Contacts of the helix formed by residues 504 - 528 (chain B) in PDB entry 1FO4
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 MET 504 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B SER* 6.0 0.4 - - - +
433B LYS* 3.1 40.2 - - + +
502B GLY 3.9 7.6 - - - +
503B GLY* 1.3 74.1 - - - +
505B ILE* 1.3 66.0 + - - +
506B GLU 3.5 2.2 - - - -
507B PHE* 4.1 13.2 - - + -
508B ARG* 3.0 27.6 + - + +
1210B GLU* 3.9 17.5 - - - +
1212B HIS* 4.0 16.2 - - + +
1301B THR* 5.1 2.0 - - - +
1303B GLU* 3.1 57.2 + - + +
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Residues in contact with ILE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LEU* 3.8 25.9 - - + +
497B SER 3.6 26.9 - - - +
498B PRO* 4.3 14.6 - - + +
500B ALA* 4.1 9.4 - - + +
503B GLY* 3.4 26.7 - - - +
504B MET* 1.3 77.1 - - - +
506B GLU* 1.3 67.5 + - + +
509B ARG* 3.0 46.0 + - - +
1317B CYS 5.5 0.4 - - - +
1319B THR* 4.2 18.4 - - + +
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Residues in contact with GLU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B MET 3.5 0.2 - - - -
505B ILE* 1.3 77.3 - - + +
507B PHE* 1.3 58.6 + - - +
509B ARG* 3.4 2.0 + - - +
510B THR* 2.9 35.5 + - - +
1307B ASN* 4.2 20.2 + - - +
1317B CYS* 4.1 11.2 - - - +
1318B VAL* 3.2 21.2 - - + +
1319B THR* 2.8 47.7 + - - +
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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
----------------------------------------------------------
423B GLN* 4.1 3.4 - - + -
424B ALA 5.0 0.7 - - - -
433B LYS* 4.1 20.0 - - + -
504B MET* 3.6 20.8 + - + +
505B ILE 3.4 0.4 - - - -
506B GLU* 1.3 78.2 - - - +
508B ARG* 1.3 60.1 + - + +
510B THR* 3.3 3.8 + - - -
511B LEU* 2.9 51.9 + - + +
1168B THR 3.5 18.2 - - - -
1302B PRO* 3.6 11.4 - - + -
1303B GLU* 3.6 48.2 + - + +
1306B ARG* 3.4 36.1 - - + -
1307B ASN* 3.4 15.7 + - - +
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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
----------------------------------------------------------
433B LYS* 3.6 24.2 - - + +
434B VAL* 3.6 18.1 - - + +
458B GLY 2.9 31.9 + - - -
459B MET* 3.8 11.6 - - - +
496B LEU* 3.8 23.2 - - + +
500B ALA* 3.6 22.2 - - - +
501B PRO 3.2 24.6 + - - -
502B GLY* 4.9 2.0 - - - -
503B GLY 2.8 28.6 + - - +
504B MET* 3.0 21.1 + - + +
505B ILE* 3.9 2.6 - - - +
507B PHE* 1.3 75.3 - - + +
509B ARG* 1.3 68.5 + - - +
511B LEU* 3.1 5.7 + - - +
512B THR* 3.1 25.3 + - - +
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Residues in contact with ARG 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B MET* 4.1 2.9 - - + -
491B ALA* 2.9 34.4 + - - +
494B LEU 3.1 24.6 + - - +
495B SER* 3.6 9.2 - - - +
496B LEU* 3.9 20.4 - - + +
505B ILE* 3.0 40.0 + - - +
506B GLU 3.8 2.9 - - - +
508B ARG* 1.3 75.5 - - - +
510B THR* 1.3 61.7 + - - +
512B THR* 2.5 27.4 + - - +
513B LEU* 3.4 4.2 + - - +
1316B LEU 3.8 20.4 + - - -
1317B CYS* 3.4 35.5 + - + +
1318B VAL 5.3 1.2 + - - -
1319B THR* 6.1 0.2 - - - +
1321B ALA* 5.9 0.6 - - - +
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Residues in contact with THR 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLU* 2.9 24.9 + - - +
507B PHE* 3.5 7.2 - - - -
509B ARG* 1.3 78.2 - - - +
511B LEU* 1.3 57.5 + - - +
513B LEU* 3.3 4.0 + - - +
514B SER* 2.8 31.8 + - - +
1306B ARG* 3.4 44.6 - - + +
1307B ASN* 4.8 3.0 + - - -
1313B PHE* 4.8 0.9 - - + -
1314B THR* 3.8 25.1 - - + +
1317B CYS* 3.5 21.0 - - - +
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLN* 3.9 20.6 - - + -
433B LYS* 4.3 5.8 - - + -
434B VAL* 3.8 30.7 - - + -
507B PHE* 2.9 47.0 + - + +
508B ARG* 3.1 7.8 + - - +
510B THR* 1.3 73.2 - - - +
512B THR* 1.3 60.7 + - - +
514B SER* 3.7 2.4 - - - -
515B PHE* 2.8 45.1 + - + -
1167B LEU 3.9 5.6 - - - +
1168B THR* 3.7 37.2 - - - +
1306B ARG* 4.8 1.8 - - + -
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Residues in contact with THR 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 4.2 3.1 - - + -
456B TYR* 2.8 45.7 + - + -
459B MET* 3.5 39.1 - - + +
490B LEU* 3.8 2.6 + - - +
494B LEU* 3.9 17.0 + - + +
508B ARG 3.1 14.8 + - - +
509B ARG* 2.5 19.9 + - - -
511B LEU* 1.3 77.8 - - - +
513B LEU* 1.3 71.4 + - - +
515B PHE 3.8 0.2 + - - -
516B PHE 3.4 9.2 + - - -
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B CYS* 3.5 34.9 - - + +
490B LEU* 3.3 39.3 - - + -
491B ALA* 3.7 9.6 - - + +
509B ARG* 3.7 9.6 - - + +
510B THR 3.3 4.8 + - - +
511B LEU 3.2 0.2 - - - -
512B THR* 1.3 88.1 + - - +
514B SER* 1.3 59.8 + - - +
516B PHE* 3.3 3.8 + - - +
517B PHE* 3.0 27.4 + - - +
1313B PHE* 4.0 29.8 - - + +
1316B LEU* 4.1 13.7 - - + -
1317B CYS* 3.7 20.6 - - - -
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Residues in contact with SER 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B THR* 2.8 23.5 + - - +
511B LEU* 3.2 5.8 + - - -
513B LEU* 1.3 74.1 - - - +
515B PHE* 1.3 68.0 + - - +
517B PHE* 3.2 9.7 + - - +
518B LYS* 3.1 27.4 + - - +
1167B LEU* 3.1 33.0 + - - +
1168B THR* 6.3 0.2 - - - -
1306B ARG* 3.0 28.1 + - - -
1313B PHE* 4.5 4.3 - - - +
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Residues in contact with PHE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PHE* 3.2 53.3 - + + -
422B LYS 3.9 1.6 - - - -
423B GLN* 3.6 31.4 - - + -
434B VAL* 3.4 37.9 - - + -
435B THR 4.3 0.2 - - - -
436B CYS* 3.6 22.7 - - + -
438B MET* 3.9 6.3 - - + -
456B TYR* 4.6 1.8 - + + -
511B LEU* 2.8 30.7 + - + +
512B THR 4.0 2.2 - - - +
514B SER* 1.3 74.7 - - - +
516B PHE* 1.3 62.8 + - - +
518B LYS* 3.3 4.4 + - + -
519B PHE* 3.0 18.2 + - - +
1168B THR* 3.9 28.0 - - + -
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Residues in contact with PHE 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B MET* 3.7 10.0 - - + +
452B LEU* 5.0 2.5 - - + -
454B LEU* 3.6 26.7 - - + -
478B TRP* 4.1 13.5 - + - -
482B LEU* 3.9 13.0 - - + -
483B LEU* 3.9 29.2 - - + -
486B VAL* 3.4 44.0 - - + -
487B CYS* 4.4 5.2 - - - -
490B LEU* 3.9 9.9 - - + -
512B THR 3.4 11.9 + - - +
513B LEU 3.3 7.5 + - - +
514B SER 3.2 0.6 - - - -
515B PHE* 1.3 76.7 - - - +
517B PHE* 1.3 56.8 + - - +
519B PHE* 3.0 25.7 + + - +
520B TYR* 2.7 38.4 + - + +
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Residues in contact with PHE 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 3.9 31.9 - - + -
513B LEU 3.0 13.8 + - - +
514B SER* 3.2 10.3 + - - +
516B PHE* 1.3 76.4 - - - +
518B LYS* 1.3 56.2 + - - +
520B TYR* 3.3 4.8 + + - +
521B LEU* 3.0 66.1 + - + +
542B TYR* 3.9 10.5 - + - -
993B TRP* 3.4 45.5 - + - -
1167B LEU* 3.8 20.6 - - + -
1312B LYS* 4.3 5.8 - - - -
1313B PHE* 3.3 35.9 - + + -
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Residues in contact with LYS 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PHE* 3.6 33.0 - - + -
514B SER 3.1 17.0 + - - +
515B PHE* 3.6 8.1 - - + +
516B PHE 3.2 0.2 - - - -
517B PHE* 1.3 73.8 - - - +
519B PHE* 1.3 57.1 + - - +
521B LEU* 3.4 7.3 + - - +
522B THR* 2.7 39.6 + - - +
545B ALA* 3.4 29.4 + - + +
546B THR* 4.5 0.3 - - - +
547B LEU 4.8 5.5 + - - -
994B LYS* 4.2 5.5 - - - +
1165B ASP* 2.7 30.7 + - - -
1167B LEU* 3.8 33.7 - - + -
1168B THR* 3.9 14.5 - - + +
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Residues in contact with PHE 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE 4.2 6.3 - - - -
418B PHE* 4.3 1.3 - - - -
419B SER* 3.4 29.6 - - - -
421B PHE* 3.8 7.1 - - + -
438B MET* 3.5 57.9 - - + -
439B ARG 3.8 13.5 - - - -
440B VAL* 3.9 12.1 - - + -
452B LEU* 4.1 5.6 - - + -
454B LEU* 3.9 9.9 - - + -
478B TRP* 3.7 20.2 - + - -
515B PHE 3.0 7.3 + - - +
516B PHE* 3.3 29.6 - + - +
518B LYS* 1.3 76.3 - - - +
520B TYR* 1.3 55.4 + - - +
522B THR* 3.3 1.6 + - - -
523B VAL* 2.9 47.3 + - + +
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Residues in contact with TYR 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B TRP* 3.1 57.8 + + - -
479B ASN* 2.7 46.1 - - - -
480B GLU* 3.0 10.5 + - - -
482B LEU* 4.3 7.9 - - + -
483B LEU* 4.0 34.1 - - + -
516B PHE* 2.7 30.7 + + + +
517B PHE* 3.5 7.0 - + - +
519B PHE* 1.3 74.2 - - - +
521B LEU* 1.3 76.4 + - + +
523B VAL 3.4 0.2 + - - -
524B LEU* 3.1 46.5 + - + +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PHE* 3.0 55.1 + - + +
518B LYS* 4.0 2.2 - - - +
520B TYR* 1.3 91.8 - - + +
522B THR* 1.3 65.7 + - - +
524B LEU* 3.3 12.5 + - + +
525B LYS* 3.0 23.9 + - - +
538B LEU* 3.9 15.5 - - + +
542B TYR* 4.0 27.8 - - + +
545B ALA* 4.0 22.0 - - + -
546B THR* 3.5 14.6 - - + -
993B TRP* 5.0 0.2 - - - +
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Residues in contact with THR 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B SER* 4.1 13.5 + - - +
421B PHE* 4.8 4.9 - - - -
518B LYS* 2.7 26.6 + - - +
519B PHE* 3.6 4.4 - - - -
521B LEU* 1.3 77.2 - - - +
523B VAL* 1.3 57.3 + - + +
525B LYS* 3.5 7.3 + - + +
526B LYS* 3.0 56.3 + - + +
546B THR* 3.5 31.1 + - - +
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE* 4.4 11.0 - - + -
440B VAL* 4.1 7.6 - - + -
442B PHE* 3.7 28.0 - - + -
478B TRP* 3.3 38.4 - - + +
519B PHE* 2.9 46.6 + - + +
521B LEU 3.2 0.2 - - - -
522B THR* 1.3 76.6 - - + +
524B LEU* 1.3 54.4 + - - +
526B LYS* 3.1 7.5 + - - +
527B LEU* 2.7 37.8 + - + +
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B MET* 3.8 27.3 - - + +
478B TRP* 3.8 22.2 - - + +
479B ASN* 5.7 0.2 - - - -
520B TYR* 3.1 46.0 + - + +
521B LEU* 3.3 9.2 + - + +
523B VAL* 1.3 75.1 - - - +
525B LYS* 1.3 64.2 + - - +
527B LEU* 3.2 14.5 + - - +
528B GLY* 3.4 8.5 + - - -
538B LEU* 3.6 27.1 - - + -
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Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU 3.0 13.6 + - - +
522B THR* 3.5 11.9 - - + +
524B LEU* 1.3 76.5 - - - +
526B LYS* 1.3 62.7 + - + +
528B GLY* 3.2 16.8 + - - -
538B LEU* 4.2 16.8 - - + +
543B THR* 4.8 11.9 - - + +
546B THR* 3.3 33.2 + - + +
547B LEU* 4.0 18.4 - - - +
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Residues in contact with LYS 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 2.7 32.3 + - - +
328B ARG* 5.0 7.8 - - - +
417B PHE* 3.6 45.3 - - + +
418B PHE 3.4 16.6 + - - +
419B SER* 4.7 0.4 + - - -
522B THR* 3.0 43.0 + - + +
523B VAL* 3.1 4.2 + - + +
525B LYS* 1.3 73.9 - - + +
527B LEU* 1.3 61.1 + - - +
528B GLY 3.1 10.5 + - - -
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ASP* 5.8 2.9 - - - +
417B PHE* 3.9 21.5 - - + -
442B PHE* 3.8 19.1 - - + -
446B SER 4.0 20.0 - - - +
447B MET* 3.8 39.0 - - + +
478B TRP* 4.1 8.5 - - + -
523B VAL* 2.7 41.2 + - + +
524B LEU* 3.2 7.3 + - - +
526B LYS* 1.3 72.4 - - - +
528B GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LEU 3.4 6.3 + - - -
525B LYS 3.2 13.7 + - - -
526B LYS 3.1 6.7 - - - -
527B LEU* 1.3 81.3 - - - +
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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