Contacts of the helix formed by residues 532 - 559 (chain A) in PDB entry 4FE1
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 GLY 532 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ASP* 3.7 16.8 - - - -
483A GLN* 4.1 7.2 - - - -
484A PRO* 3.3 21.4 - - - +
530A VAL* 4.2 0.8 + - - -
531A LEU 1.3 70.3 - - - -
533A THR* 1.3 66.5 + - - -
534A ALA* 3.2 3.8 - - - -
535A ASP* 2.4 31.0 + - - +
536A PHE 3.3 2.3 + - - -
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Residues in contact with THR 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE 4.1 4.7 - - - +
476A SER* 3.5 30.8 + - - +
477A ASP* 2.9 30.7 + - - -
481A GLN* 3.7 1.9 - - - -
482A LEU* 3.1 53.5 + - + +
483A GLN* 3.9 4.8 + - - +
532A GLY* 1.3 70.5 - - - -
534A ALA* 1.3 58.6 + - - +
536A PHE* 3.1 5.4 + - - +
537A MET* 3.0 35.6 + - - +
644A ILE* 5.1 0.9 - - + -
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Residues in contact with ALA 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TYR* 4.2 1.2 + - - -
477A ASP* 5.3 1.4 + - - +
532A GLY 3.2 0.6 - - - -
533A THR* 1.3 78.4 - - - +
535A ASP* 1.3 59.6 + - - +
537A MET* 3.3 6.4 + - - +
538A VAL* 3.0 30.7 + - - +
639A PHE* 3.8 28.6 - - + +
640A ALA* 4.1 13.4 + - - +
643A ALA* 4.4 7.1 - - + +
644A ILE* 3.7 28.4 - - + +
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Residues in contact with ASP 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PRO* 4.7 2.5 - - + -
531A LEU* 3.3 21.6 - - + +
532A GLY* 2.4 38.7 + - - +
534A ALA* 1.3 76.8 + - - +
536A PHE* 1.3 65.5 + - - +
537A MET 3.1 0.2 - - - -
538A VAL* 3.4 7.8 - - - +
539A HIS* 2.7 41.1 + - + +
612A HIS* 4.5 4.7 + - - -
616A LYS* 2.8 39.1 + - - +
639A PHE* 3.9 9.6 - - - -
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Residues in contact with PHE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A HIS 5.5 1.1 - - - -
458A LEU* 4.5 11.2 - - + -
482A LEU* 3.0 62.6 - - + +
483A GLN 4.4 9.2 - - - -
484A PRO* 4.6 12.5 - - + +
532A GLY 3.3 3.6 + - - +
533A THR 3.1 8.0 + - - +
535A ASP* 1.3 79.2 - - - +
537A MET* 1.3 67.6 + - + +
539A HIS* 3.4 3.4 + - - +
540A HIS* 2.7 72.1 + + + -
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Residues in contact with MET 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A SER* 5.0 1.7 - - - +
458A LEU* 4.2 13.2 - - + -
459A TYR* 3.1 64.0 - - + +
462A ASN* 3.8 22.4 - - - +
475A PHE* 4.3 1.6 - - - +
482A LEU* 4.4 13.7 - - + -
533A THR* 3.0 25.0 + - + +
534A ALA* 3.4 7.0 - - - +
535A ASP 3.1 0.2 - - - -
536A PHE* 1.3 79.6 - - + +
538A VAL* 1.3 63.5 + - - +
540A HIS* 3.1 6.8 + - - +
541A ILE* 3.0 23.6 + - - +
643A ALA 5.3 0.2 - - - +
644A ILE* 3.9 26.7 - - - +
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TYR* 2.9 17.2 + - + +
534A ALA 3.0 17.3 + - - +
535A ASP* 3.4 13.0 - - - +
537A MET* 1.3 72.7 - - - +
539A HIS* 1.3 62.0 + - - +
541A ILE* 3.2 8.2 + - + +
542A HIS* 3.0 32.7 + - + +
608A VAL* 5.4 4.9 - - + -
612A HIS* 3.3 45.5 - - + +
639A PHE* 4.5 4.3 - - + -
643A ALA 5.5 1.1 - - - +
649A TRP* 3.9 26.9 - - + -
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Residues in contact with HIS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 5.1 12.3 - - + -
535A ASP* 2.7 39.1 + - + +
536A PHE* 3.7 6.3 - - - +
537A MET 3.2 0.2 - - - -
538A VAL* 1.3 76.2 - - - +
540A HIS* 1.3 62.8 + - + +
542A HIS* 3.1 14.7 + - + +
543A ALA* 3.0 25.3 + - - +
612A HIS* 4.0 23.4 - + - -
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Residues in contact with HIS 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PHE* 6.5 1.3 - + - -
451A LEU* 4.5 15.6 - - + +
454A HIS 5.0 5.6 - - - +
455A SER* 3.8 17.2 - - - -
458A LEU* 6.4 0.4 - - + -
536A PHE* 2.7 73.8 + + + +
537A MET* 3.7 5.2 - - - +
539A HIS* 1.3 79.8 - - + +
541A ILE* 1.3 63.9 + - - +
543A ALA* 3.3 9.8 + - + +
544A PHE* 3.0 23.2 + - - +
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Residues in contact with ILE 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A SER* 3.6 7.4 - - - +
456A PHE* 3.4 40.2 - - + +
459A TYR* 3.5 26.9 - - + +
537A MET 3.0 19.0 + - - +
538A VAL* 3.2 10.7 + - + +
540A HIS* 1.3 76.2 - - - +
542A HIS* 1.3 57.8 + - - +
544A PHE* 3.1 9.0 - - + +
545A THR* 3.0 36.0 + - + +
608A VAL* 3.8 29.4 - - + -
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Residues in contact with HIS 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 3.0 17.8 + - + +
539A HIS* 3.3 14.8 - - + +
540A HIS 3.1 0.2 - - - -
541A ILE* 1.3 73.6 - - - +
543A ALA* 1.3 64.9 + - - +
544A PHE 3.0 1.6 - - - -
545A THR* 3.2 8.5 + - - -
546A ILE* 3.0 36.4 + - + +
605A CYS* 4.8 1.1 - - - -
608A VAL* 3.4 41.5 + - + +
609A VAL* 3.5 28.8 - - + +
612A HIS* 3.0 38.5 + + + +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 3.9 15.0 - - + -
539A HIS 3.0 12.7 + - - +
540A HIS* 3.3 14.3 + - + +
542A HIS* 1.3 74.8 - - - +
544A PHE* 1.3 56.9 + - - +
546A ILE* 3.8 6.6 - - - +
547A HIS* 2.9 44.3 + - + +
----------------------------------------------------------
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Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A CYS 3.4 13.2 - - - -
451A LEU* 3.6 21.5 - - + +
452A GLY* 3.2 35.9 - - - -
455A SER* 3.9 13.0 - - - +
456A PHE* 5.6 5.8 - - + -
540A HIS 3.0 13.4 + - - +
541A ILE* 3.1 17.7 - - + +
542A HIS 3.0 0.4 - - - -
543A ALA* 1.3 75.3 - - - +
545A THR* 1.3 74.1 + - + +
546A ILE 3.2 0.2 + - - -
547A HIS* 3.3 2.4 + - - +
548A VAL* 3.0 35.0 + - + +
601A TRP* 3.6 30.3 - + - -
604A ASN* 5.9 0.7 - - - -
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Residues in contact with THR 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ILE* 3.0 23.2 + - + +
542A HIS* 3.2 13.7 + - - -
544A PHE* 1.3 87.5 - - + +
546A ILE* 1.3 58.6 + - - +
548A VAL 3.5 0.2 + - - -
549A THR* 2.6 34.3 + - - -
601A TRP* 3.9 22.8 - - + -
604A ASN* 4.3 14.1 - - - +
605A CYS* 3.2 37.1 + - - +
608A VAL* 5.3 4.7 - - + -
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Residues in contact with ILE 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A HIS* 3.0 25.2 + - + +
543A ALA* 3.8 6.5 - - - +
545A THR* 1.3 74.3 - - - +
547A HIS* 1.3 70.2 + - + +
549A THR* 3.0 7.7 + - - -
550A VAL* 2.9 35.0 + - + +
605A CYS* 3.7 21.3 - - - -
609A VAL* 6.2 1.6 - - + -
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Residues in contact with HIS 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LEU* 3.6 16.9 - - + +
447A VAL* 3.3 23.5 - - + +
448A CYS* 3.5 13.5 - - - -
451A LEU* 3.4 24.3 - - + +
543A ALA* 2.9 36.8 + - + +
544A PHE 3.3 1.5 + - - +
546A ILE* 1.3 79.5 - - + +
548A VAL* 1.3 57.8 + - - +
550A VAL* 3.5 6.3 + - + +
551A LEU* 3.0 29.1 + - - +
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Residues in contact with VAL 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A CYS* 3.7 22.7 - - + -
544A PHE* 3.0 39.4 + - + +
547A HIS* 1.3 74.1 - - - +
549A THR* 1.3 67.4 + - - +
551A LEU* 3.2 3.0 + - + +
552A ILE* 3.0 45.2 + - + +
601A TRP* 3.4 46.9 - - + -
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Residues in contact with THR 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A VAL* 6.1 2.7 - - + -
406A VAL* 4.8 2.2 - - + -
545A THR 2.6 20.6 + - - -
546A ILE* 3.0 10.3 + - - -
548A VAL* 1.3 78.0 - - - +
550A VAL* 1.3 63.9 + - + +
552A ILE* 3.3 4.0 + - - +
553A LEU* 3.1 40.8 + - + +
598A GLY* 4.0 18.8 - - - +
601A TRP* 3.6 25.6 + - - +
602A MET* 4.3 13.3 - - + +
605A CYS* 4.5 2.6 - - - +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LEU* 4.1 14.1 - - + -
546A ILE* 2.9 31.6 + - + +
547A HIS* 3.8 6.5 - - + +
549A THR* 1.3 79.8 - - + +
551A LEU* 1.3 62.8 + - - +
553A LEU* 3.1 6.8 + - - +
554A LEU* 2.8 42.8 + - + +
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ILE* 3.7 42.8 - - + +
444A LEU* 3.5 25.8 - - + +
445A ASN* 4.0 29.2 - - + +
448A CYS* 4.1 11.7 - - + -
547A HIS 3.0 18.8 + - - +
548A VAL* 3.2 5.6 + - + +
550A VAL* 1.3 75.0 - - - +
552A ILE* 1.3 70.1 + - + +
554A LEU* 3.8 1.5 - - - +
555A LYS* 2.9 36.2 + - + +
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Residues in contact with ILE 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A VAL* 3.0 46.7 + - + +
549A THR* 3.7 7.4 - - - +
551A LEU* 1.3 90.9 - - + +
553A LEU* 1.3 57.8 + - - +
555A LYS* 3.3 4.2 + - - +
556A GLY 3.0 21.5 + - - -
594A HIS* 3.4 37.9 - - + +
597A LEU* 4.1 15.0 - - + -
598A GLY* 3.8 16.4 - - - +
601A TRP* 5.0 12.6 - - + +
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Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A VAL* 5.0 7.2 - - + +
406A VAL* 4.0 25.6 - - + +
409A ALA* 3.6 31.1 - - + +
549A THR* 3.1 34.0 + - + +
550A VAL* 3.9 4.9 - - - +
552A ILE* 1.3 73.0 - - - +
554A LEU* 1.3 60.4 + - - +
556A GLY* 3.1 3.8 + - - -
557A VAL* 2.9 32.4 + - - +
594A HIS* 3.8 21.5 - - - +
595A VAL* 4.0 15.5 - - + -
598A GLY* 3.9 15.0 - - - -
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ILE* 4.0 24.0 - - + -
441A ILE* 4.2 3.8 - - + -
444A LEU* 4.5 10.3 - - + -
550A VAL* 2.8 38.1 + - + +
551A LEU* 4.0 2.7 - - - +
553A LEU* 1.3 71.3 - - - +
555A LYS* 1.3 59.5 + - - +
557A VAL* 4.4 9.0 - - + +
558A LEU* 2.9 64.1 + - + +
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Residues in contact with LYS 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ILE* 3.8 28.9 - - + -
551A LEU* 2.9 23.0 + - + +
552A ILE* 3.5 7.2 - - - +
554A LEU* 1.3 75.5 - - - +
556A GLY* 1.3 64.9 + - - +
559A PHE* 3.0 46.6 + - + +
569A LYS* 6.1 1.0 - - - +
594A HIS* 3.0 30.4 + - + +
----------------------------------------------------------
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Residues in contact with GLY 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ALA* 4.7 1.3 - - - -
552A ILE 3.0 9.9 + - - -
553A LEU 3.1 4.9 + - - -
555A LYS* 1.3 79.4 - - - +
557A VAL* 1.3 57.1 + - - +
559A PHE 3.7 1.1 - - - -
560A ALA* 3.0 29.6 + - - +
591A GLY* 4.1 9.4 - - - -
594A HIS* 3.2 34.9 - - - -
----------------------------------------------------------
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA* 3.4 31.2 - - + +
412A GLY* 3.9 11.7 - - - +
413A ALA* 3.8 13.5 - - + +
416A MET* 3.7 29.9 - - + +
434A LEU* 4.9 0.3 - - - +
553A LEU 2.9 20.3 + - - +
554A LEU* 4.1 10.3 - - + +
555A LYS 3.4 0.2 - - - -
556A GLY* 1.3 76.3 - - - +
558A LEU* 1.3 69.3 + - + +
560A ALA* 3.3 15.6 + - - +
561A ARG 5.0 0.2 + - - -
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 6.4 0.2 - - + -
433A VAL* 3.5 31.6 - - + +
434A LEU* 3.8 20.6 - - + +
437A ARG* 3.2 36.8 + - + -
440A ILE* 4.2 22.9 - - + -
441A ILE* 3.9 17.0 - - + -
554A LEU* 2.9 51.4 + - + +
555A LYS* 4.8 0.2 - - - -
557A VAL* 1.3 83.9 - - + +
559A PHE* 1.3 67.8 + - + +
560A ALA 3.5 0.4 + - - -
561A ARG 5.3 0.5 + - - -
----------------------------------------------------------
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Residues in contact with PHE 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 3.4 45.1 - - + +
438A ASP* 4.2 17.7 - - - -
441A ILE* 3.6 29.8 - - + -
555A LYS* 3.0 43.2 + - + +
556A GLY 3.7 2.5 - - - -
558A LEU* 1.3 81.0 - - + +
560A ALA* 1.3 63.9 + - - +
561A ARG 3.3 2.9 - - - -
562A SER 3.3 21.7 - - - +
563A SER* 3.9 15.0 - - - -
564A ARG* 5.5 1.6 - - - -
569A LYS* 2.9 29.2 + - - +
589A VAL 4.9 0.2 - - - +
594A HIS* 5.7 3.4 - - + +
----------------------------------------------------------
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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