Contacts of the helix formed by residues 690 - 719 (chain A) in PDB entry 6NYY
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 690 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A LYS* 5.3 0.9 - - - +
689A TYR* 1.3 94.7 - - - +
691A GLU* 1.3 61.7 + - - +
692A ALA* 3.6 2.9 + - - +
693A THR* 2.8 31.8 + - - -
694A ALA* 3.4 7.4 + - - +
687F LYS* 3.7 5.1 - - - +
691F GLU* 3.2 14.4 - - - -
694F ALA* 3.5 25.2 + - - -
695F ARG* 3.8 7.8 - - - -
698F ASP* 2.8 15.9 + - - +
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Residues in contact with GLU 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A SER* 1.3 71.1 - - - +
692A ALA* 1.3 54.8 + - - +
693A THR 3.2 1.6 - - - -
694A ALA* 3.0 6.6 + - - +
695A ARG* 2.7 35.8 + - + +
690B SER* 3.3 14.8 - - - -
691B GLU* 2.5 48.6 + - + +
692B ALA* 3.8 2.9 + - + +
691F GLU* 2.4 35.9 + - + +
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Residues in contact with ALA 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A SER* 3.6 2.4 + - - +
691A GLU* 1.3 74.8 - - - +
693A THR* 1.3 62.6 + - - +
695A ARG* 3.9 10.1 - - - +
696A LEU* 3.2 21.5 + - - +
691F GLU* 4.1 2.0 + - - +
695F ARG* 3.7 45.1 - - + +
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Residues in contact with THR 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A VAL* 5.7 4.3 - - + -
673A ILE* 6.3 1.6 - - + -
675A PHE* 5.1 6.1 - - + -
689A TYR* 3.8 28.0 - - + -
690A SER* 2.8 23.8 + - - -
692A ALA* 1.3 78.1 - - - +
694A ALA* 1.3 52.0 + - - +
696A LEU* 2.9 10.0 + - + +
697A ILE* 2.7 50.9 + - + +
698F ASP* 3.1 21.2 + - - +
702F ARG* 3.8 19.7 + - - +
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Residues in contact with ALA 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A LYS* 5.4 9.0 - - + +
689A TYR* 3.6 25.1 - - + -
690A SER 3.4 9.4 + - - +
691A GLU* 3.0 14.8 + - - +
693A THR* 1.3 75.3 - - - +
695A ARG* 1.3 63.5 + - - +
697A ILE* 3.8 4.9 - - - +
698A ASP* 3.3 21.5 + - - +
690B SER* 3.3 27.5 - - - +
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Residues in contact with ARG 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A GLU* 2.7 20.3 + - + +
692A ALA* 3.9 10.8 - - - +
694A ALA* 1.3 72.7 - - - +
696A LEU* 1.3 60.4 + - - +
698A ASP* 4.4 1.0 - - - +
699A ASP* 2.9 46.5 + - - +
690B SER* 4.0 9.3 - - - +
692B ALA* 3.7 30.3 - - + +
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Residues in contact with LEU 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A LYS* 3.6 39.0 - - + +
670A VAL* 4.3 11.7 - - + -
692A ALA 3.2 14.5 + - - +
693A THR* 2.9 10.1 + - + +
695A ARG* 1.3 75.7 - - - +
697A ILE* 1.3 64.2 + - - +
699A ASP* 3.5 5.4 + - + -
700A GLU* 3.2 44.3 + - + +
702F ARG* 4.3 23.1 - - - +
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Residues in contact with ILE 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A TYR* 4.3 18.8 - - + -
661A ILE* 4.5 7.1 - - + +
662A VAL* 3.7 30.1 - - + -
670A VAL* 4.3 26.0 - - + -
675A PHE* 5.3 2.5 - - + -
689A TYR* 3.6 43.1 - - + +
693A THR* 2.7 31.6 + - + +
694A ALA* 4.1 4.5 - - - +
695A ARG 3.4 0.2 - - - -
696A LEU* 1.3 73.2 - - - +
698A ASP* 1.3 59.4 + - - +
700A GLU* 3.2 4.3 + - - +
701A VAL* 3.0 27.6 + - + +
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Residues in contact with ASP 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A TYR* 2.3 37.9 + - - -
694A ALA* 3.3 11.7 + - - +
695A ARG* 4.6 1.3 - - - +
697A ILE* 1.3 78.9 - - - +
699A ASP* 1.3 60.2 + - - +
701A VAL* 4.1 4.5 - - - +
702A ARG* 3.1 36.9 + - - +
675B PHE* 5.8 0.2 - - - -
689B TYR* 3.6 5.4 - - - -
690B SER* 2.9 36.3 + - - +
693B THR* 3.3 18.9 + - - +
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Residues in contact with ASP 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A ARG* 2.9 39.6 + - - +
696A LEU* 3.9 7.6 - - + +
697A ILE 3.3 0.2 - - - -
698A ASP* 1.3 76.9 - - - +
700A GLU* 1.3 60.3 + - + +
702A ARG* 2.4 36.8 + - - +
703A ILE* 3.3 31.7 + - + +
692B ALA* 6.4 0.4 - - - -
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Residues in contact with GLU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A ILE* 3.9 7.9 - - + +
667A ASN* 3.3 37.1 + - - +
669A LYS* 3.3 34.3 + - + +
696A LEU* 3.2 31.4 + - + +
697A ILE* 3.2 4.0 + - - +
698A ASP 3.2 0.2 - - - -
699A ASP* 1.3 82.3 - - - +
701A VAL* 1.3 59.4 + - - +
702A ARG 3.3 0.7 - - - -
703A ILE* 3.5 23.8 + - - +
704A LEU* 2.8 27.4 + - - +
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Residues in contact with VAL 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A THR* 5.2 3.4 - - + +
657A ALA* 3.7 27.6 - - + +
658A TYR* 3.5 35.7 - - + -
661A ILE* 3.7 17.5 - - + -
697A ILE* 3.0 19.5 + - + +
698A ASP* 3.6 4.5 + - - +
700A GLU* 1.3 75.5 - - - +
702A ARG* 1.3 55.8 + - - +
704A LEU* 3.0 6.1 + - - +
705A ILE* 2.7 49.0 + - + +
673B ILE* 5.0 6.7 - - + -
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Residues in contact with ARG 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A ASP* 3.1 25.1 + - - +
699A ASP* 2.4 42.4 + - - +
701A VAL* 1.3 77.6 - - - +
703A ILE* 1.3 60.9 + - + +
705A ILE* 4.5 5.6 - - - +
706A ASN* 2.8 41.4 + - - +
669B LYS 3.8 15.0 + - - -
670B VAL* 3.2 28.6 + - - +
671B GLY* 5.0 3.8 - - - -
673B ILE* 5.5 9.5 - - + +
693B THR* 3.6 34.1 + - - +
696B LEU* 4.3 17.4 - - - +
----------------------------------------------------------
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Residues in contact with ILE 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A LYS* 5.8 2.9 - - - +
699A ASP* 3.3 20.1 + - + +
700A GLU* 3.5 29.3 + - - +
701A VAL 3.2 0.2 - - - -
702A ARG* 1.3 77.0 - - + +
704A LEU* 1.3 65.2 + - - +
706A ASN* 3.5 6.6 + - - +
707A ASP* 3.1 45.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A LYS* 5.6 9.2 - - - -
622A LEU* 5.3 8.2 - - + +
625A MET* 3.9 10.7 - - + +
657A ALA* 3.8 27.4 - - + +
660A GLN* 3.9 29.2 - - - +
661A ILE* 3.9 22.0 - - + -
700A GLU 2.8 19.2 + - - +
701A VAL* 3.0 6.7 + - - +
703A ILE* 1.3 77.9 - - - +
705A ILE* 1.3 62.0 + - - +
707A ASP* 3.4 9.6 + - + +
708A ALA* 3.2 20.4 + - - +
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Residues in contact with ILE 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A MET* 3.6 21.3 - - + -
629A LEU* 4.2 7.4 - - + +
653A VAL* 3.8 19.5 - - + -
654A THR* 4.5 7.2 - - - +
657A ALA* 4.6 1.1 - - + -
701A VAL* 2.7 35.5 + - + +
702A ARG* 4.5 3.6 - - - +
704A LEU* 1.3 72.2 - - - +
706A ASN* 1.3 53.1 + - - +
708A ALA* 3.1 3.8 + - - +
709A TYR* 2.7 33.1 + - + +
672B GLN* 3.7 39.9 - - + +
673B ILE* 3.7 29.8 - - + -
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Residues in contact with ASN 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ARG* 2.8 32.3 + - - +
703A ILE* 3.5 7.3 + - - +
704A LEU 3.4 0.4 - - - -
705A ILE* 1.3 78.9 - - - +
707A ASP* 1.3 58.7 + - - +
709A TYR* 3.8 15.4 - - - +
710A LYS* 3.0 46.8 + - - +
668B GLU 5.6 4.2 + - - +
671B GLY* 5.5 6.5 - - - -
672B GLN* 5.1 8.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 5.0 6.0 - - + +
703A ILE* 3.1 34.4 + - - +
704A LEU* 3.8 11.2 - - + +
705A ILE 3.2 0.4 - - - -
706A ASN* 1.3 78.3 - - - +
708A ALA* 1.3 61.6 + - - +
710A LYS* 4.7 4.6 - - - +
711A ARG* 3.4 23.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 3.7 22.8 - - + +
625A MET* 3.9 24.2 - - + -
626A CYS* 3.3 18.0 - - - -
629A LEU* 3.9 8.7 - - + +
704A LEU 3.2 11.3 + - - +
705A ILE 3.1 8.5 + - - +
707A ASP* 1.3 75.5 - - - +
709A TYR* 1.3 59.4 + - - +
712A THR* 2.7 26.2 + - - -
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Residues in contact with TYR 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 4.1 14.6 - - + -
632A ARG* 5.5 7.2 - - + -
633A VAL* 3.9 22.7 - - + -
636A GLU* 2.5 39.9 + - - -
705A ILE* 2.7 22.1 + - + +
706A ASN* 3.6 17.5 - - - +
707A ASP 3.2 0.2 - - - -
708A ALA* 1.3 73.5 - - - +
710A LYS* 1.3 73.1 + - + +
712A THR* 3.1 6.4 + - - -
713A VAL* 3.0 45.1 + - + +
672B GLN* 4.3 31.9 + - + -
----------------------------------------------------------
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Residues in contact with LYS 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A ASN* 3.0 30.0 + - - +
707A ASP* 4.7 5.2 - - - +
709A TYR* 1.3 83.5 - - + +
711A ARG* 1.3 62.9 + - - +
713A VAL* 3.9 9.2 - - + +
714A ALA* 3.1 23.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A LEU* 3.8 22.6 - - + +
586A GLU 5.7 1.0 - - - +
619A GLU* 5.3 1.0 + - - +
622A LEU* 3.4 32.4 - - - +
623A ASP* 3.0 30.2 + - - -
626A CYS* 3.8 19.9 - - + -
707A ASP 3.4 18.3 + - - +
709A TYR 3.2 0.8 - - - -
710A LYS* 1.3 78.9 - - - +
712A THR* 1.3 57.5 + - - +
714A ALA* 3.5 4.9 + - - +
715A LEU* 3.0 27.1 + - + +
----------------------------------------------------------
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Residues in contact with THR 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ALA* 4.7 4.7 - - + -
585A LEU* 6.2 0.9 - - + -
626A CYS* 3.3 38.6 + - + +
629A LEU* 4.5 2.7 - - - +
630A GLY* 3.7 21.8 - - - +
633A VAL* 3.8 12.1 - - + -
708A ALA 2.7 16.5 + - - -
709A TYR* 3.1 8.3 + - - -
711A ARG* 1.3 76.6 - - - +
713A VAL* 1.3 59.5 + - - +
715A LEU* 3.3 6.1 + - + +
716A LEU* 2.9 41.7 + - + +
----------------------------------------------------------
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Residues in contact with VAL 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A VAL* 3.7 24.5 - - + -
636A GLU* 5.4 2.0 - - - +
637A ILE* 5.6 1.1 - - + -
709A TYR* 3.0 41.6 + - + +
710A LYS* 4.0 8.3 - - + +
712A THR* 1.3 76.0 - - - +
714A ALA* 1.3 52.7 + - - +
717A THR* 2.7 57.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LYS 3.1 19.2 + - - +
711A ARG* 3.8 6.5 - - - +
713A VAL* 1.3 78.0 - - - +
715A LEU* 1.3 60.6 + - - +
717A THR* 3.9 5.5 + - - -
718A GLU* 3.4 26.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ALA* 4.0 27.4 - - + +
584A TYR* 4.1 24.2 - - + +
585A LEU* 3.8 37.9 - - + -
711A ARG* 3.0 19.1 + - + +
712A THR* 3.6 7.2 - - + +
713A VAL 3.2 0.2 - - - -
714A ALA* 1.3 78.1 - - - +
716A LEU* 1.3 62.0 + - + +
718A GLU* 3.5 7.1 + - - +
719A LYS* 3.0 46.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 716 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLY* 4.3 5.2 - - - +
580A VAL* 4.2 5.8 - - + -
581A ALA* 3.9 28.0 - - + +
630A GLY* 3.4 27.6 - - - +
633A VAL* 3.8 17.7 - - + -
634A SER* 4.3 8.3 - - - +
637A ILE* 3.7 17.4 - - + +
712A THR* 2.9 28.2 + - + +
715A LEU* 1.3 79.1 - - + +
717A THR* 1.3 61.8 + - - +
719A LYS* 3.2 4.0 - - + +
720A LYS* 3.0 27.2 + - - +
723A VAL* 3.8 25.4 - - + +
----------------------------------------------------------
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Residues in contact with THR 717 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ILE* 3.7 29.2 - - + -
713A VAL* 2.7 42.5 + - + +
714A ALA* 3.9 6.1 + - - -
716A LEU* 1.3 75.3 - - - +
718A GLU* 1.3 63.3 + - - +
720A LYS* 3.5 20.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 718 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ALA 3.4 19.7 + - - +
715A LEU* 3.5 9.0 + - - +
716A LEU 3.3 0.2 - - - -
717A THR* 1.3 83.6 + - - +
719A LYS* 1.3 74.3 + - + +
720A LYS 3.3 2.5 + - - -
721A ALA 5.2 0.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A VAL* 4.6 4.7 - - + -
584A TYR* 3.6 46.0 + - + -
715A LEU* 3.0 26.7 + - + +
716A LEU* 3.2 7.2 - - + +
717A THR 3.3 0.2 - - - -
718A GLU* 1.3 97.1 + - + +
720A LYS* 1.3 62.2 + - - +
721A ALA 3.3 2.9 - - - +
722A ASP* 3.2 25.4 + - + +
723A VAL* 3.3 15.2 + - - +
----------------------------------------------------------
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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