Contacts of the helix formed by residues 590 - 621 (chain A) in PDB entry 1JB0
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 SER 590 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A LYS* 4.6 2.0 - - - -
574A PHE 3.3 15.7 - - - -
576A PHE* 3.1 39.9 + - - -
588A GLN 3.5 0.2 - - - -
589A VAL* 1.3 82.6 - - - +
591A GLY* 1.3 64.5 + - - +
592A TRP* 3.6 4.0 + - - +
593A ASP* 2.5 43.3 + - - +
594A HIS* 2.8 21.5 + - - -
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Residues in contact with GLY 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ALA* 4.5 7.3 - - - +
556A GLY* 4.2 19.6 - - - -
560A ALA* 4.9 10.6 + - - +
569A LYS* 5.3 0.4 - - - +
573A GLY 5.3 0.4 + - - -
574A PHE* 3.4 21.7 + - - +
576A PHE* 5.2 0.4 - - - -
589A VAL 3.9 0.4 + - - -
590A SER* 1.3 75.2 - - - +
592A TRP* 1.3 61.2 + - - +
594A HIS* 3.2 8.9 + - - +
595A VAL* 3.1 24.6 + - - +
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Residues in contact with TRP 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A PHE* 3.1 35.1 + + + +
575A ARG* 3.5 18.8 - - + +
590A SER* 3.1 4.2 - - - +
591A GLY* 1.3 77.1 - - - +
593A ASP* 1.3 78.7 + - - +
595A VAL* 2.9 20.8 + - + +
596A PHE* 2.9 30.3 + + + -
725A ILE* 3.6 41.7 - - + -
728A ARG* 3.8 11.7 - - + -
729A ALA* 3.8 25.4 - - + -
732A VAL* 5.6 0.7 - - + -
1128A CLA 3.0 37.6 + - + +
5001A LHG 3.1 34.3 + - + -
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Residues in contact with ASP 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A PHE 3.2 10.4 - - - +
577A PRO 3.9 0.3 - - - +
588A GLN* 3.4 36.5 - - + +
590A SER* 2.5 28.9 + - - +
592A TRP* 1.3 91.8 - - - +
594A HIS* 1.3 56.4 + - - +
596A PHE* 3.2 4.6 - - - +
597A LEU* 2.9 34.1 + - - +
725A ILE* 4.0 0.7 - - - +
728A ARG* 2.6 47.7 + - - -
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Residues in contact with HIS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ILE* 3.4 24.9 - - - +
553A LEU* 3.9 4.6 - - - +
555A LYS* 2.9 33.7 + - + +
556A GLY* 3.3 39.8 - - - -
559A PHE* 6.2 0.9 - - + -
569A LYS* 5.2 0.2 - - - -
588A GLN 3.9 11.0 + - - -
589A VAL* 3.4 26.2 + - - -
590A SER 2.8 19.7 + - - -
591A GLY 3.5 8.1 - - - +
592A TRP 3.1 0.8 - - - -
593A ASP* 1.3 79.1 - - - +
595A VAL* 1.3 59.9 + - + +
597A LEU* 3.4 3.1 + - - -
598A GLY* 2.8 25.1 + - - -
676B TYR* 3.4 18.6 - + - -
679B GLU* 4.3 3.1 + - - -
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A VAL* 3.9 19.5 - - + +
409A ALA 4.7 1.8 - - - +
410A ALA* 3.5 36.1 - - + +
413A ALA* 5.4 1.3 - - + -
553A LEU* 4.1 12.8 - - + -
574A PHE* 4.7 4.0 - - + -
591A GLY 3.1 14.5 + - - +
592A TRP* 2.9 11.1 + - - +
594A HIS* 1.3 74.9 - - + +
596A PHE* 1.3 66.1 + - - +
598A GLY* 3.2 1.4 + - - -
599A LEU* 3.0 32.3 + - + +
1128A CLA 3.8 25.6 - - + -
5001A LHG 6.0 0.2 - - + -
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Residues in contact with PHE 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A GLN* 4.0 21.8 - - - -
592A TRP* 2.9 26.8 + + + +
593A ASP* 3.2 14.8 - - - +
595A VAL* 1.3 79.2 - - - +
597A LEU* 1.3 86.0 + - + +
599A LEU* 3.3 16.4 + - - +
600A PHE* 3.2 34.8 - + - -
690A LEU* 3.6 21.3 - - + -
728A ARG* 3.1 52.3 - - + -
732A VAL* 3.7 13.4 - - + +
671B ILE* 4.0 8.5 - - + -
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Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ILE* 4.0 11.0 - - + -
588A GLN* 3.5 23.6 - - + +
593A ASP 2.9 21.8 + - - +
594A HIS* 3.9 3.6 - - - +
596A PHE* 1.3 88.1 - - + +
598A GLY* 1.3 65.7 + - - +
600A PHE* 3.1 18.6 + - + +
601A TRP* 3.4 13.2 + - - +
671B ILE 4.5 0.2 - - - +
672B SER* 3.6 25.8 - - - +
676B TYR* 3.7 37.2 - - + -
1023B CLA 4.0 30.1 - - + +
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Residues in contact with GLY 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A VAL* 4.7 5.8 - - - -
549A THR* 3.8 6.5 - - - +
552A ILE* 3.7 16.3 - - - +
553A LEU* 4.0 13.7 - - - -
594A HIS 2.8 21.8 + - - -
595A VAL 3.2 3.1 + - - -
597A LEU* 1.3 72.6 - - - +
599A LEU* 1.3 60.7 + - - +
601A TRP* 3.1 4.1 + - - +
602A MET* 2.9 24.5 + - - +
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Residues in contact with LEU 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A PHE* 4.1 15.7 - - + -
406A VAL* 3.7 22.4 - - + +
595A VAL* 3.0 24.8 + - + +
596A PHE* 3.5 12.3 - - - +
597A LEU 3.1 0.4 - - - -
598A GLY* 1.3 77.6 - - - +
600A PHE* 1.3 62.8 + - - +
602A MET* 3.2 28.1 + - + +
603A TYR* 3.0 23.6 + - - +
732A VAL* 4.0 28.3 - - + -
736A LEU* 4.2 7.9 - - + +
1128A CLA 4.2 11.9 - - + -
5001A LHG 4.2 24.2 - - + -
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Residues in contact with PHE 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A PHE* 3.2 44.6 - + - -
597A LEU* 3.1 7.2 + - - +
599A LEU* 1.3 77.7 - - - +
601A TRP* 1.3 60.3 + - - +
603A TYR* 3.3 9.1 + - - +
604A ASN* 3.0 21.8 + - - +
690A LEU* 3.8 23.8 - - + -
732A VAL* 3.6 21.8 - - + -
735A TYR* 3.7 49.4 - + + -
736A LEU* 5.5 1.3 - - + -
1022A CLA 3.5 18.4 - - + +
671B ILE* 3.8 18.8 - - + -
1023B CLA 3.4 29.4 - - + -
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Residues in contact with TRP 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A PHE* 3.8 9.6 - + - -
545A THR* 3.8 28.9 - - + -
548A VAL* 3.4 35.7 - - + -
549A THR* 3.4 19.8 + - - +
552A ILE* 3.5 22.4 - - + -
597A LEU 3.4 5.5 + - - -
598A GLY 3.1 6.9 + - - +
600A PHE* 1.3 76.3 - - - +
602A MET* 1.3 60.9 + - - +
604A ASN* 3.3 26.4 + - - +
605A CYS* 2.9 29.3 + - - +
1022A CLA 3.2 63.4 - - + +
1023B CLA 3.3 37.8 - + + -
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Residues in contact with MET 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A TRP* 3.9 20.0 - - + -
402A GLY* 3.6 23.1 - - - +
403A PHE* 3.9 47.8 - - + +
406A VAL* 3.8 10.5 - - + -
549A THR* 3.7 8.7 + - + -
598A GLY 2.9 16.1 + - - +
599A LEU* 3.6 21.3 - - + +
601A TRP* 1.3 75.4 - - - +
603A TYR* 1.3 58.9 + - - +
605A CYS* 3.2 5.1 + - - +
606A ILE* 2.8 37.0 + - + +
736A LEU* 4.9 2.5 - - + -
1124A CLA 3.4 27.4 - - + -
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Residues in contact with TYR 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A TRP* 3.4 24.1 - + - -
599A LEU 3.0 13.0 + - - +
600A PHE* 3.3 9.4 - - - +
601A TRP 3.2 0.2 - - - -
602A MET* 1.3 78.8 - - - +
604A ASN* 1.3 59.1 + - - +
607A SER* 2.8 52.1 + - - -
735A TYR* 4.1 11.0 - + + -
736A LEU* 3.8 20.6 - - + -
739A GLY* 3.2 24.5 - - - -
740A ILE* 3.7 31.6 - - + -
743A THR* 5.8 0.2 - - - -
1011A CLA 2.9 54.9 + - - +
1022A CLA 3.8 16.2 - - + -
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Residues in contact with ASN 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A THR* 4.2 3.4 - - - +
600A PHE 3.0 13.5 + - - +
601A TRP* 3.4 33.1 - - - +
603A TYR* 1.3 81.8 - - - +
605A CYS* 1.3 62.1 + - - +
607A SER* 3.8 3.8 - - - -
608A VAL* 3.3 29.1 + - - +
1011A CLA 3.6 39.5 - - - +
1022A CLA 3.4 46.5 + - + +
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Residues in contact with CYS 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A HIS* 4.8 0.4 - - - -
545A THR* 3.3 37.0 + - - +
546A ILE* 3.8 24.0 - - - -
549A THR* 4.5 1.1 - - - +
601A TRP 2.9 16.7 + - - +
602A MET* 3.4 8.1 - - - +
604A ASN* 1.3 74.2 - - - +
606A ILE* 1.3 71.7 + - - +
608A VAL* 3.3 4.6 + - - +
609A VAL* 3.1 35.1 + - - +
1124A CLA 4.4 16.4 - - + -
1135A CLA 5.3 0.4 - - - -
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ILE* 5.0 0.9 - - + -
398A MET* 3.8 30.5 - - + +
399A TRP* 3.5 51.6 - - + +
402A GLY* 4.4 7.4 - - - +
602A MET* 2.8 38.0 + - + +
605A CYS* 1.3 74.8 - - - +
607A SER* 1.3 67.6 + - - +
609A VAL* 3.2 4.4 + - + +
610A ILE* 3.0 24.4 + - + +
1124A CLA 3.8 32.1 - - + -
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Residues in contact with SER 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A TRP* 3.6 14.1 - - - -
603A TYR* 2.8 30.0 + - - -
604A ASN 3.8 4.3 - - - -
606A ILE* 1.3 78.0 - - - +
608A VAL* 1.3 58.0 + - - +
610A ILE* 3.3 13.4 - - - +
611A PHE* 3.0 35.2 + - - -
743A THR* 5.0 0.9 + - - -
1011A CLA 3.5 40.5 - - - -
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Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A VAL* 4.7 3.1 - - + -
541A ILE* 3.8 21.8 - - + -
542A HIS* 3.8 14.8 - - + +
545A THR* 5.4 1.8 - - + -
604A ASN 3.3 15.8 + - - +
605A CYS* 3.3 6.3 + - - +
606A ILE 3.2 0.6 - - - -
607A SER* 1.3 76.0 - - - +
609A VAL* 1.3 62.0 + - - +
611A PHE* 3.8 7.1 - - + +
612A HIS* 2.8 27.9 + - - +
649A TRP* 5.2 1.5 - - + -
1011A CLA 3.9 66.4 - - + -
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Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A PHE* 4.2 11.7 - - + -
398A MET* 4.1 32.3 - - + -
542A HIS* 3.5 16.6 - - + -
605A CYS* 3.1 20.3 + - - +
606A ILE* 3.5 9.0 - - - +
608A VAL* 1.3 76.9 - - - +
610A ILE* 1.3 58.1 + - - +
612A HIS* 3.1 4.2 + - - +
613A PHE* 2.8 26.5 + - - +
1124A CLA 4.4 8.5 - - + -
1135A CLA 3.5 41.9 - - + +
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Residues in contact with ILE 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A PHE* 4.2 5.8 - - + -
395A THR* 3.6 30.1 - - + +
398A MET* 4.2 15.7 - - + -
399A TRP* 3.7 33.9 - - + +
606A ILE* 3.0 14.6 + - + +
607A SER* 3.3 13.2 - - - +
609A VAL* 1.3 73.9 - - + +
611A PHE* 1.3 66.5 + - + +
613A PHE* 3.7 6.9 - - - +
614A SER* 2.9 30.0 + - - -
743A THR* 3.7 25.4 - - + -
747A PHE* 3.4 19.8 - - + -
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Residues in contact with PHE 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A SER 3.0 22.1 + - - +
608A VAL* 3.8 6.5 - - - +
610A ILE* 1.3 76.0 - - + +
612A HIS* 1.3 68.3 + - - +
614A SER* 3.9 0.5 - - - -
615A TRP* 3.0 27.0 + - - +
649A TRP* 3.8 17.0 - + + -
653A PHE* 3.5 23.5 - + + -
654A LEU* 3.7 18.2 - - + -
743A THR* 3.8 20.6 - - + -
746A PHE* 4.2 1.1 - + - -
747A PHE* 4.0 15.0 - + - -
1011A CLA 3.1 86.4 - - + -
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Residues in contact with HIS 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ASP* 4.5 6.1 + - - -
538A VAL* 3.7 35.0 - - + +
539A HIS* 4.0 13.2 - + - -
542A HIS* 3.0 26.2 - + + +
608A VAL 2.8 19.2 + - - +
609A VAL 3.2 5.6 - - - +
611A PHE* 1.3 78.2 - - - +
613A PHE* 1.3 63.0 + - - +
615A TRP* 3.9 1.0 - - - +
616A LYS* 2.9 28.7 + - + +
639A PHE* 3.9 16.6 - + - -
649A TRP* 3.9 10.3 - - - -
1135A CLA 3.2 40.7 - + + +
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Residues in contact with PHE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A TYR* 3.5 42.0 - + + -
390A GLN* 4.5 3.4 - - + -
391A LEU* 3.6 28.3 - - + -
394A PHE* 3.4 56.1 - + + -
609A VAL 2.8 11.5 + - - +
610A ILE 3.7 3.4 - - - +
611A PHE 3.3 0.2 - - - -
612A HIS* 1.3 76.3 - - - +
614A SER* 1.3 66.9 + - - +
616A LYS* 3.8 0.3 - - - +
617A MET* 3.0 46.9 + - + +
622A TRP* 4.0 17.7 - + - -
1135A CLA 3.7 27.4 - - + -
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Residues in contact with SER 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A LEU* 4.1 16.5 - - - +
610A ILE 2.9 21.6 + - - -
611A PHE 3.9 3.1 - - - -
612A HIS 3.4 0.2 - - - -
613A PHE* 1.3 82.9 - - - +
615A TRP* 1.3 61.8 + - - +
617A MET* 4.2 1.9 - - - +
618A GLN* 3.1 44.2 + - - +
622A TRP* 5.1 1.6 - - - -
653A PHE* 4.0 6.2 - - - -
657A GLN* 4.1 0.9 + - - -
747A PHE* 3.6 26.8 - - - -
750A ARG* 5.8 0.9 - - - +
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Residues in contact with TRP 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A PHE 3.0 17.1 + - - +
614A SER* 1.3 73.4 - - - +
616A LYS* 1.3 65.9 + - - +
618A GLN* 4.7 2.0 - - - +
619A SER* 3.0 29.7 + - - -
635A THR* 4.0 3.7 + - + -
638A ASN* 3.1 26.4 + - - +
639A PHE* 3.7 14.4 - + + -
642A SER* 3.5 38.4 - - - -
643A ALA* 3.5 21.1 - - + -
648A GLY 3.6 14.8 - - - -
649A TRP* 3.5 46.0 - + + -
652A ASP* 3.7 21.0 + - + -
653A PHE* 3.7 17.2 - + + -
657A GLN* 3.9 16.4 - - - +
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Residues in contact with LYS 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A ILE* 3.6 25.4 - - + -
530A VAL 2.7 29.6 + - - +
531A LEU* 5.0 1.6 - - - -
535A ASP* 2.9 28.8 + - - +
612A HIS* 2.9 30.0 + - + +
613A PHE 3.8 2.0 - - - +
615A TRP* 1.3 77.4 - - - +
617A MET* 1.3 57.9 + - - +
619A SER* 4.7 0.2 - - - -
620A ASP* 2.9 62.6 + - - +
621A VAL* 3.8 2.3 + - + +
639A PHE* 4.0 18.6 - - + -
1135A CLA 4.2 20.2 - - + -
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Residues in contact with MET 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A TYR* 3.8 37.0 - - + +
390A GLN* 5.4 1.6 - - - +
526A MET* 4.1 10.8 - - + -
529A ILE* 4.3 2.0 - - - -
613A PHE* 3.0 40.8 + - + +
614A SER 4.2 0.2 - - - +
616A LYS* 1.3 76.9 - - - +
618A GLN* 1.3 57.1 + - - +
621A VAL* 3.0 37.9 + - + -
622A TRP* 2.6 81.5 + - + +
1135A CLA 4.2 9.0 - - + -
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Residues in contact with GLN 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A LEU* 5.6 0.8 - - - +
614A SER* 3.1 32.6 + - - +
615A TRP* 4.1 3.6 - - - +
617A MET* 1.3 78.5 - - - +
619A SER* 1.3 58.2 + - - +
622A TRP* 3.9 10.9 - - + +
633A HIS* 3.7 1.4 - - - +
634A ILE* 3.1 41.6 + - + +
635A THR* 2.9 27.9 + - + +
657A GLN* 2.6 29.0 + - - +
750A ARG* 2.7 44.2 + - - +
751A ILE* 4.3 10.8 - - + +
754A VAL* 4.2 1.0 - - - +
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Residues in contact with SER 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 3.0 20.4 + - - -
616A LYS 4.0 0.4 - - - -
618A GLN* 1.3 79.8 - - - +
620A ASP* 1.3 82.0 + - - +
621A VAL 3.8 0.4 - - - -
633A HIS* 3.2 12.0 + - - +
635A THR* 3.0 17.7 - - - -
637A GLY* 2.9 20.6 + - - +
638A ASN* 3.2 10.5 + - - -
639A PHE* 3.0 29.7 + - - +
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Residues in contact with ASP 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A MET* 3.9 10.2 - - - +
528A PRO 4.5 4.7 - - - +
529A ILE* 5.3 1.2 - - + -
530A VAL* 5.6 4.7 - - + +
616A LYS* 2.9 51.3 + - - +
619A SER* 1.3 105.8 + - - +
621A VAL* 1.3 66.0 - - + +
633A HIS* 3.2 20.5 + - + -
637A GLY* 3.4 10.9 - - - -
639A PHE* 3.8 11.3 - - - +
640A ALA* 5.1 2.5 + - - +
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Residues in contact with VAL 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A VAL* 3.5 22.8 - - + +
526A MET* 4.2 17.9 - - + -
527A MET* 3.6 17.6 - - + +
529A ILE* 3.6 35.9 - - + -
616A LYS 4.2 2.5 - - - +
617A MET* 3.0 46.2 + - + +
620A ASP* 1.3 84.8 - - - +
622A TRP* 1.3 68.9 + - + +
633A HIS* 3.0 16.7 + - - -
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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