Contacts of the helix formed by residues 371 - 395 (chain D) in PDB entry 2I0J
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 THR 371 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D LEU* 1.3 79.3 - - - +
372D LEU* 1.3 60.7 + - - +
373D HIS* 4.1 6.1 + - - +
374D ASP* 3.1 23.0 + - - +
375D GLN* 2.8 27.5 + - - +
467D LYS* 3.5 34.8 - - + +
471D GLU* 3.1 23.4 + - - +
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Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D THR* 1.3 73.2 - - - +
373D HIS* 1.3 64.2 + - - +
375D GLN* 3.1 14.8 + - + +
376D VAL* 3.0 18.7 + - + +
541D LEU* 3.7 23.3 - - + -
544D LEU* 3.6 33.9 - - + +
545D ASP* 3.7 37.7 - - + +
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Residues in contact with HIS 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D THR* 3.3 5.4 + - - +
372D LEU* 1.3 79.7 - - - +
374D ASP* 1.3 79.1 + - - +
376D VAL* 3.4 4.7 + - - +
377D HIS* 3.1 37.6 + + + +
461D PHE* 5.3 7.9 - + - -
537D TYR* 2.8 36.2 + + - +
541D LEU* 5.8 2.2 - - - -
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Residues in contact with ASP 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D LEU* 4.3 8.4 - - + +
371D THR* 3.1 25.4 + - - +
373D HIS* 1.3 93.9 + - - +
375D GLN* 1.3 65.2 + - - +
377D HIS* 4.0 0.5 - - - +
378D LEU* 3.2 29.6 + - - +
461D PHE* 3.6 35.3 - - + -
468D SER* 5.8 0.5 - - - -
471D GLU* 2.8 31.2 - - - +
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Residues in contact with GLN 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D LYS* 4.1 17.8 + - - -
367D PHE* 3.6 58.8 - - + +
368D VAL* 3.7 15.7 + - - +
370D LEU* 2.9 29.1 + - + -
371D THR 2.8 18.5 + - - +
372D LEU* 3.1 13.4 + - - +
374D ASP* 1.3 76.3 - - - +
376D VAL* 1.3 62.1 + - - +
378D LEU* 3.4 0.4 + - - -
379D LEU* 3.2 21.7 + - - +
544D LEU* 3.5 16.1 - - + +
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Residues in contact with VAL 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D LEU* 3.0 21.8 + - + +
373D HIS* 3.8 4.7 - - - +
375D GLN* 1.3 77.9 - - - +
377D HIS* 1.3 54.8 + - - +
379D LEU* 4.8 1.8 - - - -
380D GLU* 2.9 27.5 + - - +
537D TYR* 3.5 50.9 - - + +
540D LEU* 3.8 8.3 - - + +
541D LEU* 3.4 32.3 - - + +
544D LEU* 3.1 23.6 - - + -
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Residues in contact with HIS 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D HIS* 3.1 31.2 + + + +
374D ASP* 4.0 3.1 - - - +
375D GLN 3.4 0.2 - - - -
376D VAL* 1.3 77.0 - - - +
378D LEU* 1.3 62.1 + - - +
380D GLU* 4.0 15.5 - - - +
381D SER* 3.1 27.3 + - - -
457D GLY* 2.8 25.7 + - - -
460D THR* 2.7 45.6 + - - -
461D PHE* 3.3 26.0 - + + -
537D TYR* 4.6 8.7 - + + -
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Residues in contact with LEU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D PHE* 3.7 20.0 - - + -
370D LEU* 3.7 30.1 - - + -
374D ASP 3.2 17.3 + - - +
375D GLN 3.8 3.6 - - - +
377D HIS* 1.3 74.3 - - - +
379D LEU* 1.3 61.5 + - - +
381D SER* 3.4 4.9 + - - -
382D ALA* 3.0 29.6 + - - +
453D LEU* 3.5 26.7 - - + +
454D LEU* 3.8 23.1 - - + +
456D SER* 4.8 0.3 - - - -
457D GLY 3.9 6.7 - - - +
458D VAL* 3.8 20.4 - - - +
461D PHE* 3.9 12.6 - - + -
475D ILE* 4.4 6.5 - - + -
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Residues in contact with LEU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D MET* 4.4 24.2 - - + -
358D ILE* 4.0 20.9 - - + -
361D ALA* 3.8 18.4 - - + -
367D PHE* 4.2 4.0 - - + -
375D GLN 3.2 12.4 + - - +
376D VAL* 4.1 2.7 - - - +
378D LEU* 1.3 77.9 - - - +
380D GLU* 1.3 66.3 + - - +
382D ALA* 5.0 0.2 - - - +
383D TRP* 2.8 30.6 + - + +
386D ILE* 4.7 1.3 - - + -
453D LEU* 3.4 27.1 - - + -
540D LEU* 4.0 15.5 - - + -
544D LEU* 4.0 33.9 - - + -
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Residues in contact with GLU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D VAL 2.9 20.3 + - - +
377D HIS* 4.0 14.1 - - - +
379D LEU* 1.3 76.2 - - - +
381D SER* 1.3 60.2 + - - +
383D TRP* 3.0 25.8 + - - -
522D MET* 5.0 4.3 - - - +
536D LEU* 5.0 8.3 - - + +
537D TYR* 3.2 45.4 + - + +
540D LEU* 3.3 19.0 - - + +
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Residues in contact with SER 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D HIS* 3.1 23.8 + - - -
378D LEU 3.6 4.7 - - - -
379D LEU 3.0 0.4 - - - -
380D GLU* 1.3 81.4 - - - +
382D ALA* 1.3 57.1 + - - +
383D TRP 3.8 0.2 - - - -
385D GLU* 3.9 12.1 - - - +
456D SER* 3.5 4.2 + - - -
457D GLY* 3.2 31.9 + - - -
460D THR* 4.7 2.6 + - - +
515D ARG* 5.2 2.6 + - - -
518D SER* 5.2 3.3 + - - -
522D MET* 6.1 1.2 - - - +
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Residues in contact with ALA 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D LEU 3.0 11.9 + - - +
379D LEU 3.0 3.3 + - - -
381D SER* 1.3 79.5 - - - +
383D TRP* 1.3 64.1 + - - +
384D LEU 3.3 2.7 - - - -
385D GLU* 3.4 6.7 + - - +
386D ILE* 3.0 34.6 + - + +
452D ILE* 3.9 16.8 - - + +
453D LEU* 4.2 2.7 - - - -
456D SER* 3.4 27.6 - - - +
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Residues in contact with TRP 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D I0G 4.3 13.7 - - + -
350D ALA* 4.9 4.5 - - + -
354D LEU* 3.9 30.3 - - + -
357D MET* 3.6 15.1 - - - +
379D LEU* 2.8 19.3 + - + +
380D GLU* 3.0 27.6 + - - -
381D SER 5.1 0.2 - - - -
382D ALA* 1.3 73.9 - - - +
384D LEU* 1.3 102.3 + - + +
386D ILE* 3.3 2.4 + - - +
387D LEU* 2.9 49.7 + - + +
522D MET* 3.4 34.4 - - + +
525D LEU* 5.1 10.8 - - + -
536D LEU* 3.7 27.2 - - + +
540D LEU* 5.3 3.4 - - + -
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Residues in contact with LEU 384 (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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1D I0G 3.5 35.2 - - + -
382D ALA 3.3 0.2 - - - -
383D TRP* 1.3 108.3 - - + +
385D GLU* 1.3 67.3 + - - +
387D LEU* 4.3 5.8 - - + -
388D MET* 2.9 50.2 + - + +
518D SER* 3.5 32.3 + - - +
521D GLY* 3.9 20.0 - - - +
522D MET* 3.8 15.5 - - + -
525D LEU* 5.7 0.4 - - + -
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Residues in contact with GLU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C SER* 4.9 0.2 + - - -
381D SER 3.9 6.3 - - - +
382D ALA* 3.4 6.4 + - - +
383D TRP 3.3 0.4 - - - -
384D LEU* 1.3 76.6 - - - +
386D ILE* 1.3 57.7 + - - +
388D MET* 3.3 2.8 + - - +
389D ILE* 2.9 29.9 + - - +
452D ILE* 3.7 22.1 - - + +
456D SER* 2.5 29.3 + - - -
511D LEU* 4.2 4.5 - - - +
514D ILE* 3.7 20.8 - - + +
515D ARG* 3.1 49.2 + - - +
518D SER* 3.4 25.7 + - - +
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Residues in contact with ILE 386 (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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357D MET* 3.9 26.7 - - + -
360D TRP* 3.6 28.3 - - + -
379D LEU* 4.7 0.7 - - + -
382D ALA 3.0 25.4 + - - +
383D TRP 3.6 3.8 - - - +
385D GLU* 1.3 74.1 - - - +
387D LEU* 1.3 65.6 + - - +
389D ILE* 3.1 11.1 - - - +
390D GLY* 3.1 19.8 + - - -
449D LYS* 4.0 27.4 - - + +
452D ILE* 3.8 15.9 - - + -
453D LEU* 3.8 27.4 - - + -
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Residues in contact with LEU 387 (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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1D I0G 3.2 38.0 + - + +
350D ALA* 3.6 35.9 - - + +
353D GLU* 3.9 26.9 - - + +
354D LEU* 5.2 0.4 - - + -
357D MET* 3.3 23.8 - - + -
383D TRP* 2.9 40.6 + - + +
384D LEU* 3.7 8.3 - - + +
386D ILE* 1.3 75.6 - - + +
388D MET* 1.3 58.2 + - - +
390D GLY* 3.3 2.3 + - - -
391D LEU 3.0 21.7 + - - -
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Residues in contact with MET 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D I0G 3.9 33.0 - - + -
384D LEU* 2.9 45.4 + - + +
385D GLU* 3.7 4.3 - - - +
387D LEU* 1.3 73.8 - - - +
389D ILE* 1.3 56.4 + - - +
390D GLY 3.0 1.6 - - - -
391D LEU* 2.9 9.6 + - - +
392D VAL* 2.7 38.2 + - - +
424D ILE* 4.3 11.9 - - + -
428D LEU* 4.1 17.9 - - + -
514D ILE* 4.7 7.9 - - + +
517D MET* 3.8 45.5 - - + +
518D SER* 4.0 5.8 - - - -
521D GLY* 4.4 3.4 - - - -
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Residues in contact with ILE 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D GLU 2.9 19.2 + - - +
386D ILE* 3.1 15.3 - - - +
388D MET* 1.3 72.3 - - - +
390D GLY* 1.3 65.1 + - - +
392D VAL* 4.0 6.5 - - - +
393D TRP* 3.1 22.7 + - - +
435D PHE* 4.2 15.9 - - + -
445D PHE* 3.3 15.1 - - + -
448D LEU* 4.0 23.8 - - + -
449D LYS* 3.5 28.7 - - + +
452D ILE* 3.8 17.9 - - + -
511D LEU* 4.2 2.9 - - + -
514D ILE* 3.6 30.8 - - + +
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Residues in contact with GLY 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ILE 3.1 7.6 + - - -
387D LEU* 3.6 4.5 - - - -
388D MET 3.0 1.2 - - - -
389D ILE* 1.3 82.3 - - - +
391D LEU* 1.3 67.1 + - - +
393D TRP* 3.2 6.4 + - - +
394D ARG* 3.0 32.0 + - - +
445D PHE* 4.0 14.8 - - - -
449D LYS* 5.7 2.0 - - - -
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D I0G 4.1 8.5 - - + -
387D LEU 3.0 12.3 + - - +
388D MET 2.9 8.1 + - - +
390D GLY* 1.3 70.5 - - - +
392D VAL* 1.3 57.8 - - - +
393D TRP 2.6 15.7 + - - -
394D ARG* 2.8 30.0 + - - +
395D SER* 3.0 32.6 + - - +
402D LEU* 4.2 10.5 - - + -
403D LEU 3.4 29.6 - - - +
404D PHE* 3.4 42.0 - - + +
428D LEU* 3.9 23.3 - - + -
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Residues in contact with VAL 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D MET 2.7 20.2 + - - +
389D ILE* 4.0 6.1 - - - +
391D LEU* 1.3 74.9 - - - +
393D TRP* 1.3 59.5 + - - +
395D SER* 3.7 2.9 + - - -
396D MET* 3.6 7.1 - - - +
402D LEU* 5.6 0.7 - - + -
428D LEU* 3.6 43.3 - - + +
431D THR* 3.3 30.5 - - + -
432D SER* 3.1 29.0 + - - -
435D PHE* 3.3 26.5 - - + -
514D ILE* 5.5 0.9 - - + -
517D MET* 4.5 3.4 - - + -
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Residues in contact with TRP 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D ILE 3.1 19.0 + - - +
390D GLY 3.3 5.2 - - - +
391D LEU 2.6 5.3 + - - -
392D VAL* 1.3 71.8 - - - +
394D ARG* 1.3 68.8 + - + +
395D SER 3.1 5.4 + - - -
396D MET* 3.1 53.0 + - + +
435D PHE* 4.7 2.7 - + + -
440D LEU* 3.4 45.3 - - + -
441D GLN 4.0 1.8 - - - -
442D GLY* 3.6 29.2 - - - -
445D PHE* 3.4 35.7 - + + -
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Residues in contact with ARG 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D I0G 2.8 33.5 + - - -
326D ILE* 4.6 33.3 - - + +
353D GLU* 4.0 11.8 + - - -
390D GLY* 3.0 33.7 + - - +
391D LEU* 2.8 24.2 + - - +
393D TRP* 1.3 83.5 - - + +
395D SER* 1.3 55.2 + - - +
396D MET 3.1 4.4 + - - -
397D GLU* 4.5 1.2 + - - +
398D HIS* 3.6 7.6 - - - -
403D LEU* 3.0 47.0 + - + +
404D PHE 3.0 22.4 + - - -
405D ALA* 5.7 0.7 - - - +
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Residues in contact with SER 395 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D LEU* 3.0 20.8 + - - +
392D VAL 4.1 1.1 - - - -
393D TRP 3.1 0.8 - - - -
394D ARG* 1.3 75.9 - - - +
396D MET* 1.3 60.1 + - - +
397D GLU 3.4 2.0 - - - -
398D HIS* 3.6 14.4 + - - -
399D PRO* 5.1 0.2 - - - +
401D LYS 3.6 20.1 - - - +
402D LEU* 3.1 12.5 - - - +
403D LEU* 2.5 31.0 + - - +
432D SER* 2.7 27.3 + - - -
436D ARG* 4.3 2.4 + - - -
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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