Contacts of the helix formed by residues 491 - 516 (chain B) in PDB entry 3IAD
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 PRO 491 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TRP* 4.7 6.3 - - + +
269B GLY* 3.8 30.1 - - - +
489B THR 4.6 1.3 - - - +
490B LYS* 1.3 87.4 - - + +
492B LEU* 1.3 56.3 + - - +
493B GLN* 3.1 18.8 - - + +
494B LEU* 2.6 34.5 + - + +
495B TYR 3.3 2.9 + - - -
564B THR* 4.1 12.8 - - + +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B LYS 3.2 4.4 + - - -
491B PRO* 1.3 68.3 - - - +
493B GLN* 1.3 64.4 + - - +
495B TYR* 3.0 14.1 + - + -
496B ARG* 2.9 51.1 + - + +
564B THR* 5.0 0.6 - - - +
568B ASN* 3.6 31.3 + - + +
571B TRP* 3.5 56.5 - - + +
572B TYR* 4.6 0.4 - - + -
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Residues in contact with GLN 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLY 5.5 0.2 - - - +
271B HIS* 3.8 18.7 + - - -
491B PRO* 3.1 17.5 - - + +
492B LEU* 1.3 79.3 - - - +
494B LEU* 1.3 62.6 + - - +
496B ARG* 3.9 6.5 + - - +
497B GLN* 3.3 25.0 + - - +
802B EPE 2.7 41.7 + - + +
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLY* 3.8 25.1 - - - +
270B LEU 3.4 22.2 - - - +
271B HIS* 5.0 0.9 - - - -
272B VAL* 3.9 17.7 - - + +
273B PHE* 3.7 31.0 - - + -
333B ASP* 5.9 0.7 - - - +
490B LYS* 4.1 15.7 - - + +
491B PRO* 2.6 25.4 + - + +
493B GLN* 1.3 80.9 - - - +
495B TYR* 1.3 65.4 + - - +
497B GLN* 3.3 9.8 + - - +
498B TRP* 3.1 33.0 + - + +
802B EPE 3.8 11.9 - - - +
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ASN* 3.4 31.6 + - + +
488B PRO* 3.4 29.6 - - + +
490B LYS 3.9 10.3 - - - +
491B PRO 3.3 2.0 + - - -
492B LEU* 3.0 12.0 + - + +
494B LEU* 1.3 77.1 - - - +
496B ARG* 1.3 57.9 + - - +
498B TRP* 3.1 6.0 + - - +
499B THR* 2.9 40.0 + - - -
535B GLN* 2.4 40.5 + - - +
539B ILE* 3.6 16.4 - - + +
568B ASN* 3.8 28.9 - - + -
572B TYR* 3.3 30.7 - + - -
901B 15X 4.3 4.7 - - - -
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 2.9 36.8 + - + +
493B GLN* 4.2 6.3 - - - +
495B TYR* 1.3 76.1 - - - +
497B GLN* 1.3 56.6 + - + +
499B THR* 3.3 2.9 + - - -
500B ASP* 3.0 35.8 + - - +
571B TRP* 3.3 46.4 - - - -
572B TYR* 4.0 14.1 + - - +
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Residues in contact with GLN 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 3.6 38.3 - - + +
493B GLN* 3.3 18.6 + - - +
494B LEU* 3.3 6.7 + - - +
496B ARG* 1.3 78.4 - - + +
498B TRP* 1.3 58.4 + - - +
500B ASP* 3.4 6.9 + - - +
501B ARG* 2.9 40.2 + - - +
802B EPE 2.9 45.0 + - - -
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Residues in contact with TRP 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 3.9 8.1 - - + -
273B PHE* 3.6 36.1 - + - -
324B ALA 5.6 0.2 - - - -
325B TYR* 3.6 29.4 - + - -
327B ASN* 5.4 0.7 - - - -
329B ILE* 3.7 12.1 - - + -
330B HIS* 3.7 37.9 - - + -
333B ASP* 3.5 34.0 + - + -
487B ASN* 3.4 39.2 - - + +
490B LYS* 5.5 3.8 - - + +
494B LEU* 3.1 34.4 + - + +
495B TYR* 3.1 7.7 + - - +
497B GLN* 1.3 75.9 - - - +
499B THR* 1.3 60.8 + - - +
501B ARG* 4.3 9.0 - - - -
502B ILE* 3.0 31.0 + - - +
901B 15X 4.2 2.0 - - - -
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Residues in contact with THR 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B TYR* 2.9 32.8 + - - -
496B ARG 3.6 4.3 - - - -
498B TRP* 1.3 77.5 - - - +
500B ASP* 1.3 59.7 + - - +
502B ILE* 3.1 3.3 - - - +
503B MET* 3.0 35.4 + - + +
531B VAL* 4.0 20.2 - - + -
535B GLN* 3.7 28.7 - - + +
572B TYR* 3.1 26.5 + - - +
901B 15X 3.7 8.2 - - - -
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Residues in contact with ASP 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ARG* 3.0 22.2 + - - +
497B GLN* 3.7 6.7 - - - +
499B THR* 1.3 81.2 - - - +
501B ARG* 1.3 58.4 + - + +
503B MET* 4.0 4.9 - - - +
504B GLU* 3.1 27.5 + - - +
531B VAL* 5.8 2.8 - - - +
572B TYR* 5.5 0.7 + - - -
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Residues in contact with ARG 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 3.2 41.7 - - - -
324B ALA* 3.0 51.1 + - + +
325B TYR* 4.1 8.5 - - + -
327B ASN* 3.6 11.5 + - - +
329B ILE* 4.3 12.6 - - - +
497B GLN* 2.9 26.3 + - - +
498B TRP* 3.8 12.7 - - - +
499B THR 3.3 0.4 - - - -
500B ASP* 1.3 77.6 - - + +
502B ILE* 1.3 64.1 + - - +
504B GLU* 3.3 1.8 + - - -
505B GLU* 3.1 19.8 + - - +
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Residues in contact with ILE 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR* 3.5 41.0 - - + -
326B HIS* 4.0 3.6 - - + -
498B TRP 3.0 16.7 + - - +
499B THR* 3.1 13.5 - - + +
501B ARG* 1.3 76.1 - - - +
503B MET* 1.3 63.7 + - + +
505B GLU* 3.5 3.0 + - - +
506B PHE* 2.9 69.8 + - + -
901B 15X 3.5 57.9 - - + +
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Residues in contact with MET 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B THR* 3.0 24.4 + - + +
500B ASP* 4.0 5.8 - - - +
502B ILE* 1.3 76.4 - - + +
504B GLU* 1.3 59.1 + - - +
506B PHE* 3.7 6.4 - - + +
507B PHE* 2.9 68.4 + - + -
523B MET* 3.4 32.5 - - + +
529B ALA* 4.9 2.9 - - + -
531B VAL* 4.1 35.7 - - + -
535B GLN* 5.3 0.2 - - - -
901B 15X 3.8 30.5 - - - -
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Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ALA* 3.7 17.7 - - + +
500B ASP 3.1 19.2 + - - +
501B ARG* 3.3 5.3 + - - +
503B MET* 1.3 75.4 - - - +
505B GLU* 1.3 63.1 + - - +
507B PHE* 3.3 9.7 + - + +
508B ARG* 3.0 22.7 + - - +
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Residues in contact with GLU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 2.8 33.8 - - + +
324B ALA* 3.7 9.7 + - + +
325B TYR* 2.8 21.2 + - + -
326B HIS* 2.5 35.4 + - - -
370B HIS* 4.0 0.5 - - - -
372B GLY* 3.6 32.4 - - - +
501B ARG 3.1 14.9 + - - +
502B ILE* 3.7 6.8 - - - +
504B GLU* 1.3 77.1 - - - +
506B PHE* 1.3 65.7 + - + +
508B ARG* 3.3 9.2 + - + +
509B GLN* 3.3 16.6 + - - +
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Residues in contact with PHE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B HIS* 5.3 2.0 - + - -
502B ILE* 2.9 42.5 + - + +
503B MET* 3.7 16.6 - - - +
505B GLU* 1.3 83.2 - - + +
507B PHE* 1.3 58.2 + - - +
509B GLN* 3.1 8.9 + - + +
510B GLY 3.0 22.2 + - - -
523B MET* 3.8 24.2 - - + +
524B CYS* 3.3 22.9 - - - +
599B PHE* 3.4 32.5 - + - -
901B 15X 3.4 57.4 - + - -
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Residues in contact with PHE 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B MET* 2.9 54.6 + - + +
504B GLU* 3.7 9.4 - - + +
506B PHE* 1.3 76.0 - - - +
508B ARG* 1.3 56.0 + - - +
510B GLY* 3.4 0.9 + - - -
511B ASP* 2.9 35.8 + - - +
523B MET 3.9 5.4 - - - -
524B CYS 3.5 18.0 - - - +
525B ASP 3.7 9.0 - - - -
526B LYS* 3.6 41.3 - - + -
529B ALA* 3.8 16.2 - - + -
531B VAL* 4.5 8.5 - - + -
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Residues in contact with ARG 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLY 5.8 1.3 - - - +
504B GLU* 3.0 15.2 + - - +
505B GLU* 3.5 12.8 - - + +
506B PHE 3.2 0.2 - - - -
507B PHE* 1.3 74.8 - - - +
509B GLN* 1.3 58.0 + - - +
511B ASP* 3.4 10.0 + - - +
512B ARG* 3.0 34.3 + - + +
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Residues in contact with GLN 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLY 4.2 3.3 + - - +
373B VAL* 3.2 18.8 - - + -
374B SER* 3.0 46.4 + - - -
377B PHE* 3.9 18.1 - - + +
505B GLU 3.3 8.3 + - - +
506B PHE* 3.1 13.6 + - + +
508B ARG* 1.3 75.9 - - - +
510B GLY* 1.3 55.2 + - - +
512B ARG* 3.0 8.3 + - - +
513B GLU* 2.7 58.9 + - - +
521B SER* 3.6 12.5 + - - -
524B CYS* 4.6 8.9 - - - -
901B 15X 5.1 2.2 + - - -
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Residues in contact with GLY 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B PHE 3.0 10.3 + - - -
507B PHE 3.4 0.4 + - - -
508B ARG 3.4 0.2 - - - -
509B GLN* 1.3 76.9 - - - +
511B ASP* 1.3 56.2 + - - +
513B GLU* 3.2 16.2 + - - +
514B ARG* 2.9 34.1 + - - +
520B ILE* 4.0 9.8 - - - +
524B CYS* 3.3 24.2 - - - +
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Residues in contact with ASP 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B PHE* 2.9 25.2 + - - +
508B ARG* 3.5 9.4 - - - +
509B GLN 3.3 0.2 - - - -
510B GLY* 1.3 74.9 - - - +
512B ARG* 1.3 62.8 + - + +
514B ARG* 2.8 30.5 + - - +
515B GLU* 3.3 31.1 + - - +
526B LYS* 3.1 32.9 + - - +
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Residues in contact with ARG 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PRO* 4.2 14.3 + - - +
373B VAL* 3.2 35.6 - - - +
377B PHE* 4.2 26.0 - - + -
508B ARG* 3.0 20.5 + - + +
509B GLN* 3.0 9.1 + - - +
511B ASP* 1.3 75.4 - - + +
513B GLU* 1.3 64.0 + - - +
515B GLU* 3.5 14.7 - - - +
516B ARG* 3.4 33.5 + - - +
282D ARG* 4.3 5.6 - - - +
317D ASP* 2.9 47.5 + - - +
318D HIS* 6.1 1.4 - - - -
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Residues in contact with GLU 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PHE* 3.8 18.5 - - + +
509B GLN* 2.7 36.3 + - - +
510B GLY* 3.5 21.4 + - - +
512B ARG* 1.3 73.0 - - - +
514B ARG* 1.3 61.3 + - - +
516B ARG* 3.3 1.7 + - - -
517B GLY 3.1 3.5 + - - -
518B MET* 2.9 49.2 + - + +
519B GLU 3.8 15.5 - - - +
520B ILE* 3.5 4.8 - - - -
521B SER* 2.6 47.4 + - - -
524B CYS* 4.1 0.7 - - - +
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B GLY 2.9 15.0 + - - +
511B ASP* 2.8 37.9 + - - +
512B ARG 3.3 0.2 - - - -
513B GLU* 1.3 73.6 - - - +
515B GLU* 1.3 66.9 + - - +
517B GLY* 3.0 14.3 + - - -
518B MET 4.7 2.9 - - - -
520B ILE* 3.2 24.9 - - + +
524B CYS 5.4 0.2 + - - -
525B ASP* 2.9 27.3 + - - +
526B LYS* 3.9 21.8 - - - +
527B HIS* 3.4 21.5 + - - -
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Residues in contact with GLU 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B ASP* 3.3 17.1 + - - +
512B ARG* 3.5 20.9 - - - +
514B ARG* 1.3 79.7 - - - +
516B ARG* 1.3 61.8 + - - +
517B GLY 3.4 0.5 + - - -
280D GLY 5.5 0.7 - - - +
282D ARG* 2.9 51.3 + - - +
309D ILE* 5.7 1.2 - - - +
313D MET* 3.8 32.4 - - + +
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Residues in contact with ARG 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PHE* 3.9 20.6 - - - -
381B THR* 3.9 17.9 - - - +
512B ARG* 3.4 25.8 + - - +
513B GLU 3.3 5.7 + - - +
514B ARG 3.2 1.0 - - - -
515B GLU* 1.3 80.4 + - - +
517B GLY* 1.3 60.4 + - - +
518B MET* 3.5 28.7 + - + +
310D THR* 4.1 25.3 + - + +
313D MET* 4.5 16.8 - - - +
314D THR* 3.3 37.3 + - - +
317D ASP* 3.5 24.2 + - - +
409D GLU* 5.1 2.6 + - - -
410D GLU 5.5 0.8 + - - -
412D CYS* 5.5 0.6 - - - -
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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