Contacts of the helix formed by residues 307 - 333 (chain B) in PDB entry 1XVP
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 PHE 307 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLU* 3.6 21.8 - - - +
397A TYR* 3.2 66.0 - + + -
398A ALA* 3.6 12.8 - - - -
401A GLU* 3.2 28.5 - - - -
415A PHE* 4.3 12.8 - + - -
305B ASP* 4.1 4.2 - - + +
306B ARG* 1.3 116.6 - - + +
308B LEU* 1.3 63.6 + - - +
309B TYR* 3.3 2.5 - - - -
310B ALA* 3.3 8.4 + - + +
311B LYS* 3.0 25.4 + - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.7 46.9 - - + +
254B LEU* 3.8 11.9 - - + -
258B GLU* 3.6 19.1 - - - +
296B ILE* 4.4 23.6 - - + +
304B ARG* 3.6 34.8 - - + +
305B ASP* 4.4 20.0 - - - +
306B ARG 3.2 5.2 + - - +
307B PHE* 1.3 76.0 - - - +
309B TYR* 1.3 63.3 - - - +
311B LYS* 3.1 9.9 + - + +
312B LEU* 3.0 27.0 + - + +
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 3.9 27.2 + - + +
419A LEU* 5.3 2.5 - - + -
420A LEU* 4.8 3.3 - - - +
265B MET* 3.9 11.8 - - + +
289B ALA* 3.5 22.3 + - - +
292B LEU* 3.5 33.7 - - + -
293B GLN* 3.4 38.4 + - + -
296B ILE* 3.4 20.7 - - + +
297B LYS* 6.5 0.9 - - - -
306B ARG 5.0 0.8 + - - +
307B PHE* 3.3 1.1 - - - -
308B LEU* 1.3 79.2 - - - +
310B ALA* 1.3 64.9 + - + +
312B LEU* 3.0 20.0 + - + +
313B LEU* 3.1 42.7 + - + +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TYR* 3.0 34.8 + - + -
415A PHE* 4.8 5.6 - - + -
419A LEU* 3.5 32.2 - - + +
422A LEU* 6.1 1.0 - - - +
307B PHE* 3.3 19.9 + - + +
309B TYR* 1.3 81.4 - - + +
311B LYS* 1.3 59.1 + - - +
313B LEU* 3.8 6.5 + - - +
314B GLY* 3.6 12.0 + - - -
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLU* 3.1 34.4 + - - +
393A ARG* 4.0 24.3 + - - +
394A GLU* 2.8 32.9 + - - -
397A TYR* 4.1 8.7 - - + -
252B LEU* 4.9 17.0 - - + +
305B ASP* 4.2 26.2 + - - +
307B PHE* 3.0 19.2 + - - +
308B LEU* 3.3 9.4 - - - +
310B ALA* 1.3 74.3 - - - +
312B LEU* 1.3 67.2 + - - +
314B GLY* 3.1 11.3 + - - -
315B LEU* 3.2 18.3 + - + +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 5.1 0.2 - - + -
252B LEU* 3.6 28.7 - - + -
254B LEU* 3.6 28.0 - - + -
258B GLU* 5.3 4.0 - - + +
262B LEU* 4.2 25.4 - - + +
292B LEU* 4.4 20.0 - - + -
296B ILE* 4.3 13.5 - - + -
308B LEU* 3.0 19.2 + - + +
309B TYR* 3.2 18.2 - - + +
311B LYS* 1.3 76.5 - - - +
313B LEU* 1.3 51.0 - - + +
315B LEU* 2.7 32.8 + - + +
316B LEU* 2.8 20.0 + - - +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA 4.5 0.2 - - - +
419A LEU* 3.8 34.3 - - + +
420A LEU* 4.0 20.6 - - + +
422A LEU* 5.0 5.4 - - + +
423A PRO* 3.6 17.0 - - + +
265B MET* 3.6 31.2 - - + -
309B TYR* 3.1 43.8 + - + +
310B ALA 3.9 8.1 - - - +
311B LYS 3.3 0.4 - - - -
312B LEU* 1.3 79.9 - - + +
314B GLY* 1.3 59.8 + - - +
316B LEU* 3.3 18.4 + - + +
317B ALA* 3.3 17.3 + - - +
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASP* 5.6 1.6 - - - -
393A ARG* 4.7 10.1 - - - -
397A TYR* 5.7 0.2 - - - -
422A LEU* 5.8 6.0 - - - +
310B ALA 3.6 6.8 + - - -
311B LYS 3.1 9.6 + - - -
312B LEU 3.0 1.0 - - - -
313B LEU* 1.3 77.1 - - - +
315B LEU* 1.3 57.5 + - - +
317B ALA* 3.3 10.1 - - - +
318B GLU* 3.1 31.2 + - - +
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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
----------------------------------------------------------
379A ASP* 4.7 7.0 - - - +
245B PHE* 3.6 32.0 - - + -
248B THR* 3.5 36.1 - - + -
249B LEU* 4.1 26.2 - - + -
252B LEU* 4.5 12.1 - - + -
262B LEU* 5.8 4.5 - - + -
311B LYS* 3.2 13.0 + - + +
312B LEU* 2.7 15.1 + - + +
314B GLY* 1.3 76.2 - - - +
316B LEU* 1.3 57.3 + - - -
317B ALA 3.0 1.6 - - - -
318B GLU* 3.2 16.1 - - + +
319B LEU* 2.7 34.9 + - + +
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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
----------------------------------------------------------
420A LEU* 6.1 0.2 - - + -
423A PRO* 3.9 12.6 - - + -
200B GLU* 4.1 3.3 - - - +
262B LEU* 3.8 25.3 - - + +
265B MET* 3.9 25.6 - - + -
266B ALA* 3.8 35.4 - - + +
312B LEU 2.8 8.8 + - - +
313B LEU* 3.3 35.0 + - + +
315B LEU* 1.3 77.2 - - - +
317B ALA* 1.3 57.4 + - - +
319B LEU* 3.5 18.7 + - + +
320B ARG* 3.0 35.8 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 4.2 5.2 - - + +
423A PRO* 3.8 11.0 - - + +
426A ARG* 3.0 54.6 + - + +
313B LEU 3.3 9.4 + - - +
314B GLY* 3.3 14.8 - - - +
316B LEU* 1.3 78.2 - - - +
318B GLU* 1.3 57.8 + - - +
320B ARG* 3.6 10.5 - - - -
321B SER 3.1 9.2 + - - -
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 4.8 5.6 + - - +
379A ASP* 4.1 26.3 - - - +
426A ARG* 2.9 34.3 + - - -
241B LEU* 4.7 13.9 - - + +
245B PHE* 3.9 15.7 - - + -
314B GLY 3.1 21.2 + - - +
315B LEU* 2.8 26.6 + - + +
317B ALA* 1.3 76.3 - - - +
319B LEU* 1.3 53.8 - - - +
320B ARG 3.0 1.8 - - - -
321B SER* 3.1 7.2 + - - -
322B ILE* 2.6 43.5 + - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLU* 3.1 57.4 - - + +
203B HIS* 4.3 7.2 - - + -
204B ILE* 3.9 27.6 - - + -
245B PHE* 3.8 30.3 - - + -
262B LEU* 5.5 6.3 - - + -
315B LEU* 2.7 16.0 + - + +
316B LEU* 3.5 26.9 - - + +
318B GLU* 1.3 77.6 - - - +
320B ARG* 1.3 52.9 + - - +
322B ILE* 3.7 11.2 - - + +
323B ASN* 2.8 25.3 + - - +
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 4.7 0.8 - - - +
423A PRO* 3.9 25.7 + - + +
424A ALA 5.0 0.2 - - - +
426A ARG* 3.9 7.9 - - + -
427A SER* 3.0 31.1 + - - +
430A LEU* 3.7 10.1 - - - +
200B GLU* 3.3 21.2 + - - -
266B ALA* 5.0 1.6 + - - +
269B SER* 2.7 29.7 + - - -
271B ASP* 2.7 37.8 + - - -
272B ARG* 3.6 24.9 - - - +
285B GLN* 5.5 1.6 - - - +
316B LEU* 3.0 24.2 + - - +
317B ALA* 3.4 13.9 - - - +
318B GLU 3.0 0.6 - - - -
319B LEU* 1.3 75.6 - - - +
321B SER* 1.3 64.8 + - - +
322B ILE 3.3 0.5 + - - -
323B ASN* 3.5 2.8 + - - +
324B GLU* 3.4 17.3 + - - +
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 3.1 36.8 + - - -
430A LEU* 3.5 21.3 - - - +
241B LEU* 5.4 6.6 - - - +
317B ALA 3.1 1.8 + - - -
318B GLU* 3.4 13.2 - - - -
320B ARG* 1.3 79.5 - - - +
322B ILE* 1.3 58.6 + - - +
324B GLU* 3.8 3.5 + - - +
325B ALA* 3.3 25.1 + - - +
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Residues in contact with ILE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 5.1 2.2 - - + -
200B GLU* 6.0 0.2 - - + -
203B HIS* 4.1 26.2 - - + +
238B PHE* 4.7 5.5 - - + -
241B LEU* 4.5 23.8 - - + +
242B LEU* 3.6 29.2 - - + -
245B PHE* 3.7 36.1 - - + -
318B GLU* 2.6 24.1 + - + +
319B LEU* 3.9 10.3 - - + +
321B SER* 1.3 72.6 - - - +
323B ASN* 1.3 68.5 + - - +
324B GLU 3.1 1.3 - - - -
325B ALA* 3.2 5.6 + - - +
326B TYR* 3.0 25.2 + - + +
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS 4.9 5.3 + - - +
196B GLY 3.0 30.7 + - - +
197B ALA* 4.1 0.4 - - - +
198B ALA 4.8 0.2 - - - +
199B VAL* 3.0 34.8 - - - +
200B GLU* 3.2 29.7 - - + +
272B ARG* 5.9 0.2 - - - +
319B LEU 2.8 20.6 + - - +
320B ARG* 3.5 4.2 + - - +
322B ILE* 1.3 76.9 - - - +
324B GLU* 1.3 61.1 + - - +
326B TYR* 3.5 2.1 + - - +
327B GLY* 3.2 19.9 + - - -
346B ILE* 5.8 0.3 - - - +
347B CYS* 5.4 2.6 - - - -
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Residues in contact with GLU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER 5.3 0.5 - - - +
430A LEU* 3.5 42.6 - - + +
431A LYS* 4.8 4.2 + - - +
433A LEU* 6.0 0.3 - - - +
434A GLU* 3.5 26.2 - - - +
320B ARG 3.4 14.3 + - - +
321B SER 4.0 4.3 - - - +
322B ILE 3.1 0.4 - - - -
323B ASN* 1.3 78.7 - - - +
325B ALA* 1.3 64.0 + - - +
327B GLY* 3.6 2.4 + - - -
328B TYR* 3.6 18.9 + - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 4.1 18.6 - - + -
241B LEU* 4.7 10.8 - - + -
321B SER 3.3 15.7 + - - +
322B ILE* 3.2 7.9 + - - +
324B GLU* 1.3 79.8 - - - +
326B TYR* 1.3 59.9 + - - +
328B TYR* 3.6 7.5 + - - +
329B GLN* 3.1 29.1 + - - +
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Residues in contact with TYR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 4.6 1.8 - + - -
165B ASN* 3.1 36.7 + - - -
199B VAL* 3.6 41.3 - - + -
203B HIS* 5.4 8.3 - + - +
234B PHE* 4.1 24.2 - + - -
238B PHE* 3.9 20.4 - + + -
322B ILE* 3.0 18.1 + - + +
323B ASN 3.9 3.1 - - - +
325B ALA* 1.3 75.1 - - - +
327B GLY* 1.3 69.7 + - - +
328B TYR 3.0 2.2 - - - -
329B GLN* 3.0 14.0 + - - +
330B ILE* 3.2 45.1 + - + +
340B MET* 4.1 3.6 - - - +
343B LEU* 3.7 12.7 - - + +
347B CYS* 4.4 2.5 - - - -
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASN 3.2 13.7 + - - -
324B GLU* 3.6 3.3 + - - -
325B ALA 3.5 0.6 - - - -
326B TYR* 1.3 85.1 - - - +
328B TYR* 1.3 58.1 + - - +
330B ILE* 3.7 9.3 - - - +
331B GLN* 3.0 27.6 + - - +
347B CYS* 4.5 21.5 - - - +
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Residues in contact with TYR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A PRO* 5.6 18.3 - - + +
235B GLN* 3.3 26.9 + - - -
324B GLU 3.6 11.6 + - - +
325B ALA* 3.7 9.4 - - - +
326B TYR 3.0 0.6 - - - -
327B GLY* 1.3 77.5 - - - +
329B GLN* 1.3 77.8 + - - +
331B GLN* 3.1 24.1 + - + +
332B HIS* 3.1 36.0 + - + +
460C GLN* 5.6 14.4 - - + -
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PHE* 3.6 21.8 - - + -
235B GLN* 3.2 52.3 + - - +
238B PHE* 3.5 41.0 - - + +
325B ALA* 3.1 15.7 + - - +
326B TYR* 3.0 8.8 + - - +
328B TYR* 1.3 83.7 - - - +
330B ILE* 1.3 56.8 + - - +
331B GLN 2.8 11.2 + - - -
332B HIS* 3.3 6.4 + - - +
333B ILE* 3.1 29.7 + - - +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PHE* 4.3 3.4 - - + -
326B TYR* 3.2 54.0 + - + +
327B GLY 3.7 15.0 - - - +
328B TYR 3.4 0.2 - - - -
329B GLN* 1.3 73.0 - - - +
331B GLN* 1.3 58.4 + - + +
333B ILE 4.1 4.6 - - - +
336B LEU* 4.0 20.4 - - + -
337B SER* 3.1 39.5 + - - +
340B MET* 3.9 22.2 - - + -
343B LEU* 4.5 12.8 - - + +
344B GLN* 5.2 2.9 - - + +
347B CYS* 4.2 19.3 - - + -
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLY 3.0 24.1 + - - +
328B TYR* 3.3 15.2 - - + +
330B ILE* 1.3 85.7 - - + +
332B HIS* 1.3 64.0 + - - +
333B ILE* 2.9 12.4 + - - +
334B GLN* 4.2 3.1 + - - +
337B SER* 4.7 12.3 - - - +
347B CYS* 5.4 7.1 + - - +
----------------------------------------------------------
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Residues in contact with HIS 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLY* 3.7 14.2 + - - -
235B GLN* 3.2 47.7 + - + +
328B TYR* 3.1 28.7 + - + +
329B GLN* 3.3 7.0 + - - +
331B GLN* 1.3 78.8 - - - +
333B ILE* 1.3 66.7 + - + +
334B GLN* 3.3 13.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 5.9 1.8 - - + -
232B VAL* 3.6 19.1 - - + +
233B GLY* 3.7 17.9 - - - +
234B PHE* 3.6 41.1 - - + +
329B GLN* 3.1 16.6 + - + +
330B ILE 4.1 2.3 - - - +
331B GLN* 2.9 6.2 - - - +
332B HIS* 1.3 80.7 - - + +
334B GLN* 1.3 68.5 + - - +
335B GLY 3.3 0.9 + - - -
336B LEU* 3.0 52.3 + - + +
337B SER* 4.1 3.1 + - - -
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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