Contacts of the helix formed by residues 50 - 78 (chain N) in PDB entry 1JY3
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 50 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N PRO* 1.3 75.3 - - - +
51N GLY* 1.3 64.7 + - - +
52N CYS* 3.2 13.0 + - - +
53N ARG* 3.1 19.4 + - - +
54N MET* 3.0 21.8 + - - +
68O ASP* 5.3 0.8 + - - -
83O CYS* 3.6 13.5 - - - +
22P THR* 4.5 0.2 - - - -
79R LEU 4.7 1.2 + - - -
81R VAL 4.1 8.9 + - - -
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Residues in contact with GLY 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N PRO 3.6 2.8 + - - -
50N SER* 1.3 73.9 + - - +
52N CYS* 1.3 57.5 + - - +
54N MET 3.4 0.6 + - - -
55N LYS* 3.0 28.6 + - - +
83O CYS* 3.9 10.1 - - - +
84O PRO* 3.6 24.9 - - - +
89O LEU* 3.8 18.1 - - - +
22P THR* 4.0 6.7 - - - +
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Residues in contact with CYS 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N SER* 3.1 5.8 + - - +
51N GLY* 1.3 72.8 - - - +
53N ARG* 1.3 65.5 + - - +
55N LYS 3.5 0.3 + - - -
56N GLY 3.1 10.2 + - - -
68O ASP* 3.5 10.7 - - + +
69O ALA 3.0 39.3 + - - +
71O GLY* 3.4 31.2 - - - -
81O VAL* 4.4 4.7 - - - -
83O CYS* 2.1 48.9 - - - +
84O PRO* 4.1 0.7 - - - -
36Q TRP* 4.5 6.1 - - + -
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Residues in contact with ARG 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N SER* 3.1 22.5 + - - +
52N CYS* 1.3 78.0 - - - +
54N MET* 1.3 67.7 + - - +
56N GLY 3.1 2.3 + - - -
57N LEU* 2.9 34.7 + - + +
66O PRO* 3.4 29.2 + - - +
67O PRO 3.2 15.8 + - - +
68O ASP* 2.9 41.3 + - - +
77R PRO 3.6 7.5 + - - -
78R ASP 2.8 43.3 + - - +
79R LEU* 4.3 9.2 - - - +
80R GLY* 3.6 14.3 - - - +
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Residues in contact with MET 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N PRO* 3.7 25.8 - - + -
50N SER 3.0 19.1 + - - +
51N GLY 3.9 3.8 - - - +
52N CYS 3.4 0.2 - - - -
53N ARG* 1.3 76.7 - - - +
55N LYS* 1.3 58.0 + - - +
57N LEU* 3.7 12.1 - - + +
58N ILE* 2.8 36.8 + - - +
89O LEU* 4.1 14.1 - - + -
22P THR* 4.0 23.8 - - + +
25P ILE* 4.2 11.4 - - + -
26P ALA* 3.6 32.5 - - + +
29P LEU* 4.0 23.8 - - + -
79R LEU* 4.0 11.4 - - + -
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Residues in contact with LYS 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N GLY 3.0 17.6 + - - +
52N CYS 3.8 4.3 - - - +
53N ARG 3.2 0.2 - - - -
54N MET* 1.3 76.9 - - - +
56N GLY* 1.3 64.1 + - - +
58N ILE* 4.4 3.1 - - + -
59N ASP* 2.7 56.2 + - - +
69O ALA* 3.9 11.7 - - + +
70O ASP* 3.0 41.5 + - + +
84O PRO* 4.4 6.7 - - + -
89O LEU* 3.7 20.1 - - + +
92O THR* 3.9 26.7 - - + +
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Residues in contact with GLY 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52N CYS 3.1 11.4 + - - -
53N ARG 3.1 0.2 + - - -
55N LYS* 1.3 79.2 - - - +
57N LEU* 1.3 55.7 + - - +
59N ASP* 3.4 4.2 + - - +
60N GLU* 3.0 28.8 + - - +
67O PRO* 3.5 35.7 - - - +
69O ALA* 4.1 12.3 - - - +
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Residues in contact with LEU 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N ARG* 2.9 27.4 + - + +
54N MET* 3.8 21.8 - - + +
56N GLY* 1.3 73.4 - - - +
58N ILE* 1.3 66.2 + - - +
60N GLU* 3.3 9.0 + - - +
61N VAL* 3.0 28.5 + - + +
64O ARG* 3.9 24.9 - - - +
67O PRO* 3.8 12.1 - - + +
29P LEU* 4.1 15.3 - - + -
78R ASP* 3.8 33.7 - - + +
79R LEU* 4.2 11.7 - - + -
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Residues in contact with ILE 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N MET* 2.8 22.1 + - - +
55N LYS* 3.7 4.5 - - + +
57N LEU* 1.3 74.8 - - - +
59N ASP* 1.3 65.2 + - - +
61N VAL* 3.3 4.5 + - - +
62N ASP* 3.0 21.3 + - - +
89O LEU* 3.9 24.5 - - + +
92O THR* 3.7 19.3 - - + -
93O LEU* 3.7 34.3 - - + -
96O GLN* 3.2 24.7 - - - +
25P ILE* 3.8 17.9 - - + -
29P LEU* 4.0 22.0 - - + -
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Residues in contact with ASP 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55N LYS* 2.7 53.4 + - - +
56N GLY* 3.8 5.2 - - - +
58N ILE* 1.3 79.1 - - - +
60N GLU* 1.3 58.2 + - - +
62N ASP* 3.3 5.7 + - - +
63N GLN* 3.0 31.2 + - - +
69O ALA* 4.8 5.8 - - + +
92O THR* 4.4 1.0 - - - +
96O GLN* 3.7 17.0 + - - -
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Residues in contact with GLU 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N GLY 3.0 17.0 + - - +
57N LEU* 3.6 14.5 - - - +
58N ILE 3.3 0.2 - - - -
59N ASP* 1.3 74.5 - - - +
61N VAL* 1.3 68.1 + - + +
63N GLN* 3.3 6.8 + - - +
64N ASP* 3.0 24.8 + - + +
64O ARG* 2.7 50.8 + - - +
67O PRO* 4.0 9.3 - - + +
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Residues in contact with VAL 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N LEU* 3.0 17.8 + - + +
58N ILE 3.3 7.8 + - - +
60N GLU* 1.3 81.7 - - + +
62N ASP* 1.3 62.0 + - - +
64N ASP* 3.3 5.9 + - - +
65N PHE* 3.0 53.3 + - + -
29P LEU* 4.2 18.4 - - + -
32P TYR* 4.3 14.4 - - + -
33P GLN* 3.7 26.0 - - + -
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Residues in contact with ASP 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58N ILE 3.0 9.5 + - - +
59N ASP* 3.3 7.6 + - - +
61N VAL* 1.3 79.1 - - - +
63N GLN* 1.3 62.0 + - - +
65N PHE* 4.0 3.5 - - - +
66N THR* 2.8 43.0 + - - -
96O GLN* 3.5 49.8 + - - +
100O ILE* 3.8 19.2 - - - +
32P TYR* 4.8 2.8 + - - -
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Residues in contact with GLN 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N ASP 3.0 17.8 + - - +
60N GLU* 3.7 6.7 - - - +
62N ASP* 1.3 78.0 + - - +
64N ASP* 1.3 66.2 + - - +
66N THR* 3.8 9.0 + - - +
67N SER* 3.0 27.6 + - - -
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Residues in contact with ASP 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60N GLU* 3.0 19.4 + - + +
61N VAL* 3.3 6.9 + - - +
63N GLN* 1.3 78.3 - - - +
65N PHE* 1.3 66.5 + - - +
67N SER* 3.3 5.7 + - - -
68N ARG* 3.0 64.9 + - - +
33P GLN* 5.0 2.6 - - - +
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Residues in contact with PHE 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N VAL* 3.0 37.8 + - + +
62N ASP* 4.0 1.8 - - - +
64N ASP* 1.3 83.6 - - - +
66N THR* 1.3 60.3 + - - +
68N ARG* 3.8 18.1 - - - +
69N ILE* 2.9 38.7 + - + +
100O ILE* 3.8 17.7 - - + -
32P TYR* 4.3 17.3 - + - -
33P GLN* 3.4 46.0 - - + -
36P VAL* 3.5 33.7 - - + -
37P ASP 4.1 3.6 - - - -
40P LEU* 3.5 18.2 - - + -
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Residues in contact with THR 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N ASP* 2.8 37.6 + - - -
63N GLN* 3.8 11.2 - - - +
65N PHE* 1.3 75.9 - - - +
67N SER* 1.3 58.3 + - - +
69N ILE* 3.4 8.2 + - - +
70N ASN* 3.0 46.9 + - - +
100O ILE* 4.4 5.6 - - - +
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Residues in contact with SER 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N GLN* 3.0 20.2 + - - -
64N ASP* 3.6 6.5 - - - -
65N PHE 3.3 0.2 - - - -
66N THR* 1.3 77.4 - - - +
68N ARG* 1.3 62.2 + - - +
70N ASN* 3.3 8.7 + - - +
71N LYS* 3.0 24.1 + - - +
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Residues in contact with ARG 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N ASP* 3.0 49.7 + - - +
65N PHE* 3.8 16.5 - - - +
67N SER* 1.3 75.7 - - - +
69N ILE* 1.3 65.7 + - - +
71N LYS* 3.4 7.9 + - + +
72N LEU* 3.2 29.2 + - - +
33P GLN* 5.0 1.0 + - - -
37P ASP* 2.9 33.5 + - - -
40P LEU* 3.4 32.2 - - + +
41P ARG* 3.8 3.6 - - - +
44P GLU* 2.9 42.8 + - - +
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Residues in contact with ILE 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65N PHE* 2.9 23.3 + - + +
66N THR* 3.8 4.7 - - - +
68N ARG* 1.3 74.3 - - - +
70N ASN* 1.3 65.5 + - - +
72N LEU* 3.2 10.4 + - - +
73N ARG* 3.0 57.3 + - - +
100O ILE* 3.9 33.2 - - + +
103O SER* 4.2 19.1 - - - -
104O ILE* 4.4 7.0 - - + -
107O LEU* 4.3 12.1 - - + +
40P LEU* 4.0 17.9 - - + -
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Residues in contact with ASN 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N THR* 3.0 39.3 + - - +
67N SER* 3.8 7.1 - - - +
68N ARG 3.3 0.2 - - - -
69N ILE* 1.3 79.0 - - - +
71N LYS* 1.3 56.6 + - - +
73N ARG* 3.3 29.3 + - - +
74N ASP* 2.9 38.6 + - - +
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Residues in contact with LYS 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67N SER* 3.0 17.9 + - - +
68N ARG* 3.7 8.3 - - + +
69N ILE 3.2 0.2 - - - -
70N ASN* 1.3 76.5 - - - +
72N LEU* 1.3 63.8 + - + +
74N ASP* 3.4 11.0 + - + +
75N SER* 3.2 22.2 + - - -
44P GLU* 6.1 0.9 - - - +
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Residues in contact with LEU 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68N ARG 3.2 18.6 + - - +
69N ILE 3.2 6.5 + - - +
71N LYS* 1.3 74.4 - - + +
73N ARG* 1.3 65.2 + - - +
75N SER* 2.9 26.4 + - - +
76N LEU* 3.1 22.0 + - + +
107O LEU* 4.0 22.7 - - + -
40P LEU* 3.7 26.7 - - + -
43P LEU* 3.9 39.0 - - + +
44P GLU* 4.1 20.6 - - + -
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Residues in contact with ARG 73 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N ILE* 3.0 32.2 + - - +
70N ASN* 3.5 26.8 + - - +
72N LEU* 1.3 77.4 - - - +
74N ASP* 1.3 59.0 + - - +
76N LEU 3.1 0.3 + - - -
77N PHE* 2.8 52.5 + - + +
78N ASN* 4.5 0.2 - - - +
103O SER* 3.0 35.0 + - - +
106O ASP* 5.8 1.4 + - - +
107O LEU* 4.1 17.8 - - + +
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Residues in contact with ASP 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N ASN* 2.9 25.4 + - - +
71N LYS* 3.6 9.7 - - + +
73N ARG* 1.3 77.2 - - - +
75N SER* 1.3 50.9 + - - +
78N ASN* 2.7 58.7 + - + +
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Residues in contact with SER 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71N LYS* 3.2 12.5 + - - -
72N LEU* 2.9 24.0 + - - +
73N ARG 3.1 0.2 - - - -
74N ASP* 1.3 79.7 - - - +
76N LEU* 1.3 66.2 + - - +
78N ASN 3.6 8.7 - - - +
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Residues in contact with LEU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72N LEU* 3.1 20.0 + - + +
75N SER* 1.3 86.6 - - - +
77N PHE* 1.3 77.2 + - + +
78N ASN 3.5 0.7 - - - -
107O LEU* 3.6 31.4 - - + -
110O THR* 3.6 20.2 - - - +
111O VAL* 4.4 23.6 - - + -
43P LEU* 6.3 0.2 - - + -
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Residues in contact with PHE 77 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73N ARG* 2.8 36.9 + - + +
76N LEU* 1.3 92.8 - - + +
78N ASN* 1.3 63.2 + - - +
107O LEU* 4.8 3.4 - - + -
110O THR* 3.7 33.4 - - + -
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Residues in contact with ASN 78 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N ASP* 2.7 45.4 + - - +
75N SER* 3.6 13.0 - - - +
76N LEU 3.5 0.9 + - - -
77N PHE* 1.3 82.0 + - - +
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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