Contacts of the helix formed by residues 4 - 35 (chain G) in PDB entry 2HTN
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 ASP 4 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G GLY* 1.3 69.8 - - - -
5G THR* 1.3 68.8 + - - +
6G LYS* 3.1 16.8 + - - +
7G VAL* 3.0 37.4 + - + +
8G ILE* 3.0 24.1 + - - +
65G LEU* 5.2 0.4 - - - +
107G TYR* 3.3 13.5 + - - -
111G VAL* 3.6 26.5 - - + +
113G ASP* 5.0 5.1 + - + +
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Residues in contact with THR 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G LYS* 5.8 3.3 - - - -
3G GLY 3.4 4.7 + - - -
4G ASP* 1.3 75.1 + - - +
6G LYS* 1.3 63.7 + - - +
8G ILE* 3.2 11.6 + - + +
9G ASN* 2.8 43.6 + - - +
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Residues in contact with LYS 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ASP* 3.1 7.0 + - - +
5G THR* 1.3 79.1 - - - +
7G VAL* 1.3 60.1 + - - +
9G ASN* 3.3 17.1 + - + +
10G TYR* 3.1 57.1 + - + -
107G TYR* 3.1 41.1 - - + +
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Residues in contact with VAL 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ASP* 3.0 32.9 + - + +
5G THR 3.1 0.6 - - - -
6G LYS* 1.3 73.4 - - - +
8G ILE* 1.3 66.7 + - - +
10G TYR* 2.9 12.7 + - + +
11G LEU* 2.9 42.0 + - + +
65G LEU* 4.5 4.0 - - + -
107G TYR* 3.9 9.0 - - + -
108G ALA* 4.6 6.5 - - + -
111G VAL* 3.5 27.4 - - + -
113G ASP* 3.5 23.8 - - + +
116G SER* 4.2 7.2 - - - +
120G MET* 5.9 0.9 - - + -
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Residues in contact with ILE 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLY 4.1 10.1 - - - +
4G ASP 3.0 16.2 + - - +
5G THR* 3.2 11.6 + - + +
7G VAL* 1.3 76.1 - - - +
9G ASN* 1.3 58.9 + - - +
11G LEU* 3.4 11.2 + - + +
12G ASN* 3.0 35.1 + - - +
62G ILE* 3.9 23.1 - - + -
65G LEU* 3.7 43.3 - - + +
66G GLU 4.7 1.1 - - - +
67G GLY* 3.9 18.2 - - - +
68G LEU 4.6 2.0 - - - +
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Residues in contact with ASN 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G THR* 2.8 44.0 + - - +
6G LYS* 3.3 19.7 - - + +
7G VAL 3.0 0.2 - - - -
8G ILE* 1.3 78.1 - - - +
10G TYR* 1.3 66.4 + - + +
12G ASN* 3.3 7.5 + - - +
13G LYS* 3.0 22.2 + - - +
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Residues in contact with TYR 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LYS* 3.1 45.2 + - + -
7G VAL* 2.9 9.4 + - - +
9G ASN* 1.3 77.7 - - - +
11G LEU* 1.3 61.1 + - + +
13G LYS* 3.1 20.0 + - + +
14G LEU* 2.8 39.2 + - + +
100G ASN* 4.9 1.3 - - + -
103G GLU* 3.0 44.3 + - + +
104G ALA* 3.7 28.5 - - + -
107G TYR* 3.6 41.8 - + + +
120G MET* 5.7 0.4 - - + -
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Residues in contact with LEU 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 2.9 27.6 + - + +
8G ILE* 3.4 12.8 - - - +
9G ASN 3.2 0.2 - - - -
10G TYR* 1.3 78.4 - - + +
12G ASN* 1.3 51.8 + - - +
14G LEU* 3.1 9.7 + - + +
15G LEU* 2.7 34.5 + - - +
58G TYR* 4.1 17.3 - - + -
61G ARG* 3.9 25.1 - - + -
62G ILE* 3.6 27.8 - - + -
65G LEU* 4.1 18.6 - - + -
116G SER* 4.5 4.0 - - - +
119G MET* 4.8 4.9 - - + -
120G MET* 4.3 25.8 - - + -
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Residues in contact with ASN 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 3.0 31.5 + - - +
9G ASN* 3.7 10.3 + - - +
11G LEU* 1.3 77.3 - - - +
13G LYS* 1.3 57.6 + - - +
15G LEU* 3.3 7.6 + - - +
16G GLY* 2.8 25.8 + - - -
62G ILE* 3.6 8.4 - - - +
68G LEU 3.1 19.5 + - - -
69G PRO* 3.3 5.5 - - - +
70G ASN* 2.6 44.6 + - + +
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Residues in contact with LYS 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ASN 3.0 13.6 + - - +
10G TYR* 3.1 29.1 + - + +
12G ASN* 1.3 75.8 - - - +
14G LEU* 1.3 61.7 + - + +
16G GLY* 3.2 3.4 + - - -
17G ASN* 3.0 36.0 + - - +
100G ASN* 3.3 36.3 + - + +
103G GLU* 5.9 3.8 - - - -
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Residues in contact with LEU 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G TYR* 2.8 25.4 + - + +
11G LEU* 3.4 7.6 - - - +
13G LYS* 1.3 81.5 - - + +
15G LEU* 1.3 64.0 + - - +
17G ASN* 3.0 19.8 + - - +
18G GLU* 3.1 16.5 + - - +
58G TYR* 3.4 35.8 - - + +
100G ASN* 4.1 26.2 - - + +
101G LEU* 3.9 13.5 - - + -
104G ALA* 3.8 15.7 - - + -
120G MET* 3.5 30.7 - - - -
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Residues in contact with LEU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU 2.7 20.4 + - - +
12G ASN* 3.4 10.8 - - - +
14G LEU* 1.3 72.6 - - - +
16G GLY* 1.3 62.8 + - - +
18G GLU* 3.1 2.9 + - - +
19G LEU* 2.9 23.6 + - + +
55G ALA* 3.8 38.4 - - + +
58G TYR* 4.0 14.3 - - + -
59G ILE* 3.9 14.1 - - + +
62G ILE* 4.2 10.1 - - + -
69G PRO* 4.2 1.8 - - + -
70G ASN 3.9 25.6 - - - +
71G LEU* 3.8 33.0 - - + -
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Residues in contact with GLY 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ASN 2.8 14.3 + - - -
13G LYS* 3.6 5.2 - - - -
14G LEU 3.2 0.2 - - - -
15G LEU* 1.3 77.7 - - - +
17G ASN* 1.3 62.8 + - - +
19G LEU* 3.4 13.6 + - - +
20G VAL* 3.2 28.6 + - - +
70G ASN 5.2 1.8 - - - -
73G ASP 5.0 7.7 - - - +
75G GLY 5.1 0.7 + - - -
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Residues in contact with ASN 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 3.0 24.1 + - - +
14G LEU* 3.0 14.4 + - - +
16G GLY* 1.3 77.0 - - - +
18G GLU* 1.3 65.3 + - + +
20G VAL* 3.3 9.7 + - - +
21G ALA* 3.1 20.5 + - - +
93G LEU* 4.8 10.9 - - + +
97G GLY* 3.7 19.3 - - - +
100G ASN* 2.8 37.6 + - - +
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Residues in contact with GLU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU 3.5 12.3 - - - +
15G LEU 3.1 7.7 + - - +
17G ASN* 1.3 74.7 - - - +
19G LEU* 1.3 57.2 + - - +
21G ALA* 2.9 3.9 + - - +
22G ILE* 2.7 38.9 + - - +
51G GLU* 3.0 24.3 - - - +
54G HIS* 2.9 20.6 + - + +
55G ALA* 4.0 17.3 - - + +
58G TYR* 3.6 21.0 + - + -
123G ILE* 3.8 6.6 - - - +
127G GLU* 2.9 7.2 - - - +
301G FE 2.0 31.9 - - - -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 2.9 24.0 + - + +
16G GLY* 3.6 11.9 - - - +
18G GLU* 1.3 77.0 - - - +
20G VAL* 1.3 61.2 + - - +
22G ILE* 3.6 8.9 + - + +
23G ASN* 3.1 29.2 + - - +
55G ALA* 4.9 2.0 - - + -
70G ASN 3.7 15.3 - - - +
71G LEU* 3.4 48.5 - - + +
73G ASP 4.6 6.7 - - - +
74G LEU* 3.9 15.8 - - + +
200G HEM 3.8 27.1 - - + -
23H ASN* 4.5 6.5 - - - +
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Residues in contact with VAL 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLY 3.2 16.5 + - - +
17G ASN* 3.5 9.4 - - - +
18G GLU 3.1 0.4 - - - -
19G LEU* 1.3 76.0 - - - +
21G ALA* 1.3 61.2 + - - +
23G ASN 3.4 1.6 + - - -
24G GLN* 3.0 28.3 + - - +
74G LEU* 4.0 5.8 - - + -
75G GLY* 3.5 35.4 - - - +
76G LYS 3.6 15.9 - - - +
77G LEU* 3.5 24.6 - - + +
93G LEU* 4.0 23.6 - - + -
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ASN 3.1 12.4 + - - +
18G GLU* 2.9 9.5 + - - +
20G VAL* 1.3 74.8 - - - +
22G ILE* 1.3 66.5 + - - +
24G GLN* 4.5 0.2 - - - -
25G TYR* 2.8 38.0 + - + +
51G GLU* 3.3 32.1 - - + +
93G LEU* 3.7 20.8 - - + +
94G GLU* 4.7 2.2 - - - +
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Residues in contact with ILE 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G GLU 2.7 24.1 + - - +
19G LEU* 3.7 15.3 - - + +
20G VAL 3.3 0.2 - - - -
21G ALA* 1.3 71.4 - - - +
23G ASN* 1.3 59.8 + - - +
25G TYR* 4.8 0.2 - - - -
26G PHE* 2.9 32.7 + - - +
48G SER* 3.2 8.4 + - - -
51G GLU* 3.7 18.6 - - + -
52G MET* 3.8 39.7 - - + +
55G ALA* 4.1 13.2 - - + -
200G HEM 3.5 56.5 - - + -
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Residues in contact with ASN 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 3.1 14.7 + - - +
20G VAL 3.4 6.4 + - - +
21G ALA 3.3 0.4 - - - -
22G ILE* 1.3 78.0 - - - +
24G GLN* 1.3 59.6 + - - +
26G PHE* 4.6 0.2 - - - -
27G LEU* 3.0 31.9 + - - +
74G LEU* 4.1 10.8 - - - +
77G LEU* 4.1 14.8 - - + -
200G HEM 3.1 27.3 - - - +
19H LEU* 4.5 7.7 - - - +
71H LEU* 3.1 47.9 + - + +
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Residues in contact with GLN 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G VAL* 3.0 18.8 + - - +
21G ALA 4.0 1.8 - - - +
23G ASN* 1.3 75.7 - - - +
25G TYR* 1.3 59.7 + - - +
27G LEU* 3.3 3.8 + - - +
28G HIS* 2.9 53.3 + - + +
76G LYS 5.0 0.3 - - - +
77G LEU* 3.9 11.6 - - + +
78G ASN* 3.0 34.8 + - - +
79G ILE* 5.1 4.5 - - + -
89G SER* 3.3 29.5 + - - -
90G ASP* 3.1 27.3 + - - +
93G LEU* 4.1 19.4 - - + +
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Residues in contact with TYR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ALA* 2.8 39.3 + - + +
24G GLN* 1.3 74.4 - - - +
26G PHE* 1.3 56.9 + - - +
28G HIS 3.6 0.2 + - - -
29G ALA* 3.0 28.4 + - - +
44G GLU* 3.1 39.9 - - - +
47G GLU* 3.1 48.5 + - + -
48G SER* 3.7 20.6 - - - +
51G GLU* 3.9 18.4 - - + -
90G ASP* 4.2 19.5 - - + -
93G LEU* 5.4 4.0 - - + -
94G GLU* 3.4 40.2 + - + +
130G HIS* 3.8 1.2 - - - +
134G LEU* 3.7 7.3 - - + +
302G FE 4.4 0.2 - - - -
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Residues in contact with PHE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G ILE 2.9 21.0 + - - +
23G ASN* 3.9 5.2 - - - +
25G TYR* 1.3 75.1 - - - +
27G LEU* 1.3 63.7 + - - +
29G ALA* 3.4 5.8 - - + +
30G ARG* 3.2 38.2 + - + +
45G TYR* 3.9 25.4 - + - -
48G SER* 3.5 19.3 + - - +
52G MET* 4.1 7.6 - - + -
200G HEM 3.7 49.8 - + + -
56H ASP* 3.5 36.3 - - + -
59H ILE* 3.8 19.7 - - + -
71H LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ASN 3.0 19.0 + - - +
24G GLN* 3.8 3.4 - - - +
26G PHE* 1.3 76.1 - - - +
28G HIS* 1.3 68.1 + - + +
30G ARG* 3.3 3.0 + - - -
31G MET* 2.9 46.7 + - + +
77G LEU* 5.9 1.6 - - + -
79G ILE* 3.7 30.3 - - + -
59H ILE* 4.0 12.3 - - + -
63H LEU* 4.5 1.1 - - + -
69H PRO* 3.8 50.3 - - + +
71H LEU* 4.1 17.2 - - + +
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Residues in contact with HIS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLN* 2.9 34.7 + - + +
25G TYR 3.8 0.2 - - - +
27G LEU* 1.3 77.2 - - - +
29G ALA* 1.3 56.1 + - - +
31G MET* 3.1 4.6 + - - +
32G PHE* 2.8 39.8 + - + -
44G GLU* 3.4 14.6 - - - +
79G ILE* 2.6 50.5 + - + -
86G MET* 3.5 43.6 + - + +
90G ASP* 3.1 33.6 + - - -
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Residues in contact with ALA 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G TYR 3.0 18.8 + - - +
26G PHE* 3.4 8.7 - - + +
28G HIS* 1.3 75.4 - - - +
30G ARG* 1.3 61.3 + - - +
32G PHE* 3.0 9.4 + - - +
33G LYS 2.8 23.9 + - - -
41G ASN* 3.2 19.0 - - - +
44G GLU* 3.4 23.2 - - + +
45G TYR* 3.7 18.8 - - + +
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Residues in contact with ARG 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G PHE* 3.2 33.3 + - + +
27G LEU 3.9 2.2 - - - +
29G ALA* 1.3 81.1 - - - +
31G MET* 1.3 53.6 + - - +
33G LYS* 3.5 18.0 - - - +
34G ASN* 2.7 33.6 + - - +
41G ASN* 3.0 29.8 + - - +
45G TYR* 3.5 37.2 - - - -
200G HEM 5.0 1.4 - - - +
56H ASP* 2.9 38.6 + - - +
59H ILE* 4.1 9.2 - - + -
60H GLU* 3.9 22.7 + - + +
63H LEU* 3.4 19.8 - - + +
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Residues in contact with MET 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 2.9 40.9 + - + +
28G HIS* 3.3 9.6 - - - +
30G ARG* 1.3 75.5 - - - +
32G PHE* 1.3 60.2 + - - +
34G ASN* 3.3 4.6 + - - +
35G TRP* 3.0 56.4 + - + -
79G ILE* 3.8 22.4 - - + -
80G GLY 3.6 21.8 - - - +
81G GLU* 4.0 14.6 - - - +
86G MET* 3.8 18.8 - - + -
63H LEU* 4.0 18.4 - - + -
68H LEU* 6.2 2.2 - - + -
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Residues in contact with PHE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G HIS* 2.8 25.7 + - + -
29G ALA* 3.3 5.8 - - - +
31G MET* 1.3 76.5 - - - +
33G LYS* 1.3 60.7 + - - +
35G TRP* 3.1 10.8 + + - +
36G GLY 3.0 5.4 + - - -
37G LEU* 2.8 40.2 + - + +
40G LEU* 3.8 35.9 - - + -
41G ASN 4.0 12.6 - - - +
44G GLU* 3.3 35.2 - - + -
83G VAL* 4.1 13.0 - - + -
86G MET* 3.5 32.3 - - + -
87G LEU* 3.7 25.6 - - + -
90G ASP* 5.7 0.2 - - - -
133G TRP* 6.6 0.2 - + - -
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Residues in contact with LYS 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F THR* 5.4 0.2 - - - +
29G ALA 2.8 5.8 + - - +
30G ARG* 3.5 35.7 - - - +
32G PHE* 1.3 77.7 - - - +
34G ASN* 1.3 63.3 + - - +
36G GLY* 3.0 14.3 + - - +
37G LEU 4.6 2.9 - - - +
38G LYS* 5.3 2.2 - - + +
41G ASN* 3.5 29.8 - - + +
60H GLU* 2.7 32.6 + - + +
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Residues in contact with ASN 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ASP* 4.2 12.3 - - - +
136F THR* 3.2 23.9 + - - +
30G ARG 2.7 21.9 + - - +
31G MET* 3.4 8.4 + - - +
33G LYS* 1.3 74.1 - - - +
35G TRP* 1.3 76.5 + - - +
36G GLY 3.4 0.5 + - - -
60H GLU 5.2 0.2 - - - +
63H LEU* 3.6 41.8 + - + +
64H PHE* 3.8 9.2 + - - +
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Residues in contact with TRP 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F THR* 3.6 9.3 - - - +
139F ASP* 5.9 5.8 - - + +
140F LEU* 3.3 25.9 - - + +
143F LYS* 3.3 30.8 + - - +
31G MET* 3.0 37.9 + - + +
32G PHE* 3.1 20.4 + + - +
34G ASN* 1.3 94.6 - - - +
36G GLY* 1.3 57.0 + - - +
37G LEU* 4.2 16.1 - - + +
81G GLU* 3.7 26.7 - - - -
82G ASP* 4.2 1.3 - - - -
83G VAL* 4.2 13.2 - - + -
86G MET* 3.6 37.0 - - + -
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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) + - + + + + + -
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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