Contacts of the helix formed by residues 390 - 413 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D HIS* 5.8 2.0 + - - -
95D MSE 5.6 0.2 - - - +
96D LEU* 3.5 14.8 - - - +
388D GLU* 2.9 33.5 + - + +
389D LEU* 1.3 74.6 - - - +
391D GLU* 1.3 73.4 + - - +
392D TYR* 3.5 9.9 + - - +
393D THR* 2.7 33.7 + - - -
394D PHE 3.0 18.2 + - - -
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Residues in contact with GLU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 3.9 16.1 - - + +
224D GLY 5.0 0.2 - - - +
225D LEU* 3.7 27.9 - - + +
226D ASN* 2.9 54.6 + - - +
229D GLU* 4.3 5.3 - - + +
230D MSE 3.3 23.4 - - + +
390D ASN* 1.3 79.6 - - - +
392D TYR* 1.3 65.7 + - - +
394D PHE* 3.3 2.4 + - - +
395D GLY 3.0 18.5 + - - -
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Residues in contact with TYR 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D HIS* 3.7 42.6 - + + +
229D GLU* 3.4 38.7 + - + +
232D LYS* 3.9 10.8 - - + -
233D GLY* 3.4 37.2 - - - -
236D ALA* 3.3 21.2 - - + +
390D ASN* 3.3 12.4 + - - +
391D GLU* 1.3 76.7 - - - +
393D THR* 1.3 64.5 + - - +
395D GLY 3.2 2.4 + - - -
396D TYR* 3.1 22.2 + + - +
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Residues in contact with THR 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D HIS* 2.8 39.5 + - + +
5D VAL* 4.1 8.3 - - + -
386D ILE* 3.5 22.7 - - + -
387D PRO* 4.2 4.3 - - + +
388D GLU* 3.4 24.7 + - - +
389D LEU* 5.2 0.2 - - - -
390D ASN* 2.7 26.4 + - - -
392D TYR* 1.3 73.5 - - - +
394D PHE* 1.3 60.6 + - - +
396D TYR* 3.7 0.6 - - - +
397D LEU* 2.8 30.9 + - + +
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Residues in contact with PHE 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLY* 4.1 8.5 - - - -
91D ALA* 4.6 1.6 - - + -
92D ALA* 3.4 39.9 - - + -
95D MSE 3.8 28.6 - - + -
96D LEU* 4.0 11.4 - - + -
211D VAL* 4.3 13.5 - - + -
212D LEU* 4.8 2.5 - - + -
230D MSE 3.6 30.5 - - + -
281D PHE* 4.1 18.6 - + - -
284D TRP* 6.3 1.8 - + - -
390D ASN 3.0 14.0 + - - +
391D GLU 3.3 7.8 + - - +
393D THR* 1.3 77.1 - - - +
395D GLY* 1.3 58.1 + - - +
397D LEU* 3.8 5.5 - - + +
398D VAL* 3.0 56.1 + - + +
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Residues in contact with GLY 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D LEU* 4.9 2.5 - - - -
230D MSE 3.5 30.3 - - - -
234D ALA* 3.5 22.2 - - - +
391D GLU 3.0 11.5 + - - -
392D TYR 3.7 0.9 - - - -
394D PHE* 1.3 79.9 - - - +
396D TYR* 1.3 59.8 + - - +
398D VAL* 3.5 4.8 + - - +
399D TYR 3.2 16.8 + - - -
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Residues in contact with TYR 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 3.3 18.5 - - - -
4D HIS* 3.6 22.4 + - + -
5D VAL* 3.3 40.6 - - + -
233D GLY* 3.3 28.8 - - - +
234D ALA* 4.3 0.9 - - - +
236D ALA* 3.7 11.0 - - + -
237D GLY* 3.4 16.4 - - - -
240D ASP* 2.5 35.3 + - - +
241D PHE* 3.5 25.4 - + - -
392D TYR* 3.1 15.6 + + + +
393D THR* 3.7 7.0 - - - +
394D PHE 3.3 0.2 - - - -
395D GLY* 1.3 77.2 - - - +
397D LEU* 1.3 57.3 + - - +
399D TYR* 3.2 4.5 + - - +
400D PHE* 2.9 24.9 + - + +
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Residues in contact with LEU 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 3.9 19.1 - - + -
95D MSE 4.9 12.8 - - + -
278D LEU* 5.6 0.2 - - + -
281D PHE* 3.8 32.3 - - + -
330D LEU* 5.2 0.4 - - + -
384D VAL* 3.8 22.9 - - + -
386D ILE* 3.6 31.0 - - + -
393D THR* 2.8 18.8 + - + +
394D PHE* 3.8 4.7 - - - +
396D TYR* 1.3 74.5 - - - +
398D VAL* 1.3 65.3 + - - +
400D PHE* 3.4 8.0 + - + +
401D PHE* 3.1 50.1 + - + -
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Residues in contact with VAL 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D VAL* 3.8 16.6 - - + -
212D LEU* 4.2 11.9 - - + -
281D PHE* 4.2 7.0 - - + -
284D TRP* 3.8 25.0 - - + -
394D PHE* 3.0 53.1 + - + +
395D GLY* 3.8 5.6 - - - +
396D TYR 3.3 0.2 - - - -
397D LEU* 1.3 75.7 - - - +
399D TYR* 1.3 58.8 + - - +
401D PHE 3.4 1.2 + - - -
402D GLU* 2.9 53.8 + - - +
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Residues in contact with TYR 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TRP* 3.8 18.2 - + - -
49D VAL* 2.7 46.0 + - - +
52D PRO* 3.9 23.1 - - + -
212D LEU* 5.4 1.3 - - + -
234D ALA* 3.9 15.3 - - + +
237D GLY* 3.6 19.7 - - - -
238D ARG* 3.4 25.3 + - + +
241D PHE* 4.2 4.7 - + + -
395D GLY 3.2 14.4 + - - +
396D TYR 3.7 3.8 - - - +
398D VAL* 1.3 80.0 - - + +
400D PHE* 1.3 64.7 + - - +
402D GLU* 3.8 13.6 - - - +
403D LYS* 3.0 50.0 + - + +
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Residues in contact with PHE 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 5.0 9.0 - - + -
6D THR 5.8 0.4 - - - -
7D PHE* 4.3 15.9 - + + -
241D PHE* 3.7 34.9 - + + -
250D PRO* 3.7 11.4 - - + -
251D ALA* 3.5 31.1 - - - +
254D TYR* 4.0 26.5 - + + -
384D VAL* 4.3 13.5 - - + -
396D TYR* 2.9 15.6 + - + +
397D LEU* 3.5 16.2 - - + +
399D TYR* 1.3 77.0 - - - +
401D PHE* 1.3 95.5 + + - +
404D ALA* 3.0 29.8 + - - +
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Residues in contact with PHE 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D TYR* 3.5 34.1 - + - -
271D LEU* 4.4 5.8 - - + -
281D PHE* 3.7 27.8 - + - -
284D TRP* 4.0 4.9 - - + -
285D TRP* 3.5 29.8 - + - -
288D LEU* 3.7 17.7 - - + +
289D PHE* 3.8 5.7 - + + -
330D LEU* 4.0 18.4 - - + -
384D VAL* 4.3 6.7 - - + -
397D LEU* 3.1 43.1 + - + +
398D VAL 4.0 2.2 - - - +
400D PHE* 1.3 93.7 - + - +
402D GLU* 1.3 58.4 + - - +
404D ALA* 4.3 1.6 - - - -
405D CYS* 2.8 31.0 + - - +
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Residues in contact with GLU 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D TRP* 3.7 26.0 - - + +
209D PHE* 3.7 54.9 - - + +
211D VAL* 4.2 5.0 - - - +
212D LEU* 4.9 6.1 - - - +
284D TRP* 4.1 14.9 - - + -
288D LEU* 4.0 4.9 - - + -
398D VAL* 2.9 45.0 + - + +
399D TYR* 3.3 15.8 + - - +
401D PHE* 1.3 71.0 - - - +
403D LYS* 1.3 58.8 + - - +
405D CYS* 3.2 3.8 + - - +
406D ALA* 3.0 27.7 + - - +
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Residues in contact with LYS 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ILE* 4.1 17.2 - - + +
36D HIS* 3.0 39.2 + - - -
48D TRP* 4.0 16.9 - - + -
49D VAL* 4.5 2.0 - - - -
238D ARG 5.2 0.4 + - - -
241D PHE* 2.6 42.9 + - + +
242D GLY* 3.9 0.4 - - - -
251D ALA* 4.3 7.6 - - + -
252D TYR* 3.1 24.3 + - + -
399D TYR* 3.0 44.1 + - + +
400D PHE 4.1 2.2 - - - +
402D GLU* 1.3 73.9 - - - +
404D ALA* 1.3 65.8 + - - +
406D ALA* 3.4 2.3 + - - +
407D MSE 3.2 22.9 + - - +
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Residues in contact with ALA 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ALA* 3.3 30.4 - - + +
254D TYR* 3.7 27.1 - - + -
255D ALA* 3.5 6.9 - - - +
289D PHE* 4.4 1.6 - - + -
400D PHE* 3.0 20.1 + - + +
401D PHE* 3.8 5.2 - - - +
402D GLU 3.3 0.2 - - - -
403D LYS* 1.3 76.9 - - - +
405D CYS* 1.3 57.4 + - - +
407D MSE 3.4 1.2 + - - -
408D SER* 2.8 31.7 + - - -
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Residues in contact with CYS 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D PHE* 4.4 3.6 - - + -
288D LEU* 3.5 29.2 - - + -
289D PHE* 3.7 26.0 - - + -
292D SER* 3.4 35.4 - - - -
293D GLU* 5.2 1.6 - - - -
401D PHE 2.8 19.1 + - - +
402D GLU 3.2 4.5 + - - +
404D ALA* 1.3 74.5 - - - +
406D ALA* 1.3 60.5 + - - +
408D SER* 3.7 1.1 - - - -
409D GLY* 2.9 28.6 + - - -
416D PRO* 4.7 2.0 - - - +
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Residues in contact with ALA 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 4.0 15.9 - - + -
48D TRP* 3.7 34.1 - - + -
209D PHE* 5.0 0.6 - - - -
402D GLU 3.0 5.8 + - - +
403D LYS* 3.6 8.5 - - - +
405D CYS* 1.3 76.3 - - - +
407D MSE 1.3 61.2 + - - +
410D TYR* 3.2 31.0 + - - -
416D PRO* 4.0 4.5 - - - +
417D PHE* 3.9 19.7 - - + -
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Residues in contact with MSE 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 3.6 34.5 - - + +
31D THR* 3.7 31.4 - - + -
32D HIS 3.9 4.9 - - - +
35D ILE* 4.2 7.3 - - + +
252D TYR* 3.5 54.1 - - + +
255D ALA* 3.5 20.4 - - + -
403D LYS 3.2 9.2 + - - +
406D ALA* 1.3 74.9 - - - +
408D SER* 1.3 65.7 + - - +
410D TYR* 3.3 1.6 + - - -
411D LEU* 2.9 46.0 + - + +
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Residues in contact with SER 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ALA* 3.6 13.0 - - - +
258D ARG* 2.8 22.4 + - - -
259D ASN* 2.9 30.8 + - - +
289D PHE* 4.4 1.8 - - - -
293D GLU* 2.6 23.9 + - - +
404D ALA 2.8 23.4 + - - -
405D CYS* 3.7 6.1 - - - -
407D MSE 1.3 73.6 - - - +
409D GLY* 1.3 55.3 + - - +
411D LEU* 4.6 0.2 - - - -
412D LEU* 3.0 25.6 + - - +
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Residues in contact with GLY 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D GLU* 3.1 19.8 + - - -
405D CYS 2.9 15.6 + - - -
406D ALA 4.1 0.9 - - - -
408D SER* 1.3 76.0 - - - +
410D TYR* 1.3 62.4 + - - +
412D LEU* 3.3 2.4 + - - +
413D GLY 3.2 15.9 + - - -
414D VAL* 3.2 21.2 + - - +
416D PRO* 4.0 14.8 - - - -
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Residues in contact with TYR 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 6.5 1.1 - - + -
24A LEU* 5.6 3.1 - - - +
31D THR* 3.3 36.3 - - + +
34D ALA* 5.0 7.5 + - + -
35D ILE* 3.7 26.2 - - + -
40D GLY* 3.8 10.7 + - - -
41D ALA* 2.6 42.3 + - + -
46D LEU* 4.6 9.1 - - + +
406D ALA 3.2 23.0 + - - +
407D MSE 3.8 0.7 - - - +
409D GLY* 1.3 77.3 - - - +
411D LEU* 1.3 58.5 + - - +
413D GLY* 3.0 19.8 + - - -
414D VAL 4.2 6.1 - - - -
416D PRO* 3.7 17.7 - - + +
417D PHE* 3.5 23.2 - + - -
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.9 2.6 - - - +
263A ASN* 5.5 1.2 + - - -
24D LEU* 4.6 12.3 - - + -
27D ALA* 4.1 29.8 - - + -
28D VAL* 4.6 3.6 - - + +
31D THR* 4.5 5.6 - - - +
255D ALA 4.3 5.4 - - - +
256D VAL* 3.8 38.4 - - + +
259D ASN* 4.0 12.8 - - + +
407D MSE 2.9 45.6 + - + +
408D SER 3.7 3.8 - - - +
410D TYR* 1.3 76.5 - - - +
412D LEU* 1.3 59.7 + - - +
413D GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.8 29.7 + - + +
259D ASN* 3.6 16.5 + - - +
262D TYR* 3.9 29.6 - - + -
293D GLU* 3.7 43.5 - - + +
298D LYS* 4.3 13.1 + - + +
299D GLY* 4.0 13.5 - - - +
300D ILE 5.4 0.2 - - - +
408D SER 3.0 17.0 + - - +
409D GLY 3.5 5.6 - - - +
411D LEU* 1.3 76.7 - - - +
413D GLY* 1.3 58.0 + - - +
414D VAL* 4.0 15.5 - - + -
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Residues in contact with GLY 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 4.7 6.4 - - - +
23A TYR* 3.7 19.3 - - - +
24A LEU* 4.1 24.0 - - - +
296D ASP* 4.8 2.1 - - - +
298D LYS* 4.2 11.8 + - - -
409D GLY 3.2 0.4 + - - -
410D TYR 3.0 15.6 + - - -
411D LEU 3.2 1.3 - - - -
412D LEU* 1.3 80.2 - - - +
414D VAL* 1.3 64.3 + - - +
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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