Contacts of the helix formed by residues 371 - 395 (chain B) in PDB entry 4MG5
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASP 3.9 0.6 + - - +
370B LEU* 1.3 77.7 - - - +
372B LEU* 1.3 65.2 + - - +
373B HIS* 3.8 8.1 + - - +
374B ASP* 3.1 33.0 + - - +
375B GLN* 3.0 20.1 + - - +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU 3.8 0.8 + - - -
371B THR* 1.3 74.1 - - - +
373B HIS* 1.3 65.2 + - + +
375B GLN* 3.3 14.9 + - - +
376B VAL* 2.9 40.0 + - + +
691D HIS* 4.5 18.2 - - + +
694D LEU* 3.9 32.3 - - + +
695D GLN* 3.9 38.8 - - + +
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Residues in contact with HIS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B THR* 3.2 8.2 - - - +
372B LEU* 1.3 87.9 - - + +
374B ASP* 1.3 61.0 + - - +
376B VAL* 3.5 7.6 + - - +
377B HIS* 3.0 27.0 + - - +
691D HIS* 4.9 21.5 + + - -
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Residues in contact with ASP 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 4.0 22.4 - - + +
371B THR* 3.1 28.7 + - - +
373B HIS* 1.3 77.6 - - - +
375B GLN* 1.3 61.8 + - - +
377B HIS* 3.3 6.8 + - - +
378B LEU* 2.9 36.1 + - - +
461B PHE* 4.2 28.2 - - + -
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Residues in contact with GLN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LYS* 4.7 5.0 - - - +
367B PHE* 3.4 55.6 + - + +
368B VAL* 3.4 18.8 + - - +
370B LEU* 2.9 25.4 + - + +
371B THR 3.0 15.0 + - - +
372B LEU* 3.6 17.8 - - - +
374B ASP* 1.3 76.5 - - - +
376B VAL* 1.3 63.9 + - - +
378B LEU 3.3 0.2 + - - -
379B LEU* 3.1 25.5 + - - +
694D LEU* 3.8 28.3 - - + +
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 2.9 24.4 + - + +
373B HIS* 3.5 8.5 - - - +
375B GLN* 1.3 75.8 - - - +
377B HIS* 1.3 57.8 + - - +
379B LEU 3.4 0.2 + - - -
380B GLU* 2.9 59.8 + - - +
690D LEU* 3.7 12.0 - - + +
691D HIS* 3.9 41.1 - - + +
694D LEU* 3.6 21.5 - - + +
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Residues in contact with HIS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS 3.0 17.8 + - - +
374B ASP* 3.3 7.8 + - - +
376B VAL* 1.3 79.9 - - + +
378B LEU* 1.3 65.3 + - + +
380B GLU* 3.8 9.4 + - - +
381B CSO 3.1 28.0 + - + +
457B GLY* 2.9 36.0 + - - -
460B THR* 3.2 37.8 + - + -
461B PHE* 3.4 20.0 - + + -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B PHE* 3.9 15.7 - - + -
370B LEU* 3.5 31.4 - - + -
374B ASP 2.9 17.4 + - - +
375B GLN 3.8 3.6 - - - +
377B HIS* 1.3 81.1 - - + +
379B LEU* 1.3 58.1 + - - +
381B CSO 3.3 4.7 + - - +
382B ALA* 3.0 31.9 + - - +
453B LEU* 3.6 25.1 - - + +
454B LEU* 3.9 19.1 - - + +
457B GLY* 3.8 32.4 + - - +
458B VAL* 4.0 2.7 - - - +
461B PHE* 4.5 6.1 - - + -
475B ILE* 4.0 12.1 - - + -
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B MET* 4.2 29.2 - - + +
358B ILE* 4.5 10.5 - - + -
361B ALA* 3.9 16.2 - - + -
367B PHE* 4.0 13.7 - - + -
375B GLN 3.1 16.9 + - - +
376B VAL 4.0 2.7 - - - +
378B LEU* 1.3 73.6 - - - +
380B GLU* 1.3 61.6 + - - +
382B ALA 4.4 0.4 - - - +
383B TRP* 2.9 35.7 + - + +
386B ILE* 4.9 1.8 - - + -
453B LEU* 3.9 17.7 - - + -
543B MET* 3.6 4.4 - - + +
690D LEU* 4.2 18.2 - - + -
694D LEU* 3.7 33.9 - - + -
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 2.9 42.7 + - - +
377B HIS* 3.8 10.7 + - - +
378B LEU 3.3 0.2 - - - -
379B LEU* 1.3 75.7 - - - +
381B CSO 1.3 50.8 + - - +
383B TRP* 3.1 12.6 - - - -
542B GLU 4.8 3.8 - - - +
543B MET* 3.9 13.5 - - + +
546B ALA* 3.5 30.6 - - + +
547B HIS* 2.6 30.4 + - - -
688D LYS* 5.3 3.8 - - - +
690D LEU* 3.5 17.9 - - + +
691D HIS* 5.0 4.7 - - - -
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Residues in contact with CSO 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A HIS* 3.9 17.8 + - - -
377B HIS* 3.1 22.3 + - + +
378B LEU 3.8 4.0 - - - +
379B LEU 3.2 0.2 - - - -
380B GLU* 1.3 77.9 + - - +
382B ALA* 1.3 58.0 + - - +
383B TRP* 5.2 0.2 - - - -
384B LEU 5.2 0.7 + - - -
385B GLU* 4.1 8.8 - - - +
456B SER* 3.2 31.8 + - - -
457B GLY* 3.8 12.3 - - - +
460B THR* 4.6 8.1 + - - +
515B ARG* 3.8 15.7 + - - -
518B SER* 5.1 2.8 + - - -
547B HIS* 3.5 23.0 + - - -
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU 3.0 16.4 + - - +
379B LEU 4.7 0.2 - - - +
381B CSO 1.3 78.8 + - - -
383B TRP* 1.3 65.4 + - - +
384B LEU 3.3 2.9 - - - -
385B GLU* 3.1 11.6 + - - +
386B ILE* 3.0 37.3 + - + +
452B ILE* 3.8 28.0 - - + +
453B LEU* 4.1 5.2 - - + +
456B SER* 4.1 6.1 - - - -
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Residues in contact with TRP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 3.8 19.3 - - + -
357B MET* 3.3 25.1 - - - +
379B LEU 2.9 13.5 + - - +
380B GLU 3.1 25.6 + - - -
381B CSO 5.0 0.2 - - - -
382B ALA* 1.3 75.0 - - - +
384B LEU* 1.3 81.4 + - + +
386B ILE* 3.2 1.1 + - - +
387B LEU* 3.0 51.3 + - + +
522B MET* 3.7 34.5 - - + +
525B LEU* 3.8 24.7 - - + -
540B LEU* 3.9 21.8 - - + -
543B MET* 3.2 57.1 + - + -
544B LEU 4.3 2.0 - - - -
547B HIS* 4.2 1.3 - - - -
602B 27E 4.9 2.9 - - + -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B CSO 5.2 0.6 + - - -
382B ALA 3.3 0.6 - - - -
383B TRP* 1.3 96.8 - - + +
385B GLU* 1.3 68.0 + - - +
387B LEU* 3.4 3.3 + - + +
388B MET* 3.0 29.5 + - + +
518B SER* 3.4 35.2 - - - +
521B GLY* 3.8 7.9 - - - -
522B MET* 3.6 36.3 - - + +
602B 27E 3.4 52.7 - - + -
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A SER* 4.7 0.9 + - - -
381B CSO 4.1 8.5 - - - +
382B ALA* 3.1 9.6 + - - +
384B LEU* 1.3 76.9 - - - +
386B ILE* 1.3 58.2 + - - +
388B MET* 3.3 3.5 + - - +
389B ILE* 2.9 31.5 + - - +
452B ILE* 3.7 16.5 - - + +
456B SER* 2.8 33.8 + - - -
511B LEU* 4.1 4.2 - - - +
514B ILE* 3.8 20.0 - - + +
515B ARG* 3.4 41.7 + - - +
518B SER* 3.4 25.2 + - - +
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B MET* 4.0 25.4 - - + -
360B TRP* 3.8 28.3 - - + -
379B LEU* 4.9 0.9 - - + -
382B ALA* 3.0 30.3 + - + +
383B TRP* 3.6 6.7 - - - +
385B GLU* 1.3 74.9 - - - +
387B LEU* 1.3 64.5 + - - +
389B ILE* 3.4 8.3 - - - +
390B GLY* 3.2 18.7 + - - -
449B LYS* 3.7 30.8 - - + +
452B ILE* 3.9 15.5 - - + -
453B LEU* 4.2 15.3 - - + -
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ALA* 4.3 13.5 - - + -
353B GLU* 3.5 42.0 - - + +
354B LEU* 4.6 5.4 - - + +
357B MET* 3.5 24.9 - - + -
383B TRP* 3.0 42.7 + - + +
384B LEU* 3.4 8.5 + - + +
386B ILE* 1.3 76.1 - - - +
388B MET* 1.3 58.1 + - + +
390B GLY* 3.3 2.0 + - - -
391B LEU* 2.9 28.2 + - - +
394B ARG* 5.0 2.6 + - - -
602B 27E 3.9 20.4 - - + -
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Residues in contact with MET 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 3.0 21.3 + - + +
385B GLU* 3.7 4.7 - - - +
387B LEU* 1.3 75.2 - - - +
389B ILE* 1.3 60.4 + - - +
391B LEU* 3.3 7.2 + - - +
392B VAL* 2.9 35.1 + - - +
424B ILE* 3.4 29.2 - - + -
428B LEU* 4.0 19.5 - - + +
514B ILE* 4.9 4.0 - - + +
517B MET* 3.4 37.2 - - + +
518B SER* 3.7 19.1 - - - -
521B GLY* 4.6 0.9 - - - -
602B 27E 3.0 39.9 - - + -
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Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLU 2.9 16.6 + - - +
386B ILE* 3.4 17.3 - - - +
388B MET* 1.3 75.3 - - - +
390B GLY* 1.3 60.8 + - - +
392B VAL* 3.8 5.7 - - - +
393B TRP* 2.9 28.4 + - - +
435B PHE* 4.0 20.6 - - + -
445B PHE* 3.5 14.7 - - + -
448B LEU* 4.0 24.5 - - + -
449B LYS* 4.2 18.8 - - + +
452B ILE* 3.8 18.4 - - + -
511B LEU* 4.6 1.3 - - + -
514B ILE* 3.7 31.8 - - + +
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ILE 3.2 9.2 + - - -
387B LEU* 3.7 4.0 - - - -
389B ILE* 1.3 82.1 - - - +
391B LEU* 1.3 65.1 + - - +
393B TRP* 3.2 2.9 + - - +
394B ARG* 2.9 40.6 + - - +
445B PHE* 4.1 15.9 - - - -
449B LYS* 5.5 2.2 - - - -
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU 2.9 14.5 + - - +
388B MET* 3.3 8.5 + - - +
390B GLY* 1.3 75.4 - - - +
392B VAL* 1.3 58.4 + - - +
394B ARG* 3.4 16.0 + - - +
395B SER* 2.7 40.2 + - - +
402B LEU* 4.3 12.1 - - + -
403B LEU 3.6 20.6 - - - +
404B PHE* 3.6 46.0 - - + +
428B LEU* 3.8 24.7 - - + -
602B 27E 3.6 17.3 - - + -
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B MET 2.9 22.4 + - - +
389B ILE* 3.8 7.2 - - - +
390B GLY 3.3 0.2 - - - -
391B LEU* 1.3 75.0 - - + +
393B TRP* 1.3 63.5 + - - +
395B SER* 3.2 5.1 + - - -
396B MET* 3.2 19.2 + - - +
402B LEU* 5.5 1.3 - - + -
428B LEU* 3.9 34.1 - - + +
431B THR* 3.7 14.1 - - + -
432B SER* 3.4 31.6 + - - +
435B PHE* 3.2 32.1 - - + -
517B MET* 4.7 2.9 - - + -
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Residues in contact with TRP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE 2.9 18.1 + - - +
390B GLY 3.5 3.8 - - - +
392B VAL* 1.3 77.3 - - - +
394B ARG* 1.3 72.9 + - + +
396B MET* 3.1 46.8 + - + +
397B GLU 4.9 0.2 + - - -
435B PHE* 4.6 3.8 - - + -
440B LEU* 3.4 49.1 - - + -
442B GLY* 3.4 36.3 - - - -
445B PHE* 3.4 35.7 - + + -
601B GOL 3.0 30.1 + - - -
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 4.0 43.7 - - + +
349B LEU* 5.3 0.4 - - - +
353B GLU* 3.5 22.7 + - - -
387B LEU 5.0 2.2 + - - -
390B GLY* 2.9 34.6 + - - +
391B LEU* 3.7 26.7 - - - +
393B TRP* 1.3 84.3 - - + +
395B SER* 1.3 59.9 + - - +
396B MET 3.2 1.1 + - - -
397B GLU* 4.5 1.4 + - - +
398B HIS* 3.7 15.9 - - - -
403B LEU* 3.2 34.3 + - + +
404B PHE* 3.1 25.4 + - - +
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Residues in contact with SER 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU* 2.7 23.9 + - - +
392B VAL* 3.7 5.4 - - - -
393B TRP 3.1 0.4 - - - -
394B ARG* 1.3 76.6 - - - +
396B MET* 1.3 64.4 + - - +
397B GLU 3.4 1.3 - - - -
398B HIS* 2.9 24.8 + - - +
401B LYS 3.4 17.9 - - - -
402B LEU* 3.3 14.6 - - - +
403B LEU* 2.8 28.6 + - - +
432B SER* 3.4 11.2 + - - -
604B GOL 3.6 0.5 + - - -
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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