Contacts of the helix formed by residues 343 - 373 (chain B) in PDB entry 2PID
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 ARG 343 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 3.8 20.5 + - + -
308B ARG* 4.3 12.1 + - - +
309B GLN 3.4 11.3 + - - -
310B PRO* 4.7 2.8 - - - +
311B ASP* 3.8 10.3 + - - -
336B HIS* 4.2 3.8 + - - -
339B GLU 4.2 0.8 + - - -
340B PRO 3.1 17.2 + - - +
341B GLU* 3.3 15.0 - - - +
342B ARG* 1.3 75.8 - - - +
344B GLY* 1.3 64.4 + - - +
345B PRO* 3.5 2.9 - - - -
346B GLN* 3.3 43.7 + - + +
347B LYS* 3.1 31.9 + - + +
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Residues in contact with GLY 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ILE* 4.6 3.6 - - - -
336B HIS* 4.2 2.2 - - - +
342B ARG* 3.1 11.4 - - - +
343B ARG* 1.3 75.5 - - - +
345B PRO* 1.3 72.8 - - - +
347B LYS* 3.2 7.7 + - - +
348B ARG* 2.9 24.6 + - - +
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Residues in contact with PRO 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B VAL* 3.3 25.3 - - + +
318B LEU* 4.1 4.9 - - + +
332B ILE* 3.6 26.0 - - + +
333B MET* 3.7 17.5 - - - -
336B HIS* 3.4 44.0 - - + +
343B ARG 3.6 1.3 - - - -
344B GLY* 1.3 88.3 - - - +
346B GLN* 1.3 66.0 + - - +
348B ARG* 3.1 4.1 + - + +
349B LEU* 2.9 24.1 + - - +
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Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE 4.2 4.5 - - - +
307B VAL* 3.1 39.8 - - + +
309B GLN* 2.9 26.6 + - + +
310B PRO 3.9 0.6 - - - -
311B ASP* 2.7 37.1 + - - +
314B VAL* 3.6 17.6 - - + +
336B HIS* 4.0 1.2 + - - -
343B ARG* 3.3 35.5 - - + +
344B GLY 3.3 0.2 - - - -
345B PRO* 1.3 80.1 - - - +
347B LYS* 1.3 56.4 + - - +
349B LEU* 3.3 4.9 + - - +
350B ALA* 2.8 30.7 + - - +
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 4.1 19.1 + - - +
307B VAL* 4.1 15.5 - - + -
341B GLU 5.4 0.6 + - - -
342B ARG* 3.1 28.7 + - - +
343B ARG* 3.1 19.7 + - - +
344B GLY* 3.8 5.2 - - - +
346B GLN* 1.3 73.5 - - - +
348B ARG* 1.3 66.3 + - - +
350B ALA* 3.9 0.9 - - - +
351B ALA* 3.0 26.0 + - - +
370B THR* 6.2 4.3 - - + -
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 4.4 3.6 - - + -
324B LEU* 3.5 26.3 - - + +
328B GLU* 2.7 36.5 + - - -
332B ILE* 3.5 24.9 - - + +
344B GLY 2.9 13.9 + - - +
345B PRO* 3.5 9.2 - - + +
347B LYS* 1.3 76.9 - - - +
349B LEU* 1.3 64.7 + - - +
351B ALA* 3.4 5.4 + - - +
352B GLU* 3.1 50.4 + - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE* 3.8 38.1 - - + +
309B GLN* 4.3 3.6 - - + -
314B VAL* 4.5 12.3 - - + +
317B TYR* 3.6 50.9 - - + +
318B LEU* 3.7 13.8 - - + +
321B PHE* 4.0 11.9 - - + -
322B THR* 3.9 15.5 - - + -
345B PRO 2.9 17.7 + - - +
346B GLN 3.5 2.5 - - - +
348B ARG* 1.3 76.3 - - - +
350B ALA* 1.3 63.8 + - - +
352B GLU* 3.3 1.7 + - - +
353B VAL* 3.2 27.7 + - + +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 3.4 50.7 - - + +
306B PHE* 3.9 11.4 - - - -
307B VAL* 3.9 7.0 - - + +
346B GLN 2.8 18.7 + - - +
347B LYS 3.9 0.7 - - - +
349B LEU* 1.3 77.0 - - - +
351B ALA* 1.3 55.4 + - - +
353B VAL* 4.2 0.7 - - - +
354B THR* 2.6 38.1 + - - -
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 3.9 3.7 - - + -
347B LYS 3.0 18.3 + - - +
348B ARG* 3.8 7.4 - - - +
350B ALA* 1.3 75.0 - - - +
352B GLU* 1.3 67.8 + - + +
355B LYS* 3.0 28.3 + - - +
363B LEU* 3.6 31.9 - - + +
367B LYS* 5.8 2.7 - - + -
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PHE* 3.6 33.9 - - + -
321B PHE 5.6 0.7 - - - -
322B THR* 3.9 22.1 - - + -
323B PHE* 5.3 0.9 + - - +
324B LEU* 3.4 32.4 - - + +
348B ARG* 3.1 45.2 + - - +
349B LEU 3.3 4.2 + - - +
351B ALA* 1.3 79.9 - - - +
353B VAL* 1.3 62.2 + - - +
355B LYS* 3.7 11.7 + - - +
356B LEU* 3.2 17.7 + - - +
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.8 22.0 - - + -
302B LEU* 4.6 1.6 - - + -
306B PHE* 3.5 38.1 - - + -
321B PHE* 3.7 38.6 - - + +
349B LEU* 3.2 24.0 + - + +
350B ALA 4.4 0.2 - - - +
352B GLU* 1.3 75.0 - - + +
354B THR* 1.3 67.3 + - - +
356B LEU* 3.1 7.6 + - + +
357B VAL* 2.8 29.3 + - + +
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Residues in contact with THR 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO* 4.1 15.7 - - + +
302B LEU* 4.2 10.7 - - + +
303B TYR* 3.5 23.4 + - - +
306B PHE* 5.5 0.3 - - - -
350B ALA 2.6 24.0 + - - -
353B VAL* 1.3 76.5 - - - +
355B LYS* 1.3 54.8 + - - +
358B HIS* 2.7 43.3 + - + +
359B GLY 3.7 0.4 + - - -
362B GLY 3.9 8.1 - - - +
363B LEU* 3.8 33.7 - - - +
366B ALA* 4.1 5.4 - - + -
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 4.1 0.5 + - - -
158B LEU* 3.5 36.8 + - + +
159B PHE* 3.6 25.5 - - + -
351B ALA 3.0 19.1 + - - +
352B GLU* 3.7 13.3 + - - +
354B THR* 1.3 79.6 - - - +
356B LEU* 1.3 56.9 + - - +
359B GLY* 2.8 39.6 + - - -
360B ARG* 4.2 27.1 - - + +
363B LEU* 4.2 16.7 - - + +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.6 17.3 - - + -
96B LEU* 3.8 29.4 - - + -
99B PHE* 4.2 11.2 - - + -
151B LEU* 3.6 15.5 - - + +
154B ASN* 3.0 22.2 + - - +
155B HIS* 3.8 39.7 - - + +
159B PHE* 3.7 19.7 - - + -
321B PHE 5.2 4.9 - - - +
323B PHE* 4.7 6.5 - - + -
352B GLU 3.2 12.5 + - - +
353B VAL* 3.1 10.6 + - + +
355B LYS* 1.3 77.9 - - - +
357B VAL* 1.3 61.3 + - + +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.1 17.0 - - + -
150B ALA* 5.9 1.4 - - - +
151B LEU* 3.7 15.8 - - + +
154B ASN* 3.5 8.9 + - - -
292B LEU* 3.7 33.8 - - + +
302B LEU* 3.5 20.6 - - + -
353B VAL* 2.8 30.8 + - + +
356B LEU* 1.3 83.2 - - + +
358B HIS* 1.3 86.8 + - + +
----------------------------------------------------------
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Residues in contact with HIS 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 4.0 3.6 - - - +
291B TRP 5.1 0.2 + - - -
292B LEU* 3.3 28.1 + - - -
294B ARG* 3.9 32.0 - - + +
297B THR 4.3 3.6 + - - -
299B PRO* 3.6 32.8 - - + +
302B LEU* 3.6 29.7 - - + +
354B THR* 2.7 18.2 + - + +
357B VAL* 1.3 85.3 + - + +
359B GLY* 1.3 64.0 + - - +
361B GLU* 4.3 4.9 + - - +
362B GLY* 3.2 28.1 + - - -
----------------------------------------------------------
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Residues in contact with GLY 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 3.4 13.5 - - - +
158B LEU* 3.6 11.0 - - - -
355B LYS* 2.8 31.8 + - - -
358B HIS* 1.3 82.6 - - - +
360B ARG* 1.3 64.9 + - - -
361B GLU* 3.3 0.9 - - - -
363B LEU 3.1 13.5 + - - -
----------------------------------------------------------
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLN 5.3 1.8 + - - -
158B LEU* 3.9 37.1 + - + +
355B LYS* 4.2 25.5 - - + +
359B GLY* 1.3 69.0 - - - -
361B GLU* 1.3 67.7 + - - +
363B LEU* 3.2 9.6 + - + +
364B ASP* 2.9 36.0 + - - +
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Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 3.2 38.0 + - - -
358B HIS 4.6 4.4 - - - +
359B GLY* 5.7 0.2 - - - -
360B ARG* 1.3 78.0 - - - +
362B GLY* 1.3 66.7 + - - +
364B ASP* 3.3 8.5 + - - +
365B SER* 3.1 26.5 + - - -
368B ARG* 5.2 5.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 5.1 0.2 - - - -
299B PRO* 3.5 16.5 - - - +
354B THR* 4.0 6.5 - - - -
358B HIS* 3.2 31.6 + - - -
359B GLY 3.7 0.4 - - - -
361B GLU* 1.3 87.6 + - - +
363B LEU* 1.3 55.3 + - - +
365B SER* 3.5 2.4 + - - -
366B ALA* 2.9 28.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 4.1 9.0 - - + -
351B ALA* 3.6 47.8 - - + +
354B THR* 3.8 18.7 - - + +
355B LYS* 4.2 20.9 - - + +
359B GLY 3.1 12.3 + - - +
360B ARG* 3.7 10.5 - - + +
362B GLY* 1.3 76.9 - - - +
364B ASP* 1.3 53.2 + - - +
366B ALA* 3.2 2.3 + - - +
367B LYS* 2.8 66.1 + - + +
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ARG* 2.9 30.5 + - - +
361B GLU* 3.6 7.7 - - - +
363B LEU* 1.3 75.4 - - - +
365B SER* 1.3 61.1 + - - +
367B LYS* 3.1 24.0 + - - +
368B ARG* 2.8 46.5 + - + +
----------------------------------------------------------
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Residues in contact with SER 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ARG* 4.0 21.1 + - - -
299B PRO* 4.3 7.8 - - - +
300B PHE* 5.0 2.1 + - - +
361B GLU* 3.1 17.6 + - - -
362B GLY 3.7 4.5 + - - -
364B ASP* 1.3 77.5 - - - +
366B ALA* 1.3 65.9 + - - +
368B ARG* 3.0 26.6 + - - +
369B CYS* 3.1 30.6 + - - -
----------------------------------------------------------
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Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO 4.2 0.7 - - - +
300B PHE* 3.7 22.2 - - - +
303B TYR* 3.9 35.4 - - + -
354B THR* 4.1 5.2 - - + -
362B GLY 2.9 15.6 + - - +
363B LEU* 3.3 12.1 - - - +
365B SER* 1.3 79.4 + - - +
367B LYS* 1.3 56.9 + - - +
369B CYS 3.5 0.3 + - - -
370B THR* 3.0 32.0 + - - -
----------------------------------------------------------
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Residues in contact with LYS 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 4.9 9.0 - - + +
351B ALA* 5.8 2.9 - - + -
363B LEU* 2.8 53.5 + - + +
364B ASP* 3.1 25.6 + - - +
366B ALA* 1.3 72.5 - - - +
368B ARG* 1.3 64.1 + - - +
370B THR* 3.7 5.9 - - - -
371B GLN* 2.8 44.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLU* 5.2 4.2 + - - -
364B ASP* 2.8 26.4 + - + +
365B SER* 3.0 45.8 - - - +
367B LYS* 1.3 73.7 - - - +
369B CYS* 1.3 60.1 + - - +
371B GLN* 3.3 11.8 + - - +
372B ALA* 3.0 28.2 + - - +
----------------------------------------------------------
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Residues in contact with CYS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.5 40.2 - - + -
365B SER* 3.1 18.4 + - - -
366B ALA 3.7 2.2 - - - +
368B ARG* 1.3 82.7 - - - +
370B THR* 1.3 61.1 + - - +
372B ALA* 3.4 8.1 + - - +
373B LEU* 3.2 26.7 + - - +
----------------------------------------------------------
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Residues in contact with THR 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.5 15.8 - - - -
303B TYR* 3.4 33.4 - - + +
304B GLN* 4.1 4.3 + - - +
307B VAL* 6.2 1.3 - - + -
347B LYS* 6.2 4.3 - - + -
366B ALA 3.0 17.5 + - - -
367B LYS* 3.2 8.3 + - - -
369B CYS* 1.3 76.5 - - - +
371B GLN* 1.3 65.4 + - + +
373B LEU* 3.5 18.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LYS* 2.8 38.1 + - - +
368B ARG* 3.5 10.1 - - - +
370B THR* 1.3 77.1 - - + +
372B ALA* 1.3 68.0 + - - +
373B LEU 3.1 5.9 + - - -
----------------------------------------------------------
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ARG 3.0 12.8 + - - +
369B CYS* 3.5 13.0 - - - +
371B GLN* 1.3 77.6 - - - +
373B LEU* 1.3 66.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.7 29.6 - - + -
304B GLN* 5.0 4.3 - - - +
369B CYS 3.2 12.7 + - - +
370B THR* 3.8 12.8 - - - +
371B GLN 3.1 8.3 + - - -
372B ALA* 1.3 85.4 - - + +
----------------------------------------------------------
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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