Contacts of the helix formed by residues 296 - 319 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A LEU* 1.3 83.5 - - - +
297A GLY* 1.3 51.6 + - - +
299A MET* 4.5 8.3 - - + -
300A LEU* 2.7 38.0 + - - +
407A PHE* 3.2 61.7 - - + +
410A ASN* 4.4 13.7 - - + +
413A MET* 4.3 23.8 - - + -
414A LEU* 4.6 13.3 - - + +
422A LEU* 4.7 7.2 - - + -
426A PHE* 4.9 1.6 - - + -
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Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE* 3.8 40.2 - - - -
295A LEU* 2.7 7.5 + - - +
296A PRO* 1.3 79.8 - - - +
298A LEU* 1.3 62.7 + - - +
300A LEU* 3.1 13.5 - - - +
301A TYR* 3.3 12.6 + - - -
407A PHE* 4.1 4.9 - - - -
426A PHE* 4.1 9.0 - - - -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE* 4.3 4.7 - - + +
203A GLN* 3.2 40.6 - - + +
204A HIS* 3.7 22.5 + - + +
207A HIS* 5.9 1.8 - - + -
291A VAL* 5.1 5.8 - - + +
292A PHE* 3.5 48.0 - - + +
294A LEU* 5.1 2.7 - - + +
295A LEU* 2.7 39.9 + - + +
297A GLY* 1.3 70.8 - - - -
299A MET* 1.3 64.3 + - - +
300A LEU 2.9 1.0 + - - -
301A TYR* 3.0 6.1 + - - +
302A ALA* 2.9 22.1 + - - +
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Residues in contact with MET 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PRO* 4.5 2.5 - - - -
275A TYR* 4.7 3.4 - - - +
285A MET* 3.9 35.7 - - - +
287A VAL* 3.7 31.0 - - + -
292A PHE* 2.8 40.2 - - + +
293A GLY* 3.5 15.0 - - - +
295A LEU 3.3 7.1 + - - +
296A PRO* 4.1 9.4 - - + +
298A LEU* 1.3 79.1 - - - +
300A LEU* 1.3 57.0 + - - +
302A ALA* 3.6 5.0 - - + +
303A THR* 2.9 30.7 + - - +
414A LEU* 4.0 14.6 - - + -
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A MET* 4.6 6.1 - - - -
200A PHE* 6.4 0.2 - - + -
296A PRO 2.7 23.9 + - - +
297A GLY* 3.1 8.7 - - - +
298A LEU 2.9 0.2 + - - -
299A MET* 1.3 74.9 - - - +
301A TYR* 1.3 75.8 + - + +
303A THR* 3.1 10.2 + - - -
304A ILE* 3.1 23.6 + - + +
414A LEU* 3.8 20.8 - - + +
419A VAL* 3.7 44.4 - - + +
422A LEU* 4.4 5.6 - - + -
423A VAL* 3.7 20.0 - - + -
426A PHE* 4.3 24.0 - - + -
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Residues in contact with TYR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A MET* 2.8 51.2 + - + +
200A PHE* 3.8 11.4 - - + -
201A PHE* 3.2 59.2 - + - +
204A HIS* 4.0 23.6 - + + +
297A GLY 3.3 10.7 + - - -
298A LEU 3.0 7.1 + - - +
300A LEU* 1.3 84.7 - - + +
302A ALA* 1.3 64.0 + - - +
304A ILE* 2.9 22.4 + - + +
305A TRP* 2.9 37.8 + + + -
426A PHE* 6.5 0.4 - + - -
564A LEU* 4.4 10.4 - - + +
567A LEU* 5.4 3.4 - - + -
580A PHE* 3.6 3.5 - - - -
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A HIS* 3.9 16.9 - - + -
232A HIS 6.0 1.3 - - - +
233A ILE* 5.8 4.0 - - + +
263A PRO* 4.8 3.8 - - + +
287A VAL* 4.6 21.9 - - + +
292A PHE* 4.6 9.6 - - + -
298A LEU 2.9 13.4 + - - +
299A MET* 3.6 15.0 - - + +
301A TYR* 1.3 75.7 - - - +
303A THR* 1.3 58.2 + - - +
305A TRP* 4.3 3.3 - - - +
306A LEU* 3.1 27.4 + - - +
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Residues in contact with THR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A VAL 3.8 4.9 - - - +
262A TYR* 3.8 10.7 - - + -
263A PRO* 2.9 29.8 - - - +
299A MET 2.9 12.6 + - - -
300A LEU* 3.5 7.2 - - - -
301A TYR 3.1 0.2 - - - -
302A ALA* 1.3 75.6 - - - +
304A ILE* 1.3 67.1 + - - +
306A LEU* 3.1 5.7 + - - +
307A ARG* 2.8 56.6 + - - +
414A LEU* 3.9 6.6 - - + +
419A VAL* 3.7 16.2 - - + -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A MET* 5.0 0.2 - - + -
300A LEU* 3.1 34.5 + - + +
301A TYR* 2.9 21.9 + - + +
303A THR* 1.3 75.9 - - - +
305A TRP* 1.3 59.4 + - + +
307A ARG* 3.0 11.5 + - - +
308A GLU* 2.8 26.7 + - - +
419A VAL* 4.1 17.3 - - + -
423A VAL* 4.1 8.5 - - + -
567A LEU* 3.5 46.4 - - + +
568A VAL* 4.1 23.1 - - + -
571A ASN* 3.9 4.4 + - + +
572A THR* 6.1 0.4 - - + -
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Residues in contact with TRP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE* 4.7 16.1 - + - -
204A HIS* 3.7 30.3 + + - -
232A HIS* 5.9 1.3 - + - -
233A ILE* 3.4 29.6 - - + +
301A TYR* 2.9 25.4 + + + +
302A ALA* 4.3 2.5 - - - +
304A ILE* 1.3 77.4 - - + +
306A LEU* 1.3 62.0 + - - +
308A GLU* 3.4 4.3 + - + +
309A HIS* 3.1 22.3 + - - +
336A LEU* 3.6 36.6 - - + +
339A GLU* 3.9 16.8 - - + -
340A THR* 3.4 43.7 - - + -
343A ILE* 4.3 6.7 - - + -
567A LEU* 3.3 42.6 - - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 5.3 4.7 - - + +
252A LEU* 4.3 24.2 - - + -
253A LYS 3.4 24.5 - - - +
254A TYR* 4.1 18.2 - - + -
261A VAL* 4.9 4.0 - - + -
262A TYR* 4.8 5.8 - - - +
263A PRO* 4.1 23.6 - - + -
264A PRO* 4.7 1.8 - - + -
302A ALA 3.1 18.3 + - - +
303A THR* 3.1 7.2 + - - +
305A TRP* 1.3 72.5 - - - +
307A ARG* 1.3 82.1 + - + +
308A GLU 3.1 0.3 + - - -
309A HIS* 3.1 7.4 + - - +
310A ASN* 3.0 29.4 + - - +
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 4.3 20.5 + - - +
261A VAL* 2.7 65.9 + - + +
262A TYR* 4.2 6.3 + - - -
303A THR* 2.8 28.8 + - - +
304A ILE* 3.3 9.9 - - - +
306A LEU* 1.3 86.9 - - + +
308A GLU* 1.3 61.8 + - - +
310A ASN* 3.2 4.8 + - - +
311A ARG* 3.0 21.5 + - - +
419A VAL* 3.6 25.2 - - - +
420A GLU* 4.6 0.8 + - - -
571A ASN* 2.9 45.4 + - + +
572A THR* 3.5 20.6 - - - +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE 2.8 10.7 + - - +
305A TRP* 3.5 17.0 - - + +
307A ARG* 1.3 72.7 - - - +
309A HIS* 1.3 66.9 + - - +
311A ARG* 2.6 51.7 + - - +
312A VAL* 3.0 18.2 + - - +
336A LEU* 4.0 11.0 - - + -
339A GLU* 2.7 38.6 - - - +
558A LEU* 4.9 0.2 - - - +
567A LEU* 4.1 15.4 - - + -
570A LEU* 5.4 0.5 - - - +
571A ASN* 3.1 24.3 + - - +
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Residues in contact with HIS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ILE* 5.5 0.4 - - + -
234A TYR* 2.5 43.1 + + + +
250A GLY 2.8 27.3 + - - -
252A LEU* 3.5 25.1 + - + +
305A TRP 3.1 11.6 + - - +
306A LEU 3.1 6.3 + - - +
308A GLU* 1.3 78.4 - - - +
310A ASN* 1.3 79.7 + - - +
312A VAL* 3.5 2.2 + - - +
313A CYS* 3.1 22.2 + - - -
329A PHE* 3.8 17.8 - + - -
332A ALA* 3.6 24.7 - - + +
336A LEU* 3.8 14.8 - - + +
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Residues in contact with ASN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 3.3 21.1 - - + +
252A LEU* 2.7 35.3 + - - +
254A TYR* 2.8 44.6 - - + -
261A VAL* 5.5 0.4 - - - +
306A LEU* 3.0 19.3 + - + +
307A ARG* 3.6 9.2 - - - +
308A GLU 3.0 0.2 + - - -
309A HIS* 1.3 81.7 - - - +
311A ARG* 1.3 62.2 + - - +
313A CYS* 3.1 17.3 + - - +
314A ASP* 3.3 12.3 + - - +
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ARG 3.0 12.2 + - - +
308A GLU* 2.6 50.7 + - - +
310A ASN* 1.3 74.4 - - - +
312A VAL* 1.3 73.7 + - - +
314A ASP* 3.1 21.3 + - - +
315A LEU* 3.3 31.0 + - + +
339A GLU* 4.7 1.0 + - - -
558A LEU* 4.6 11.7 - - - +
566A LYS* 5.8 2.8 - - - +
570A LEU* 3.4 40.5 - - - +
571A ASN* 3.5 20.0 - - - +
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLU* 3.0 36.2 + - - +
309A HIS 4.0 4.0 - - - +
311A ARG* 1.3 76.1 - - - +
313A CYS* 1.3 65.7 + - - +
315A LEU* 2.9 20.2 + - + +
316A LEU* 3.0 34.8 + - + +
332A ALA* 4.6 5.8 - - + -
335A ILE* 3.6 24.2 - - + -
336A LEU* 4.0 15.9 - - + -
339A GLU* 4.3 0.4 - - - +
558A LEU* 3.6 22.4 - - + -
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Residues in contact with CYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ASP* 3.2 17.5 - - - +
250A GLY* 3.0 35.7 - - - -
251A LYS* 4.0 8.7 - - + -
309A HIS* 3.1 27.5 + - - -
310A ASN 3.1 10.0 + - - +
312A VAL* 1.3 75.6 - - - +
314A ASP* 1.3 63.8 + - - +
316A LEU* 3.2 8.8 + - - +
317A LYS* 2.9 23.8 + - - +
328A LEU* 3.9 7.5 - - - +
332A ALA* 3.9 13.0 - - - -
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ASP* 5.2 2.6 - - - +
251A LYS* 3.2 34.2 + - - -
310A ASN 3.3 5.4 + - - +
311A ARG* 3.1 15.1 + - - +
313A CYS* 1.3 80.5 - - - +
315A LEU* 1.3 61.5 + - + +
317A LYS* 3.4 7.9 + - - +
318A ALA* 3.2 19.1 + - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG* 3.6 27.8 - - + +
312A VAL* 2.9 24.0 + - + +
314A ASP* 1.3 73.4 - - + +
316A LEU* 1.3 73.1 + - + +
318A ALA* 2.9 23.4 + - + +
319A GLU* 3.3 9.3 + - - +
554A VAL* 4.7 15.7 - - + -
558A LEU* 3.8 29.2 - - + -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A VAL* 3.0 47.9 + - + +
313A CYS* 3.5 4.9 - - - +
315A LEU* 1.3 82.5 - - + +
317A LYS* 1.3 51.7 + - - +
319A GLU* 3.2 5.1 + - + -
320A HIS* 2.6 53.9 + - + +
323A TRP* 4.1 4.3 - - + -
328A LEU* 3.4 21.8 - - + +
331A THR* 3.9 18.8 - - + -
332A ALA* 4.7 6.3 - - + +
335A ILE* 3.8 11.0 - - + -
550A PHE 4.1 18.2 - - - +
551A GLY* 4.6 2.2 - - - +
554A VAL* 5.4 4.7 - - + -
555A GLY* 5.1 6.7 - - - +
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ASP* 3.7 27.3 - - + +
313A CYS 2.9 16.6 + - - +
314A ASP* 3.6 11.0 - - - +
316A LEU* 1.3 73.2 - - - +
318A ALA* 1.3 68.4 + - - +
320A HIS 3.9 5.4 - - - +
321A PRO* 3.2 39.5 + - - +
323A TRP 2.9 27.1 + - - -
328A LEU* 3.5 23.5 - - + +
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASP 3.2 10.5 + - - +
315A LEU* 2.9 14.4 + - + +
317A LYS* 1.3 79.1 - - - +
319A GLU* 1.3 71.6 + - - +
321A PRO* 3.7 8.5 - - - +
51B GLY* 5.8 0.2 - - - -
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU 3.3 7.1 + - - +
316A LEU* 3.2 8.8 + - + +
318A ALA* 1.3 85.6 - - - +
320A HIS* 1.3 85.5 + - + +
321A PRO* 2.8 12.1 - - - +
551A GLY 5.0 1.3 - - - +
554A VAL* 3.8 33.5 - - + +
50B PHE* 4.0 19.9 - - + +
51B GLY* 3.2 14.7 + - - -
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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