Contacts of the helix formed by residues 63 - 93 (chain A) in PDB entry 1J5N
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 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP 4.4 1.2 + - - -
60A LYS* 3.8 10.0 + - - +
61A ALA 3.6 3.6 + - - -
62A LEU* 1.3 91.0 + - - +
64A PRO* 1.3 85.8 - - + +
65A GLU* 3.6 17.0 - - + +
66A GLU* 2.7 27.2 + - - +
67A LYS* 3.0 14.9 + - - +
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Residues in contact with PRO 64 (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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60A LYS 5.6 1.3 - - - +
63A THR* 1.3 91.6 - - + +
65A GLU* 1.3 61.3 + - - +
67A LYS* 2.9 41.0 + - + +
68A GLN* 3.0 13.1 + - - +
71A GLU* 3.9 5.8 - - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.1 10.2 - - + +
64A PRO* 1.3 82.4 - - - +
66A GLU* 1.3 73.4 + - - +
68A GLN* 2.8 48.1 + - + +
69A PRO* 3.4 2.3 - - - +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.1 59.5 - - + +
63A THR* 2.7 15.3 + - - +
65A GLU* 1.3 88.2 - - - +
67A LYS* 1.3 49.1 + - - -
69A PRO* 3.0 12.6 - - - +
70A TYR* 2.7 31.9 + - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 3.4 48.1 - - + +
60A LYS* 5.4 6.2 - - + +
62A LEU* 5.2 0.2 - - + -
63A THR 3.1 18.6 - - - +
64A PRO* 2.9 25.0 + - + +
66A GLU* 1.3 75.5 - - + +
68A GLN* 1.3 66.0 + - - +
69A PRO* 3.0 4.3 - - - -
70A TYR* 2.7 13.4 + - - -
71A GLU* 2.7 57.9 + - + +
123C A 5.2 8.7 + - - -
124C T 4.5 6.9 + - - -
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO 3.0 8.9 + - - +
65A GLU* 2.8 45.5 + - - +
67A LYS* 1.3 73.8 - - - +
69A PRO* 1.3 60.0 - - + +
71A GLU* 4.6 3.1 - - - -
72A ALA* 2.5 41.9 + - + +
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Residues in contact with PRO 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 6.1 0.9 - - - +
65A GLU 3.4 4.0 - - - +
66A GLU* 3.0 21.8 - - - +
67A LYS 3.0 0.7 - - - -
68A GLN* 1.3 97.6 - - + +
70A TYR* 1.3 72.7 + - + +
72A ALA* 4.1 1.1 - - + +
73A LYS* 3.0 28.6 + - - +
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA 3.7 4.0 - - - +
30A PHE* 3.6 12.1 - - + -
31A PHE* 3.2 57.8 - + + +
34A GLU* 4.2 21.1 - - + -
35A ASN* 4.8 1.0 + - - -
59A TRP* 3.2 27.4 - + - -
62A LEU* 4.4 10.3 - - + +
66A GLU* 2.7 29.2 + - - +
67A LYS* 2.7 17.6 + - - -
69A PRO* 1.3 80.4 - - + +
71A GLU* 1.3 50.7 + - - +
72A ALA 3.0 1.6 - - - -
73A LYS* 2.4 34.1 + - - +
74A ALA* 2.5 16.5 + - - -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 3.5 19.3 - - + +
64A PRO* 3.9 8.5 - - - +
67A LYS* 2.7 59.6 + - + +
68A GLN* 4.4 2.3 + - - +
70A TYR* 1.3 72.7 - - - +
72A ALA* 1.3 53.1 + - - +
74A ALA* 2.6 30.2 + - + +
75A GLN* 3.2 21.8 + - - +
124C T 3.9 21.7 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 2.5 27.5 + - + +
69A PRO* 4.1 1.3 - - + +
71A GLU* 1.3 72.0 - - - +
73A LYS* 1.3 58.3 + - - +
74A ALA 2.9 9.6 + - - -
75A GLN* 3.0 30.0 + - - +
76A ALA* 3.0 11.9 + - - +
79A LYS* 5.6 0.2 + - - -
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Residues in contact with LYS 73 (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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30A PHE* 3.8 29.7 - - + -
69A PRO 3.0 20.3 + - - +
70A TYR* 2.4 26.9 + - - +
72A ALA* 1.3 69.2 - - - +
74A ALA* 1.3 54.7 + - - -
76A ALA* 3.4 18.0 - - + +
77A ASP* 3.0 30.6 + - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 5.0 0.9 - - - +
25A LEU 5.1 2.7 - - - +
26A SER* 4.2 0.7 - - - -
27A ALA* 3.7 15.0 - - + +
30A PHE* 2.9 26.4 - - + -
70A TYR 2.5 8.0 + - - +
71A GLU* 2.6 22.1 + - + +
73A LYS* 1.3 72.1 - - - +
75A GLN* 1.3 50.9 + - + +
76A ALA 3.1 1.1 - - - -
77A ASP* 3.1 3.5 + - - +
78A LYS* 2.7 35.9 + - - +
124C T 4.8 2.5 - - - +
125C C 4.3 15.0 - - - +
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.5 32.6 + - - +
72A ALA* 3.0 18.8 + - - +
74A ALA* 1.3 76.4 - - - +
76A ALA* 1.3 58.8 + - - +
78A LYS* 3.2 10.8 - - - +
79A LYS* 3.0 47.4 + - - +
125C C 4.7 15.9 - - - +
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 3.0 11.3 + - - +
73A LYS* 3.4 25.6 - - + +
75A GLN* 1.3 79.3 - - - +
77A ASP* 1.3 57.6 + - - +
79A LYS* 3.4 15.0 + - - +
80A ARG* 3.1 23.4 + - - +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 2.9 19.3 - - - +
25A LEU* 3.0 41.1 + - - +
30A PHE* 3.4 29.0 - - + -
73A LYS* 3.0 13.3 + - - +
74A ALA 3.1 0.4 + - - +
76A ALA* 1.3 73.5 - - - +
78A LYS* 1.3 65.2 + - - +
80A ARG* 3.1 29.3 - - - +
81A TYR* 3.2 4.2 + - - +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.3 13.2 - - + +
74A ALA 2.7 14.3 + - - +
75A GLN* 3.2 16.8 - - + +
77A ASP* 1.3 76.0 - - - +
79A LYS* 1.3 62.5 + - - +
81A TYR* 3.2 10.7 - - + -
82A GLU* 2.9 57.6 + - - +
85A LYS* 4.4 3.8 - - - +
125C C 3.2 20.6 - - - +
126C A 2.5 59.4 + - - +
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Residues in contact with LYS 79 (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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75A GLN* 3.0 41.0 + - - +
76A ALA* 3.8 10.6 - - - +
78A LYS* 1.3 78.5 - - + +
80A ARG* 1.3 62.6 + - - +
82A GLU* 2.6 47.0 + - + +
83A SER* 3.0 10.1 + - - -
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 3.1 9.1 + - - +
77A ASP* 3.1 32.8 - - - +
79A LYS* 1.3 77.0 - - - +
81A TYR* 1.3 63.8 + - + +
83A SER* 2.9 29.5 + - - -
84A GLU* 4.0 9.3 + - - +
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 3.3 25.7 - - + +
23A ARG* 2.5 63.9 + - - +
24A ALA* 4.1 2.9 - - + -
77A ASP* 3.2 6.9 + - - +
78A LYS* 3.2 12.6 - - - +
79A LYS 3.2 0.4 - - - -
80A ARG* 1.3 77.5 - - + +
82A GLU* 1.3 70.0 + - - +
83A SER 2.6 7.1 + - - -
84A GLU* 2.6 57.8 + - - +
85A LYS* 2.9 33.9 + - + +
126C A 3.3 39.3 + - - -
127C C 3.8 11.6 - - - -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 2.9 25.1 + - - +
79A LYS* 2.6 33.4 + - - +
81A TYR* 1.3 84.2 - - - +
83A SER* 1.3 57.5 + - - -
85A LYS* 3.1 27.6 - - - +
86A GLU* 3.0 37.8 + - + +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS 3.0 7.2 + - - -
80A ARG* 2.9 33.1 + - - -
81A TYR 2.6 4.8 + - - -
82A GLU* 1.3 74.3 + - - +
84A GLU* 1.3 60.6 + - - -
85A LYS 3.0 4.0 - - - -
86A GLU* 2.9 34.6 - - - +
87A LEU* 3.1 8.8 + - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 5.1 1.2 - - - +
21A PRO* 2.7 43.9 - - + +
23A ARG 3.6 1.7 - - - +
80A ARG* 4.0 11.9 + - - +
81A TYR* 2.6 53.1 + - - +
83A SER* 1.3 75.0 - - - +
85A LYS* 1.3 54.0 + - - -
87A LEU* 3.4 15.1 - - + +
88A TYR* 2.9 27.3 + - - +
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 3.8 5.6 - - + -
78A LYS* 4.4 2.2 - - - +
81A TYR* 2.9 40.4 + - + +
82A GLU* 3.1 30.5 - - - +
84A GLU* 1.3 76.9 - - - +
86A GLU* 1.3 74.5 + - - +
87A LEU 3.0 1.3 - - - -
88A TYR* 2.9 26.9 + - + +
89A ASN* 3.0 13.4 + - - +
126C A 2.8 28.6 + - - +
127C C 2.9 29.2 + - - +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.0 17.9 + - + +
83A SER* 2.9 35.3 - - - +
85A LYS* 1.3 86.9 - - + +
87A LEU* 1.3 58.8 + - + +
89A ASN* 2.7 24.9 + - - +
90A ALA* 3.0 17.7 + - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 4.9 6.7 - - + -
83A SER 3.1 9.1 + - - +
84A GLU* 3.4 19.3 - - + +
85A LYS 3.0 0.4 - - - -
86A GLU* 1.3 82.0 - - + +
88A TYR* 1.3 76.2 + - - +
89A ASN 2.9 2.2 - - - -
90A ALA* 2.5 30.7 + - + +
91A THR* 2.6 35.5 + - + +
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 2.5 36.4 + - - -
18A PRO* 3.1 22.8 - - + +
19A ASN* 2.3 47.6 - - + +
20A ALA 3.2 15.9 - - - -
21A PRO* 3.2 23.1 - - + -
84A GLU 2.9 21.0 + - - +
85A LYS* 3.0 18.2 - - + +
87A LEU* 1.3 74.7 - - - +
89A ASN* 1.3 55.6 + - + -
92A LEU* 2.6 49.1 + - + +
127C C 5.3 9.6 - - - -
128C C 4.5 15.9 - - - -
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 3.0 20.8 + - - +
86A GLU* 2.7 26.6 + - - +
87A LEU 2.7 2.6 + - - -
88A TYR* 1.3 80.3 - - + +
90A ALA* 1.3 61.4 + - - +
91A THR 3.0 9.2 + - - -
92A LEU* 3.9 10.1 - - + -
93A ALA* 2.5 37.8 + - + +
127C C 5.8 0.6 + - - -
128C C 5.7 3.8 - - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 3.0 19.7 + - + +
87A LEU* 2.5 17.9 + - + +
89A ASN* 1.3 79.8 + - - +
91A THR* 1.3 55.8 + - - +
93A ALA* 4.6 3.8 - - - -
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 2.7 34.1 - - - +
87A LEU* 2.6 40.2 + - + +
89A ASN 3.0 1.0 - - - -
90A ALA* 1.3 76.2 + - - +
92A LEU* 1.3 63.6 + - - +
93A ALA* 3.3 3.8 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 2.9 44.4 - - + +
19A ASN* 3.1 6.1 - - - +
88A TYR* 2.6 55.3 + - + +
89A ASN* 3.9 5.2 - - + -
91A THR* 1.3 82.3 - - - +
93A ALA* 1.3 76.0 + - + +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASN* 2.5 27.7 + - + +
90A ALA* 4.6 2.8 - - - -
91A THR 3.3 4.7 + - - +
92A LEU* 1.3 99.7 - - + +
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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