Contacts of the helix formed by residues 390 - 413 (chain B) in PDB entry 3IFS
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 ASN 390 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B MSE 5.6 0.2 - - - +
96B LEU* 3.6 14.2 - - - +
388B GLU* 3.5 32.6 + - + +
389B LEU* 1.3 76.2 - - - +
391B GLU* 1.3 73.1 + - - +
392B TYR* 3.5 10.0 + - - +
393B THR* 2.7 33.4 + - - -
394B PHE* 3.0 18.5 + - - +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.0 16.7 - - + +
224B GLY 4.8 0.7 - - - +
225B LEU* 3.5 27.6 - - + +
226B ASN* 2.8 55.7 + - - +
229B GLU* 4.1 5.3 - - + +
230B MSE 3.4 23.5 - - + +
390B ASN* 1.3 81.8 - - - +
392B TYR* 1.3 64.2 + - - +
394B PHE* 3.3 3.1 + - - +
395B GLY 3.1 17.7 + - - -
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Residues in contact with TYR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR 5.1 10.2 + - - -
4B HIS* 5.9 4.6 - - + +
229B GLU* 3.4 38.2 + - + +
232B LYS* 3.9 12.6 - - + -
233B GLY* 3.2 39.8 - - - -
236B ALA* 3.2 20.8 - - + +
390B ASN* 3.3 10.8 + - - +
391B GLU* 1.3 79.2 - - - +
393B THR* 1.3 70.5 + - - +
396B TYR* 3.1 30.7 + + + +
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Residues in contact with THR 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B HIS* 6.5 0.2 - - - -
5B VAL* 4.0 16.2 - - + -
386B ILE* 3.5 23.3 - - + -
387B PRO* 4.5 9.8 - - + +
388B GLU* 3.3 28.3 + - - +
389B LEU* 5.1 0.9 - - + -
390B ASN* 2.7 27.3 + - - -
392B TYR* 1.3 81.9 - - - +
394B PHE* 1.3 60.5 + - - +
396B TYR* 3.3 4.3 + - - +
397B LEU* 2.8 31.1 + - + +
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY* 4.0 10.5 - - - -
91B ALA* 4.3 3.6 - - + -
92B ALA* 3.5 37.9 - - + -
95B MSE 3.7 28.0 - - + -
96B LEU* 4.0 13.9 - - + -
211B VAL* 4.3 14.1 - - + -
212B LEU* 5.1 1.6 - - + -
230B MSE 3.7 27.6 - - + -
281B PHE* 4.0 22.2 - + - -
284B TRP* 6.2 1.8 - + - -
390B ASN 3.0 14.4 + - - +
391B GLU 3.3 7.2 + - - +
393B THR* 1.3 75.8 - - - +
395B GLY* 1.3 58.5 + - - +
397B LEU* 3.6 5.5 - - - +
398B VAL* 2.9 55.6 + - + +
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Residues in contact with GLY 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 5.1 2.9 - - - -
230B MSE 3.5 30.1 - - - -
234B ALA* 3.4 21.7 - - - +
391B GLU 3.1 10.5 + - - -
392B TYR 3.8 0.7 - - - -
394B PHE* 1.3 79.1 - - - +
396B TYR* 1.3 61.2 + - - +
398B VAL* 3.5 5.4 + - - +
399B TYR 3.1 17.7 + - - -
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Residues in contact with TYR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B HIS* 4.3 16.5 - - + +
5B VAL* 3.6 44.3 + - + -
233B GLY 3.2 27.0 - - - +
234B ALA* 4.3 1.1 - - - +
236B ALA* 3.5 12.6 - - + -
237B GLY 3.4 16.2 - - - -
240B ASP* 2.3 40.1 + - - +
241B PHE* 3.5 27.0 - + - -
392B TYR* 3.1 26.2 + + + +
393B THR* 3.6 7.9 - - - +
395B GLY* 1.3 75.7 - - - +
397B LEU* 1.3 57.0 + - - +
399B TYR* 3.3 5.7 + - - +
400B PHE* 3.0 28.3 + - + +
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.1 18.8 - - + +
95B MSE 4.6 15.5 - - + -
281B PHE* 3.7 32.3 - - + -
330B LEU* 4.9 0.9 - - + -
384B VAL* 3.9 22.4 - - + -
386B ILE* 3.7 28.9 - - + -
393B THR* 2.8 18.2 + - + +
394B PHE* 3.6 5.2 - - - +
396B TYR* 1.3 75.3 - - - +
398B VAL* 1.3 66.0 + - - +
400B PHE* 3.3 6.7 + - + +
401B PHE* 3.1 50.1 + - + -
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B VAL* 3.6 18.4 - - + -
212B LEU* 4.1 12.8 - - + -
281B PHE* 4.2 10.1 - - + -
284B TRP* 3.8 17.6 - - + -
394B PHE* 2.9 55.1 + - + +
395B GLY* 3.7 5.8 - - - +
397B LEU* 1.3 75.3 - - - +
399B TYR* 1.3 58.9 + - - +
401B PHE 3.3 0.7 + - - -
402B GLU* 2.9 58.2 + - - +
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Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 3.7 21.3 - + - -
49B VAL* 2.6 45.0 + - - +
52B PRO* 3.9 21.5 - - + -
212B LEU* 5.4 2.0 - - + -
234B ALA* 3.8 14.6 - - + +
237B GLY* 3.5 20.0 - - - -
238B ARG* 3.4 24.1 + - + +
241B PHE* 4.0 5.2 - + + -
395B GLY 3.1 17.4 + - - +
396B TYR 3.3 4.2 + - - +
397B LEU 3.2 0.2 - - - -
398B VAL* 1.3 75.8 - - + +
400B PHE* 1.3 64.8 + - - +
402B GLU* 3.8 14.3 - - - -
403B LYS* 2.9 48.9 + - + +
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Residues in contact with PHE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.9 10.3 - - + -
6B THR 5.7 0.2 - - - -
7B PHE* 4.2 13.5 - - + -
241B PHE* 3.6 34.9 - + + -
250B PRO* 3.7 12.3 - - + -
251B ALA* 3.6 31.1 - - - +
254B TYR* 4.0 25.6 - + + -
384B VAL* 4.0 17.5 - - + -
396B TYR 3.0 14.5 + - - +
397B LEU* 3.4 15.3 - - + +
399B TYR* 1.3 75.3 - - - +
401B PHE* 1.3 98.1 + + - +
403B LYS 3.5 0.2 + - - -
404B ALA* 2.9 30.3 + - - +
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Residues in contact with PHE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.6 34.8 - + - -
271B LEU* 4.5 5.2 - - + -
281B PHE* 3.8 27.1 - + - -
284B TRP* 4.0 5.6 - + + -
285B TRP* 3.7 27.6 - + - -
288B LEU* 3.6 16.1 - - + +
289B PHE* 3.8 5.0 - + + -
330B LEU* 4.0 19.7 - - + -
384B VAL* 4.2 7.6 - - + -
397B LEU* 3.1 42.7 + - + +
398B VAL 4.0 2.2 - - - +
400B PHE* 1.3 94.3 - + - +
402B GLU* 1.3 60.0 + - - +
404B ALA* 4.3 1.3 - - - -
405B CYS* 2.8 32.1 + - - +
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 3.7 27.3 - - + +
209B PHE* 3.7 53.2 - - + +
211B VAL* 4.2 4.7 - - - +
212B LEU* 5.0 6.0 - - - +
284B TRP* 4.1 16.7 - - + -
288B LEU* 4.0 7.4 - - + -
398B VAL* 2.9 40.2 + - - +
399B TYR* 3.8 14.7 - - - +
401B PHE* 1.3 76.8 - - - +
403B LYS* 1.3 58.4 + - - +
405B CYS* 3.2 2.8 + - - +
406B ALA* 3.0 27.9 + - - +
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Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.3 15.0 - - + -
36B HIS* 2.8 35.9 + - - -
48B TRP* 4.0 19.2 - - + -
49B VAL* 4.5 2.7 - - - -
238B ARG* 5.6 0.2 - - - +
241B PHE* 2.9 36.4 + - + +
242B GLY* 4.2 0.4 - - - -
251B ALA* 4.2 6.5 - - + -
252B TYR* 2.8 32.9 + - + +
399B TYR* 2.9 42.7 + - + +
400B PHE 4.0 1.6 - - - +
402B GLU* 1.3 76.6 - - - +
404B ALA* 1.3 63.2 + - - +
406B ALA* 3.4 3.3 + - - +
407B MSE 3.2 22.2 + - - +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA* 3.2 32.0 - - - +
254B TYR* 3.6 27.6 - - + -
255B ALA* 3.4 6.2 - - + +
289B PHE* 4.4 1.1 - - - -
400B PHE* 2.9 20.0 + - + +
401B PHE* 3.8 5.2 - - - +
403B LYS* 1.3 76.1 - - - +
405B CYS* 1.3 57.3 + - - +
407B MSE 3.3 1.5 + - - -
408B SER* 2.8 32.5 + - - -
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Residues in contact with CYS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 4.4 3.8 - - + -
288B LEU* 3.4 28.9 - - + -
289B PHE* 3.6 27.3 - - + -
292B SER* 3.2 37.4 - - - -
293B GLU* 5.2 1.8 - - - -
401B PHE 2.8 17.8 + - - +
402B GLU 3.5 4.9 - - - +
404B ALA* 1.3 73.8 - - - +
406B ALA* 1.3 65.5 + - - +
408B SER* 3.7 1.0 - - - -
409B GLY* 2.9 21.8 + - - -
416B PRO* 4.7 2.0 - - - +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.1 16.6 - - + -
48B TRP* 3.8 20.0 - - + -
209B PHE* 5.1 0.6 - - - -
402B GLU 3.0 12.8 + - - +
403B LYS* 3.6 9.0 - - + +
404B ALA 3.4 0.2 - - - -
405B CYS* 1.3 76.1 - - - +
407B MSE 1.3 63.5 + - - +
409B GLY 3.5 0.2 + - - -
410B TYR* 3.2 30.6 + - - -
416B PRO* 3.9 6.1 - - - +
417B PHE* 3.9 25.1 - - + -
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Residues in contact with MSE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.6 31.2 - - + +
31B THR* 3.7 24.5 - - + -
32B HIS* 3.9 11.7 - - - +
35B ILE* 4.2 5.8 - - + +
252B TYR* 3.5 57.7 - - + +
255B ALA* 3.5 17.5 - - + -
403B LYS 3.2 5.3 + - - +
404B ALA 3.6 7.2 - - - +
406B ALA* 1.3 79.2 - - - +
408B SER* 1.3 58.7 + - - +
410B TYR* 3.3 1.7 + - - +
411B LEU* 2.9 53.3 + - + +
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ALA* 3.8 14.4 - - - -
258B ARG* 2.8 22.1 + - - -
259B ASN* 3.3 26.8 + - - +
289B PHE* 4.4 2.7 - - - -
293B GLU* 2.4 24.4 + - - +
404B ALA 2.8 21.4 + - - -
405B CYS* 3.3 7.8 + - - -
407B MSE 1.3 71.3 - - - +
409B GLY* 1.3 55.9 + - - +
411B LEU 3.2 1.4 + - - -
412B LEU* 2.9 25.5 + - - +
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Residues in contact with GLY 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B SER* 5.9 0.2 - - - -
293B GLU* 3.2 14.3 + - - -
405B CYS 2.9 15.2 + - - -
406B ALA 4.0 1.1 - - - -
408B SER* 1.3 72.9 - - - +
410B TYR* 1.3 66.0 + - - +
412B LEU* 3.2 2.7 + - - +
413B GLY 3.1 16.6 + - - -
414B VAL* 3.1 30.4 + - - +
416B PRO* 4.0 10.5 - - - -
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Residues in contact with TYR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 3.3 35.9 - - + +
34B ALA* 5.2 7.0 + - + -
35B ILE* 3.8 24.9 - - + -
40B GLY* 3.7 11.6 + - - -
41B ALA* 2.5 48.3 + - + -
42B GLY 4.8 1.2 - - - -
43B ASN 4.8 0.2 + - - -
46B LEU* 4.8 6.6 - - + +
406B ALA 3.2 23.4 + - - +
407B MSE 3.8 0.7 - - - +
409B GLY* 1.3 76.0 - - - +
411B LEU* 1.3 63.0 + - - +
413B GLY* 3.0 14.2 + - - -
414B VAL 4.0 6.1 - - - -
416B PRO* 3.7 13.0 - - + +
417B PHE* 3.5 24.9 - + - -
23C TYR* 6.5 1.8 - + + -
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.6 12.1 - - + -
27B ALA* 4.0 28.7 - - + -
28B VAL* 4.5 1.6 - - + +
31B THR* 4.3 8.7 - - - +
255B ALA 4.4 0.2 - - - -
256B VAL* 3.9 34.3 - - + +
259B ASN* 3.8 18.8 - - + +
407B MSE 2.9 51.0 + - + +
408B SER 3.2 4.7 + - - +
410B TYR* 1.3 77.2 - - - +
412B LEU* 1.3 59.9 + - - +
413B GLY* 3.3 0.7 + - - -
263C ASN* 5.5 1.2 + - - -
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 3.7 15.9 + - - +
262B TYR* 3.8 30.1 - - + -
293B GLU* 3.7 43.5 - - + +
298B LYS* 4.2 14.3 + - + +
299B GLY* 3.9 14.8 - - - +
300B ILE 5.3 0.4 - - - +
408B SER 2.9 13.2 + - - +
409B GLY* 3.2 9.8 + - - +
411B LEU* 1.3 76.1 - - - +
413B GLY* 1.3 59.3 + - - +
414B VAL* 4.0 14.8 - - + +
263C ASN* 3.7 29.4 + - + +
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Residues in contact with GLY 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ASP* 4.8 2.4 - - - +
298B LYS* 4.3 10.8 + - - -
410B TYR 3.0 15.1 + - - -
411B LEU 3.1 1.5 - - - -
412B LEU* 1.3 79.8 - - - +
414B VAL* 1.3 63.3 + - - +
20C GLU* 4.8 6.2 - - - +
23C TYR* 3.6 20.9 - - - +
24C LEU* 4.3 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