Contacts of the helix formed by residues 677 - 706 (chain A) in PDB entry 5XJY
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 677 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ARG* 5.2 4.2 + - - -
676A LEU* 1.3 75.8 - - - +
678A ASN* 1.3 95.6 + - - +
679A SER* 3.1 16.1 + - - +
680A ILE* 3.2 23.9 + - - +
681A LEU* 3.8 4.8 + - - +
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Residues in contact with ASN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LYS* 5.0 2.4 - - - -
672A ARG* 2.5 40.2 + - - +
677A ASP* 1.3 87.0 + - - +
679A SER* 1.3 58.0 + - - +
681A LEU* 3.2 18.2 + - - +
682A TRP* 2.9 55.8 + - + +
843A GLU* 6.1 3.0 - - - +
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Residues in contact with SER 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A ASP* 4.1 15.0 + - - +
678A ASN* 1.3 77.3 - - - +
680A ILE* 1.3 69.8 + - - +
682A TRP* 4.4 2.6 - - - +
683A PHE* 2.9 33.5 + - - +
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Residues in contact with ILE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CYS* 4.9 7.4 - - + +
6A GLN* 4.7 15.0 - - + +
7A LEU* 3.7 45.9 - - + +
10A LEU* 3.4 15.5 - - + +
676A LEU* 4.1 28.0 - - + -
677A ASP 3.2 14.8 + - - +
679A SER* 1.3 82.8 + - - +
681A LEU* 1.3 63.2 + - + +
683A PHE* 4.4 5.2 - - + -
684A SER* 3.0 29.6 + - - -
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Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.3 20.2 - - + -
13A LYS* 4.6 8.3 - - - +
662A GLU* 6.1 0.7 - - - +
668A LYS* 4.0 43.5 - - + +
671A MET* 3.9 26.0 - - + -
672A ARG* 5.5 2.9 - - + +
676A LEU* 5.6 2.0 - - + -
677A ASP 4.4 8.3 - - - +
678A ASN* 3.2 25.8 + - - +
680A ILE* 1.3 78.9 - - + +
682A TRP* 1.3 64.8 + - + +
684A SER* 2.9 6.4 + - - -
685A TRP* 2.9 45.7 + - + +
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Residues in contact with TRP 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A ILE* 4.6 23.3 - - + -
668A LYS* 3.3 33.2 - - + +
678A ASN* 2.9 46.5 + - + +
679A SER* 4.4 2.7 - - - +
681A LEU* 1.3 77.8 - - + +
683A PHE* 1.3 57.3 + - - +
685A TRP* 3.6 5.0 + + - +
686A PHE* 3.0 28.4 + - - +
734A PHE* 3.8 57.4 - + + -
737A SER* 5.7 0.4 - - - -
738A THR* 5.0 19.7 - - - -
839A THR* 5.6 13.5 - - - -
843A GLU* 5.4 13.7 - - + +
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Residues in contact with PHE 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.7 33.7 - - + -
679A SER 2.9 22.4 + - - +
680A ILE* 4.1 5.6 - - + +
682A TRP* 1.3 77.9 - - - +
684A SER* 1.3 57.7 + - - +
686A PHE* 3.2 17.3 + + - +
687A ILE* 3.0 60.2 + - + +
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Residues in contact with SER 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.9 7.2 - - - -
10A LEU* 3.4 24.1 + - - +
11A LEU* 3.4 18.6 - - - +
14A ASN* 2.3 35.1 + - - -
680A ILE 3.0 20.0 + - - -
681A LEU* 2.9 5.8 + - - -
683A PHE* 1.3 77.4 - - - +
685A TRP* 1.3 58.3 + - - +
687A ILE* 3.2 2.3 + - - +
688A SER* 3.0 26.5 + - - -
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Residues in contact with TRP 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 4.9 7.3 - - - +
14A ASN* 3.2 35.4 - - + +
17A PHE* 4.1 23.6 - + - -
18A ARG* 5.2 8.3 - - - -
655A ILE* 3.9 25.7 - - + +
658A GLY* 4.1 22.7 - - - -
659A ILE* 3.4 21.3 - - + -
662A GLU* 3.6 36.3 + - + -
668A LYS* 5.7 0.8 - - + +
681A LEU* 2.9 42.9 + - + +
682A TRP* 4.1 6.1 - + - +
684A SER* 1.3 72.8 - - - +
686A PHE* 1.3 54.5 + - - +
688A SER* 5.2 0.4 - - - -
689A SER* 2.6 42.9 + - - +
734A PHE* 3.8 19.2 - - + -
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Residues in contact with PHE 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A TRP 3.0 20.5 + - - +
683A PHE* 3.4 20.9 - + + +
684A SER 3.2 0.2 - - - -
685A TRP* 1.3 78.1 - - - +
687A ILE* 1.3 71.7 + - + +
689A SER* 3.9 2.7 - - - -
690A LEU* 3.0 49.3 + - + +
727A VAL* 3.7 34.1 - - + -
730A ILE* 3.7 26.1 - - + +
731A LEU* 4.4 15.7 - - + -
734A PHE* 4.0 10.5 - + + -
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Residues in contact with ILE 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.2 26.5 - - + -
683A PHE* 3.0 51.7 + - + +
684A SER* 3.8 3.4 - - - +
686A PHE* 1.3 86.8 - - + +
688A SER* 1.3 58.9 + - - +
690A LEU* 2.7 28.9 + - + +
691A ILE* 3.1 25.8 + - + +
----------------------------------------------------------
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Residues in contact with SER 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.9 7.4 - - - -
14A ASN* 3.6 32.6 - - - +
15A LEU* 3.4 31.5 + - - +
18A ARG* 3.6 16.1 + - - -
655A ILE* 5.4 0.4 - - - -
684A SER 3.0 12.2 + - - -
685A TRP* 5.2 1.8 - - - -
687A ILE* 1.3 74.8 - - - +
689A SER* 1.3 64.7 + - - +
691A ILE* 4.3 5.4 - - - +
692A PRO* 3.3 16.5 - - - +
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Residues in contact with SER 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 5.0 1.6 - - - +
655A ILE* 3.3 40.3 - - - +
685A TRP* 2.6 25.5 + - - +
686A PHE* 3.9 1.3 - - - -
688A SER* 1.3 78.6 - - - +
690A LEU* 1.3 62.6 + - - +
691A ILE 3.5 0.3 + - - -
692A PRO* 3.6 11.7 - - - +
693A LEU* 3.6 15.9 - - - +
730A ILE* 3.4 27.8 - - - +
734A PHE* 5.1 0.4 - - - -
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Residues in contact with LEU 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A PHE* 3.0 38.1 + - + +
687A ILE* 2.7 20.0 + - + +
689A SER* 1.3 72.8 - - - +
691A ILE* 1.3 64.1 + - + +
693A LEU* 3.3 4.0 + - - +
694A LEU* 2.8 61.5 + - + +
726A ALA* 5.4 6.5 - - + -
727A VAL* 3.7 30.3 - - + -
730A ILE* 3.6 15.0 - - + -
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Residues in contact with ILE 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.8 7.6 - - + -
687A ILE* 3.1 25.9 + - + +
688A SER* 4.9 3.8 - - - +
690A LEU* 1.3 88.1 - - + +
692A PRO* 1.3 65.0 - - + +
694A LEU* 3.1 13.2 + - + +
695A VAL* 3.0 31.5 + - + +
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Residues in contact with PRO 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.9 3.4 - - + -
18A ARG* 4.5 11.9 - - - +
25A LEU* 5.0 12.6 - - + -
28A GLU* 4.5 26.4 - - + +
29A VAL* 5.1 6.8 - - + +
688A SER 3.3 19.1 - - - +
689A SER* 3.6 8.7 - - - +
691A ILE* 1.3 94.4 - - + +
693A LEU* 1.3 58.2 + - + +
695A VAL* 3.3 13.5 - - + +
696A SER* 3.0 27.2 + - - -
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 4.7 1.1 - - - +
648A TRP* 3.6 46.6 - - + +
651A SER* 3.6 26.2 - - - +
652A VAL* 5.9 2.5 - - + +
655A ILE* 5.8 3.4 - - + -
689A SER* 3.6 18.6 - - - +
690A LEU* 3.3 8.0 + - - +
691A ILE 3.3 0.4 - - - -
692A PRO* 1.3 80.0 - - + +
694A LEU* 1.3 58.7 + - - +
696A SER* 2.4 22.6 + - - +
697A ALA* 2.9 14.6 + - - +
726A ALA* 4.5 16.2 - - + +
729A THR* 4.8 7.0 - - + -
730A ILE* 3.8 27.4 - - + -
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Residues in contact with LEU 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU* 2.8 42.0 + - + +
691A ILE* 3.1 15.7 + - + +
693A LEU* 1.3 73.5 - - - +
695A VAL* 1.3 60.4 + - - +
697A ALA* 3.1 7.1 + - + +
698A GLY* 3.0 23.0 + - - -
719A PHE* 3.8 27.3 - - + -
723A SER* 3.9 32.8 - - - +
726A ALA* 5.3 4.5 - - + -
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Residues in contact with VAL 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.7 15.5 - - + -
691A ILE* 3.0 18.3 + - + +
692A PRO* 3.3 20.9 - - + +
694A LEU* 1.3 73.7 - - - +
696A SER* 1.3 60.1 + - - +
698A GLY* 3.9 2.1 - - - +
699A LEU* 3.0 31.0 + - + +
----------------------------------------------------------
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Residues in contact with SER 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 5.4 7.6 - - - -
29A VAL* 5.8 4.5 - - - +
32A PRO* 4.4 24.1 - - - +
36A PHE* 5.6 0.5 - - - -
648A TRP* 3.2 24.8 + - - -
692A PRO 3.0 13.2 + - - -
693A LEU* 2.4 28.9 + - - +
695A VAL* 1.3 80.0 - - - +
697A ALA* 1.3 55.2 + - - +
699A LEU* 3.4 9.3 + - - +
700A LEU* 2.9 25.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TRP* 4.1 11.2 - - + -
693A LEU 2.9 14.0 + - - +
694A LEU* 3.1 13.4 + - + +
696A SER* 1.3 75.0 + - - +
698A GLY* 1.3 59.3 + - - +
700A LEU* 3.0 7.5 + - - +
701A VAL* 3.0 29.3 + - - +
719A PHE* 4.2 9.6 - - + -
722A LEU* 3.9 37.9 - - + +
726A ALA* 5.6 0.9 - - + -
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Residues in contact with GLY 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LEU 3.0 12.4 + - - -
695A VAL* 3.5 3.1 + - - -
697A ALA* 1.3 75.8 - - - +
699A LEU* 1.3 56.8 + - - +
701A VAL* 3.2 5.0 + - - +
702A VAL* 3.0 33.8 + - - +
719A PHE* 3.5 24.1 - - - -
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Residues in contact with LEU 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.0 4.9 - - + +
32A PRO* 4.8 11.2 - - + +
33A LEU* 3.7 52.0 - - + +
36A PHE* 5.5 1.8 - - + -
695A VAL* 3.0 18.8 + - + +
696A SER* 3.7 8.3 - - - +
697A ALA 3.2 0.2 - - - -
698A GLY* 1.3 75.2 - - - +
700A LEU* 1.3 60.8 + - - +
702A VAL* 3.8 8.0 - - + +
703A ILE* 3.0 32.3 + - + +
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.5 41.1 - - + -
640A MET* 5.5 5.4 - - - -
643A PHE* 6.0 0.9 - - + -
644A MET* 3.8 23.6 - - + -
696A SER 2.9 14.1 + - - +
697A ALA* 3.0 9.4 + - - +
699A LEU* 1.3 74.9 - - - +
701A VAL* 1.3 55.9 + - + +
703A ILE* 3.7 11.4 - - + -
704A LEU* 2.7 71.3 + - + +
718A VAL* 5.9 0.4 - - + -
722A LEU* 3.6 24.9 - - + -
----------------------------------------------------------
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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
----------------------------------------------------------
697A ALA 3.0 13.9 + - - +
698A GLY* 3.2 8.7 + - - +
700A LEU* 1.3 78.6 - - + +
702A VAL* 1.3 60.6 + - + +
704A LEU* 3.5 5.3 - - - +
705A LYS* 3.0 31.7 + - + +
715A PRO* 3.4 31.6 - - + +
718A VAL* 3.9 13.7 - - + +
719A PHE* 3.6 38.8 - - + +
722A LEU* 4.8 4.7 - - + -
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Residues in contact with VAL 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A GLY 3.0 17.5 + - - +
699A LEU* 4.0 7.9 - - + +
700A LEU 3.3 0.2 - - - -
701A VAL* 1.3 79.5 - - + +
703A ILE* 1.3 61.7 + - + +
704A LEU 3.4 0.3 + - - -
706A LEU* 3.4 43.3 + - + +
707A GLY 4.0 0.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 6.3 2.0 - - + -
36A PHE* 4.0 27.1 - - + +
37A LEU* 3.7 33.7 - - + -
40A ILE* 4.4 14.4 - - + +
699A LEU* 3.0 21.6 + - + +
700A LEU* 3.3 31.2 - - + +
702A VAL* 1.3 79.6 - - + +
704A LEU* 1.3 57.5 + - + +
707A GLY* 3.3 27.9 - - - +
709A LEU* 5.3 1.6 - - + +
----------------------------------------------------------
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Residues in contact with LEU 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A MET* 4.7 9.6 - - + -
700A LEU* 2.7 45.5 + - + +
701A VAL* 3.1 4.7 + - - +
703A ILE* 1.3 78.7 - - + +
705A LYS* 1.3 65.2 + - - +
709A LEU* 3.4 29.2 + - + +
710A LEU* 3.2 65.6 + - + -
718A VAL* 4.1 29.8 - - + -
----------------------------------------------------------
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Residues in contact with LYS 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A VAL* 3.0 13.5 + - + +
702A VAL* 5.8 0.2 - - - -
704A LEU* 1.3 77.8 - - - +
706A LEU* 1.3 76.2 + - + +
707A GLY 3.2 1.4 + - - -
708A ASN* 3.3 12.6 + - - -
709A LEU 4.2 0.7 + - - -
710A LEU 4.0 15.7 + - - +
711A PRO* 3.6 32.2 - - + +
712A TYR 4.2 4.4 - - - +
713A SER 5.1 3.3 + - - +
715A PRO* 3.7 39.5 - - + +
718A VAL* 6.5 0.2 - - + -
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Residues in contact with LEU 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A VAL* 3.4 35.5 + - + +
705A LYS* 1.3 91.6 - - + +
707A GLY* 1.3 57.5 + - - +
708A ASN* 3.2 5.9 + - - +
----------------------------------------------------------
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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