Contacts of the helix formed by residues 391 - 416 (chain D) in PDB entry 3IKM
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 ASP 391 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D TRP* 4.9 7.8 + - - +
387D GLU 5.3 1.1 - - - +
388D ASN 3.7 3.2 + - - +
389D PHE 3.1 1.4 - - - -
390D GLN* 1.3 106.4 - - + +
392D LEU* 1.3 54.4 + - + +
393D MET 2.6 17.9 + - - -
394D GLN* 2.8 14.3 + - - +
395D TYR* 2.7 39.7 + - + +
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Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D LYS* 3.0 23.7 + - + +
374D ARG* 2.8 71.6 - - + +
375D GLU* 4.8 0.4 - - - +
378D VAL* 5.6 4.0 - - + -
388D ASN* 3.5 25.8 - - + +
391D ASP* 1.3 79.0 - - + +
393D MET* 1.3 58.8 + - - +
395D TYR* 2.5 39.4 - - + +
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Residues in contact with MET 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 5.5 13.5 - - + -
221D TYR* 3.2 26.4 + - + +
371D LYS* 3.1 22.7 - - - +
375D GLU* 4.0 14.6 - - - +
385D ILE* 3.8 30.7 - - + +
388D ASN* 2.9 18.6 - - + +
389D PHE* 2.7 52.5 - - + +
391D ASP 2.6 5.1 + - - -
392D LEU* 1.3 75.6 - - - +
394D GLN* 1.3 60.8 + - - +
395D TYR 2.8 5.4 - - - -
396D CYS* 2.9 4.3 + - + +
397D ALA 2.9 21.8 + - - -
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Residues in contact with GLN 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D PRO 4.8 0.4 - - - +
167D PRO* 3.0 45.1 - - + +
169D TRP* 4.2 20.2 - - + +
170D ALA* 4.8 6.8 - - + +
220D TRP* 6.2 3.1 - - + -
221D TYR* 3.9 6.0 + - - -
389D PHE 4.6 1.6 + - - -
390D GLN 5.4 1.1 - - - +
391D ASP* 2.8 13.8 + - - +
393D MET* 1.3 73.7 - - - +
395D TYR* 1.3 75.8 + - + +
397D ALA* 3.8 4.8 - - - +
398D GLN* 2.8 54.1 + - - +
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Residues in contact with TYR 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D GLU* 4.4 11.3 - - + +
371D LYS* 3.7 19.3 - - + +
374D ARG* 4.6 17.3 - - - -
391D ASP* 2.7 56.9 + - + +
392D LEU* 2.5 26.0 - - - +
393D MET 2.8 0.2 - - - -
394D GLN* 1.3 95.8 - - - +
396D CYS* 1.3 64.7 + - - +
398D GLN* 3.6 2.3 - - - +
399D ASP* 2.9 23.3 + - - +
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Residues in contact with CYS 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D GLU* 5.4 4.9 - - - -
211D LEU* 4.3 20.2 - - + -
370D GLU 4.5 0.7 - - - -
371D LYS* 2.9 51.7 - - - +
372D GLU* 5.2 6.1 - - - -
375D GLU* 5.7 4.3 - - - -
392D LEU 3.2 0.2 + - - -
393D MET* 2.9 5.8 + - - +
395D TYR* 1.3 81.1 - - - +
397D ALA* 1.3 67.3 + - - +
399D ASP* 3.2 1.2 + - - +
400D VAL* 2.9 35.7 + - - +
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Residues in contact with ALA 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ASP* 4.7 2.0 - - - -
211D LEU* 5.3 4.2 - - + +
212D ALA 4.6 2.9 - - - +
213D VAL* 3.2 36.3 - - + -
220D TRP* 6.3 1.1 - - + -
221D TYR* 4.2 12.3 - - + +
393D MET 2.9 13.7 + - - +
394D GLN* 3.8 6.1 - - - +
396D CYS* 1.3 79.7 - - - +
398D GLN* 1.3 64.0 + - - +
400D VAL* 3.3 16.9 + - - +
401D TRP* 3.5 14.0 + - - -
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Residues in contact with GLN 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LYS* 4.4 27.6 - - + +
166D PRO 2.6 29.7 + - - +
167D PRO* 3.8 6.9 - - - +
213D VAL* 5.0 0.2 - - - +
370D GLU* 4.8 6.1 - - - +
394D GLN* 2.8 41.5 + - - +
395D TYR* 3.7 2.9 - - - +
397D ALA* 1.3 73.1 - - - +
399D ASP* 1.3 63.1 + - - +
401D TRP* 3.2 25.8 + - + +
402D ALA* 3.3 10.1 + - - +
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Residues in contact with ASP 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D LEU* 5.2 2.9 - - - +
366D GLY 3.8 10.2 - - - +
367D PRO* 3.4 18.6 - - - +
369D LEU 3.8 0.3 - - - -
370D GLU* 2.8 69.3 + - + +
372D GLU* 5.6 0.2 - - - +
395D TYR 2.9 11.4 + - - +
396D CYS 3.9 0.9 - - - +
398D GLN* 1.3 73.6 - - - +
400D VAL* 1.3 51.8 + - + +
402D ALA* 2.8 38.4 + - - +
403D THR* 2.8 23.2 + - - +
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Residues in contact with VAL 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ASP* 2.9 35.0 - - + -
270D ASN* 5.6 3.4 - - + -
372D GLU* 5.3 7.0 - - - +
396D CYS* 2.9 40.4 + - - +
397D ALA 3.3 9.2 - - - +
398D GLN 3.2 0.2 - - - -
399D ASP* 1.3 76.0 - - + +
401D TRP* 1.3 57.0 + - - +
403D THR* 3.0 20.9 - - + +
404D HIS* 2.9 28.3 + - + +
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Residues in contact with TRP 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LYS* 5.9 4.9 - - + -
166D PRO* 4.8 19.3 - - + -
177D ARG* 6.1 1.1 - - + -
196D VAL* 3.4 14.8 + - + -
198D ASP 3.6 3.0 - - - +
213D VAL* 2.7 45.8 - - + +
214D ALA* 2.4 55.9 - - - -
215D ILE* 4.5 15.9 - - + -
218D SER 4.6 2.7 - - - -
220D TRP* 5.4 4.9 - + - -
397D ALA 3.8 10.1 - - - -
398D GLN* 3.2 16.2 + - + +
399D ASP 2.9 1.2 - - - -
400D VAL* 1.3 78.1 - - + +
402D ALA* 1.3 68.8 + - - +
403D THR 2.9 1.3 - - - -
404D HIS* 2.6 47.3 + + + +
405D GLU* 2.8 19.8 + - - +
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Residues in contact with ALA 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D GLY 6.4 0.4 - - - -
367D PRO* 6.3 1.1 - - + -
370D GLU* 5.9 0.2 - - - +
398D GLN 3.3 5.0 + - - +
399D ASP* 2.8 27.3 + - - +
401D TRP* 1.3 78.1 - - - +
403D THR* 1.3 60.5 + - - +
405D GLU* 3.1 8.9 + - - +
406D VAL* 2.6 37.8 + - + +
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Residues in contact with THR 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ASN* 3.8 22.6 + - - +
355D SER* 4.0 23.1 + - - +
356D LEU* 5.6 6.7 - - + -
359D VAL* 5.4 2.0 - - - -
367D PRO 6.2 0.2 - - - +
399D ASP* 2.8 23.3 + - - +
400D VAL* 3.0 25.1 + - + +
402D ALA* 1.3 77.0 - - - +
404D HIS* 1.3 52.6 + - - -
406D VAL* 3.3 11.4 - - - +
407D PHE* 2.7 41.3 + - - +
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Residues in contact with HIS 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D VAL* 4.1 13.7 - - + -
197D PHE 4.1 12.2 + - - -
198D ASP* 5.3 0.2 - - - -
268D GLY 3.1 25.8 + - - +
270D ASN* 2.6 43.1 + - + -
294D THR* 4.0 0.8 - - - +
400D VAL* 2.9 30.4 + - + +
401D TRP* 2.6 44.9 + + + +
403D THR* 1.3 71.6 + - - +
405D GLU* 1.3 57.3 + - - +
407D PHE* 3.9 5.6 - - - -
408D GLN* 2.3 49.9 + - - +
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Residues in contact with GLU 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D PRO* 5.9 4.2 - - - +
196D VAL* 5.7 0.9 - - - +
215D ILE* 3.5 28.8 - - - +
401D TRP* 2.8 20.6 + - - +
402D ALA* 3.4 8.7 - - - +
404D HIS* 1.3 76.5 - - - +
406D VAL* 1.3 69.4 + - - +
408D GLN* 2.7 17.5 + - - +
409D GLN* 2.7 46.0 + - - +
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Residues in contact with VAL 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D HIS* 4.7 1.3 - - - +
359D VAL* 3.1 45.3 - - + -
362D LEU* 4.3 3.0 - - + +
363D TYR* 3.9 31.2 - - + -
367D PRO* 5.9 2.9 - - + -
402D ALA* 2.6 45.4 + - + +
403D THR* 3.3 9.0 - - - +
405D GLU* 1.3 74.3 - - - +
407D PHE* 1.3 70.6 + - + +
410D GLN* 2.9 30.6 - - - +
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Residues in contact with PHE 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D GLY* 4.6 4.0 - - - -
270D ASN* 4.0 2.2 - - - -
292D LEU 4.4 7.0 - - - -
293D ASP 4.2 0.9 - - - -
294D THR* 2.7 53.2 - - + -
297D MET* 3.4 16.8 - - + -
298D HIS* 2.9 31.2 - + + +
359D VAL* 5.7 0.9 - - + -
403D THR* 2.7 19.6 + - - +
404D HIS* 3.7 14.1 - - - -
405D GLU 2.8 0.4 + - - -
406D VAL* 1.3 84.0 - - + +
408D GLN* 1.3 76.8 + - + -
411D LEU* 2.6 64.7 + - + +
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Residues in contact with GLN 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ALA* 6.0 0.2 - - - +
157D LEU* 5.3 8.3 - - - +
158D LEU* 4.1 27.2 - - + +
196D VAL* 4.0 7.4 - - - +
265D LEU* 6.3 0.2 - - - +
266D VAL* 4.8 9.5 + - - +
267D VAL 5.0 0.6 + - - -
268D GLY* 3.1 35.3 - - - +
297D MET* 5.5 3.1 - - - -
404D HIS* 2.3 38.9 + - - +
405D GLU* 2.7 4.2 + - - +
407D PHE* 1.3 87.4 - - + +
409D GLN* 1.3 53.4 + - + +
411D LEU* 2.8 9.6 - - + +
412D PRO* 2.7 35.1 - - + +
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Residues in contact with GLN 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D LEU 4.1 2.6 + - - -
158D LEU* 2.6 45.6 + - + +
160D ALA 2.6 21.8 + - - -
161D GLN* 5.5 2.8 - - - +
405D GLU* 2.7 39.5 + - - +
408D GLN* 1.3 77.1 - - + +
410D GLN* 1.3 63.4 + - + +
412D PRO* 2.6 25.5 - - - +
413D LEU* 4.3 6.6 - - - +
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Residues in contact with GLN 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D LEU* 3.7 39.7 + - + +
363D TYR* 4.8 14.7 - - + -
406D VAL* 2.9 28.6 + - - +
408D GLN 3.2 1.2 - - - -
409D GLN* 1.3 86.0 - - + +
411D LEU* 1.3 50.0 + - - +
412D PRO* 2.7 13.9 - - - +
413D LEU* 3.9 6.1 + - - +
414D PHE* 2.6 41.1 - - + -
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D MET* 2.9 40.8 - - + +
298D HIS* 2.9 28.0 - - + +
301D ILE* 5.1 6.5 - - + -
361D ARG* 5.3 0.7 - - - +
362D LEU* 4.0 11.2 - - + +
407D PHE* 2.6 54.1 + - + +
408D GLN* 2.8 29.2 - - + +
410D GLN* 1.3 70.6 - - - +
412D PRO* 1.3 52.2 - - + +
413D LEU 3.3 0.2 - - - -
414D PHE* 3.8 9.8 - - + -
415D LEU* 2.5 46.1 + - + +
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Residues in contact with PRO 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 3.5 31.9 - - + -
297D MET* 4.5 6.7 - - - -
408D GLN* 2.7 15.7 - - + +
409D GLN 2.6 31.0 - - - +
410D GLN 2.7 8.7 - - - +
411D LEU* 1.3 79.3 - - + +
413D LEU* 1.3 71.0 + - + +
415D LEU* 2.8 7.9 - - + +
416D GLU* 2.7 47.1 + - + +
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Residues in contact with LEU 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 5.7 1.6 - - + -
409D GLN 4.3 8.5 - - - +
410D GLN* 4.4 5.6 - - - +
412D PRO* 1.3 93.5 - - + +
414D PHE* 1.3 67.6 + - + +
415D LEU 2.8 5.2 - - - -
416D GLU* 2.7 30.4 + - - +
417D ARG* 2.9 30.6 + - - +
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Residues in contact with PHE 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ILE* 2.7 32.9 - - + +
361D ARG* 6.1 2.0 - - - +
362D LEU* 4.0 17.0 - - + -
410D GLN* 2.6 61.7 - - + -
411D LEU* 3.8 5.8 - - + -
412D PRO 3.6 0.2 - - - -
413D LEU* 1.3 84.7 - - + +
415D LEU* 1.3 51.0 + - - +
417D ARG* 2.6 54.6 - - - +
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D LEU* 5.2 0.2 - - + -
297D MET* 3.0 70.2 - - + +
301D ILE* 3.6 22.4 - - + +
411D LEU* 2.5 30.3 + - + +
412D PRO* 2.8 9.4 - - + +
413D LEU 2.8 0.8 - - - -
414D PHE* 1.3 76.1 - - - +
416D GLU* 1.3 53.0 + - + +
417D ARG 2.6 13.1 + - - -
418D CYS* 3.2 17.5 + - - +
424D LEU* 5.5 11.8 - - + +
427D MET* 5.1 9.0 - - + -
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Residues in contact with GLU 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 6.0 1.4 - - - +
412D PRO* 2.7 26.7 + - + +
413D LEU* 2.7 44.4 + - - +
415D LEU* 1.3 70.2 - - + +
417D ARG* 1.3 56.2 + - - +
418D CYS 2.7 11.0 + - - +
419D PRO* 3.2 23.1 - - + +
424D LEU* 5.0 19.1 - - + -
----------------------------------------------------------
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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