7 32.5 - - + -
228B VAL* 3.8 12.6 - - + -
230B LEU* 3.7 22.1 - - + +
232B HIS* 6.2 0.4 - - - +
305B TRP* 3.4 28.6 - - + +
336B LEU 2.7 21.3 + - - -
337B ILE 3.6 4.3 - - - -
339B GLU* 1.3 72.5 - - - +
341B ILE* 1.3 57.3 + - - +
343B ILE* 3.5 2.7 + - - +
344B VAL* 2.9 37.6 + - + +
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Residues in contact with ILE 341 (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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228B VAL* 4.7 10.1 - - + -
337B ILE* 3.0 33.3 + - + +
338B GLY 3.2 3.1 + - - +
340B THR* 1.3 74.8 - - - +
342B LYS* 1.3 61.6 + - - +
344B VAL* 3.6 5.4 + - - +
345B ILE* 3.2 24.1 + - + +
361B PHE* 3.6 27.6 - - + -
534B LEU* 3.7 47.3 - - + +
537B ASN* 4.2 15.9 - - + +
539B ILE* 4.5 7.2 - - + -
540B CYS* 4.4 10.1 - - - -
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Residues in contact with LYS 342 (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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338B GLY 3.1 10.7 + - - +
339B GLU 2.9 9.4 + - - +
341B ILE* 1.3 74.9 - - - +
343B ILE* 1.3 67.5 + - - +
345B ILE 3.1 1.4 + - - -
346B GLU* 2.9 65.9 + - + +
361B PHE* 4.0 30.3 + - + +
559B VAL 3.1 22.0 - - - +
560B LYS* 3.0 26.3 + - - +
561B THR* 3.9 3.8 - - - +
562B ALA* 3.4 25.4 - - + +
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Residues in contact with ILE 343 (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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201B PHE* 3.8 27.4 - - + -
305B TRP* 4.3 10.1 - - + -
339B GLU* 3.0 17.1 + - + +
340B THR* 4.0 3.8 - - - +
342B LYS* 1.3 75.2 - - - +
344B VAL* 1.3 64.5 + - - +
347B GLU* 3.1 31.2 + - - +
348B TYR 3.0 20.6 + - - -
562B ALA* 4.2 7.6 - - + -
563B THR 3.9 25.1 - - - +
564B LEU* 3.9 7.4 - - + +
567B LEU* 3.7 30.3 - - + -
580B PHE* 4.2 15.9 - - + -
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 3.8 26.0 - - + -
205B PHE* 3.7 34.8 - - + -
340B THR* 2.9 24.9 + - + +
341B ILE* 3.9 5.4 - - - +
342B LYS 3.1 0.2 - - - -
343B ILE* 1.3 77.4 - - - +
345B ILE* 1.3 51.5 + - - +
348B TYR* 3.0 14.5 - - + +
349B VAL* 2.7 39.5 + - + +
530B 0AH 5.6 2.2 - - - +
534B LEU* 3.4 31.9 - - + -
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Residues in contact with ILE 345 (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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113B MET* 4.3 8.5 - - + -
341B ILE* 3.2 16.2 + - + +
342B LYS 3.1 3.1 + - - +
344B VAL* 1.3 75.6 - - - +
346B GLU* 1.3 65.9 + - - +
349B VAL* 3.5 9.9 - - + +
350B GLN 3.5 18.0 + - - -
359B LEU* 3.7 24.4 - - + +
360B LYS 4.2 18.4 - - - +
361B PHE* 3.8 32.8 - - + -
531B LEU* 4.7 10.8 - - + -
534B LEU* 3.6 26.0 - - + -
535B LEU* 4.4 17.7 - - + -
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ARG* 4.2 5.3 + - - -
342B LYS* 2.9 56.7 + - - +
345B ILE* 1.3 76.7 - - + +
347B GLU* 1.3 65.8 + - + +
350B GLN* 3.2 21.9 - - - +
358B GLN* 5.5 4.5 - - + +
359B LEU* 3.4 23.5 - - - +
360B LYS* 3.4 13.0 - - - +
361B PHE* 3.0 29.4 + - + +
562B ALA 5.3 0.7 - - - +
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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) + - + + + + + -
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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