Contacts of the helix formed by residues 646 - 677 (chain A) in PDB entry 3RCW
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 THR 646 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ASN* 3.4 13.3 - - + +
643A ALA* 2.7 37.7 + - + +
644A ARG 3.2 0.6 - - - -
645A ASP* 1.3 85.0 - - + +
647A VAL* 1.3 62.9 + - - +
648A PHE* 4.1 6.7 - - - -
649A TYR* 3.2 15.9 + - - +
650A ARG* 3.2 30.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ILE* 5.1 12.1 - - + -
646A THR* 1.3 71.8 - - - +
648A PHE* 1.3 72.7 + - + +
650A ARG* 3.2 24.6 + - - +
651A ALA* 2.8 30.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ILE* 3.5 39.7 - - + -
587A PHE* 4.3 0.7 - - - -
638A CYS* 3.2 17.8 - - - -
642A ASN* 3.4 37.9 - - + +
646A THR* 3.4 5.5 + - - -
647A VAL* 1.3 83.9 - - + +
649A TYR* 1.3 62.8 + - - +
651A ALA* 3.4 4.4 + - - +
652A ALA 3.1 15.6 + - - -
----------------------------------------------------------
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Residues in contact with TYR 649 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A CYS* 4.1 7.1 - - - -
639A MET* 3.7 38.6 - - + +
642A ASN* 3.4 21.5 - - + +
643A ALA 3.2 17.3 - - - +
644A ARG* 3.6 35.6 - - + +
646A THR* 3.2 9.8 + - - +
648A PHE* 1.3 78.1 - - - +
650A ARG* 1.3 65.6 + - + +
652A ALA* 3.3 5.2 + - - +
653A VAL* 3.1 48.5 + - + +
----------------------------------------------------------
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Residues in contact with ARG 650 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ARG 4.4 10.8 - - - +
645A ASP 4.8 6.3 - - - -
646A THR 3.2 16.9 + - - +
647A VAL* 3.2 40.5 + - - +
649A TYR* 1.3 81.3 - - + +
651A ALA* 1.3 63.6 + - - +
653A VAL* 3.0 8.7 + - - +
654A ARG* 3.0 22.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ASP* 5.9 0.2 - - - +
586A ILE* 3.9 26.0 - - + -
587A PHE* 4.5 9.2 - - + -
647A VAL* 2.8 22.2 + - + +
648A PHE 3.9 3.1 - - - +
650A ARG* 1.3 73.0 - - - +
652A ALA* 1.3 52.3 + - - +
654A ARG* 3.2 10.8 + - - +
655A LEU* 2.8 37.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A PHE* 3.9 13.4 - - + -
635A ILE* 3.7 17.1 - - + +
638A CYS* 3.7 20.6 - - + -
639A MET* 4.0 17.0 - - + -
648A PHE 3.1 13.1 + - - +
649A TYR 3.4 9.6 - - - +
651A ALA* 1.3 77.5 - - - +
653A VAL* 1.3 57.4 + - - +
655A LEU* 3.3 0.6 + - - -
656A ARG* 2.8 31.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A MET* 4.0 14.4 - - - -
649A TYR* 3.1 40.3 + - + +
650A ARG* 3.0 8.8 + - - +
652A ALA* 1.3 75.7 - - - +
654A ARG* 1.3 61.2 - - - +
656A ARG* 3.1 29.9 + - - +
657A ASP* 3.0 37.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LYS 6.2 0.2 - - - +
650A ARG 3.0 12.4 + - - +
651A ALA* 3.4 12.8 - - - +
653A VAL* 1.3 77.0 - - - +
655A LEU* 1.3 56.9 + - - +
657A ASP* 3.6 6.3 + - - +
658A GLN* 2.9 59.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A LEU* 3.5 28.5 - - + +
581A LYS* 3.5 28.9 - - + +
582A ASP* 4.4 2.0 - - + +
587A PHE* 3.8 25.1 - - + -
609A PHE* 3.8 24.2 - - + -
631A PHE* 3.9 10.8 - - + -
634A ILE* 4.8 1.1 - - + -
635A ILE* 3.8 20.0 - - + -
651A ALA 2.8 20.8 + - - +
652A ALA* 3.7 4.3 - - - +
654A ARG* 1.3 70.8 - - - +
656A ARG* 1.3 61.4 + - - +
658A GLN* 4.6 4.0 - - - +
659A GLY* 2.9 27.5 + - - -
----------------------------------------------------------
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Residues in contact with ARG 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A PHE* 4.6 6.1 - - + -
632A ASP* 6.2 0.4 - - - +
635A ILE* 3.8 32.2 - - + +
636A ASP* 5.8 0.7 - - - -
639A MET* 4.3 20.1 - - - +
652A ALA 2.8 21.8 + - - +
653A VAL* 3.1 27.6 + - - +
655A LEU* 1.3 72.6 - - - +
657A ASP* 1.3 78.5 + - - +
659A GLY 3.8 0.3 - - - -
660A GLY* 2.9 28.2 + - - -
----------------------------------------------------------
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Residues in contact with ASP 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A VAL* 3.0 28.1 + - - +
654A ARG* 3.8 5.3 - - - +
656A ARG* 1.3 102.0 + - - +
658A GLN* 1.3 66.2 + - + +
660A GLY* 3.2 7.8 + - - -
661A VAL* 3.6 13.1 + - - +
664A ARG* 5.0 2.4 + - - -
----------------------------------------------------------
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Residues in contact with GLN 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LYS* 3.6 45.9 - - + +
654A ARG* 2.9 45.7 + - + +
655A LEU* 4.2 2.6 - - - +
657A ASP* 1.3 74.4 - - + +
659A GLY* 1.3 59.7 + - - +
661A VAL* 3.3 25.2 + - - +
662A VAL* 3.5 11.3 - - - +
----------------------------------------------------------
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Residues in contact with GLY 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A LEU* 3.6 24.2 - - - -
581A LYS* 5.4 1.1 - - - +
631A PHE* 4.5 4.0 - - - -
655A LEU* 2.9 18.4 + - - -
656A ARG 3.8 0.7 - - - -
658A GLN* 1.3 73.2 - - - +
660A GLY* 1.3 60.0 + - - +
661A VAL 3.1 1.6 - - - -
662A VAL* 3.2 4.6 + - - +
663A LEU* 2.8 41.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A PHE* 5.1 0.6 - - - -
656A ARG 2.9 16.5 + - - -
657A ASP 3.2 4.4 + - - -
659A GLY* 1.3 78.6 - - - +
661A VAL* 1.3 61.4 + - - +
663A LEU* 3.3 6.9 + - - +
664A ARG* 2.9 45.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ASP 3.6 10.8 + - - +
658A GLN* 3.3 16.5 + - - +
659A GLY 3.1 0.4 - - - -
660A GLY* 1.3 74.9 - - - +
662A VAL* 1.3 62.8 + - + +
664A ARG* 3.5 26.4 + - - +
665A GLN* 3.0 28.4 + - + +
668A ARG* 5.2 1.2 + - - -
----------------------------------------------------------
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Residues in contact with VAL 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 4.5 18.8 - - + +
577A GLN* 3.9 48.7 - - + +
578A LEU* 4.4 7.0 - - + -
581A LYS* 4.7 14.1 - - + -
658A GLN 3.5 16.4 - - - +
659A GLY* 3.2 10.5 + - - +
661A VAL* 1.3 84.2 - - + +
663A LEU* 1.3 57.6 + - - +
665A GLN* 3.3 9.0 + - + +
666A ALA* 2.9 25.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A VAL* 3.7 27.6 - - + -
578A LEU* 4.8 4.0 - - + -
624A LEU* 4.0 16.3 - - + +
627A PHE* 4.2 8.5 - - + -
628A GLU* 3.9 39.0 - - + +
631A PHE* 3.5 35.9 - - + -
632A ASP* 5.6 1.3 - - - +
659A GLY 2.8 20.5 + - - +
660A GLY* 4.1 5.6 - - - +
662A VAL* 1.3 73.9 - - - +
664A ARG* 1.3 61.0 + - + +
666A ALA* 3.0 5.7 + - + +
667A ARG* 2.8 28.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ASP 5.0 2.2 + - - -
660A GLY* 2.9 35.9 + - - +
661A VAL* 3.7 27.9 - - - +
663A LEU* 1.3 76.7 - - - +
665A GLN* 1.3 61.4 + - - +
667A ARG* 3.3 15.2 + - - +
668A ARG* 3.3 38.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A VAL* 3.0 17.6 + - + +
662A VAL* 3.4 12.1 - - + +
663A LEU 3.2 0.2 - - - -
664A ARG* 1.3 77.2 - - - +
666A ALA* 1.3 61.9 + - - +
668A ARG* 2.7 47.5 + - - +
669A GLU* 3.1 30.7 + - + +
----------------------------------------------------------
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Residues in contact with ALA 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU* 4.0 8.7 - - + +
571A LEU* 5.9 0.4 - - + -
574A VAL* 3.6 26.5 - - + -
624A LEU* 4.1 17.9 - - + -
662A VAL 2.9 14.9 + - - +
663A LEU* 3.0 12.8 + - - +
665A GLN* 1.3 77.2 - - - +
667A ARG* 1.3 56.9 + - - +
669A GLU* 3.1 8.7 + - - +
670A VAL* 2.9 31.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU* 3.8 19.9 - - + +
628A GLU* 5.5 3.4 - - - +
663A LEU 2.8 12.7 + - - +
664A ARG* 3.3 11.4 + - - +
666A ALA* 1.3 74.9 - - - +
668A ARG* 1.3 63.4 + - + +
670A VAL* 3.1 9.1 + - - +
671A ASP* 3.1 36.0 + - - +
581D LYS* 5.3 10.8 - - - +
----------------------------------------------------------
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Residues in contact with ARG 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A VAL* 5.2 1.4 + - - +
664A ARG* 3.6 31.6 - - - +
665A GLN* 2.7 54.8 + - - +
667A ARG* 1.3 77.4 - - + +
669A GLU* 1.3 58.4 + - - +
671A ASP* 3.3 10.9 + - - +
672A SER* 2.8 28.4 + - - -
661D VAL* 4.2 38.0 - - + +
665D GLN* 5.7 0.7 - - - +
----------------------------------------------------------
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Residues in contact with GLU 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU* 3.8 30.1 - - + -
665A GLN* 3.1 21.2 + - + +
666A ALA* 3.6 8.1 - - - +
667A ARG 3.1 1.0 - - - -
668A ARG* 1.3 78.9 - - - +
670A VAL* 1.3 64.6 + - - +
672A SER* 3.5 21.8 + - - -
673A ILE* 3.0 38.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU* 4.5 13.9 - - + -
570A LEU* 3.7 17.5 - - + -
571A LEU* 6.2 0.2 - - + -
624A LEU* 4.2 26.7 - - + -
666A ALA 2.9 20.5 + - - +
667A ARG* 3.1 10.1 + - - +
669A GLU* 1.3 75.0 - - - +
671A ASP* 1.3 59.7 + - - +
673A ILE* 3.6 7.1 + - + +
674A GLY* 3.0 22.5 + - - -
----------------------------------------------------------
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Residues in contact with ASP 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A ARG* 3.1 24.5 + - - +
668A ARG* 3.4 11.8 - - - +
670A VAL* 1.3 76.7 - - - +
672A SER* 1.3 66.5 + - - +
674A GLY 2.9 9.9 + - - -
675A LEU* 3.0 5.9 + - - +
577D GLN* 3.0 46.9 + - - +
581D LYS* 2.9 37.4 + - - -
661D VAL* 5.7 2.6 - - + +
662D VAL* 4.4 6.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ARG 2.8 21.0 + - - -
669A GLU* 3.3 27.9 + - - -
671A ASP* 1.3 71.8 - - - +
673A ILE* 1.3 61.1 + - - -
675A LEU* 3.0 14.8 + - - +
676A GLU* 3.2 11.1 + - - +
665D GLN* 3.2 43.4 + - - +
669D GLU* 5.3 2.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PRO* 5.0 26.5 - - + +
570A LEU* 4.4 21.3 - - + -
669A GLU* 3.0 35.3 + - + +
670A VAL* 4.0 6.3 - - + +
672A SER* 1.3 73.4 - - - +
674A GLY* 1.3 63.8 + - - +
676A GLU* 3.2 28.1 + - + +
677A GLU* 3.8 22.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A VAL 3.0 12.8 + - - -
671A ASP 2.9 10.4 + - - -
673A ILE* 1.3 77.8 - - - +
675A LEU* 1.3 59.6 + - - +
677A GLU* 3.6 26.9 + - - +
573D SER* 4.0 7.4 + - - -
577D GLN* 3.9 11.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ASP 3.0 14.3 + - - +
672A SER* 3.0 8.4 + - - +
674A GLY* 1.3 71.0 - - - +
676A GLU* 1.3 67.2 + - - +
677A GLU 2.9 12.4 + - - +
678A ALA 3.6 8.7 + - - -
570D LEU* 3.9 14.7 - - + +
573D SER* 3.7 23.5 + - - -
574D VAL* 3.6 27.4 - - + +
577D GLN* 3.8 16.4 - - - +
662D VAL* 4.1 7.2 - - + +
665D GLN* 4.0 19.7 - - + -
666D ALA* 3.9 31.0 - - - +
669D GLU* 4.3 16.1 - - + +
----------------------------------------------------------
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Residues in contact with GLU 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A SER 3.2 10.1 + - - +
673A ILE* 3.2 21.2 + - + +
675A LEU* 1.3 73.8 - - - +
677A GLU* 1.3 59.9 + - + +
678A ALA* 3.0 18.4 - - - +
669D GLU* 4.1 18.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PRO* 6.2 0.2 - - - +
673A ILE* 3.8 29.9 - - - +
674A GLY* 3.6 20.0 + - - +
675A LEU 2.9 5.0 + - - -
676A GLU* 1.3 80.2 - - + +
678A ALA* 1.3 52.3 + - - +
569D VAL* 4.6 5.5 - - - +
573D SER* 3.9 12.7 + - - -
----------------------------------------------------------
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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