Contacts of the helix formed by residues 22 - 54 (chain E) in PDB entry 1F33
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 22 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ASP 3.6 3.2 + - - -
21E VAL* 1.3 74.0 - - - +
23E ASP* 1.3 61.4 + - - +
24E SER* 3.6 10.6 - - - -
25E GLU* 3.0 32.3 + - - +
26E LYS* 2.8 25.3 + - - +
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Residues in contact with ASP 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 4.0 15.5 - - + +
21E VAL 3.3 4.1 + - - +
22E SER* 1.3 72.7 - - - +
24E SER* 1.3 62.7 + - - +
26E LYS* 3.6 14.2 + - - +
27E LYS* 2.9 34.9 + - + +
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Residues in contact with SER 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E SER* 3.6 12.3 - - - -
23E ASP* 1.3 81.3 - - - +
25E GLU* 1.3 63.9 + - - +
27E LYS* 3.7 5.0 - - - +
28E ALA* 3.1 20.8 + - - +
140E LYS* 4.3 12.3 + - - -
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Residues in contact with GLU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 3.7 18.1 - - + +
22E SER* 3.0 19.4 + - - +
24E SER* 1.3 78.7 - - - +
26E LYS* 1.3 57.7 + - - +
28E ALA* 3.6 6.2 - - - +
29E THR* 2.6 43.5 + - - +
140E LYS* 3.2 44.1 - - + +
141E ASP* 3.4 16.1 + - - +
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Residues in contact with LYS 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 3.2 24.8 - - + +
15E LEU 5.1 2.4 + - - -
17E THR* 3.4 23.8 + - - +
19E ASN* 2.9 30.1 + - - -
20E ASP* 4.9 0.2 - - - +
21E VAL* 2.9 37.3 + - + +
22E SER 2.8 21.2 + - - +
23E ASP* 4.4 7.6 + - - -
25E GLU* 1.3 72.2 - - - +
27E LYS* 1.3 57.9 + - - +
29E THR* 3.7 2.3 - - - -
30E VAL* 2.8 37.6 + - - +
87E LEU* 3.1 33.9 - - + +
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Residues in contact with LYS 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 3.3 50.4 - - + +
13E ASN* 5.6 0.2 - - - +
14E LEU* 3.9 14.8 - - + +
23E ASP* 2.9 23.9 + - - +
24E SER* 3.7 4.5 - - - +
26E LYS* 1.3 77.3 - - - +
28E ALA* 1.3 61.4 + - - +
30E VAL* 3.4 3.0 + - - +
31E GLU* 3.0 25.7 + - - +
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Residues in contact with ALA 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E SER 3.1 14.7 + - - +
25E GLU* 3.6 3.8 - - - +
27E LYS* 1.3 80.3 - - - +
29E THR* 1.3 56.9 + - - +
31E GLU* 3.3 10.2 + - - +
32E LEU* 3.0 28.0 + - - +
140E LYS* 3.8 30.5 - - + +
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Residues in contact with THR 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 5.7 0.2 - - - +
25E GLU* 2.6 31.2 + - - +
28E ALA* 1.3 70.9 - - - +
30E VAL* 1.3 66.1 + - - +
32E LEU* 3.1 7.2 + - - +
33E LEU* 2.9 32.4 + - + +
87E LEU* 3.3 25.5 - - + +
140E LYS* 5.3 3.6 + - - +
141E ASP* 3.8 19.0 + - - +
144E THR* 3.1 36.1 - - + +
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Residues in contact with VAL 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 4.0 15.3 - - + +
14E LEU* 4.2 5.2 - - + -
26E LYS 2.8 27.8 + - - +
27E LYS* 3.7 6.5 - - - +
29E THR* 1.3 73.1 - - - +
31E GLU* 1.3 58.1 + - - +
33E LEU* 3.6 0.9 + - - +
34E ASN* 3.0 47.0 + - - +
84E ALA* 3.7 24.7 - - + +
87E LEU* 4.2 7.9 - - + -
89E GLY* 3.6 36.3 - - - +
90E VAL 4.2 2.0 - - - +
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Residues in contact with GLU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 6.1 1.8 - - + -
27E LYS 3.0 14.5 + - - +
28E ALA* 3.5 11.9 - - - +
29E THR 3.1 0.2 - - - -
30E VAL* 1.3 77.4 - - - +
32E LEU* 1.3 66.0 + - - +
34E ASN* 3.5 4.6 + - - +
35E ARG* 3.1 28.3 + - - +
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ALA 3.0 14.5 + - - +
29E THR* 3.6 10.3 - - + +
31E GLU* 1.3 76.7 - - - +
33E LEU* 1.3 63.0 + - + +
35E ARG* 3.2 40.5 + - - +
36E GLN* 3.2 20.7 + - + +
135E ALA* 3.9 30.5 - - + +
138E GLU* 3.6 20.0 - - + +
139E ALA* 4.0 24.0 - - + +
144E THR* 5.0 5.6 - - + -
148E LEU* 4.2 11.0 - - + -
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E THR* 2.9 28.1 + - + +
30E VAL 3.9 2.9 - - - +
32E LEU* 1.3 72.7 - - - +
34E ASN* 1.3 60.6 + - - +
35E ARG 3.0 2.0 - - - -
36E GLN* 2.8 9.2 + - - +
37E VAL* 2.8 30.7 + - - +
80E MET* 3.6 35.1 - - + +
83E ARG* 3.5 20.4 - - + -
84E ALA* 3.4 38.4 - - + +
144E THR* 3.5 24.9 - - + -
147E ILE* 5.1 2.5 - - + -
148E LEU* 4.6 10.3 - - + -
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Residues in contact with ASN 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E VAL* 3.0 40.1 + - - +
31E GLU* 4.0 5.6 - - - +
33E LEU* 1.3 75.8 - - - +
35E ARG* 1.3 61.4 + - - +
37E VAL* 3.7 9.0 - - - +
38E ILE* 3.1 33.6 + - + +
84E ALA* 4.5 4.6 - - - +
90E VAL 3.0 21.6 + - - -
91E ALA* 3.3 6.0 - - - +
92E LEU* 2.6 51.0 + - + +
101E LYS* 6.3 0.4 - - - +
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Residues in contact with ARG 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLU* 3.1 18.0 + - - +
32E LEU* 3.2 38.3 - - - +
33E LEU 3.0 0.6 - - - -
34E ASN* 1.3 76.3 - - - +
36E GLN* 1.3 70.0 + - - +
38E ILE* 3.6 9.3 + - - +
39E GLN* 3.4 23.9 + - - +
131E ASP* 2.8 40.4 + - - -
135E ALA* 4.4 3.8 - - - +
138E GLU* 3.8 14.5 + - - -
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Residues in contact with GLN 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.5 15.9 - - + +
33E LEU* 2.8 8.1 + - - +
35E ARG* 1.3 83.0 + - - +
37E VAL* 1.3 61.0 + - - +
39E GLN* 2.9 27.4 + - - +
40E PHE* 2.8 54.4 + - - -
80E MET* 3.6 19.3 - - - -
131E ASP* 3.7 10.2 - - - +
132E VAL* 3.6 20.8 - - - +
135E ALA* 3.6 20.1 - - - +
148E LEU* 3.9 18.6 - - + -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU 2.8 23.2 + - - +
34E ASN* 3.7 14.6 - - - +
36E GLN* 1.3 72.0 - - - +
38E ILE* 1.3 58.2 + - - +
40E PHE* 3.7 2.0 - - - +
41E ILE* 2.8 54.0 + - + +
77E LEU* 4.0 13.0 - - + +
80E MET* 4.0 14.6 - - + +
81E ALA* 3.8 32.1 - - + +
84E ALA* 6.2 0.7 - - + -
92E LEU 3.5 22.4 - - - +
52F TRP* 4.6 7.4 - - + -
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Residues in contact with ILE 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ASN* 3.1 21.5 + - + +
35E ARG* 3.8 8.1 - - - +
37E VAL* 1.3 76.6 - - - +
39E GLN* 1.3 62.4 + - - +
42E ASP* 3.1 23.2 + - - +
92E LEU* 4.0 17.9 - - + +
97E VAL* 3.6 23.3 - - + -
98E ILE* 3.5 38.8 - - + +
101E LYS* 3.9 27.1 - - + +
102E THR* 4.0 23.3 - - - +
103E PRO* 5.0 1.1 - - + -
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Residues in contact with GLN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ARG* 3.4 10.5 + - - +
36E GLN* 2.9 33.1 + - - +
38E ILE* 1.3 80.4 - - - +
40E PHE* 1.3 57.8 + - + +
42E ASP* 3.3 5.8 + - - +
43E LEU* 2.9 29.2 + - - +
102E THR* 5.2 0.2 - - - -
103E PRO* 3.3 39.3 - - + +
104E LEU* 4.0 3.3 - - + +
127E ILE* 4.3 7.1 - - - +
128E VAL* 3.4 36.5 - - + +
131E ASP* 3.0 34.8 + - - +
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Residues in contact with PHE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E GLN* 2.8 50.4 + - - +
37E VAL 3.7 3.1 - - - +
39E GLN* 1.3 70.7 - - - +
41E ILE* 1.3 67.1 + - - +
43E LEU* 3.1 8.0 + - + +
44E SER* 2.9 24.3 + - - -
73E LEU* 3.8 32.4 - - + +
76E HIS* 4.0 19.1 - - + -
77E LEU* 4.0 15.9 - - + -
80E MET* 3.6 18.4 - - + -
128E VAL* 3.6 19.1 - - + -
132E VAL* 4.3 9.2 - - + -
151E ALA* 3.9 13.9 - - + -
155E LEU* 3.2 34.1 - - + -
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Residues in contact with ILE 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E VAL* 2.8 41.5 + - + +
38E ILE 3.9 3.4 - - - +
40E PHE* 1.3 71.5 - - - +
42E ASP* 1.3 62.9 + - - +
44E SER* 2.6 22.0 + - - +
45E LEU* 3.0 17.1 + - + +
77E LEU* 3.3 25.8 - - + +
93E GLY* 3.7 27.4 - - - +
98E ILE* 3.9 16.4 - - + -
45F LEU* 3.6 28.9 - - + -
52F TRP* 4.3 11.4 - - + -
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Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ILE 3.1 18.3 + - - +
39E GLN 3.7 3.8 - - - +
41E ILE* 1.3 75.9 - - - +
43E LEU* 1.3 59.6 + - - +
45E LEU* 3.2 6.2 + - - +
46E ILE* 2.9 43.0 + - - +
98E ILE* 3.8 9.2 - - + +
102E THR* 2.6 31.7 + - - +
104E LEU* 3.4 20.2 - - + +
95F THR* 3.0 37.0 + - - +
96F GLN* 4.9 1.2 - - - +
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E GLN 2.9 17.4 + - - +
40E PHE* 3.1 6.9 + - + +
42E ASP* 1.3 77.2 - - - +
44E SER* 1.3 53.9 + - - +
46E ILE* 3.3 7.3 + - + +
47E THR* 2.7 37.5 + - - -
73E LEU* 4.0 11.2 - - + -
104E LEU* 3.9 12.1 - - + +
124E ARG* 3.8 28.3 - - + +
125E TYR* 3.5 51.8 - - + -
128E VAL* 4.0 11.2 - - + -
155E LEU* 3.9 23.3 - - + -
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Residues in contact with SER 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PHE 2.9 12.6 + - - -
41E ILE* 2.6 25.7 + - - +
43E LEU* 1.3 74.7 - - - +
45E LEU* 1.3 67.8 + - - +
47E THR* 3.3 5.3 + - - -
48E LYS* 3.3 20.3 + - - +
70E ARG* 4.1 19.4 - - - +
73E LEU* 3.9 26.2 - - - +
74E ILE* 4.6 13.5 - - - +
77E LEU* 4.7 2.2 - - - +
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Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ILE* 3.0 26.5 + - + +
42E ASP* 3.5 11.4 - - - +
44E SER* 1.3 84.8 + - - +
46E ILE* 1.3 64.2 + - + +
48E LYS* 3.3 8.3 + - - +
49E GLN* 3.1 21.8 + - - +
52E TRP* 5.3 0.5 - - - -
98E ILE* 5.2 2.2 - - + -
41F ILE* 3.6 31.9 - - + -
45F LEU* 4.7 18.2 - - + -
93F GLY 3.9 17.1 - - - +
94F THR* 5.0 1.1 - - - -
95F THR* 4.1 33.7 - - - +
98F ILE* 5.3 1.1 - - + -
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Residues in contact with ILE 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ASP* 2.9 33.2 + - - +
43E LEU* 3.5 7.4 - - + +
45E LEU* 1.3 74.9 - - + +
47E THR* 1.3 65.3 + - - +
49E GLN* 3.0 18.4 + - - +
50E ALA* 3.0 13.0 + - - +
104E LEU* 3.7 30.1 - - + -
105E LYS 4.7 2.2 - - - +
107E TYR* 3.4 41.7 - - + +
121E LEU* 3.9 11.0 - - + -
124E ARG* 4.1 24.5 - - + +
94F THR* 5.3 6.7 - - + -
96F GLN* 5.9 2.7 - - - +
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Residues in contact with THR 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU 2.7 27.7 + - - -
44E SER* 3.5 9.4 - - - -
46E ILE* 1.3 72.6 - - - +
48E LYS* 1.3 59.1 + - + +
50E ALA* 3.6 2.8 + - - +
51E HIS* 3.0 28.5 + - + +
66E LEU* 3.3 44.2 - - + +
70E ARG* 4.4 10.3 - - + +
73E LEU* 3.9 2.8 - - - +
121E LEU* 4.2 9.4 - - - -
125E TYR* 2.6 34.1 + - - +
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Residues in contact with LYS 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E SER 3.3 9.1 + - - +
45E LEU* 3.3 10.4 + - + +
46E ILE 3.1 0.6 - - - -
47E THR* 1.3 78.2 - - + +
49E GLN* 1.3 59.0 + - - +
51E HIS* 3.1 33.9 + - + +
52E TRP* 2.8 65.3 + - + +
67E ASP* 2.8 24.7 + - - +
70E ARG* 2.9 49.1 - - + +
78F ASP* 2.8 24.3 + - - +
82F GLU* 5.4 1.0 + - - -
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Residues in contact with GLN 49 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU 3.1 9.6 + - - +
46E ILE* 3.0 13.6 + - - +
48E LYS* 1.3 77.1 - - - +
50E ALA* 1.3 62.3 + - - +
52E TRP* 4.0 6.0 - - - -
53E ASN* 2.9 37.8 + - - +
107E TYR* 4.2 16.1 - - + -
108E PRO 4.4 3.6 + - - -
109E LEU* 4.0 19.3 - - - +
117E HIS* 4.5 1.7 - - - -
90F VAL* 5.3 1.2 - - - +
91F ALA 2.7 23.8 - - - +
92F LEU* 3.2 4.0 - - - +
93F GLY* 3.0 18.9 + - - +
94F THR* 3.2 38.1 - - + +
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Residues in contact with ALA 50 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ILE 3.0 2.9 + - - +
47E THR 3.8 2.7 - - - +
49E GLN* 1.3 78.1 - - - +
51E HIS* 1.3 65.5 + - - +
53E ASN 3.3 2.4 + - - -
54E MET* 3.2 31.7 + - + +
107E TYR* 3.4 23.6 - - - +
117E HIS* 3.5 18.5 + - + +
121E LEU* 3.6 35.7 - - + -
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Residues in contact with HIS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E THR* 3.0 20.8 + - + +
48E LYS* 3.1 37.8 + - + +
50E ALA* 1.3 76.7 - - - +
52E TRP* 1.3 80.1 + + - +
54E MET* 3.5 9.8 - - - +
59E PHE* 4.6 0.9 - - - -
63E HIS* 2.7 82.5 + + - -
64E GLU* 5.0 0.4 - - - -
66E LEU* 4.0 18.3 - - + +
67E ASP* 3.8 20.5 + - + -
82F GLU* 4.7 4.9 + - - -
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Residues in contact with TRP 52 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D TRP* 3.9 10.1 + + - -
45E LEU 5.3 0.7 - - - -
48E LYS* 2.8 54.0 + - + +
49E GLN* 4.0 7.0 - - - -
51E HIS* 1.3 94.8 + + - +
53E ASN* 1.3 61.9 + - - +
54E MET 3.6 2.3 + - - +
63E HIS* 4.6 3.4 - + - -
37F VAL* 4.6 2.5 - - + -
41F ILE* 4.3 10.5 - - + -
77F LEU* 3.6 21.8 - - + -
78F ASP* 3.3 30.5 + - - +
81F ALA* 3.4 26.7 - - + +
82F GLU* 4.3 15.4 + - + +
85F VAL* 3.4 26.8 - - + +
91F ALA* 3.8 29.4 - - + -
92F LEU 4.8 0.7 - - - -
93F GLY* 4.1 24.2 - - - -
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Residues in contact with ASN 53 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLN* 2.9 32.9 + - - +
50E ALA 3.3 4.7 + - - -
52E TRP* 1.3 82.5 - - - +
54E MET* 1.3 60.6 + - - +
55E ARG* 4.7 2.8 - - - +
111E ILE 4.6 2.0 - - - +
112E HIS* 3.1 32.8 + - + +
117E HIS* 3.4 16.3 + - + +
85F VAL* 3.5 11.4 - - - +
89F GLY 4.3 0.9 - - - +
90F VAL* 3.4 16.5 - - + +
91F ALA* 2.9 46.3 + - - +
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Residues in contact with MET 54 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D TRP* 5.2 1.6 + - - -
164D SER* 4.4 1.2 + - - -
50E ALA* 3.2 16.9 + - + +
51E HIS 3.5 11.2 - - - +
52E TRP 3.6 3.1 - - - +
53E ASN* 1.3 79.5 - - - +
55E ARG* 1.3 69.8 + - - +
59E PHE* 3.3 33.0 - - + +
62E VAL* 3.5 28.3 - - + -
63E HIS* 4.0 16.8 - - - -
66E LEU* 3.4 26.9 - - + -
112E HIS 3.2 6.3 - - - +
114E VAL* 4.3 15.9 - - + +
117E HIS* 3.7 30.3 - - + -
118E LEU* 5.0 0.9 - - + -
121E LEU* 4.7 2.0 - - + -
85F VAL* 6.1 0.2 - - - +
----------------------------------------------------------
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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