Contacts of the helix formed by residues 13 - 42 (chain H) in PDB entry 5JKL
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 HIS 13 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ARG* 3.7 2.2 + - - -
11H ASN 3.9 2.8 + - - -
12H TYR* 1.3 76.5 - - - +
14H GLN* 1.3 74.7 + - + +
15H ASP* 3.0 50.3 + - - +
16H SER* 3.0 29.7 + - - +
17H GLU 3.1 9.2 + - - -
124H LYS* 3.6 39.1 + - + +
126H ASP* 4.8 1.2 + - - +
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Residues in contact with GLN 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASP* 3.2 25.9 + - - -
9H ARG* 3.6 16.6 - - - +
12H TYR 3.7 0.2 + - - -
13H HIS* 1.3 80.9 + - + +
15H ASP* 1.3 61.2 + - - +
17H GLU* 3.2 8.9 + - - +
18H GLU* 2.7 58.9 + - + +
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Residues in contact with ASP 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LYS* 5.6 6.6 + - - -
13H HIS* 3.0 31.0 + - - +
14H GLN* 1.3 81.0 - - - +
16H SER* 1.3 57.7 + - - +
18H GLU* 3.5 14.1 + - - +
19H ALA* 2.9 29.3 + - - +
22H ARG* 4.8 1.6 + - - -
120H LEU* 3.5 24.1 - - + +
124H LYS* 3.5 14.9 + - - -
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Residues in contact with SER 16 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H TYR* 4.2 12.1 - - - -
13H HIS* 3.0 23.8 + - - +
15H ASP* 1.3 74.3 - - - +
17H GLU* 1.3 60.7 + - - +
19H ALA* 3.3 2.4 + - - +
20H ILE* 2.9 34.0 + - - +
117H LEU* 4.5 0.8 - - - +
120H LEU* 4.0 14.6 - - - +
121H ALA* 4.7 2.8 - - - -
124H LYS* 4.2 14.9 - - - +
126H ASP* 4.6 3.5 + - - +
129H LEU* 3.9 24.9 - - - +
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Residues in contact with GLU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ARG* 2.9 32.8 + - - +
12H TYR* 3.7 21.7 - - + -
13H HIS 3.1 8.6 + - - +
14H GLN* 3.4 15.7 - - - +
16H SER* 1.3 76.9 - - - +
18H GLU* 1.3 65.4 + - + +
20H ILE 3.3 1.4 + - - -
21H ASN* 3.1 13.0 + - - +
73H GLN* 3.0 37.4 + - - +
78H GLY* 3.5 3.2 - - - -
79H ARG* 2.8 35.5 + - - +
81H PHE* 4.6 6.7 - - + -
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASP* 3.4 17.7 - - - +
14H GLN* 2.7 55.1 + - + +
15H ASP* 3.8 13.8 - - - +
17H GLU* 1.3 82.3 - - + +
19H ALA* 1.3 61.9 + - - +
21H ASN* 3.1 13.2 + - - +
22H ARG* 3.0 50.6 + - - +
81H PHE* 6.5 0.9 - - + -
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Residues in contact with ALA 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ASP 2.9 18.4 + - - +
16H SER 3.3 1.8 + - - +
18H GLU* 1.3 75.9 - - - +
20H ILE* 1.3 61.1 + - - +
22H ARG* 3.3 20.9 + - - +
23H GLN* 3.0 22.3 + - - +
117H LEU* 3.4 28.8 - - + +
120H LEU* 3.7 12.1 - - + -
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Residues in contact with ILE 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H TYR* 3.6 15.9 - - - +
16H SER 2.9 20.7 + - - +
17H GLU 3.7 4.5 - - - +
19H ALA* 1.3 71.7 - - - +
21H ASN* 1.3 61.5 + - - +
23H GLN* 3.1 4.6 + - - +
24H ILE* 2.9 37.2 + - + +
69H LEU* 3.8 43.5 - - + +
72H LEU* 4.2 6.7 - - + -
73H GLN* 3.6 21.3 - - + +
117H LEU* 3.9 20.4 - - + -
129H LEU* 3.9 26.7 - - + -
132H PHE* 5.0 2.0 - - + -
133H ILE* 5.5 0.9 - - + -
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Residues in contact with ASN 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 3.1 14.6 + - - +
18H GLU* 3.1 13.0 + - - +
20H ILE* 1.3 77.0 - - - +
22H ARG* 1.3 62.0 + - + +
24H ILE* 3.3 16.1 + - - +
25H ASN* 3.2 20.8 + - - +
73H GLN* 3.0 19.3 + - - +
79H ARG 2.9 21.6 + - - -
80H ILE* 3.4 16.8 - - - +
81H PHE* 3.4 42.2 + - + +
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Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 3.7 23.1 + - - +
86B GLN* 3.0 55.9 + - - +
87B LYS 5.2 3.4 + - - -
15H ASP 4.8 1.8 + - - -
18H GLU* 3.0 41.2 + - - +
19H ALA* 3.3 32.2 + - - +
21H ASN* 1.3 78.2 - - + +
23H GLN* 1.3 61.6 + - - +
25H ASN* 3.2 8.8 + - - +
26H LEU* 3.0 22.1 + - - +
83H GLN* 5.7 3.4 - - - +
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Residues in contact with GLN 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ALA 3.0 13.4 + - - +
20H ILE* 3.1 8.9 + - - +
22H ARG* 1.3 75.0 - - - +
24H ILE* 1.3 64.4 + - - +
26H LEU* 3.1 12.2 + - - +
27H GLU* 2.8 53.3 + - - +
69H LEU* 3.6 20.9 - - + -
110H VAL* 3.7 11.7 + - - +
113H SER* 2.7 34.3 + - - +
114H LEU* 3.6 24.3 - - + +
117H LEU* 3.9 20.0 - - + +
----------------------------------------------------------
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Residues in contact with ILE 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ILE* 2.9 24.7 + - + +
21H ASN* 3.5 25.8 - - - +
22H ARG 3.3 0.2 - - - -
23H GLN* 1.3 76.7 - - - +
25H ASN* 1.3 65.4 + - - +
27H GLU* 3.3 4.4 + - - +
28H LEU* 3.0 40.4 + - + +
66H ALA* 4.1 4.6 - - + +
69H LEU* 3.5 30.5 - - + +
70H MET* 3.8 41.3 - - + +
73H GLN* 4.8 2.9 - - + -
80H ILE* 4.9 4.7 - - + -
82H LEU* 4.2 16.2 - - + -
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Residues in contact with ASN 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 5.9 0.9 + - - -
32G TYR* 4.2 5.0 + - - -
21H ASN 3.2 9.4 + - - +
22H ARG* 3.2 10.5 + - - +
24H ILE* 1.3 80.7 - - - +
26H LEU* 1.3 59.8 + - - +
28H LEU* 3.2 8.2 + - - +
29H TYR* 2.9 30.5 + - - +
83H GLN* 3.5 30.3 + - + +
84H ASP 2.9 28.8 + - - +
85H ILE* 4.3 6.6 - - - +
86H GLN* 5.3 1.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ARG 3.0 13.4 + - - +
23H GLN* 3.1 17.7 + - - +
25H ASN* 1.3 79.6 + - - +
27H GLU* 1.3 56.5 + - - +
29H TYR* 3.3 23.9 + - + +
30H ALA* 2.8 28.6 + - - +
106H LEU* 5.5 1.6 - - + -
109H ASN* 4.5 4.9 - - + +
110H VAL* 4.0 27.1 - - + +
113H SER* 3.5 35.7 - - - +
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Residues in contact with GLU 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H GLN* 2.8 44.9 + - - +
24H ILE 3.8 3.6 - - - +
26H LEU* 1.3 74.4 - - - +
28H LEU* 1.3 57.6 + - - +
30H ALA* 3.3 5.9 + - - +
31H SER* 2.9 24.6 + - - -
62H GLU* 2.8 17.8 - - - +
65H HIS* 3.3 11.1 - - + +
66H ALA* 3.8 18.2 - - + +
69H LEU* 3.7 18.8 - - + -
110H VAL* 3.5 10.9 - - - +
114H LEU* 4.5 0.5 - - - +
137H TYR* 4.2 11.7 - - - -
201H FE 2.0 32.8 - - - -
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Residues in contact with LEU 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G TYR* 3.7 36.3 - - + +
35G LEU* 4.1 12.6 - - + -
24H ILE* 3.0 35.6 + - + +
25H ASN* 3.6 9.2 - - - +
27H GLU* 1.3 76.2 - - - +
29H TYR* 1.3 61.7 + - - +
31H SER* 3.3 8.9 + - - -
32H TYR* 3.0 22.0 + - - +
63H ARG* 4.0 26.5 - - - +
66H ALA* 3.6 20.9 - - + -
82H LEU* 4.9 0.9 - - + -
85H ILE* 3.9 23.1 - - + +
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Residues in contact with TYR 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H ASN* 2.9 18.2 + - - +
26H LEU* 3.4 27.1 - - + +
28H LEU* 1.3 73.6 - - - +
30H ALA* 1.3 69.5 + - - +
32H TYR* 3.1 4.3 + - - +
33H VAL* 2.9 48.0 + - + +
85H ILE* 3.9 11.1 - - + +
86H GLN* 3.3 41.5 - - + +
87H LYS 3.8 11.1 + - - -
88H PRO* 4.2 1.8 - - + -
89H ASP* 3.9 27.2 + - - -
106H LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H LEU 2.8 19.4 + - - +
27H GLU* 3.6 5.6 - - - +
29H TYR* 1.3 77.4 - - - +
31H SER* 1.3 64.2 + - - +
33H VAL* 3.2 2.7 + - - +
34H TYR* 3.0 27.8 + - + -
62H GLU* 4.0 23.1 - - + +
106H LEU* 4.0 29.4 - - + -
107H GLU* 5.7 0.9 - - - +
110H VAL* 4.5 9.4 - - + -
----------------------------------------------------------
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Residues in contact with SER 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ARG* 3.5 13.9 + - - -
27H GLU 2.9 13.9 + - - -
28H LEU* 3.4 14.8 - - - -
29H TYR 3.2 0.2 - - - -
30H ALA* 1.3 75.4 - - - +
32H TYR* 1.3 57.7 + - - +
35H LEU* 3.0 15.5 + - - +
59H SER* 2.7 53.7 + - - +
62H GLU* 3.5 13.8 - - - +
63H ARG* 3.9 13.4 + - - +
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Residues in contact with TYR 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ASN* 4.2 2.1 + - - -
28G LEU* 3.7 30.0 - - + +
63G ARG* 5.8 0.9 - - - +
82G LEU* 3.5 34.3 - - + +
83G GLN 2.6 31.7 + - - -
85G ILE* 3.6 28.3 - - + +
28H LEU 3.0 12.5 + - - +
29H TYR 3.1 9.6 + - - +
31H SER* 1.3 74.3 - - - +
33H VAL* 1.3 64.6 + - - +
35H LEU* 3.2 16.3 + - + +
36H SER* 2.9 22.7 + - - -
85H ILE* 3.9 8.7 - - + -
86H GLN 3.4 18.8 - - - +
87H LYS* 3.8 15.0 - - - -
88H PRO* 3.8 7.4 - - + -
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Residues in contact with VAL 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H TYR* 2.9 53.9 + - + +
30H ALA 3.2 5.6 + - - +
32H TYR* 1.3 75.6 - - - +
34H TYR* 1.3 66.0 + - - +
36H SER* 3.3 4.3 + - - -
37H MET* 3.0 46.1 + - + +
88H PRO* 3.8 15.5 - - + -
89H ASP 5.5 0.2 - - - +
93H TRP* 4.2 13.0 - - + -
106H LEU* 4.0 22.9 - - + -
----------------------------------------------------------
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Residues in contact with TYR 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ALA 3.0 23.2 + - - +
33H VAL* 1.3 77.3 - - - +
35H LEU* 1.3 58.0 + - - +
37H MET* 3.3 8.2 + - - -
38H SER* 2.9 28.8 + - - -
55H PHE* 3.5 49.9 - + - +
58H GLN* 3.7 27.4 + - + +
59H SER* 3.7 8.7 - - - +
62H GLU* 3.8 21.8 - - + -
103H ALA* 3.9 23.1 + - + +
106H LEU* 4.2 16.4 - - + -
107H GLU* 2.4 44.6 + - - +
148H LEU* 4.0 6.0 - - + +
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Residues in contact with LEU 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G LEU* 4.1 21.8 - - + -
63G ARG* 3.7 30.1 - - - +
67G GLU* 3.9 7.2 - - + +
70G MET* 3.9 24.0 - - + +
31H SER 3.0 17.8 + - - +
32H TYR* 3.2 22.6 + - + +
34H TYR* 1.3 75.8 - - - +
36H SER* 1.3 64.1 + - - +
38H SER* 3.2 5.7 + - - -
39H TYR* 3.2 54.5 + - + +
56H LEU* 3.8 7.6 - - + -
59H SER* 3.7 8.7 + - - +
----------------------------------------------------------
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Residues in contact with SER 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G MET* 4.9 3.4 - - - -
80G ILE* 6.3 0.4 - - - -
82G LEU* 3.5 29.4 - - - +
32H TYR 2.9 10.7 + - - -
33H VAL 3.5 8.3 - - - -
35H LEU* 1.3 78.2 - - - +
37H MET* 1.3 61.5 + - - +
39H TYR* 3.4 1.4 + - - +
40H TYR* 3.0 22.7 + - - +
88H PRO* 3.8 12.1 - - - +
90H GLU 3.9 8.0 + - - -
91H ASP* 4.6 5.4 + - - +
93H TRP* 2.9 20.1 + - - -
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Residues in contact with MET 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H VAL* 3.0 31.0 + - + +
34H TYR* 3.8 15.7 - - - +
35H LEU 3.3 0.2 - - - -
36H SER* 1.3 74.6 - - - +
38H SER* 1.3 64.9 + - - +
40H TYR* 3.1 9.2 + - - +
41H PHE* 3.1 24.0 + - + -
55H PHE* 3.9 34.8 - - + -
93H TRP* 3.7 49.6 - - + -
99H ALA* 3.6 29.6 - - + +
102H GLU* 3.8 12.3 - - + -
103H ALA* 3.9 8.3 - - - +
----------------------------------------------------------
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Residues in contact with SER 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H TYR 2.9 18.2 + - - -
35H LEU 3.2 6.5 + - - -
37H MET* 1.3 75.4 - - - +
39H TYR* 1.3 67.0 + - - +
41H PHE 3.1 15.9 + - - -
42H ASP* 3.3 1.4 + - - -
52H ALA* 2.7 46.8 + - - +
55H PHE* 3.7 7.3 - - - +
56H LEU* 3.4 27.4 - - - +
----------------------------------------------------------
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Residues in contact with TYR 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G GLU* 3.4 30.7 + - + +
70G MET* 3.5 36.1 - - + -
71G LYS* 3.7 23.4 - - + +
74G ASN* 2.9 24.8 + - - -
80G ILE* 3.5 21.7 - - + +
35H LEU* 3.2 34.4 + - + +
36H SER 4.4 1.3 - - - +
38H SER* 1.3 79.2 - - - +
40H TYR* 1.3 65.2 + - - +
42H ASP* 3.4 26.9 + - + -
43H ARG* 3.4 3.6 + - - +
56H LEU* 4.1 23.2 - - + +
----------------------------------------------------------
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Residues in contact with TYR 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H SER 3.0 14.4 + - - +
37H MET 3.1 7.6 + - - +
39H TYR* 1.3 77.0 - - - +
41H PHE* 1.3 91.3 + + - +
42H ASP 3.2 0.2 - - - -
43H ARG* 3.1 50.3 + - - +
46H VAL* 3.4 31.4 - - + +
91H ASP 4.4 4.3 - - - +
92H ASP* 3.5 27.3 + - - -
93H TRP* 3.6 25.4 - - + -
94H GLU* 3.2 38.4 + - - -
95H SER* 4.2 3.0 - - - -
157I LYS* 5.9 0.5 + - - -
----------------------------------------------------------
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Residues in contact with PHE 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H MET* 3.1 23.5 + - + -
38H SER 3.1 9.1 + - - +
40H TYR* 1.3 96.8 - + - +
42H ASP* 1.3 57.1 + - - +
43H ARG 3.4 0.4 - - - -
46H VAL* 3.6 17.9 - - + -
47H ALA* 3.3 8.0 + - - -
48H LEU* 2.9 53.3 + - + +
49H LYS* 5.0 0.3 - - - -
51H PHE* 3.5 17.0 - + + -
52H ALA* 3.7 9.6 - - - +
55H PHE* 3.7 21.5 - + - -
93H TRP* 4.9 0.2 - - + -
95H SER* 3.6 10.1 - - - -
96H GLY* 3.6 37.0 - - - -
99H ALA* 3.6 20.4 - - + -
----------------------------------------------------------
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Residues in contact with ASP 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LYS* 4.2 17.4 + - - +
74G ASN* 3.0 32.8 + - - +
38H SER 3.3 9.8 + - - +
39H TYR* 3.6 24.6 - - + +
40H TYR 3.2 0.6 - - - -
41H PHE* 1.3 75.1 - - - +
43H ARG* 1.3 59.4 + - - +
47H ALA* 5.3 0.9 - - - +
49H LYS* 6.2 0.7 - - - +
52H ALA* 4.4 9.5 - - + +
146I LYS* 2.8 38.0 + - - +
----------------------------------------------------------
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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