Contacts of the helix formed by residues 52 - 81 (chain E) in PDB entry 1O9I
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 ALA 52 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLN 3.3 7.5 + - - +
266B GLY* 3.3 25.6 + - - +
49E SER* 4.7 0.5 + - - -
51E GLY* 1.3 71.5 - - - +
53E GLU* 1.3 65.2 + - - +
54E LYS* 4.2 7.6 - - + +
55E TYR* 3.1 27.1 + - + +
56E LYS* 3.1 18.5 + - - +
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Residues in contact with GLU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B HIS* 4.5 9.7 + - - -
6C ARG* 2.8 44.7 + - - -
222D GLY* 5.5 1.4 - - - -
224D GLY* 3.9 13.9 + - - +
51E GLY 3.2 5.0 + - - +
52E ALA* 1.3 69.4 - - - +
54E LYS* 1.3 65.8 + - - +
56E LYS* 3.6 16.1 - - - +
57E ASP* 2.9 32.2 + - - +
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Residues in contact with LYS 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D GLY* 3.4 22.2 - - - +
225D SER* 3.9 4.2 - - - -
227D ALA* 3.7 21.2 + - + +
228D PHE* 3.6 36.9 - - + -
231D GLN* 2.8 39.4 + - - +
52E ALA* 3.2 6.4 - - + +
53E GLU* 1.3 80.5 - - - +
55E TYR* 1.3 83.9 + - + +
58E LEU* 3.3 22.5 + - - +
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Residues in contact with TYR 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLN 3.9 11.7 - - - +
266B GLY* 4.4 9.9 - - - -
228D PHE* 4.1 15.9 - + - -
52E ALA* 3.1 26.0 + - + +
53E GLU 3.1 0.4 - - - -
54E LYS* 1.3 109.6 + - + +
56E LYS* 1.3 64.3 + - - +
57E ASP 3.3 0.4 - - - -
58E LEU* 3.3 5.4 + - + +
59E LEU* 2.9 30.6 + - - +
137E LEU* 4.2 15.0 - - + -
141E MET* 4.0 22.8 - - + +
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Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO* 5.2 9.5 + - - +
253B HIS* 5.6 3.4 - - + -
6C ARG* 3.3 37.7 - - - +
46E GLY* 2.7 32.7 + - - +
47E TRP* 3.3 15.2 + - - +
49E SER* 2.8 43.0 + - - +
50E THR* 5.4 0.9 - - - -
51E GLY 4.8 3.4 - - - +
52E ALA 3.1 16.3 + - - +
53E GLU* 3.6 13.7 - - - +
55E TYR* 1.3 75.1 - - - +
57E ASP* 1.3 62.2 + - - +
59E LEU* 3.3 7.5 + - - +
60E LEU* 3.1 27.9 + - + +
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Residues in contact with ASP 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 4.6 7.1 + - - +
218D ASN* 4.2 0.2 - - - +
220D SER* 3.5 9.2 + - - +
222D GLY* 3.1 38.5 + - - +
224D GLY 3.9 4.0 - - - +
225D SER* 2.9 37.7 + - - +
53E GLU* 2.9 27.4 + - - +
56E LYS* 1.3 73.9 - - - +
58E LEU* 1.3 61.3 + - - +
60E LEU* 3.7 2.9 - - - +
61E ASP* 2.8 45.1 + - - +
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Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D LEU* 3.8 28.9 - - + -
225D SER* 4.1 2.2 - - - -
228D PHE* 3.7 26.7 - - + -
54E LYS 3.3 18.3 + - - +
55E TYR* 3.3 6.6 + - + +
57E ASP* 1.3 78.4 - - - +
59E LEU* 1.3 63.3 + - - +
61E ASP* 3.4 7.5 + - + +
62E THR* 2.8 31.4 + - - +
141E MET* 4.4 12.6 - - + -
184E GLN* 3.5 39.0 - - + +
185E PHE* 3.8 26.2 - - + -
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Residues in contact with LEU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.6 35.5 - - + +
45E GLN* 3.3 42.2 - - + +
46E GLY* 3.7 10.5 - - - +
49E SER* 5.2 0.4 - - - -
55E TYR 2.9 22.4 + - - +
56E LYS* 3.6 6.1 - - - +
58E LEU* 1.3 77.8 - - - +
60E LEU* 1.3 55.6 + - - +
62E THR* 3.4 1.5 + - - -
63E GLY* 2.8 26.0 + - - -
137E LEU* 4.1 21.8 - - + -
141E MET* 3.9 15.0 - - + -
144E ASN* 3.4 15.9 - - - +
185E PHE* 4.9 5.6 - - + -
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 4.1 9.6 - - + +
6C ARG* 3.5 38.4 - - - +
220D SER* 3.8 17.0 - - - +
43E LEU* 4.0 18.1 - - + +
46E GLY* 3.8 24.7 - - - +
47E TRP* 3.7 32.8 - - + +
56E LYS* 3.1 20.7 + - + +
57E ASP* 3.9 2.2 - - - +
59E LEU* 1.3 72.8 - - - +
61E ASP* 1.3 64.6 + - - +
64E THR* 2.8 31.0 + - - -
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Residues in contact with ASP 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D LEU* 3.9 8.8 - - + +
217D MET 3.7 15.5 - - - +
218D ASN* 3.3 5.7 - - - +
219D PHE* 3.3 17.3 - - - +
220D SER* 3.0 38.0 + - - +
225D SER* 2.6 35.5 + - - -
57E ASP* 2.8 26.4 + - - +
58E LEU* 3.5 5.4 - - - +
60E LEU* 1.3 73.9 - - - +
62E THR* 1.3 59.5 + - - +
65E GLU* 3.0 24.4 + - - +
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Residues in contact with THR 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.7 24.9 - - + -
58E LEU* 2.8 19.3 + - - +
59E LEU* 4.1 2.5 - - - -
61E ASP* 1.3 74.2 - - - +
63E GLY* 1.3 63.6 + - - +
65E GLU* 3.1 8.3 + - - +
66E GLU* 2.8 32.5 + - - +
181E HIS* 3.6 37.4 - - + +
184E GLN* 2.8 27.3 + - - +
185E PHE* 5.4 1.5 - - + -
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Residues in contact with GLY 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E MET* 3.9 7.8 - - - +
42E PHE* 3.7 20.1 - - - +
43E LEU* 3.8 18.8 - - - -
59E LEU 2.8 17.7 + - - -
62E THR* 1.3 77.8 - - - +
64E THR* 1.3 60.0 + - - +
66E GLU* 3.2 6.5 + - - +
67E MET* 3.2 23.4 + - - +
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Residues in contact with THR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PHE* 3.7 36.7 - - + +
3C LYS* 4.0 4.5 - - - -
4C HIS* 3.4 21.2 - - + +
219D PHE* 3.8 20.6 - - + +
2E PHE* 3.5 13.5 - - + -
43E LEU* 3.9 2.5 - - - +
60E LEU 2.8 20.8 + - - -
61E ASP 3.6 3.8 - - - -
63E GLY* 1.3 74.6 - - - +
65E GLU* 1.3 65.5 + - - +
67E MET* 3.2 25.9 + - - +
68E ALA* 3.5 4.0 + - - +
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D MET* 4.2 2.6 - - - +
219D PHE* 3.5 31.8 - - + -
9E GLN* 3.2 18.8 + - - +
61E ASP 3.0 9.9 + - - +
62E THR* 3.1 10.1 + - - +
64E THR* 1.3 77.0 - - - +
66E GLU* 1.3 57.6 + - - +
68E ALA* 2.9 29.0 + - - +
69E HIS* 3.2 27.1 + - + +
177E ARG* 2.7 44.5 + - - -
181E HIS* 2.9 21.3 + - + -
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Residues in contact with GLU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E GLU* 3.1 29.2 - - - +
39E MET* 3.6 24.0 - - + +
42E PHE* 3.5 19.6 - - + -
62E THR 2.8 22.2 + - - +
63E GLY 3.2 5.3 + - - +
65E GLU* 1.3 73.9 - - - +
67E MET* 1.3 56.9 + - - +
69E HIS* 2.9 14.4 + - - +
70E VAL* 2.8 31.7 + - - +
147E ARG* 3.2 13.1 + - - -
148E GLU* 2.8 25.6 - - - +
181E HIS* 3.1 17.0 + - - -
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Residues in contact with MET 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PHE* 3.6 46.2 - - + -
43C LEU* 5.1 6.3 - - + -
47C TRP* 4.7 1.4 - - - -
67C MET* 3.7 36.6 - - + -
2E PHE* 3.5 33.2 - - + -
39E MET* 3.5 28.0 - - + +
43E LEU* 4.3 1.6 - - - -
63E GLY 3.2 13.9 + - - +
64E THR* 3.2 13.5 - - - +
66E GLU* 1.3 76.8 - - - +
68E ALA* 1.3 61.8 + - - +
70E VAL* 3.3 4.6 + - - +
71E GLU* 3.0 22.3 + - - +
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Residues in contact with ALA 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 4.1 19.3 - - + -
2C PHE* 4.1 6.4 - - - +
219D PHE* 5.4 0.9 - - + -
9E GLN* 4.0 30.7 + - + +
64E THR 3.5 4.5 + - - +
65E GLU* 2.9 16.2 + - - +
67E MET* 1.3 79.1 - - - +
69E HIS* 1.3 58.5 + - - +
71E GLU* 3.3 11.0 + - - +
72E MET* 2.9 30.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 2.8 28.7 + - - -
35E GLU* 3.1 32.7 + - + +
65E GLU* 3.3 33.7 + - + +
66E GLU* 2.9 19.0 + - - +
68E ALA* 1.3 76.5 - - - +
70E VAL* 1.3 59.3 + - - +
72E MET* 3.2 11.0 + - - +
73E ILE* 2.9 37.4 + - + +
173E PHE* 4.2 3.0 - - - -
174E LEU* 3.8 27.6 - - + +
177E ARG* 4.1 13.2 - - + -
178E GLU* 6.2 1.9 - - + +
181E HIS* 4.3 4.9 - + - -
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Residues in contact with VAL 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 4.6 11.9 - - + -
47C TRP* 3.8 22.4 - - + -
29E LEU* 3.8 22.2 - - + +
35E GLU* 3.7 32.3 - - + +
36E THR* 3.8 14.6 - - - +
39E MET* 4.1 16.2 - - + -
66E GLU 2.8 19.1 + - - +
67E MET* 3.5 8.3 - - - +
69E HIS* 1.3 77.6 - - - +
71E GLU* 1.3 60.3 + - - +
73E ILE* 3.4 0.6 + - - -
74E SER* 2.9 29.6 + - - -
118E LEU* 5.5 0.2 - - + -
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Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 2.7 30.5 + - - -
2C PHE* 4.5 2.5 - - + -
47C TRP* 2.9 45.6 + - + +
4E HIS* 2.7 30.1 + - - -
5E THR 4.3 0.7 - - - +
6E ARG* 4.8 4.6 - - - +
8E LEU* 3.8 22.7 - - + +
9E GLN 5.0 0.2 + - - -
67E MET 3.0 11.4 + - - +
68E ALA* 3.4 9.1 - - - +
70E VAL* 1.3 77.2 - - - +
72E MET* 1.3 57.3 + - - +
74E SER* 3.4 2.3 + - - -
75E THR* 2.8 35.5 + - - +
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Residues in contact with MET 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.1 17.0 - - + -
9E GLN* 3.9 13.0 - - - +
10E TYR* 3.6 52.3 - - + +
11E ASN 3.9 0.2 - - - +
12E ALA* 3.5 12.0 - - + +
68E ALA 2.9 18.3 + - - +
69E HIS* 3.2 20.4 + - - +
71E GLU* 1.3 75.9 - - - +
73E ILE* 1.3 59.2 + - + +
75E THR* 3.2 2.3 + - - -
76E MET* 2.8 30.3 + - - +
170E MET* 3.8 28.7 - - + -
173E PHE* 4.0 11.4 - - + -
174E LEU* 4.2 7.9 - - + -
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Residues in contact with ILE 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LEU* 3.6 33.7 - - + +
28E SER* 4.2 15.7 - - - +
29E LEU* 3.8 21.1 - - + +
35E GLU* 4.2 17.0 - - + -
69E HIS* 2.9 24.4 + - - +
70E VAL* 4.1 2.5 - - - +
72E MET* 1.3 73.5 - - + +
74E SER* 1.3 63.2 + - - +
76E MET* 3.3 3.6 + - - +
77E ILE* 2.9 30.4 + - + +
170E MET* 3.7 26.7 - - + -
174E LEU* 3.9 19.3 - - + -
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Residues in contact with SER 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C SER* 6.0 0.9 - - - -
47C TRP* 3.6 33.1 - - - -
254D ILE* 5.2 0.5 - - - +
29E LEU* 3.4 28.8 - - - +
70E VAL 2.9 20.2 + - - -
71E GLU 3.6 4.9 - - - -
73E ILE* 1.3 77.6 - - - +
75E THR* 1.3 61.8 + - - +
77E ILE* 3.5 2.4 + - - +
78E GLY* 3.2 18.7 + - - -
116E ALA* 4.1 12.2 + - - +
118E LEU* 5.2 2.1 - - - +
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Residues in contact with THR 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C TRP* 4.9 11.4 + - - +
252D PRO* 3.5 35.4 - - + +
254D ILE* 3.7 12.4 - - + +
8E LEU* 4.0 15.9 - - + +
12E ALA 4.0 4.3 - - - +
71E GLU* 2.8 26.4 + - - +
72E MET* 3.5 6.7 - - - -
74E SER* 1.3 75.1 - - - +
76E MET* 1.3 65.0 + - - +
78E GLY* 3.1 3.1 + - - -
79E TYR* 3.0 38.5 + - + -
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Residues in contact with MET 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ALA* 3.4 30.7 + - - +
13E LYS 3.7 7.6 - - - +
14E PRO* 3.5 28.7 - - - -
25E LEU* 3.7 26.9 - - + -
72E MET 2.8 19.5 + - - +
73E ILE* 3.8 4.5 - - - +
75E THR* 1.3 72.2 - - - +
77E ILE* 1.3 56.8 + - - +
79E TYR* 3.2 3.7 + - - +
80E LEU* 2.9 36.6 + - + +
166E GLY 4.0 0.4 - - - +
167E VAL* 3.8 31.9 - - - -
170E MET* 3.8 28.7 - - + -
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Residues in contact with ILE 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ALA* 3.7 24.2 - - + +
25E LEU* 3.9 20.4 - - + +
26E GLN* 3.6 28.7 - - - +
29E LEU* 4.1 11.0 - - + -
73E ILE* 2.9 35.2 + - + +
74E SER 3.8 4.0 - - - +
76E MET* 1.3 76.2 - - - +
78E GLY* 1.3 62.2 + - - +
80E LEU* 3.1 8.3 + - - +
81E LEU* 3.0 37.2 + - + +
108E HIS* 4.2 1.1 - - - +
116E ALA* 3.7 23.3 - - + -
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Residues in contact with GLY 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ILE* 3.8 22.6 - - - +
74E SER 3.2 10.8 + - - -
75E THR 3.1 6.7 + - - -
77E ILE* 1.3 77.2 - - - +
79E TYR* 1.3 63.3 + - - +
81E LEU* 3.3 11.5 + - - +
82E GLU* 3.5 11.8 + - - +
114E LEU 4.5 12.7 - - - +
115E ASN* 4.8 10.5 - - - -
116E ALA 4.9 0.9 - - - +
----------------------------------------------------------
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Residues in contact with TYR 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D PRO* 3.4 8.2 - - + +
253D HIS* 3.0 43.0 + - - +
254D ILE* 3.8 8.9 - - + +
8E LEU* 5.7 0.9 - - + -
12E ALA 3.3 23.6 - - - -
13E LYS* 3.3 45.3 - - + +
14E PRO* 3.2 25.3 - - + +
16E ARG 5.4 0.2 - - - -
17E SER* 4.3 5.9 - - - -
75E THR* 3.0 38.2 + - + -
76E MET 3.6 2.2 - - - +
78E GLY* 1.3 75.5 - - - +
80E LEU* 1.3 63.4 + - - +
82E GLU* 3.1 42.9 + - - +
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Residues in contact with LEU 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E PRO* 3.6 13.9 - - + -
16E ARG 3.5 21.5 - - - +
17E SER* 3.6 6.0 - - - +
18E ASP* 2.9 54.4 + - + +
19E PRO* 3.5 2.4 - - - +
21E MET* 4.1 7.0 - - + -
22E ALA* 3.8 19.7 - - + +
25E LEU* 3.5 32.8 - - + -
76E MET* 2.9 29.8 + - + +
77E ILE* 3.1 5.1 + - - +
79E TYR* 1.3 76.9 - - - +
81E LEU* 1.3 58.8 + - - +
82E GLU 3.3 0.2 - - - -
164E ASP* 5.2 0.4 - - + +
167E VAL* 4.0 9.4 - - + -
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PRO* 3.9 19.1 - - + -
22E ALA* 3.7 19.7 - - + -
77E ILE* 3.0 26.9 + - + +
78E GLY 3.8 2.7 - - - +
79E TYR 3.1 0.6 - - - -
80E LEU* 1.3 73.8 - - - +
82E GLU* 1.3 67.1 - - - +
83E ASP 3.3 0.9 + - - -
84E ALA* 3.1 19.1 + - + +
104E MET* 4.8 2.0 - - + -
108E HIS* 3.7 31.2 - - + +
114E LEU* 3.6 54.8 - - + +
115E ASN* 3.7 19.1 - - - +
----------------------------------------------------------
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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