Contacts of the helix formed by residues 383 - 409 (chain D) in PDB entry 1S77
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 ALA 383 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D ALA 4.3 11.8 + - - +
381D ALA* 3.5 1.5 - - - -
382D ALA* 1.3 75.4 - - - +
384D VAL* 1.3 54.4 + - - +
385D TYR 3.1 0.7 - - - -
386D ARG* 2.5 43.8 + - + +
387D LYS* 3.0 6.7 + - + +
660D ASP* 4.3 22.2 - - + +
16N T 6.1 0.7 - - - -
17N A 5.6 0.4 + - - -
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Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D GLU* 3.1 46.2 - - + +
360D LEU 5.5 0.2 - - - -
361D PRO* 3.7 42.6 - - + -
381D ALA 4.3 6.5 - - - +
382D ALA 2.8 1.8 - - - -
383D ALA* 1.3 77.2 - - - +
385D TYR* 1.3 60.2 + - + +
386D ARG 2.8 0.5 + - - -
387D LYS* 3.0 16.6 + - - +
388D ASP* 2.7 35.2 + - + +
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Residues in contact with TYR 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D PRO* 3.4 32.3 - - + +
382D ALA* 3.6 14.6 - - + +
383D ALA* 3.1 0.6 - - - -
384D VAL* 1.3 76.5 - - + +
386D ARG* 1.3 56.7 + - - +
388D ASP* 5.0 2.9 - - - +
389D LYS* 3.3 25.1 + - - +
15N T 4.6 1.9 + - - -
16N T 3.0 88.4 + + + +
17N A 6.3 0.4 - - - -
110T T 5.1 9.9 - - - -
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Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D ALA* 2.5 27.5 + - + +
385D TYR* 1.3 72.8 - - - +
387D LYS* 1.3 64.1 + - + +
389D LYS* 3.1 20.3 - - - +
390D ALA* 3.3 7.6 + - - +
652D GLU* 3.6 22.4 + - - -
656D GLN* 3.9 27.7 - - - +
660D ASP* 4.3 14.5 + - - +
16N T 5.2 2.0 + - - +
17N A 5.3 18.4 - - + +
5R G 4.5 16.8 + - - -
6R G 3.8 39.3 + - - +
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Residues in contact with LYS 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D GLU* 3.2 47.5 + - - +
383D ALA* 3.0 6.4 + - + +
384D VAL* 3.0 19.1 + - - +
386D ARG* 1.3 83.4 - - + +
388D ASP* 1.3 60.5 + - - +
390D ALA* 3.4 8.7 + - - +
391D ARG* 3.1 25.8 + - + +
660D ASP* 5.4 13.2 - - + +
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Residues in contact with ASP 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D ARG* 2.9 48.1 - - - +
358D GLU* 3.1 20.2 - - - +
384D VAL* 2.7 22.0 + - + +
385D TYR* 5.0 2.7 - - - +
387D LYS* 1.3 72.8 - - - +
389D LYS* 1.3 64.3 + - - +
391D ARG* 3.2 23.5 + - - -
392D LYS* 3.0 23.7 + - - +
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Residues in contact with LYS 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D TYR 3.3 17.1 + - - +
386D ARG* 3.1 14.3 + - - +
388D ASP* 1.3 81.9 - - - +
390D ALA* 1.3 62.0 + - - +
392D LYS* 3.6 5.5 + - - +
393D SER* 3.3 18.0 + - - -
6R G 3.6 35.0 + - - +
7R C 5.4 8.1 - - - +
111T T 2.9 48.5 + - + +
112T G 5.2 1.0 - - - -
113T T 4.3 19.7 + - - -
114T G 5.3 8.1 - - - +
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Residues in contact with ALA 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ARG* 3.3 5.7 + - - +
387D LYS* 3.5 11.0 - - - +
388D ASP 3.2 0.2 - - - -
389D LYS* 1.3 78.0 - - - +
391D ARG* 1.3 54.9 + - - +
393D SER* 3.1 2.8 + - - -
394D ARG* 2.7 54.6 + - - +
5R G 3.4 25.4 - - - +
6R G 3.0 18.8 + - - +
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Residues in contact with ARG 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D PRO* 3.7 13.5 - - + +
354D ALA* 2.9 23.6 + - - +
355D ILE 2.4 27.5 + - - -
356D GLU* 2.9 29.8 + - - +
357D ARG* 4.1 7.3 - - - +
358D GLU* 5.0 3.4 - - - -
387D LYS* 3.1 16.1 + - + +
388D ASP* 3.2 38.3 + - - +
389D LYS 3.4 0.2 - - - -
390D ALA* 1.3 76.1 - - - +
392D LYS* 1.3 82.7 + - - +
394D ARG* 3.1 10.0 + - - +
395D ARG* 2.6 42.8 + - - +
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Residues in contact with LYS 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ASP* 3.0 21.3 + - - +
389D LYS* 3.9 5.8 - - - +
391D ARG* 1.3 97.1 - - - +
393D SER* 1.3 59.7 + - - +
395D ARG* 3.6 6.9 - - - +
396D ILE* 3.2 43.1 + - + +
111T T 5.2 8.3 + - - +
112T G 4.7 11.9 + - - -
113T T 5.2 19.4 + - - -
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Residues in contact with SER 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D LYS 3.3 10.7 + - - -
390D ALA 3.1 7.2 + - - -
392D LYS* 1.3 77.8 - - - +
394D ARG* 1.3 66.5 + - - +
395D ARG 3.0 1.6 - - - -
396D ILE* 3.2 18.3 + - - +
397D SER* 3.4 13.0 + - - -
5R G 4.4 11.9 + - - -
6R G 4.1 28.8 + - - -
113T T 5.6 4.9 - - - -
114T G 4.9 14.0 + - - -
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Residues in contact with ARG 394 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D ASP* 2.8 32.6 + - - -
353D PRO* 3.8 27.8 - - + +
390D ALA* 2.7 42.7 + - - +
391D ARG* 3.6 6.3 - - - +
393D SER* 1.3 73.4 - - - +
395D ARG* 1.3 58.4 + - - +
397D SER* 3.0 19.0 + - - +
398D LEU* 3.4 12.5 + - - +
4R C 3.3 32.7 + - - +
5R G 3.4 32.0 + - - +
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Residues in contact with ARG 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D THR* 3.0 32.9 + - - -
343D LYS* 4.7 4.8 - - - +
352D ILE* 4.4 1.2 - - - +
353D PRO* 2.5 45.5 + - + +
354D ALA 3.8 16.8 - - - +
355D ILE* 3.3 28.0 - - - +
391D ARG* 2.6 23.0 + - + +
392D LYS* 3.6 9.9 - - - +
394D ARG* 1.3 77.5 - - - +
396D ILE* 1.3 66.2 + - + +
398D LEU* 3.2 31.7 + - - +
399D GLU* 3.0 49.6 + - - +
402D LEU* 5.9 0.2 - - - +
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Residues in contact with ILE 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D LYS* 3.2 36.7 + - + +
393D SER* 3.5 12.3 - - - +
395D ARG* 1.3 77.4 - - + +
397D SER* 1.3 60.5 + - - +
399D GLU* 3.4 8.2 + - + +
400D PHE* 3.0 26.5 + - + +
113T T 6.1 1.6 - - - -
114T G 4.1 36.6 - - - +
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Residues in contact with SER 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D SER 3.4 9.5 + - - -
394D ARG* 3.0 19.8 + - - +
396D ILE* 1.3 79.5 - - - +
398D LEU* 1.3 54.8 + - - +
400D PHE* 3.5 6.9 - - - +
401D MET* 2.7 54.4 + - - +
437D ASN* 5.7 3.3 + - - -
4R C 6.1 0.7 - - - -
5R G 4.8 5.4 + - - -
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Residues in contact with LEU 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D THR* 4.4 6.3 - - + -
352D ILE* 3.8 22.0 - - + -
353D PRO* 3.4 32.8 - - + -
394D ARG 3.4 9.6 + - - +
395D ARG* 3.2 42.5 + - - +
397D SER* 1.3 80.5 + - - +
399D GLU* 1.3 66.5 + - + +
401D MET* 3.8 5.2 - - - +
402D LEU* 2.9 44.4 + - + +
437D ASN* 6.0 4.9 - - - +
439D MET* 3.9 16.4 - - - +
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Residues in contact with GLU 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ILE* 5.5 1.6 - - - +
395D ARG* 3.0 53.3 + - - +
396D ILE* 3.9 7.4 - - + +
398D LEU* 1.3 80.6 - - + +
400D PHE* 1.3 60.8 + - - +
402D LEU* 4.2 3.4 - - + -
403D GLU* 2.8 49.2 + - - +
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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
----------------------------------------------------------
46D MET* 4.9 8.5 - - + -
267D MET* 4.7 12.6 - - + -
268D PHE 5.3 2.7 - - - -
269D GLN* 6.3 0.9 - - + -
396D ILE* 3.0 16.7 + - + +
397D SER* 3.5 8.7 - - - +
399D GLU* 1.3 76.9 - - - +
401D MET* 1.3 89.7 + - + +
403D GLU* 3.2 6.2 + - + +
404D GLN* 3.0 55.8 + - + +
431D MET* 3.4 57.4 - - + -
432D PHE 4.2 2.2 - - - -
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Residues in contact with MET 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D SER* 2.7 53.2 + - - +
398D LEU* 3.8 4.0 - - - +
400D PHE* 1.3 96.5 - - + +
402D LEU* 1.3 57.8 + - - +
404D GLN* 3.3 3.3 + - - +
405D ALA* 2.9 28.9 + - - +
431D MET* 3.8 9.0 - - + +
432D PHE* 3.6 43.8 - - + -
437D ASN* 5.7 3.4 - - - +
439D MET* 4.0 12.8 - - + -
440D THR* 3.2 28.0 - - - +
443D LEU* 5.3 0.2 - - - -
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Residues in contact with LEU 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LEU* 3.9 23.1 - - + -
338D ALA* 3.8 16.4 - - + +
339D ASN* 3.5 21.1 - - - +
342D THR* 3.6 26.9 - - + +
395D ARG* 5.9 0.2 - - - +
398D LEU* 2.9 31.0 + - + +
399D GLU* 3.8 7.4 - - + +
401D MET* 1.3 78.0 - - - +
403D GLU* 1.3 67.5 + - - +
405D ALA* 3.4 2.2 + - - +
406D ASN* 3.1 29.8 + - - -
439D MET* 3.9 16.6 - - + -
443D LEU* 4.0 7.9 - - + -
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Residues in contact with GLU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ASN* 5.1 1.0 + - - -
399D GLU* 2.8 44.3 + - - +
400D PHE* 3.2 8.0 + - + +
402D LEU* 1.3 83.5 - - - +
404D GLN* 1.3 62.8 + - + +
406D ASN* 3.4 14.0 + - - +
407D LYS* 2.8 30.1 + - - +
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Residues in contact with GLN 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D MET* 5.3 5.3 - - - +
268D PHE 5.1 0.5 - - - +
269D GLN* 3.2 28.0 + - - +
270D PRO* 3.5 15.4 - - - +
400D PHE* 3.0 52.2 + - + +
401D MET 3.5 4.5 - - - +
403D GLU* 1.3 76.5 - - + +
405D ALA* 1.3 65.4 + - - +
407D LYS* 3.1 15.6 + - - +
408D PHE* 2.9 46.6 + - + +
432D PHE* 3.7 22.4 + - + +
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Residues in contact with ALA 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ILE* 3.6 20.1 - - + +
335D LEU* 3.8 20.4 - - + -
401D MET 2.9 17.4 + - - +
402D LEU* 3.6 6.3 - - - +
403D GLU 3.3 0.2 - - - -
404D GLN* 1.3 77.3 - - - +
406D ASN* 1.3 57.7 + - - +
408D PHE 3.2 2.6 + - - -
409D ALA* 2.9 26.2 + - - +
432D PHE* 4.0 9.6 - - + -
443D LEU* 3.8 21.3 - - + -
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Residues in contact with ASN 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LEU* 3.1 20.5 - - - +
339D ASN* 2.8 43.5 + - - +
402D LEU 3.1 24.8 + - - +
403D GLU* 4.0 13.3 + - - +
405D ALA* 1.3 73.1 - - - +
407D LYS* 1.3 66.6 + - - +
408D PHE 3.3 0.3 + - - -
409D ALA* 3.5 12.1 + - - +
410D ASN* 5.3 2.8 + - - -
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Residues in contact with LYS 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 4.3 6.5 - - - -
42D GLU* 2.9 36.3 + - - -
46D MET* 4.6 2.6 - - - +
269D GLN* 2.8 23.7 + - - +
403D GLU 2.8 18.6 + - - +
404D GLN* 3.1 23.5 + - - +
406D ASN* 1.3 79.2 - - - +
408D PHE* 1.3 75.0 + - + +
409D ALA 4.2 2.1 - - - +
411D HIS* 4.0 13.3 + - - -
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Residues in contact with PHE 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 5.5 0.4 - - - -
39D LEU* 3.7 36.1 - - + -
269D GLN* 4.0 11.0 - - + -
270D PRO* 3.4 35.4 - - + -
272D VAL* 4.2 6.5 - - + -
330D ILE* 3.3 21.6 + - + +
404D GLN* 2.9 44.2 + - + +
407D LYS* 1.3 94.7 - - + +
409D ALA* 1.3 65.6 + - - +
411D HIS* 3.4 38.7 + + - +
414D ILE* 4.1 23.1 - - + +
432D PHE* 5.1 2.2 - + - -
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Residues in contact with ALA 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ILE* 3.6 14.4 - - + -
332D LYS* 3.8 17.9 - - + +
335D LEU* 3.8 21.3 - - + -
405D ALA 2.9 13.2 + - - +
406D ASN* 3.9 8.8 - - - +
407D LYS 3.5 4.3 - - - +
408D PHE* 1.3 84.4 - - - +
410D ASN* 1.3 75.4 + - - +
411D HIS* 2.8 7.6 + - - -
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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