Contacts of the helix formed by residues 293 - 317 (chain D) in PDB entry 2GPV
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 SER 293 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D THR 4.0 0.2 + - - -
292D LEU* 1.3 77.3 - - - +
294D LEU* 1.3 63.8 + - - +
295D ALA* 3.6 2.3 + - - -
296D ASP* 2.9 30.5 + - - +
297D GLN* 2.8 21.9 + - - +
383D GLU* 3.3 24.2 + - - +
384D ASP* 6.1 2.6 - - - +
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Residues in contact with LEU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR 5.9 2.2 - - - +
258B PRO* 4.2 19.3 - - + -
451B LEU* 5.8 4.3 - - + -
454B LEU* 4.0 32.3 - - + +
455B GLU* 3.7 30.7 - - + +
292D LEU 3.7 1.0 + - - -
293D SER* 1.3 71.4 - - - +
295D ALA* 1.3 56.2 + - - +
297D GLN* 3.3 21.9 + - - +
298D MET* 2.8 39.6 + - + +
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO* 3.9 24.1 - - + +
259B ASP 4.2 8.7 - - - +
260B SER* 5.9 4.5 - - - -
293D SER* 3.1 1.4 + - - +
294D LEU* 1.3 78.3 - - - +
296D ASP* 1.3 58.5 + - - +
298D MET* 3.6 6.8 - - - +
299D SER* 2.8 30.0 + - - -
381D HIS 5.7 0.7 - - - +
383D GLU* 3.0 41.3 - - + +
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Residues in contact with ASP 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D LEU* 4.3 13.5 - - + +
293D SER* 2.9 24.6 + - - +
295D ALA* 1.3 72.7 - - - +
297D GLN* 1.3 67.7 + - - +
298D MET 3.0 1.6 - - - -
299D SER* 3.1 4.5 + - - -
300D LEU* 2.9 30.8 + - - +
381D HIS 4.3 1.2 - - - +
382D ILE* 3.4 16.6 - - + +
383D GLU* 2.6 31.8 + - - +
384D ASP* 2.9 33.0 + - - +
388D VAL* 4.2 10.6 - - + +
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Residues in contact with GLN 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B LEU* 3.7 31.1 - - + +
284D LYS* 5.1 2.9 - - - +
289D PHE* 3.5 50.4 + - + +
290D SER* 3.5 23.4 + - - +
292D LEU* 2.9 24.4 + - + +
293D SER 2.8 17.9 + - - +
294D LEU* 3.7 25.7 - - - +
296D ASP* 1.3 71.9 - - - +
298D MET* 1.3 56.6 + - - +
300D LEU* 4.0 1.5 - - - +
301D LEU* 3.2 27.0 + - - +
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Residues in contact with MET 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO* 4.9 5.2 - - + -
260B SER* 4.9 3.8 - - - +
447B HIS* 3.0 49.1 - - + +
450B PHE* 3.7 28.3 - - + -
451B LEU* 3.8 25.4 - - + -
454B LEU* 3.8 12.1 - - + -
294D LEU* 2.8 29.5 + - + +
295D ALA* 3.6 7.6 - - - +
297D GLN* 1.3 74.5 - - - +
299D SER* 1.3 54.8 + - - +
301D LEU* 2.9 5.4 + - - +
302D GLN* 2.4 50.5 + - + +
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Residues in contact with SER 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 6.1 0.7 - - - -
295D ALA 2.8 20.2 + - - -
296D ASP* 3.1 5.4 + - - -
298D MET* 1.3 76.3 - - - +
300D LEU* 1.3 63.5 + - - +
302D GLN* 3.2 11.8 + - - +
303D SER* 2.9 28.1 + - - -
379D SER* 3.6 21.2 + - - -
381D HIS* 3.6 14.7 + - - +
382D ILE* 3.9 14.6 - - - -
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Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D PHE* 3.9 16.4 - - + -
292D LEU* 3.4 33.0 - - + -
296D ASP 2.9 15.9 + - - +
297D GLN 4.0 3.1 - - - +
299D SER* 1.3 75.5 - - - +
301D LEU* 1.3 59.0 + - - +
303D SER* 3.3 0.4 + - - -
304D ALA* 2.9 31.5 + - - +
374D LEU* 3.1 31.0 - - + +
375D ALA* 3.8 15.7 - - - +
377D SER* 3.4 14.4 + - - +
378D ASP 5.6 1.1 - - - +
379D SER* 5.2 2.2 - - - +
382D ILE* 4.8 11.4 - - + -
388D VAL* 4.3 17.9 - - + -
391D LEU* 4.6 8.5 - - + -
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B PHE* 3.7 33.2 - - + -
454B LEU* 3.9 28.3 - - + -
279D ILE* 4.5 12.1 - - + -
280D ILE* 4.0 12.3 - - + -
283D ALA* 4.3 14.1 - - + -
289D PHE* 4.2 8.5 - - + -
297D GLN 3.2 15.6 + - - +
298D MET* 2.9 4.7 + - - +
300D LEU* 1.3 77.8 - - - +
302D GLN* 1.3 65.6 + - - +
303D SER 3.1 0.7 + - - -
304D ALA 4.3 0.4 - - - +
305D TRP* 3.2 32.1 + - + +
308D ILE* 4.5 12.8 - - + -
374D LEU* 3.8 18.8 - - + -
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Residues in contact with GLN 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 5.5 2.2 - - - -
261B ASP* 3.7 24.8 + - - +
262B ILE* 4.0 6.4 - - - +
443B LYS* 3.8 22.9 - - + +
446B MET* 5.2 1.7 - - + +
447B HIS* 3.7 31.2 + - - +
450B PHE* 4.8 21.1 - - + -
298D MET* 2.4 38.1 + - + +
299D SER* 3.8 12.8 + - - +
301D LEU* 1.3 68.1 - - - +
303D SER* 1.3 57.7 + - - +
305D TRP* 3.2 23.1 + - - -
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Residues in contact with SER 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D SER 2.9 13.4 + - - -
300D LEU 3.6 0.2 - - - -
302D GLN* 1.3 80.0 - - - +
304D ALA* 1.3 61.9 + - - +
305D TRP* 3.5 3.6 + - - -
306D MET* 4.9 1.6 + - - +
307D GLU* 4.8 5.2 - - - +
377D SER* 3.6 31.8 + - - -
379D SER* 3.4 26.4 + - - -
428D SER* 5.3 4.7 + - - -
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D LEU 2.9 20.3 + - - +
301D LEU 3.3 0.2 + - - -
303D SER* 1.3 72.4 - - - +
305D TRP* 1.3 66.8 + - - +
306D MET 3.3 2.0 - - - -
307D GLU* 2.7 30.9 + - + +
308D ILE* 3.2 10.2 + - + -
373D ALA 4.3 2.0 - - - +
374D LEU* 3.5 37.9 - - + +
377D SER* 3.8 11.4 - - - -
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Residues in contact with TRP 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B MET* 3.3 34.7 - - + -
450B PHE* 4.6 12.3 - + + -
276D LEU* 3.7 30.5 - - + -
279D ILE* 4.7 2.3 - - + +
301D LEU* 3.2 17.8 + - + +
302D GLN* 3.2 30.0 + - - +
303D SER 4.5 2.6 + - - -
304D ALA* 1.3 75.4 - - - +
306D MET* 1.3 107.3 + - + +
308D ILE* 3.1 14.8 + - - +
309D LEU* 3.0 35.2 + - + +
432D VAL* 4.6 12.8 - - + +
435D PHE* 5.4 4.9 - + - -
436D TYR* 4.5 10.1 - + - -
503D OHT 3.8 27.6 - + - -
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Residues in contact with MET 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D SER 4.9 1.3 + - - +
304D ALA 3.0 0.8 + - - -
305D TRP* 1.3 116.1 - - + +
307D GLU* 1.3 57.4 + - - +
309D LEU* 3.2 8.6 + - - +
310D ILE* 2.9 45.1 + - + +
428D SER* 3.6 28.7 - - - +
431D ALA* 3.8 14.1 - - + +
432D VAL* 3.9 31.9 - - + +
435D PHE* 5.2 2.5 - - + -
503D OHT 3.7 32.3 - - + -
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Residues in contact with GLU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PRO* 6.0 0.3 - - - +
303D SER 4.8 7.4 - - - +
304D ALA* 2.7 23.2 + - - +
306D MET* 1.3 74.1 - - - +
308D ILE* 1.3 54.6 + - + +
310D ILE 3.5 0.2 + - - -
311D LEU* 3.0 31.2 + - - +
373D ALA* 4.1 23.2 - - + +
377D SER* 5.0 5.2 - - - +
421D LEU* 4.5 5.0 - - - +
424D LEU* 3.5 34.5 - - + +
425D ARG* 2.9 46.4 + - - +
428D SER* 3.3 25.0 + - - +
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Residues in contact with ILE 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ILE* 3.6 36.6 - - + +
282D TRP* 3.7 26.2 - - + -
301D LEU* 4.5 5.2 - - + -
304D ALA* 3.8 28.3 - - + +
305D TRP* 3.1 7.5 + - - +
307D GLU* 1.3 75.2 - - + +
309D LEU* 1.3 65.7 + - - +
311D LEU* 4.1 4.9 - - - +
312D GLY* 3.2 17.8 + - - -
370D LYS* 3.9 35.6 - - + +
373D ALA* 5.4 1.8 - - + -
374D LEU* 4.2 15.5 - - + +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ALA* 4.1 15.7 - - + +
275D GLU* 3.8 39.3 - - + +
276D LEU* 4.8 4.0 - - + +
279D ILE* 3.8 15.3 - - + -
305D TRP* 3.0 43.1 + - + +
306D MET* 3.4 9.6 - - - +
308D ILE* 1.3 77.6 - - - +
310D ILE* 1.3 57.7 + - - +
312D GLY* 3.1 4.4 + - - -
313D VAL 3.0 24.3 + - - -
316D ARG* 4.9 0.2 + - - -
503D OHT 3.8 50.6 + - + +
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D MET* 2.9 43.1 + - + +
307D GLU 4.0 2.9 - - - +
309D LEU* 1.3 72.2 - - - +
311D LEU* 1.3 61.4 + - - +
313D VAL* 3.1 8.7 - - - +
314D VAL* 2.9 43.1 + - + +
349D ILE* 4.2 24.0 - - + -
352D LEU* 4.6 3.4 - - + -
424D LEU* 3.9 15.9 - - + -
427D THR* 4.0 15.7 - - + +
428D SER* 3.7 19.7 - - - +
431D ALA* 3.9 14.1 - - + -
503D OHT 4.7 10.1 - - + -
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLU 3.0 16.0 + - - +
308D ILE* 4.1 3.8 - - - +
310D ILE* 1.3 72.8 - - - +
312D GLY* 1.3 59.4 + - - +
314D VAL* 3.2 9.6 + - + +
315D TYR* 2.8 27.2 + - - +
352D LEU* 5.5 0.4 - - + -
356D TYR* 3.7 35.2 - - + +
361D LEU* 5.9 1.6 - - + -
366D PHE* 3.3 22.4 - - + +
369D LEU* 4.1 13.5 - - + +
370D LYS* 3.6 39.9 - - + +
373D ALA* 5.3 1.8 - - + -
421D LEU* 5.8 0.7 - - + -
424D LEU* 3.6 27.8 - - + +
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Residues in contact with GLY 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLU* 5.7 1.1 - - - -
308D ILE 3.2 10.1 + - - -
309D LEU* 3.1 9.9 + - - -
311D LEU* 1.3 80.5 - - - +
313D VAL* 1.3 61.2 + - - +
315D TYR* 3.2 9.2 + - - +
316D ARG* 3.1 33.5 + - - +
366D PHE* 3.9 15.4 - - - -
370D LYS* 5.2 2.0 - - - -
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Residues in contact with VAL 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU 3.0 12.1 + - - +
310D ILE* 3.1 31.0 - - - +
312D GLY* 1.3 71.3 - - - +
314D VAL* 1.3 59.6 + - - +
316D ARG* 3.1 18.9 + - - +
317D SER* 2.6 41.4 + - - +
324D LEU* 4.2 9.9 - - + -
325D VAL 3.7 17.5 - - - +
326D TYR* 3.6 40.4 - - + +
349D ILE* 4.0 17.5 - - + -
503D OHT 4.4 2.5 - - + +
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ILE* 2.9 39.9 + - + +
311D LEU* 3.4 10.5 - - + +
313D VAL* 1.3 72.9 - - - +
315D TYR* 1.3 65.9 + - - +
317D SER* 3.1 10.6 + - - -
318D LEU* 3.5 12.2 + - + +
349D ILE* 4.1 16.8 - - + +
352D LEU* 3.9 22.0 - - + -
353D VAL* 3.6 30.1 - - + +
356D TYR* 3.5 32.5 - - + -
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Residues in contact with TYR 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D LEU 2.8 9.9 + - - -
312D GLY 3.6 3.4 - - - +
314D VAL* 1.3 75.1 - - - +
316D ARG* 1.3 70.5 + - + +
317D SER 2.9 1.6 + - - -
318D LEU* 3.1 48.4 + - + +
361D LEU* 4.0 9.9 + - + -
362D GLU* 3.9 5.7 - - - -
363D LYS* 3.2 49.9 + - + +
366D PHE* 3.4 63.3 - + + -
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Residues in contact with ARG 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D LYS* 6.5 0.9 - - - -
249D ILE 5.9 0.2 + - - -
275D GLU* 3.9 15.3 + - - -
312D GLY* 3.1 33.0 + - - +
313D VAL* 3.1 17.6 + - - +
315D TYR* 1.3 84.3 - - + +
317D SER* 1.3 58.9 + - - +
318D LEU 3.4 0.9 + - - -
319D SER* 4.9 1.9 + - - -
320D PHE* 3.8 10.4 - - - -
325D VAL* 3.2 44.8 + - + +
326D TYR 3.1 26.4 + - - -
327D ALA* 4.7 2.3 - - - +
328D ASP* 5.3 6.3 - - - -
366D PHE* 5.7 1.4 - - + -
503D OHT 3.5 20.8 + - - -
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Residues in contact with SER 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D VAL* 2.6 22.0 + - - +
314D VAL 3.5 6.3 - - - -
315D TYR 2.9 1.2 + - - -
316D ARG* 1.3 77.3 - - - +
318D LEU* 1.3 62.8 + - - +
319D SER 3.4 2.5 - - - -
320D PHE* 3.1 26.8 + - - +
323D GLU 3.8 17.2 - - - +
324D LEU* 3.5 9.2 - - - +
325D VAL* 3.1 21.1 + - - -
353D VAL* 3.8 22.3 - - - +
----------------------------------------------------------
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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