Contacts of the helix formed by residues 552 - 584 (chain E) in PDB entry 1XSK
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 ASP 552 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521E ALA* 4.1 8.2 - - + +
525E LYS* 3.0 23.4 + - - +
548E PRO 3.5 2.2 + - - +
549E TRP* 4.5 5.1 - - - +
551E TYR* 1.3 83.7 - - - +
553E ASP* 1.3 63.1 + - - +
554E GLU* 3.0 9.6 + - - +
555E SER* 2.4 56.6 + - - -
556E CYS* 3.4 12.7 - - - -
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Residues in contact with ASP 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552E ASP* 1.3 72.7 - - - +
554E GLU* 1.3 67.2 + - - +
556E CYS* 2.8 24.7 + - - +
557E ASP* 3.0 18.0 + - - +
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Residues in contact with GLU 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E LYS* 2.9 25.6 + - - -
552E ASP* 3.0 12.4 + - - +
553E ASP* 1.3 78.5 - - - +
555E SER* 1.3 57.5 + - - +
557E ASP* 3.0 18.7 + - + +
558E VAL* 2.8 38.6 + - + +
656E PHE* 3.3 27.4 + - + +
657E LEU* 4.5 13.0 - - + +
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Residues in contact with SER 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521E ALA* 4.7 0.3 - - - +
524E TYR* 3.7 18.8 - - - -
525E LYS* 3.3 24.4 - - - +
548E PRO* 3.6 17.0 - - - -
551E TYR* 3.4 12.6 - - - +
552E ASP* 2.4 45.8 + - - -
554E GLU* 1.3 69.5 - - - +
556E CYS* 1.3 57.1 + - - +
558E VAL* 3.3 1.6 + - - +
559E VAL* 2.9 34.3 + - - +
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Residues in contact with CYS 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E ARG* 4.1 14.8 - - - -
298E LEU* 3.2 18.4 - - + +
548E PRO* 3.6 11.9 - - + -
549E TRP* 3.5 34.5 - - - -
552E ASP 3.4 15.7 - - - -
553E ASP* 2.8 15.7 + - - +
555E SER* 1.3 77.1 - - - +
557E ASP* 1.3 58.0 + - - +
560E ARG* 3.0 41.0 + - - +
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Residues in contact with ASP 557 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553E ASP* 3.1 18.4 - - - +
554E GLU* 3.0 19.9 + - + +
556E CYS* 1.3 74.7 - - - +
558E VAL* 1.3 60.3 + - + +
560E ARG* 2.6 33.1 + - - +
561E PHE* 2.8 34.3 + - - +
657E LEU* 4.9 15.9 - - + -
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Residues in contact with VAL 558 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E LYS* 3.4 48.0 - - + +
528E CYS* 3.8 11.6 - - + +
554E GLU* 2.8 22.5 + - + +
555E SER 3.6 5.8 - - - +
557E ASP* 1.3 78.1 - - + +
559E VAL* 1.3 63.0 + - + +
561E PHE* 3.5 3.0 + - - +
562E PHE* 3.1 46.0 + - + +
656E PHE* 3.4 33.7 - - + +
657E LEU* 5.0 4.5 - - + -
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Residues in contact with VAL 559 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E LEU* 4.1 18.6 - - + -
293E MET* 5.2 0.7 - - + -
298E LEU* 4.2 10.5 - - + -
299E PRO* 5.9 0.7 - - + +
524E TYR* 3.9 13.2 - - - +
528E CYS* 3.9 20.2 - - + -
532E LEU* 4.9 6.8 - - + +
539E LEU* 4.8 6.3 - - + -
548E PRO* 3.6 28.0 - - + -
555E SER 2.9 21.9 + - - +
556E CYS 3.9 4.0 - - - +
558E VAL* 1.3 76.5 - - - +
560E ARG* 1.3 59.7 + - - +
562E PHE* 4.2 1.9 - - - +
563E THR* 2.5 43.2 + - - +
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Residues in contact with ARG 560 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E ARG* 2.5 32.7 + - - +
297E ASN* 3.2 31.4 - - - +
298E LEU* 3.5 21.7 - - + +
299E PRO* 4.6 3.6 - - + -
556E CYS* 3.0 24.1 + - - +
557E ASP* 2.6 42.8 + - - +
559E VAL* 1.3 77.2 - - - +
561E PHE* 1.3 63.1 + - - +
563E THR* 3.3 4.6 + - - -
564E GLN* 3.0 53.9 + - - +
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Residues in contact with PHE 561 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E ASP 2.8 21.8 + - - +
558E VAL* 3.7 4.3 - - - +
560E ARG* 1.3 74.0 - - - +
562E PHE* 1.3 77.7 + + + +
564E GLN* 3.5 6.9 + - - +
565E LEU* 3.1 29.2 + - + +
639E TRP* 3.8 37.9 - + - -
657E LEU* 3.3 49.4 - - + -
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Residues in contact with PHE 562 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528E CYS* 4.7 1.3 - - + +
529E ALA* 3.8 24.2 - - + -
532E LEU* 3.7 25.2 - - + +
533E LEU* 4.5 7.2 - - + -
558E VAL* 3.1 36.1 + - + +
559E VAL 4.6 0.2 - - - +
561E PHE* 1.3 87.3 - + - +
563E THR* 1.3 60.0 + - - +
565E LEU* 3.5 16.3 + - + +
566E LYS* 3.0 27.0 + - - +
569E MET* 5.3 0.2 - - - +
639E TRP* 3.9 13.7 - + - -
656E PHE 3.7 20.0 - - - -
657E LEU* 3.5 24.2 - - - -
658E SER* 3.9 1.6 - - - -
659E LEU* 3.4 33.0 - - + -
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Residues in contact with THR 563 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E LEU* 4.0 14.2 - - + +
299E PRO* 3.9 35.3 + - + +
301E HIS* 4.2 15.3 - - + -
532E LEU* 3.9 18.5 - - + +
559E VAL* 2.5 36.0 + - - +
560E ARG* 3.8 4.9 - - - -
562E PHE* 1.3 73.3 - - - +
564E GLN* 1.3 67.3 + - - +
566E LYS* 3.3 2.6 + - + +
567E CYS* 3.0 26.1 + - - -
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Residues in contact with GLN 564 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E ASN 5.0 1.0 + - - -
299E PRO* 4.9 4.7 - - + -
560E ARG* 3.0 44.1 + - + +
561E PHE* 3.8 5.6 - - - +
563E THR* 1.3 77.7 - - - +
565E LEU* 1.3 63.3 + - - +
567E CYS* 3.2 3.6 + - - +
568E ARG* 2.9 28.2 + - + +
675E ASP* 2.4 49.9 - - + +
676E GLN* 4.4 10.2 - - - +
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Residues in contact with LEU 565 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E LEU* 4.5 6.7 - - + -
561E PHE* 3.1 20.6 + - + +
562E PHE* 3.6 20.4 - - + +
563E THR 3.2 0.2 - - - -
564E GLN* 1.3 78.2 - - - +
566E LYS* 1.3 62.6 + - - +
568E ARG* 3.0 11.7 + - + +
569E MET* 2.9 59.8 + - + +
638E LEU* 3.9 13.7 - - + -
639E TRP* 3.4 37.9 - - + -
671E LEU* 6.1 3.8 - - + -
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Residues in contact with LYS 566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E PHE* 3.0 33.5 + - - +
270E GLY* 5.5 0.9 - - - -
532E LEU* 3.1 35.4 - - + +
534E SER 3.2 17.7 + - - -
535E SER* 3.2 23.5 + - - +
536E HIS* 3.7 0.6 - - - +
537E SER* 2.7 25.5 + - - +
562E PHE 3.0 17.3 + - - +
563E THR* 3.7 4.5 - - + +
565E LEU* 1.3 76.2 - - - +
567E CYS* 1.3 65.3 + - - +
569E MET* 3.1 22.7 + - + +
570E MET* 3.2 16.5 + - - +
573E LEU* 3.8 16.6 - - + +
678E PRO* 6.3 0.4 - - + -
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Residues in contact with CYS 567 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E GLY* 5.8 1.6 - - - -
301E HIS* 4.3 14.4 - - - -
563E THR* 3.0 24.1 + - - -
564E GLN 3.7 5.8 - - - +
566E LYS* 1.3 77.9 - - - +
568E ARG* 1.3 54.6 + - - +
570E MET* 3.4 16.9 + - - +
674E ASN 3.5 9.6 - - - +
675E ASP 3.9 8.3 - - - -
676E GLN 4.0 4.7 - - - -
677E ARG* 3.5 39.9 - - - +
678E PRO* 3.9 6.1 - - - -
680E TYR* 2.6 30.1 + - - -
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Residues in contact with ARG 568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564E GLN* 2.9 19.8 + - - +
565E LEU* 3.0 15.0 + - + +
567E CYS* 1.3 77.2 - - - +
569E MET* 1.3 58.6 + - + +
571E PRO* 3.1 6.1 - - - +
671E LEU* 3.5 37.8 - - + +
672E GLY 2.8 54.6 + - - +
673E ASN* 4.8 4.0 - - - +
674E ASN 4.0 0.7 - - - -
675E ASP* 3.8 21.5 - - + +
680E TYR* 3.8 4.9 - - - -
687E ALA* 4.0 16.0 - - - +
689E HIS* 5.3 2.0 + - - -
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Residues in contact with MET 569 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532E LEU 5.2 0.2 - - - +
533E LEU* 3.5 28.5 - - + -
562E PHE 5.3 0.2 - - - +
565E LEU* 2.9 52.1 + - + +
566E LYS* 3.1 16.7 + - + +
568E ARG* 1.3 75.4 - - + +
570E MET* 1.3 57.5 + - - +
571E PRO* 3.2 4.0 - - - -
572E TYR* 2.8 33.0 + - + +
573E LEU* 2.9 39.0 + - + -
610E LEU* 5.3 3.4 - - + -
614E VAL* 6.1 4.9 - - - -
638E LEU* 4.0 18.2 - - + -
661E VAL* 5.9 1.1 - - - -
669E LEU* 6.5 0.9 - - + -
670E ALA 5.0 2.0 - - - -
671E LEU* 5.1 9.6 - - + -
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Residues in contact with MET 570 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E ALA 4.4 2.0 - - - +
269E PHE* 3.7 42.0 - - + +
566E LYS* 3.2 18.0 + - - +
567E CYS* 3.5 9.6 - - - +
568E ARG 3.3 0.2 - - - -
569E MET* 1.3 76.9 - - - +
571E PRO* 1.3 66.2 - - + +
573E LEU* 4.1 17.5 - - - -
574E TYR* 3.1 58.6 + - + +
678E PRO* 3.4 36.3 - - + +
682E TRP* 3.5 23.3 - - + +
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Residues in contact with PRO 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568E ARG 3.1 18.2 - - - +
569E MET 3.3 2.0 - - - -
570E MET* 1.3 91.3 - - + +
572E TYR* 1.3 58.0 + - - +
575E ARG* 3.9 2.6 - - - +
670E ALA* 3.5 25.0 - - + +
671E LEU 3.8 2.0 - - - +
672E GLY* 3.5 24.2 - - - +
680E TYR* 3.6 7.2 - - - +
682E TRP* 3.8 39.7 - - + +
686E THR* 5.3 0.2 - - + -
702E GLU 4.5 2.6 - - - +
703E VAL* 4.8 5.1 - - + -
704E PRO* 3.3 26.5 - - + +
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Residues in contact with TYR 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569E MET* 2.8 17.4 + - + +
571E PRO* 1.3 80.1 - - - +
573E LEU* 1.3 94.4 + - + +
575E ARG* 3.0 17.8 + - + +
576E GLU* 3.2 34.1 + - + +
610E LEU* 2.7 23.6 + - + -
611E GLY* 3.4 2.8 - - - -
613E ASN* 3.1 38.0 + - + -
614E VAL* 3.1 24.8 - - + +
669E LEU* 3.3 36.1 - - + -
670E ALA* 3.6 10.7 + - - +
671E LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E PHE* 5.5 3.6 - - + -
534E SER 6.0 1.1 - - - +
535E SER* 6.4 0.2 - - - -
566E LYS* 3.8 28.0 - - + +
569E MET* 2.9 50.5 + - + +
570E MET* 3.9 14.8 - - - +
572E TYR* 1.3 96.7 - - + +
574E TYR* 1.3 57.9 + - - +
576E GLU* 2.9 11.0 + - + +
577E ALA* 2.9 25.2 + - - +
587E MET* 3.8 19.9 - - + +
610E LEU* 4.1 27.8 - - + +
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Residues in contact with TYR 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E LEU* 3.5 20.0 + - + +
264E PRO 3.0 19.1 + - - -
265E PRO* 4.1 2.1 - - - +
266E ALA* 3.7 18.8 + - + -
269E PHE* 3.4 40.4 - + - -
570E MET* 3.1 28.8 + - + +
573E LEU* 1.3 78.5 - - - +
575E ARG* 1.3 59.3 + - - +
577E ALA* 3.5 6.6 - - + +
578E ALA* 3.3 17.3 + - - +
682E TRP* 3.5 27.1 - + + -
704E PRO* 4.2 6.6 - - + +
705E ALA 4.0 4.5 - - - -
706E ALA 3.2 27.9 + - - -
707E ASP 4.9 0.2 - - - -
708E GLY* 3.8 17.3 - - - -
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Residues in contact with ARG 575 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571E PRO 3.9 7.2 - - - +
572E TYR* 3.0 13.6 + - + +
574E TYR* 1.3 75.5 - - - +
576E GLU* 1.3 68.1 + - - +
577E ALA 3.1 0.2 - - - -
578E ALA* 3.0 23.4 + - - +
579E ARG* 3.1 47.9 + - - +
702E GLU* 2.9 63.1 + - + +
704E PRO* 4.0 15.9 - - + +
708E GLY 5.3 0.9 - - - -
710E VAL* 3.8 14.8 - - - +
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Residues in contact with GLU 576 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572E TYR* 3.5 35.1 - - + +
573E LEU* 2.9 9.1 + - - +
575E ARG* 1.3 80.0 - - - +
577E ALA* 1.3 58.4 + - - +
579E ARG* 2.5 56.7 + - - +
580E ALA* 3.4 5.0 + - - +
585E THR 4.7 1.9 - - - +
587E MET* 4.2 16.7 - - + +
589E ARG* 3.6 6.3 + - - +
611E GLY* 3.2 20.9 - - - -
612E ASP* 2.5 43.3 + - - +
613E ASN* 5.8 0.6 + - - -
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Residues in contact with ALA 577 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E LEU* 3.5 20.2 - - + +
269E PHE* 3.9 11.9 - - + -
507E PHE* 3.5 24.1 - - + -
573E LEU 2.9 11.5 + - - +
574E TYR* 3.5 13.2 - - - +
575E ARG 3.1 0.2 - - - -
576E GLU* 1.3 76.6 - - - +
578E ALA* 1.3 62.8 + - - +
580E ALA* 3.3 13.0 + - - +
581E ASN 3.4 7.4 + - - -
587E MET* 3.7 16.3 - - - -
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Residues in contact with ALA 578 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E LEU* 3.9 11.6 - - + +
574E TYR 3.3 9.6 + - - +
575E ARG* 3.0 25.8 + - - +
577E ALA* 1.3 80.1 - - - +
579E ARG* 1.3 59.1 + - - +
581E ASN* 3.3 6.9 + - - +
582E ALA* 3.1 23.3 + - - +
708E GLY* 3.7 28.3 - - - +
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Residues in contact with ARG 579 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575E ARG* 3.1 53.1 + - - +
576E GLU* 2.5 40.9 + - - +
578E ALA* 1.3 76.2 - - - +
580E ALA* 1.3 58.9 + - - +
582E ALA* 4.3 4.7 - - - +
583E ARG* 2.7 39.5 + - + +
584E GLY 3.4 2.8 + - - -
585E THR* 3.8 16.5 + - - +
589E ARG* 4.2 12.3 - - - +
612E ASP* 3.2 25.3 + - - -
702E GLU* 3.9 7.5 + - - -
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Residues in contact with ALA 580 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E PRO* 3.5 11.4 - - + +
506E GLY* 4.1 16.6 - - - +
507E PHE* 3.7 23.6 - - + -
576E GLU 3.4 4.4 + - - +
577E ALA* 3.3 13.7 + - - +
579E ARG* 1.3 77.1 - - - +
581E ASN* 1.3 60.5 + - - +
584E GLY* 2.8 27.3 + - - -
585E THR 3.1 25.0 + - - +
587E MET* 5.0 1.6 - - + -
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Residues in contact with ASN 581 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E ARG* 3.8 22.2 + - - +
261E PRO* 2.8 29.5 + - - +
262E ALA* 3.6 12.3 - - - +
263E LEU* 3.7 29.0 - - + +
507E PHE* 5.0 0.6 - - - -
577E ALA 3.4 4.1 + - - +
578E ALA* 3.3 10.3 + - - +
579E ARG 3.2 0.4 - - - -
580E ALA* 1.3 80.8 - - - +
582E ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 582 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E ARG* 3.3 23.8 + - - +
578E ALA 3.1 15.2 + - - +
579E ARG* 3.1 4.7 + - - +
581E ASN* 1.3 82.3 - - - +
583E ARG* 1.3 67.4 + - + +
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Residues in contact with ARG 583 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E LYS* 3.6 34.8 + - - +
249E ALA* 4.0 7.9 - - - +
252E ASP* 3.0 46.1 + - - +
260E ARG* 3.6 11.2 - - - +
579E ARG* 2.7 17.6 + - + +
582E ALA* 1.3 82.2 - - + +
584E GLY* 1.3 65.5 + - - +
585E THR* 3.3 19.0 + - - +
3006E SO4 3.0 33.8 + - - -
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Residues in contact with GLY 584 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E LEU* 3.9 14.7 - - - +
255E THR* 3.6 28.1 + - - +
260E ARG* 4.1 0.4 - - - +
261E PRO* 4.2 7.1 - - - +
501E GLY 5.0 0.7 - - - +
504E GLY 5.1 4.7 - - - +
506E GLY* 5.5 1.1 - - - -
580E ALA* 2.8 19.9 + - - -
581E ASN 4.8 0.2 - - - -
582E ALA 3.8 0.4 - - - -
583E ARG* 1.3 78.7 - - - +
585E THR* 1.3 63.7 + - - +
586E PRO* 3.2 10.7 - - - +
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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