Contacts of the helix formed by residues 7 - 43 (chain A) in PDB entry 2VRZ
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 7 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MSE 1.3 75.0 - - - +
8A PRO* 1.4 71.5 - - - +
9A GLU* 3.3 18.5 + - - +
10A GLU* 3.2 22.7 + - - +
11A ILE* 3.0 23.5 + - - +
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Residues in contact with PRO 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 1.4 82.0 - - - +
9A GLU* 1.3 67.3 + - - +
11A ILE* 3.4 5.5 + - + +
12A ARG* 3.0 43.2 + - - +
80A ALA* 3.8 14.1 - - + +
83A VAL* 3.6 28.9 - - + -
84A GLN* 3.6 42.2 - - + +
1098A ZN 4.5 4.9 - - - -
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 3.3 17.7 - - - +
8A PRO* 1.3 79.1 - - - +
10A GLU* 1.3 57.4 + - - +
12A ARG* 3.5 23.5 + - - +
13A ALA* 3.1 26.2 + - - +
84A GLN* 5.8 0.7 - - - -
1098A ZN 2.1 36.8 - - - -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MSE 3.8 25.5 - - + +
7A SER* 3.2 17.2 + - - +
9A GLU* 1.3 75.4 - - - +
11A ILE* 1.3 61.3 + - - +
13A ALA* 3.1 8.3 + - + +
14A LYS* 2.9 50.5 + - + +
1097A ZN 1.9 38.7 - - - -
38B GLU* 3.1 2.7 - - - +
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.0 20.0 - - + -
6A MSE 3.6 38.4 - - + +
7A SER 3.0 23.2 + - - +
8A PRO* 3.7 11.2 - - + +
10A GLU* 1.3 75.8 - - - +
12A ARG* 1.3 57.3 + - - +
14A LYS* 3.3 5.6 + - - +
15A SER* 2.9 27.0 + - - +
76A LEU* 3.1 47.4 - - + +
79A THR* 4.5 3.1 - - + -
80A ALA* 3.8 9.0 - - + +
83A VAL* 4.2 17.7 - - + -
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 3.0 26.0 + - - +
9A GLU* 3.8 33.2 - - - +
11A ILE* 1.3 72.4 - - - +
13A ALA* 1.3 66.5 + - - +
15A SER* 3.4 8.0 + - - -
16A GLN* 3.1 22.2 + - - +
77A ASN* 3.9 16.0 + - - +
80A ALA* 3.8 17.6 - - + +
81A ASP* 5.6 0.4 - - - +
84A GLN* 2.8 34.1 + - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU 3.1 16.0 + - - +
10A GLU* 3.1 13.0 + - + +
12A ARG* 1.3 78.6 - - - +
14A LYS* 1.3 62.9 + - + +
16A GLN* 3.4 21.2 + - - +
17A SER* 3.5 6.4 + - - -
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Residues in contact with LYS 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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6A MSE 4.5 5.2 - - - -
10A GLU* 2.9 50.1 + - + +
11A ILE* 3.6 7.6 - - - +
13A ALA* 1.3 72.8 - - - +
15A SER* 1.3 66.8 + - - +
17A SER* 2.6 26.6 + - - +
18A TYR* 3.1 12.9 + - + -
76A LEU* 4.2 12.1 - - + -
1097A ZN 3.8 1.0 - - - -
35B ALA* 3.8 33.7 - - + +
38B GLU* 3.0 26.9 + - - -
39B ILE* 4.3 13.0 - - + -
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE 2.9 17.9 + - - -
12A ARG 3.6 3.6 - - - -
13A ALA 3.3 0.2 - - - -
14A LYS* 1.3 74.0 - - - +
16A GLN* 1.3 62.9 + - - +
18A TYR* 3.2 3.5 - - - -
19A GLY 2.9 19.1 - - - -
73A LYS* 2.9 43.6 + - - +
76A LEU* 3.7 16.5 - - - +
77A ASN* 3.1 26.6 + - - -
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Residues in contact with GLN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG 3.1 12.9 + - - +
13A ALA* 3.4 15.6 + - - +
15A SER* 1.3 77.3 + - - +
17A SER* 1.3 55.8 + - - +
19A GLY* 3.2 3.2 + - - -
20A GLN* 2.9 58.7 + - + +
73A LYS* 5.3 3.4 - - - +
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Residues in contact with SER 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 ALA 3.5 5.9 + - - -
14A LYS* 2.6 28.3 + - - +
16A GLN* 1.3 75.7 - - - +
18A TYR* 1.3 61.8 + - - +
20A GLN* 3.6 15.3 + - - -
21A GLY* 2.9 25.8 - - - -
31B ASP* 6.4 0.9 - - - -
32B LEU* 3.4 23.4 - - - +
35B ALA* 5.1 1.2 - - - +
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 3.1 24.9 + - + -
15A SER 3.6 6.1 - - - -
17A SER* 1.3 82.8 + - - +
19A GLY* 1.3 56.5 + - - +
21A GLY* 3.3 1.0 + - - -
22A SER* 2.9 30.7 + - - -
69A LEU* 3.5 39.8 - - + +
72A ILE* 3.6 25.4 - - + -
73A LYS 4.0 5.6 - - - +
76A LEU* 3.8 22.4 - - + -
32B LEU* 3.7 20.4 + - + -
35B ALA* 3.6 16.6 - - + +
36B GLN* 2.5 56.1 + - - +
39B ILE* 3.8 10.8 - - + +
55B PHE* 4.6 0.7 - + - -
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER 2.9 11.7 - - - -
16A GLN* 3.6 4.0 - - - -
18A TYR* 1.3 75.3 - - - +
20A GLN* 1.3 60.3 + - - +
22A SER* 3.4 4.0 + - - -
23A ASP* 3.1 32.1 + - - -
70A GLU* 4.0 6.7 - - - +
73A LYS* 3.8 29.6 - - - +
1099A ZN 4.2 0.9 - - - -
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 2.9 51.3 + - + +
17A SER* 3.6 16.6 + - - -
19A GLY* 1.3 67.9 - - - +
21A GLY* 1.3 66.5 - - - +
23A ASP* 3.3 6.9 - - - +
24A GLN* 3.0 41.6 - - - +
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Residues in contact with GLY 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 SER 2.9 16.4 - - - -
18A TYR 3.3 2.9 + - - -
20A GLN* 1.3 74.3 + - - +
22A SER* 1.3 62.4 + - - +
24A GLN* 4.0 1.7 - - - +
25A ILE* 3.0 31.0 + - - +
69A LEU* 3.8 9.4 - - - -
28B ILE* 3.9 28.7 - - - -
32B LEU* 4.4 0.4 - - - -
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Residues in contact with SER 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 TYR 2.9 16.2 + - - -
19A GLY 3.6 5.8 - - - -
21A GLY* 1.3 77.3 - - - +
23A ASP* 1.3 64.8 + - - +
26A ARG* 3.0 32.8 + - - +
66A ALA* 2.8 35.6 + - - +
67A GLN* 5.0 0.2 + - - -
69A LEU* 3.7 7.2 - - - +
70A GLU* 3.6 26.8 + - - +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 3.1 14.5 + - - +
20A GLN* 3.3 6.3 - - - +
22A SER* 1.3 78.0 + - - +
24A GLN* 1.3 60.7 + - + +
26A ARG* 2.8 29.9 + - - +
27A GLN* 2.9 29.2 + - - +
70A GLU* 5.1 0.5 - - - +
1099A ZN 2.1 37.3 - - - -
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Residues in contact with GLN 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 GLN* 3.0 32.0 - - - +
21A GLY* 4.5 0.4 - - - -
23A ASP* 1.3 75.0 - - + +
25A ILE* 1.3 59.7 + - - +
27A GLN* 3.2 6.6 + - - +
28A ILE* 2.9 38.9 + - + +
24B GLN* 5.4 9.1 - - - +
28B ILE* 3.4 32.9 - - + +
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Residues in contact with ILE 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 GLY 3.0 21.6 + - - +
22A SER 4.0 2.7 - - - +
24A GLN* 1.3 76.2 - - - +
26A ARG* 1.3 56.2 + - - +
28A ILE* 3.3 7.7 + - - +
29A LEU* 2.8 30.1 + - + +
62A VAL* 3.6 30.7 - - + +
65A PHE* 3.7 33.2 - - + -
66A ALA* 3.9 16.2 - - + -
69A LEU* 4.0 4.5 - - + -
25B ILE* 4.5 23.2 - - + +
28B ILE* 3.8 27.1 - - + -
62B VAL* 5.1 0.9 - - + -
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.0 25.3 + - - +
23A ASP* 2.8 42.5 + - - +
25A ILE* 1.3 77.1 - - - +
27A GLN* 1.3 63.4 - - - +
29A LEU* 3.9 7.2 - - + +
30A SER* 3.0 24.8 - - - -
63A GLU* 6.0 7.0 - - + +
66A ALA* 4.0 15.7 - - + +
67A GLN* 6.0 0.7 - - - +
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Residues in contact with GLN 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 ASP 2.9 18.8 + - - +
24A GLN* 3.6 6.5 - - - +
26A ARG* 1.3 76.2 + - - +
28A ILE* 1.3 63.6 + - + +
30A SER* 2.9 29.4 + - - -
31A ASP* 3.0 44.8 + - - +
34A ARG* 4.7 4.2 - - - +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN 2.9 26.3 + - - +
25A ILE* 3.7 5.2 - - - +
27A GLN* 1.3 75.9 - - + +
29A LEU* 1.3 60.4 + - - +
31A ASP* 3.3 5.6 + - - +
32A LEU* 2.8 53.9 + - + +
21B GLY* 3.9 16.6 - - - +
24B GLN* 3.4 43.5 - - + +
25B ILE* 3.9 32.3 - - + +
28B ILE* 5.0 3.1 - - + -
65B PHE* 5.3 0.9 - - + -
69B LEU* 4.6 0.4 - - + -
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Residues in contact with LEU 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 ILE* 2.8 21.0 + - + +
26A ARG* 3.9 7.4 - - + +
28A ILE* 1.3 74.8 - - - +
30A SER* 1.3 54.2 + - - +
32A LEU* 4.9 1.8 - - - -
33A THR* 2.8 45.4 + - - +
55A PHE* 4.2 2.2 - - + -
59A SER* 3.5 46.7 - - - +
62A VAL* 4.4 9.4 - - + -
63A GLU* 3.8 30.3 - - + +
65B PHE* 3.7 26.0 - - + -
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG 3.0 15.3 - - - -
27A GLN* 2.9 31.4 + - - -
29A LEU* 1.3 74.7 - - - +
31A ASP* 1.3 64.6 + - - +
33A THR* 3.4 5.5 - - - -
34A ARG* 3.1 32.9 + - - +
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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
----------------------------------------------------------
27A GLN* 3.0 38.4 + - - +
28A ILE* 3.8 5.6 - - - +
30A SER* 1.3 80.7 + - - +
32A LEU* 1.3 64.8 + - + +
34A ARG* 2.7 40.6 + - - +
35A ALA* 3.0 24.6 + - - +
17B SER* 6.4 0.9 - - - -
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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
----------------------------------------------------------
28A ILE* 2.8 32.4 + - + +
29A LEU* 4.3 1.3 - - - +
31A ASP* 1.3 81.3 - - + +
33A THR* 1.3 60.4 + - - +
35A ALA* 3.3 5.6 + - + +
36A GLN* 2.8 32.9 + - - +
55A PHE* 3.8 16.2 - - + -
17B SER* 3.5 39.0 - - - +
18B TYR* 3.8 30.4 + - + +
21B GLY* 4.4 0.9 - - - -
65B PHE* 5.5 1.1 - - + -
69B LEU* 3.7 37.7 - - + -
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Residues in contact with THR 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 LEU* 2.8 32.3 + - - +
30A SER* 3.7 6.7 - - - -
32A LEU* 1.3 74.8 - - - +
34A ARG* 1.3 65.8 + - + +
36A GLN* 3.3 3.7 + - + +
37A GLY* 3.1 19.1 + - - -
55A PHE* 3.6 23.1 - - + -
59A SER* 5.1 1.4 - - - -
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 4.7 4.9 - - - +
30A SER* 3.1 19.6 + - - +
31A ASP* 2.7 33.9 + - - +
33A THR* 1.3 77.7 - - + +
35A ALA* 1.3 62.4 + - - +
37A GLY* 3.2 12.0 + - - -
38A GLU* 3.2 11.6 + - - +
14B LYS* 5.8 0.4 - - - -
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Residues in contact with ALA 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 3.0 14.0 + - - +
32A LEU* 3.3 13.9 + - + +
34A ARG* 1.3 75.3 - - - +
36A GLN* 1.3 62.0 + - - +
38A GLU* 3.1 4.7 + - - +
39A ILE* 3.0 27.9 + - - +
14B LYS* 4.6 25.9 - - + +
17B SER* 4.9 1.3 - - - +
18B TYR* 3.3 28.9 - - + +
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 2.8 22.6 + - - +
33A THR* 3.7 7.2 - - - +
34A ARG 3.3 0.2 - - - -
35A ALA* 1.3 71.4 - - - +
37A GLY* 1.3 57.9 + - - +
39A ILE* 3.3 9.8 + - - +
40A ALA* 2.9 33.0 + - - +
51A PHE* 4.2 2.1 - - - +
52A GLU* 3.9 19.8 + - + +
55A PHE* 3.5 48.7 - - + +
18B TYR* 2.6 33.5 + - - +
72B ILE* 3.7 15.5 - - - +
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR 3.1 10.2 + - - -
34A ARG 3.2 5.8 + - - -
36A GLN* 1.3 79.2 - - - +
38A GLU* 1.3 59.7 + - - +
40A ALA* 3.8 5.6 - - - +
41A ALA* 3.1 22.3 + - - +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG 3.2 9.5 + - - +
35A ALA* 3.1 10.4 + - - +
37A GLY* 1.3 72.6 - - - +
39A ILE* 1.3 66.0 + - - +
41A ALA* 3.3 6.3 + - + +
42A ASN* 2.8 42.1 + - - +
6B MSE 3.9 13.5 - - - +
10B GLU* 3.4 6.5 - - - +
14B LYS* 2.7 27.0 + - + -
1090B ZN 2.0 37.0 - - - -
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA 3.0 21.8 + - - +
36A GLN* 3.8 12.3 - - - +
38A GLU* 1.3 75.0 - - - +
40A ALA* 1.3 52.8 - - - +
42A ASN 2.9 4.0 - - - -
43A TRP* 2.8 59.7 - - + -
48A PHE* 3.7 22.9 - - + -
6B MSE 4.1 18.6 - - + -
14B LYS* 4.5 15.9 - - + -
18B TYR* 3.7 17.3 - - + +
72B ILE* 5.5 2.9 - - + -
76B LEU* 4.0 28.5 - - + -
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Residues in contact with ALA 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 GLN 2.9 17.8 + - - +
37A GLY* 3.8 5.8 - - - +
39A ILE* 1.3 74.1 + - - +
41A ALA* 1.3 62.8 + - - +
42A ASN 3.3 0.5 + - - -
43A TRP 3.5 13.6 + - - +
44A GLU* 2.8 28.4 - - - +
52A GLU* 4.0 28.0 - - + +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 3.1 14.7 + - - +
38A GLU* 3.5 13.7 - - + +
39A ILE 3.2 0.2 - - - +
40A ALA* 1.3 76.6 - - - +
42A ASN* 1.3 67.8 - - - +
44A GLU* 3.8 12.8 - - - +
----------------------------------------------------------
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 2.8 30.9 + - - +
39A ILE 2.9 4.5 - - - -
41A ALA* 1.3 87.2 - - - +
43A TRP* 1.3 72.0 + - + +
44A GLU* 4.4 1.7 - - - +
4B ILE 4.6 2.1 - - - +
5B LYS* 2.8 62.3 + - - +
6B MSE 3.2 29.8 + - + +
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Residues in contact with TRP 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 2.8 45.8 - - + -
40A ALA* 3.5 13.7 - - - +
42A ASN* 1.3 85.1 - - + +
44A GLU* 1.3 64.7 + - - +
45A GLY 3.8 0.9 - - - +
48A PHE* 3.5 55.7 - + + +
52A GLU* 4.7 4.2 - - - +
5B LYS* 3.5 20.7 - - - +
6B MSE 4.0 24.0 - - + -
11B ILE* 3.6 38.4 - - + -
76B LEU* 4.2 5.8 - - + -
79B THR* 3.7 28.0 - - + +
83B VAL* 5.1 7.5 - - + +
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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) + - + + + + + -
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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