Contacts of the helix formed by residues 608 - 640 (chain A) in PDB entry 3F7F
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 608 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER* 3.8 16.1 - - - -
466A TYR* 4.0 6.4 + - - -
604A ALA* 4.9 1.3 - - + -
606A LYS 3.2 3.5 + - - +
607A PHE* 1.3 76.2 - - - +
609A GLY* 1.3 63.3 + - - +
610A PHE* 3.0 13.4 + - - +
611A THR* 2.9 40.1 + - - +
612A SER* 3.0 22.7 + - - -
688A PHE 4.1 3.2 + - - -
689A GLY* 5.3 0.4 - - - -
690A VAL 4.2 7.9 - - - +
691A LYS* 2.7 40.0 + - - +
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Residues in contact with GLY 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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11A LEU* 4.8 5.6 - - - -
14A TYR* 5.0 2.8 - - - -
85A SER 3.0 16.4 + - - -
86A ASP* 5.7 0.9 - - - -
607A PHE* 3.6 26.7 + - - -
608A ASP* 1.3 71.6 - - - +
610A PHE* 1.3 62.4 + - - +
612A SER* 3.4 1.6 + - - -
613A ILE* 3.0 27.2 + - - +
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Residues in contact with PHE 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.3 9.2 - - + -
11A LEU* 3.8 22.2 - - + -
84A LEU* 3.7 34.6 + - + +
85A SER* 4.2 6.4 + - - +
466A TYR* 3.6 49.1 - + - +
472A LEU* 3.8 30.1 - - + -
481A HIS* 4.8 3.8 - - + -
483A LEU* 4.4 8.7 - - + -
608A ASP* 3.0 7.4 + - - +
609A GLY* 1.3 78.8 - - - +
611A THR* 1.3 67.1 + - + +
613A ILE* 3.3 2.6 - - - +
614A ILE* 3.0 54.7 + - + +
692A PHE* 5.0 2.9 - + - -
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Residues in contact with THR 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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466A TYR* 3.6 21.1 - - + +
608A ASP* 2.9 29.5 + - - +
610A PHE* 1.3 73.9 - - + +
612A SER* 1.3 60.5 + - - +
614A ILE* 3.7 8.2 - - - +
615A SER* 2.7 37.6 + - - -
689A GLY* 5.3 1.0 - - - -
690A VAL* 3.1 29.2 + - - +
691A LYS* 4.9 3.8 - - - -
692A PHE* 3.4 32.1 - - + -
701A TYR* 6.0 0.6 - - - -
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Residues in contact with SER 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.3 23.2 + - - -
607A PHE* 3.6 24.7 - - - -
608A ASP 3.0 19.1 + - - -
609A GLY 3.5 6.5 - - - -
610A PHE 3.1 0.2 - - - -
611A THR* 1.3 80.9 + - - +
613A ILE* 1.3 58.6 + - - +
615A SER* 3.4 5.0 - - - -
616A LEU* 2.9 24.3 + - - +
676A ALA* 4.2 5.9 - - - +
680A LEU* 4.1 20.3 - - - +
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Residues in contact with ILE 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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8A ASP 5.0 0.9 - - - +
9A ALA* 4.4 21.3 - - + -
10A ASN 4.6 4.7 - - - +
11A LEU* 4.5 18.4 - - + -
13A GLN* 3.1 33.2 - - + +
14A TYR* 3.2 33.4 - - + +
609A GLY 3.0 19.1 - - - +
610A PHE* 3.3 11.4 - - - +
612A SER* 1.3 73.5 + - - +
614A ILE* 1.3 59.8 + - - +
616A LEU* 5.2 1.1 - - + -
617A GLU* 2.8 57.4 + - + +
672A LYS* 5.1 0.9 - - + -
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Residues in contact with ILE 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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7A ILE* 4.0 14.7 - - + +
8A ASP 5.2 0.2 - - - -
9A ALA* 3.6 27.1 - - + -
483A LEU* 3.8 36.1 - - + +
610A PHE* 3.0 48.8 + - + +
611A THR* 3.7 5.8 - - - +
613A ILE* 1.3 76.9 - - - +
615A SER* 1.3 57.4 + - - +
617A GLU* 4.8 0.2 - - - -
618A SER* 2.6 40.9 + - - +
692A PHE* 4.0 20.0 - - + -
698A LEU* 4.4 7.4 - - + -
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Residues in contact with SER 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 THR* 2.7 23.8 + - - -
612A SER* 3.4 4.7 - - - -
614A ILE* 1.3 73.6 - - - +
616A LEU* 1.3 61.7 + - - +
618A SER* 3.1 2.6 + - - -
619A LEU* 2.8 31.0 + - - +
680A LEU* 6.0 3.6 - - - -
692A PHE* 4.3 8.5 - - - -
698A LEU* 5.0 0.2 - - - +
701A TYR* 2.9 39.7 - - - -
702A ILE* 3.6 14.3 - - - +
705A LEU* 4.2 7.4 - - - -
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Residues in contact with LEU 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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14A TYR* 3.6 31.6 - - + +
612A SER 2.9 8.1 + - - +
613A ILE* 3.9 3.1 - - + +
615A SER* 1.3 76.1 - - - +
617A GLU* 1.3 64.8 + - - +
619A LEU* 3.1 11.7 + - + +
620A HIS* 2.9 22.3 + - + +
664A LEU* 6.3 0.2 - - + -
668A TYR* 4.1 18.6 - - + -
672A LYS* 3.6 33.4 - - + +
675A LEU* 3.7 29.4 - - + -
676A ALA* 4.1 10.1 - - + +
679A LEU* 4.5 14.1 - - + -
680A LEU* 6.3 1.8 - - + -
705A LEU* 5.8 0.7 - - - -
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Residues in contact with GLU 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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7A ILE* 3.4 23.3 - - + +
8A ASP 3.7 20.6 + - - +
13A GLN* 3.4 9.3 - - - +
387A VAL* 4.5 8.7 - - - +
613A ILE* 2.8 49.6 + - + +
616A LEU* 1.3 72.8 - - - +
618A SER* 1.3 62.3 + - - +
620A HIS* 3.1 8.2 + - - +
621A GLN* 3.0 21.8 + - - +
668A TYR* 2.5 37.7 + - - -
672A LYS* 3.9 3.1 - - - +
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Residues in contact with SER 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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7A ILE* 4.0 18.3 - - - +
483A LEU* 5.5 0.2 - - - +
485A LYS* 4.0 23.7 - - - +
491A GLU* 5.0 1.9 - - - +
614A ILE* 2.6 30.2 + - - +
615A SER 3.1 4.0 + - - -
617A GLU* 1.3 76.2 - - - +
619A LEU* 1.3 63.8 + - - +
621A GLN* 3.2 13.3 + - - +
622A LEU* 3.2 15.1 + - - +
698A LEU* 5.1 1.4 - - - +
702A ILE* 3.6 25.1 - - - +
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Residues in contact with LEU 619 (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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615A SER 2.8 20.7 + - - +
616A LEU* 3.1 12.1 + - + +
618A SER* 1.3 73.6 - - - +
620A HIS* 1.3 57.1 + - - +
622A LEU* 3.6 2.5 + - + +
623A LEU* 3.1 37.8 + - + +
664A LEU* 4.0 19.7 - - + -
679A LEU* 3.5 32.5 - - + -
702A ILE* 3.9 15.8 - - + +
705A LEU* 4.2 19.5 - - + +
706A ASN* 3.9 32.8 - - + +
709A VAL* 4.4 4.7 - - + -
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Residues in contact with HIS 620 (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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386A LEU* 5.9 1.9 - - + +
387A VAL* 3.8 23.5 - - + +
390A GLN* 4.9 5.8 - - - -
616A LEU* 2.9 13.6 + - + +
617A GLU* 3.4 9.7 + - - +
619A LEU* 1.3 76.5 - - - +
621A GLN* 1.3 65.1 + - - +
623A LEU* 4.9 0.7 - - - -
624A SER* 2.7 43.6 + - - -
664A LEU* 5.4 3.4 - - + -
665A LEU* 3.4 24.3 - - + +
668A TYR* 3.1 56.8 + + + -
669A ARG* 2.6 32.5 + - - -
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Residues in contact with GLN 621 (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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5A SER* 3.1 28.0 + - - -
6A ARG 4.3 3.3 - - - +
7A ILE* 3.9 14.1 - - + +
386A LEU* 3.9 21.2 - - + +
485A LYS* 3.6 9.5 - - - +
491A GLU* 2.7 27.0 + - - +
495A TYR* 2.6 27.3 + - - -
617A GLU 3.0 11.8 + - - +
618A SER* 3.2 8.4 + - - +
620A HIS* 1.3 79.8 + - - +
622A LEU* 1.3 58.3 + - - +
624A SER* 3.1 3.5 + - - -
625A ILE* 2.9 43.9 + - + +
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Residues in contact with LEU 622 (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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488A THR* 4.3 11.4 - - + +
490A VAL* 5.2 5.6 - - + -
491A GLU* 4.1 31.0 - - + +
618A SER 3.2 12.9 + - - +
619A LEU* 3.9 5.4 - - + +
621A GLN* 1.3 79.8 - - - +
623A LEU* 1.3 59.6 + - + +
625A ILE* 3.4 6.0 + - + +
626A HIS* 2.8 49.7 + - + +
702A ILE* 4.3 20.2 - - + -
703A ASP* 4.4 15.3 - - - +
706A ASN* 3.6 28.5 - - + +
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Residues in contact with LEU 623 (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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619A LEU* 3.1 32.1 + - + +
620A HIS 4.3 2.2 - - - +
622A LEU* 1.3 75.1 - - + +
624A SER* 1.3 56.5 + - - +
626A HIS* 3.5 8.3 - - + +
627A TYR* 2.7 35.0 + - - +
661A GLN* 4.1 11.5 - - + +
664A LEU* 2.8 40.8 - - + -
665A LEU* 4.3 10.0 - - + +
706A ASN* 3.8 17.0 - - - +
709A VAL* 3.9 19.1 - - + -
710A TYR* 3.4 29.6 - - + +
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Residues in contact with SER 624 (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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386A LEU* 4.0 15.9 - - - -
390A GLN* 4.5 17.4 + - - -
494A PHE* 5.9 0.2 - - - -
620A HIS* 2.7 36.3 + - - -
621A GLN 3.1 4.2 + - - -
623A LEU* 1.3 72.3 - - - +
625A ILE* 1.3 68.7 + - - +
627A TYR* 3.1 6.2 + - - +
628A ARG* 3.1 22.0 + - - +
665A LEU* 3.2 26.1 - - - +
669A ARG* 4.5 1.6 + - - -
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Residues in contact with ILE 625 (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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386A LEU* 4.0 8.7 - - + -
490A VAL* 4.3 13.9 - - + +
491A GLU* 4.1 21.3 - - + -
494A PHE* 3.5 59.2 - - + -
495A TYR* 4.2 6.1 - - + -
621A GLN* 2.9 40.1 + - + +
622A LEU* 3.6 5.4 - - + +
624A SER* 1.3 76.4 - - - +
626A HIS* 1.3 64.1 + - + +
628A ARG* 3.1 12.4 + - - +
629A ILE* 3.1 28.7 + - + +
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Residues in contact with HIS 626 (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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490A VAL* 4.7 17.9 - - + +
590A GLN 4.6 3.6 + - - -
591A MET* 3.4 47.8 - - + +
622A LEU* 2.8 48.1 + - + +
623A LEU* 3.5 10.2 - - + +
625A ILE* 1.3 73.2 - - + +
627A TYR* 1.3 53.8 + - - +
629A ILE* 3.4 3.9 + - - +
630A THR* 2.7 38.9 + - - -
661A GLN* 3.7 1.6 - - - +
703A ASP* 6.0 0.2 - - - -
706A ASN* 3.2 25.2 + - - -
710A TYR* 2.6 29.1 + - - +
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Residues in contact with TYR 627 (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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397A ILE* 3.8 26.2 - - + +
398A VAL* 3.7 18.2 - - + -
529A SER* 2.5 28.3 + - - -
623A LEU 2.7 20.5 + - - +
624A SER* 3.1 6.9 + - - +
626A HIS* 1.3 72.6 - - - +
628A ARG* 1.3 67.9 + - + +
630A THR* 3.9 0.2 - - - -
631A LEU* 3.1 28.4 + - + +
658A HIS* 3.5 27.6 - + - -
661A GLN* 3.2 28.3 - - + +
662A PHE* 3.7 24.4 - + + -
665A LEU* 3.9 19.7 - - + -
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Residues in contact with ARG 628 (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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390A GLN* 6.3 0.4 - - - +
395A LEU* 4.5 28.1 - - - +
397A ILE* 6.5 0.7 - - + -
494A PHE* 3.6 39.4 + - + -
497A MET* 4.6 12.8 - - - +
514A ASN* 3.4 29.6 + - - +
518A SER* 6.0 1.2 - - - -
624A SER 3.1 11.5 + - - +
625A ILE 3.7 7.0 - - - +
627A TYR* 1.3 78.7 - - + +
629A ILE* 1.3 69.8 + - - +
631A LEU* 3.3 7.3 + - + +
632A GLN* 2.9 48.7 + - + +
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Residues in contact with ILE 629 (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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490A VAL* 3.5 34.1 - - + +
493A TRP* 6.2 0.2 - - + -
494A PHE* 5.8 4.5 - - + +
497A MET* 6.0 4.7 - - + -
510A LEU* 3.9 39.3 - - + -
513A LEU* 5.1 0.2 - - - +
586A LEU* 3.9 24.2 - - + -
591A MET* 4.3 7.4 - - + -
625A ILE* 3.1 21.8 + - + +
626A HIS* 3.6 10.1 - - + +
628A ARG* 1.3 82.9 - - + +
630A THR* 1.3 65.6 + - - +
632A GLN* 3.1 12.7 + - - +
633A VAL* 2.9 26.3 + - + +
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Residues in contact with THR 630 (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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591A MET* 2.8 13.4 - - - +
626A HIS 2.7 27.9 + - - -
627A TYR 3.9 0.7 - - - -
629A ILE* 1.3 74.7 - - - +
631A LEU* 1.3 63.0 + - - +
633A VAL* 3.3 6.7 + - - +
634A LEU* 2.9 27.9 + - + +
654A LEU* 3.7 37.9 - - + +
657A LEU* 4.7 1.3 - - + -
658A HIS* 3.7 12.8 - - + +
661A GLN* 2.8 30.9 + - - +
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Residues in contact with LEU 631 (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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397A ILE* 4.1 26.5 - - + -
525A LEU* 4.2 24.7 - - + +
528A ILE* 4.3 4.7 - - + -
529A SER* 3.8 14.4 - - - +
532A PHE* 3.6 31.9 - - + -
627A TYR* 3.1 26.5 + - + +
628A ARG* 3.8 6.7 - - + +
630A THR* 1.3 78.3 - - - +
632A GLN* 1.3 60.4 + - + +
634A LEU* 3.2 8.6 + - - +
635A LEU* 2.8 30.8 + - + +
658A HIS* 3.7 19.5 - - + +
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Residues in contact with GLN 632 (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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497A MET* 4.8 3.8 - - - +
510A LEU* 4.1 5.5 + - - +
513A LEU* 3.9 16.2 - - + +
514A ASN* 2.9 55.4 + - - +
517A ALA* 3.5 22.1 - - + +
525A LEU* 6.3 0.7 - - + -
628A ARG* 2.9 36.8 + - + +
629A ILE* 3.4 15.5 - - - +
631A LEU* 1.3 79.2 - - + +
633A VAL* 1.3 60.9 + - - +
635A LEU* 3.1 24.8 + - - +
636A THR* 3.3 12.8 + - - +
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Residues in contact with VAL 633 (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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509A TYR* 3.9 8.7 - - + +
510A LEU* 4.9 0.7 - - + -
513A LEU* 3.6 21.8 - - + -
583A LEU* 3.6 24.5 - - + -
586A LEU* 4.0 24.7 - - + -
629A ILE* 2.9 22.7 + - + +
630A THR* 3.7 7.9 - - - +
632A GLN* 1.3 71.0 - - - +
634A LEU* 1.3 67.7 + - - +
636A THR* 2.6 24.1 + - - -
637A PHE* 3.3 21.7 - - + -
654A LEU* 3.8 15.9 - - + -
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Residues in contact with LEU 634 (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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532A PHE* 3.6 28.0 - - + -
550A PHE* 5.1 3.8 - - + -
630A THR* 2.9 24.0 + - + +
631A LEU* 3.5 4.3 - - - +
633A VAL* 1.3 76.4 - - - +
635A LEU* 1.3 62.4 + - - +
637A PHE* 3.0 19.8 + - + +
638A VAL* 3.3 15.8 + - - +
651A ILE* 4.1 10.5 - - + +
654A LEU* 3.5 30.5 - - + +
655A LEU* 3.7 37.7 - - + -
658A HIS* 3.9 24.0 - - + -
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Residues in contact with LEU 635 (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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516A PHE* 4.1 12.3 - - + -
517A ALA* 4.1 21.5 - - + -
520A LEU* 3.8 23.6 - - + -
525A LEU* 4.9 6.5 - - + -
528A ILE* 4.1 13.0 - - + -
532A PHE* 4.3 8.9 - - + -
558A LEU* 3.4 37.9 - - + -
631A LEU* 2.8 14.9 + - + +
632A GLN* 3.1 13.7 - - - +
634A LEU* 1.3 77.5 - - - +
636A THR* 1.3 65.4 + - + +
638A VAL* 3.1 14.5 + - + +
639A LEU* 3.3 20.5 + - + +
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Residues in contact with THR 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A TYR* 4.2 8.2 + - - -
513A LEU* 3.6 30.3 - - + -
516A PHE* 6.2 0.2 - - + -
570A LEU* 4.6 13.7 - - + -
574A LEU* 4.6 11.0 - - + -
632A GLN 3.6 13.2 - - - +
633A VAL* 2.6 18.0 + - - -
635A LEU* 1.3 79.3 - - + +
637A PHE* 1.3 62.9 + - - +
639A LEU* 4.5 3.8 - - - -
640A PHE* 3.0 45.6 + - - +
642A LEU* 4.6 8.0 - - - +
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Residues in contact with PHE 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A TYR* 5.4 0.7 - - - -
550A PHE* 3.0 31.4 - - + -
583A LEU* 3.5 27.1 - - + -
633A VAL* 3.3 43.0 + - + -
634A LEU* 3.0 14.5 + - + +
636A THR* 1.3 84.6 + - - +
638A VAL* 1.3 59.9 + - - +
639A LEU 3.3 0.2 - - - -
640A PHE 3.5 12.2 - - - +
642A LEU* 3.2 38.5 + - + +
647A PHE* 3.6 30.5 - + + -
650A HIS* 5.0 2.0 - - + -
651A ILE* 3.9 21.5 - - + -
654A LEU* 4.0 12.3 - - + -
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Residues in contact with VAL 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ILE* 6.2 0.2 - - + -
532A PHE* 3.8 27.1 - - + -
550A PHE* 3.5 49.6 - - + +
553A ILE* 4.4 12.8 - - + -
554A PHE* 4.6 10.7 - - + +
558A LEU* 3.7 27.1 - - + -
634A LEU 3.3 15.9 - - - +
635A LEU* 3.1 10.9 + - + +
637A PHE* 1.3 76.7 - - - +
639A LEU* 1.3 63.0 + - - +
640A PHE 4.7 0.9 - - - -
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Residues in contact with LEU 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PHE* 3.5 35.0 - - + -
554A PHE* 3.8 32.0 - - + -
558A LEU* 4.1 11.0 - - + -
562A PHE* 4.2 17.0 - - + -
567A LEU* 3.8 19.4 - - + +
570A LEU* 4.7 6.3 - - + -
635A LEU* 3.3 22.0 + - + +
636A THR* 3.3 4.8 + - - +
638A VAL* 1.3 80.9 - - - +
640A PHE* 1.3 72.7 + - + +
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Residues in contact with PHE 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU* 3.4 37.7 - - + -
570A LEU* 3.7 24.5 - - + -
571A PHE* 3.9 40.8 - + + -
574A LEU* 3.6 30.7 - - + -
636A THR* 3.0 27.3 + - - +
637A PHE 3.5 15.2 - - - +
638A VAL 4.7 0.5 - - - -
639A LEU* 1.3 88.3 - - + +
641A ASP* 1.3 61.5 + - - +
642A LEU* 3.0 20.8 + - + +
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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