Contacts of the helix formed by residues 11 - 43 (chain A) in PDB entry 1O9R
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 PRO 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP 3.2 7.4 - - - +
10A LEU* 1.3 98.2 - - + +
12A SER* 1.3 66.2 + - - +
13A ASN* 4.5 2.9 - - + +
14A ALA* 3.0 16.9 + - + +
15A LYS* 2.8 19.8 + - - +
132A GLY 5.6 0.2 - - - +
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Residues in contact with SER 12 (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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10A LEU 3.4 3.1 + - - -
11A PRO* 1.3 72.0 - - - +
13A ASN* 1.3 67.0 + - - +
15A LYS* 3.3 15.4 + - - +
16A SER* 3.0 23.7 + - - -
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Residues in contact with ASN 13 (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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11A PRO* 3.3 3.8 - - + +
12A SER* 1.3 80.2 - - - +
14A ALA* 1.3 57.4 + - - +
16A SER* 3.4 7.7 + - - -
17A THR* 3.1 33.0 + - - +
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Residues in contact with ALA 14 (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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10A LEU* 3.8 23.6 - - + -
11A PRO* 3.0 18.9 + - + +
13A ASN* 1.3 76.3 - - - +
15A LYS* 1.3 66.4 + - - +
17A THR* 3.3 5.8 + - - -
18A VAL* 2.9 28.8 + - - +
131A ALA* 3.3 31.2 - - + +
133A ASP* 5.4 0.2 - - + -
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Residues in contact with LYS 15 (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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6A THR* 4.0 15.9 + - + +
8A ASN* 2.7 38.8 + - - +
9A ASP 4.2 0.6 - - - -
10A LEU* 2.7 39.9 + - + +
11A PRO 2.8 16.1 + - - +
12A SER* 3.3 16.7 + - - +
14A ALA* 1.3 77.1 - - - +
16A SER* 1.3 57.9 + - - +
18A VAL* 3.8 0.3 - - - +
19A ILE* 2.9 38.9 + - + +
76A LEU* 3.4 37.7 - - + +
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Residues in contact with SER 16 (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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12A SER 3.0 16.2 + - - -
13A ASN* 3.7 8.1 - - - -
15A LYS* 1.3 77.8 - - - +
17A THR* 1.3 62.9 + - - +
19A ILE* 3.5 9.4 + - - +
20A GLY* 3.2 18.0 + - - -
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Residues in contact with THR 17 (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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13A ASN* 3.1 18.4 + - - +
14A ALA* 3.7 5.3 - - - -
16A SER* 1.3 76.4 - - - +
18A VAL* 1.3 64.1 + - - +
20A GLY* 3.2 4.0 + - - -
21A ILE* 3.2 37.4 + - + +
127A ASP* 5.1 1.8 - - + +
131A ALA* 4.2 18.2 - - + -
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Residues in contact with VAL 18 (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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14A ALA 2.9 20.8 + - - +
15A LYS 4.2 1.1 - - - +
17A THR* 1.3 75.9 - - - +
19A ILE* 1.3 65.1 + - - +
21A ILE* 3.1 9.2 + - + +
22A LEU* 2.9 33.5 + - + +
76A LEU* 4.0 6.1 - - + -
128A SER* 4.4 12.6 - - - +
131A ALA* 3.8 24.0 - - + -
133A ASP* 3.6 21.8 - - + +
136A THR* 3.4 37.9 - - + +
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Residues in contact with ILE 19 (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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15A LYS* 2.9 25.7 + - + +
16A SER* 3.8 7.2 - - - +
18A VAL* 1.3 74.5 - - - +
20A GLY* 1.4 58.8 + - - +
22A LEU* 3.7 7.0 - - - +
23A ASN* 2.9 46.5 + - - +
73A VAL* 4.1 19.7 - - + +
76A LEU* 3.9 27.6 - - + +
77A GLY 4.5 0.9 - - - -
78A GLY* 3.7 29.8 - - - +
79A THR 5.2 0.7 - - - +
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Residues in contact with GLY 20 (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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16A SER 3.2 10.0 + - - -
17A THR 3.2 7.5 + - - -
18A VAL 3.2 1.0 - - - -
19A ILE* 1.4 76.5 - - - +
21A ILE* 1.3 57.1 + - - +
23A ASN* 4.0 3.0 - - - +
24A GLU* 3.0 31.8 + - - +
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Residues in contact with ILE 21 (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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17A THR* 3.2 30.6 + - + +
18A VAL* 3.1 12.5 + - - +
20A GLY* 1.3 75.5 - - - +
22A LEU* 1.3 63.8 + - - +
24A GLU* 3.7 10.9 - - - +
25A SER* 3.0 28.9 + - - +
124A ALA* 3.7 31.9 - - + -
127A ASP* 3.6 39.5 - - + +
128A SER* 4.1 6.1 - - - +
140A PHE* 3.7 12.3 - - + -
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Residues in contact with LEU 22 (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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18A VAL* 2.9 41.0 + - + +
19A ILE* 3.7 2.5 - - - +
21A ILE* 1.3 73.8 - - - +
23A ASN* 1.4 61.3 + - - +
25A SER* 3.2 1.7 + - - -
26A LEU* 2.8 25.5 + - - +
69A ILE* 3.3 38.3 - - + +
72A ARG* 3.7 26.0 - - + +
73A VAL* 3.4 30.1 - - + +
76A LEU* 4.4 2.9 - - + -
136A THR* 4.0 6.5 - - + -
139A ILE* 5.2 2.5 - - + -
140A PHE* 3.6 27.4 - - + -
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Residues in contact with ASN 23 (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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19A ILE* 2.9 27.7 + - - +
20A GLY* 4.3 3.6 - - - +
22A LEU* 1.4 73.8 - - - +
24A GLU* 1.3 63.6 + - - +
26A LEU* 3.4 9.9 + - - +
27A ALA* 3.3 21.8 + - - +
73A VAL* 3.8 16.2 - - - +
79A THR 2.9 22.8 + - - -
80A ALA* 3.6 5.2 - - - -
81A LEU* 3.0 49.0 + - + +
90A THR* 4.2 4.4 - - + +
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Residues in contact with GLU 24 (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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20A GLY 3.0 20.3 + - - +
21A ILE* 3.7 10.9 - - - +
23A ASN* 1.3 77.0 - - - +
25A SER* 1.3 64.4 + - - +
27A ALA* 3.3 12.8 + - - +
28A SER* 3.5 12.5 + - - -
90A THR* 4.0 22.6 - - + +
92A LYS* 5.3 13.4 - - + +
120A MET* 4.5 15.6 - - - +
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Residues in contact with SER 25 (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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21A ILE* 3.0 18.8 + - - +
22A LEU 3.6 3.6 - - - -
24A GLU* 1.3 77.9 + - - +
26A LEU* 1.3 64.1 + - - +
28A SER* 3.2 3.8 + - - -
29A VAL* 3.0 27.7 + - - +
69A ILE* 4.5 3.6 - - - -
120A MET* 4.0 19.9 - - - +
121A ILE* 3.7 17.6 - - - +
124A ALA* 4.2 5.9 - - - +
140A PHE* 3.5 27.1 - - - -
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Residues in contact with LEU 26 (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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22A LEU 2.8 20.5 + - - +
23A ASN* 3.6 17.0 - - - +
24A GLU 3.3 0.2 - - - -
25A SER* 1.3 73.1 - - - +
27A ALA* 1.3 59.4 + - - +
29A VAL* 3.7 4.0 - - - +
30A ILE* 2.9 53.6 + - + +
66A GLY* 3.4 36.8 - - - +
69A ILE* 4.0 8.5 - - + +
70A ALA* 3.9 24.9 - - + +
81A LEU 3.6 30.3 - - - +
82A GLY* 4.2 4.5 - - - +
41B TRP* 4.4 6.1 - - + -
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Residues in contact with ALA 27 (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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23A ASN 3.3 5.4 + - - +
24A GLU 3.7 2.7 - - - +
25A SER 3.2 1.0 - - - -
26A LEU* 1.3 81.2 - - - +
28A SER* 1.3 57.4 + - - +
31A ASP* 3.0 24.1 + - - +
81A LEU 5.0 3.6 + - - +
86A ALA 4.3 0.7 - - - +
87A VAL* 3.4 31.2 - - + +
90A THR* 3.5 39.7 - - + -
91A THR* 3.8 11.0 - - - +
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Residues in contact with SER 28 (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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24A GLU 3.5 4.0 + - - -
25A SER 3.2 3.3 + - - -
27A ALA* 1.3 76.6 - - - +
29A VAL* 1.3 61.1 + - - +
31A ASP* 3.5 1.7 + - - +
32A LEU* 2.9 28.8 + - - +
90A THR 4.6 0.2 + - - -
91A THR* 3.8 8.3 - - - -
92A LYS* 3.0 37.2 + - - +
93A LEU* 3.8 7.0 + - - +
117A VAL* 4.0 12.0 - - - +
120A MET* 3.7 30.4 - - - +
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Residues in contact with VAL 29 (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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25A SER 3.0 23.1 + - - +
26A LEU* 3.7 6.5 - - - +
28A SER* 1.3 74.8 - - - +
30A ILE* 1.3 61.9 + - + +
32A LEU* 3.3 7.1 + - - +
33A ALA* 2.9 26.8 + - + +
62A LEU* 3.7 38.0 - - + +
65A HIS* 4.9 3.4 - - + -
66A GLY* 3.9 18.2 - - - +
69A ILE* 4.4 15.5 - - + -
117A VAL* 4.2 20.4 - - + -
121A ILE* 4.4 8.5 - - + -
147A LEU* 5.6 2.5 - - + -
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Residues in contact with ILE 30 (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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26A LEU* 2.9 41.7 + - + +
27A ALA 3.9 3.4 - - - +
29A VAL* 1.3 78.5 - - + +
31A ASP* 1.4 63.2 + - - +
33A ALA* 3.0 9.8 + - + +
34A LEU* 3.0 26.6 + - + +
66A GLY* 5.8 1.8 - - - -
82A GLY* 3.6 34.8 - - - +
87A VAL* 3.8 18.6 - - + -
34B LEU* 3.7 28.9 - - + -
41B TRP* 4.5 9.2 - - + -
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Residues in contact with ASP 31 (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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27A ALA 3.0 18.3 + - - +
28A SER 3.8 3.1 - - - +
29A VAL 3.3 0.2 - - - -
30A ILE* 1.4 76.0 - - - +
32A LEU* 1.4 58.8 + - - +
34A LEU* 3.0 9.5 + - - +
35A VAL* 2.8 39.0 + - - +
87A VAL* 4.1 8.3 - - + +
91A THR* 2.6 35.6 + - - +
93A LEU* 3.4 21.4 - - + +
94A LYS 5.3 1.0 - - - +
84B LEU* 3.7 23.9 + - - +
85B GLN* 5.0 3.6 + - - +
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Residues in contact with LEU 32 (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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28A SER 2.9 19.7 + - - +
29A VAL* 3.6 6.3 - - - +
31A ASP* 1.4 75.8 - - - +
33A ALA* 1.3 53.9 + - - +
35A VAL* 3.3 9.7 + - + +
36A THR* 2.8 37.5 + - - -
62A LEU* 3.9 21.3 - - + -
93A LEU* 3.9 6.4 - - + +
113A ARG* 3.6 35.9 - - + +
114A TYR* 3.8 45.5 - - + -
117A VAL* 3.9 23.8 - - + -
147A LEU* 4.2 1.6 - - + -
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Residues in contact with ALA 33 (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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29A VAL* 2.9 13.7 + - + +
30A ILE* 3.0 12.8 + - + +
32A LEU* 1.3 77.9 - - - +
34A LEU* 1.3 60.7 + - + +
36A THR* 3.4 8.5 + - - -
37A LYS 3.4 5.9 + - - -
59A ARG* 3.0 48.7 + - - +
62A LEU* 3.8 19.0 - - + +
63A ASP* 4.3 4.7 - - - +
59B ARG* 6.2 0.2 - - - +
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Residues in contact with LEU 34 (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 ILE* 3.0 27.3 + - + +
31A ASP* 3.5 8.7 - - - +
33A ALA* 1.3 73.1 - - + +
35A VAL* 1.3 65.6 + - - +
37A LYS* 3.3 4.0 + - - +
38A GLN* 3.0 23.4 + - - +
41A TRP* 5.4 0.3 - - - -
59A ARG* 4.1 17.7 - - - +
30B ILE* 3.8 30.1 - - + -
34B LEU* 4.7 18.6 - - + -
82B GLY 4.0 17.7 - - - +
83B SER* 5.1 1.3 - - - -
84B LEU* 3.9 43.5 - - + +
87B VAL* 5.3 1.8 - - + -
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Residues in contact with VAL 35 (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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31A ASP* 2.8 29.7 + - - +
32A LEU* 3.4 20.4 - - + +
34A LEU* 1.3 77.7 - - + +
36A THR* 1.4 62.5 + - - +
38A GLN* 3.2 7.9 + - - +
39A ALA* 3.0 23.9 + - - +
93A LEU* 4.8 1.1 - - + -
94A LYS 5.6 1.3 - - - +
96A TYR* 3.6 42.4 - - + +
110A LEU* 3.7 18.2 - - + -
113A ARG* 4.2 17.0 - - - +
83B SER* 5.8 3.4 - - - +
84B LEU 6.1 0.4 - - - +
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Residues in contact with THR 36 (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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32A LEU 2.8 20.8 + - - -
33A ALA* 3.5 8.3 - - - -
34A LEU 3.2 0.2 - - - -
35A VAL* 1.4 79.6 - - - +
37A LYS* 1.3 58.0 - - + +
39A ALA* 3.5 2.8 + - - +
40A HIS* 3.0 27.1 + - - +
55A LEU* 3.1 42.0 - - + +
58A PHE* 4.2 0.7 - - + -
59A ARG* 4.0 13.2 - - + +
62A LEU* 3.6 3.1 - - - +
110A LEU* 4.4 6.7 - - - -
114A TYR* 2.8 33.9 + - - +
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Residues in contact with LYS 37 (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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33A ALA 3.4 1.2 + - - -
34A LEU* 3.3 4.8 + - - +
35A VAL 3.3 0.2 - - - -
36A THR* 1.3 76.4 - - - +
38A GLN* 1.3 66.8 + - - +
40A HIS* 3.1 20.5 + - + +
41A TRP* 3.0 49.3 + - + -
55A LEU 6.0 0.4 - - - +
56A ASP* 2.6 36.5 + - - +
59A ARG* 3.4 49.1 - - + +
67B ASP* 2.6 40.1 + - - +
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Residues in contact with GLN 38 (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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34A LEU 3.0 18.7 + - - +
35A VAL* 3.4 9.9 - - - +
37A LYS* 1.3 76.2 - - - +
39A ALA* 1.3 61.0 + - - +
41A TRP* 3.7 7.5 + - - -
42A ASN* 3.0 36.0 + - - +
96A TYR* 3.7 25.1 - - + -
97A PRO 5.1 0.7 - - - +
98A THR* 4.0 22.0 - - + +
106A HIS* 4.5 0.8 - - + -
79B THR* 4.7 0.7 - - - +
80B ALA 3.0 21.0 + - - +
81B LEU* 3.8 0.6 - - - -
82B GLY* 2.7 34.5 - - - +
83B SER* 3.2 20.7 - - - +
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Residues in contact with ALA 39 (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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35A VAL 3.0 15.2 + - - +
36A THR 3.8 3.8 - - - +
38A GLN* 1.3 73.9 - - - +
40A HIS* 1.3 65.8 + - - +
42A ASN 3.1 12.3 + - - -
43A LEU* 3.1 20.0 + - - +
55A LEU* 4.2 2.2 - - + -
96A TYR* 3.4 24.2 - - + +
106A HIS* 3.5 17.0 - - + +
110A LEU* 3.9 22.9 - - + -
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Residues in contact with HIS 40 (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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36A THR 3.0 18.7 + - - +
37A LYS* 3.5 17.6 + - + +
39A ALA* 1.3 77.3 - - - +
41A TRP* 1.3 86.6 + + - +
43A LEU* 3.7 11.9 + - - +
48A PHE* 4.4 0.7 - - - -
52A HIS* 2.7 75.3 + + - -
55A LEU* 3.7 19.7 - - + +
56A ASP* 3.0 36.7 + - - -
1163B FE 3.6 14.6 - - - -
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Residues in contact with TRP 41 (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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34A LEU 5.4 0.2 - - - -
37A LYS* 3.0 47.6 + - + +
38A GLN* 3.8 10.8 - - - -
39A ALA 3.2 0.2 + - - -
40A HIS* 1.3 98.2 + + - +
42A ASN* 1.3 61.5 + - - +
43A LEU 3.5 2.3 + - - +
48A PHE* 5.1 0.2 - - - -
52A HIS* 4.6 3.6 - + - -
26B LEU* 4.5 4.7 - - + -
30B ILE* 4.5 16.6 - - + -
66B GLY 4.5 1.6 - - - -
67B ASP* 3.4 35.4 + - - +
70B ALA* 3.2 30.6 - - + +
71B GLU* 4.2 17.2 - - + +
74B VAL* 3.5 25.8 - - + +
80B ALA* 3.8 26.5 - - + -
82B GLY* 4.0 25.1 - - - -
152D TRP* 3.7 11.4 + + + -
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 3.0 32.6 + - - +
39A ALA 3.1 3.7 + - - -
41A TRP* 1.3 78.4 - - - +
43A LEU* 1.3 62.6 + - - +
44A LYS* 3.5 9.2 + - - +
100A ILE 4.5 5.2 - - - +
101A TYR* 3.7 22.9 - - + -
106A HIS* 3.5 22.0 + - + +
74B VAL* 3.5 8.6 - - - +
78B GLY 4.4 0.9 - - - +
79B THR* 3.5 17.6 + - - +
80B ALA* 3.0 49.2 + - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA 3.1 22.3 + - - +
40A HIS 3.7 4.9 - - - +
41A TRP 3.5 2.8 - - - +
42A ASN* 1.3 77.2 - - - +
44A LYS* 1.3 69.2 + - - +
48A PHE* 3.3 31.0 - - + +
51A VAL* 3.7 20.9 - - + -
52A HIS* 3.5 40.8 - - + +
55A LEU* 4.1 10.5 - - + -
101A TYR 3.8 4.5 - - - -
103A ILE* 3.9 17.5 - - + -
106A HIS* 3.7 28.5 - - + -
110A LEU* 5.6 0.4 - - + -
152D TRP* 5.2 0.2 + - - -
156D ALA* 4.1 1.2 - - - +
----------------------------------------------------------
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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