Contacts of the helix formed by residues 22 - 54 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP 3.6 3.8 + - - -
21A VAL* 1.3 74.0 - - - +
23A ASP* 1.3 61.9 + - - +
24A SER* 3.7 10.1 - - - -
25A GLU* 3.0 31.7 + - - +
26A LYS 2.8 26.2 + - - -
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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
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12A THR 5.6 1.7 - - - +
14A LEU* 4.0 26.1 - - + +
21A VAL 3.4 3.9 + - - +
22A SER* 1.3 72.8 - - - +
24A SER* 1.3 62.0 - - - +
26A LYS* 4.0 4.9 + - - +
27A LYS* 3.0 38.9 + - - +
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Residues in contact with SER 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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22A SER* 2.9 12.0 - - - -
23A ASP* 1.3 80.6 - - - +
25A GLU* 1.3 58.9 + - - +
27A LYS* 3.8 3.9 - - - +
28A ALA* 3.0 27.1 + - - +
140A LYS* 4.3 11.8 + - - -
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Residues in contact with GLU 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 VAL* 3.7 18.4 - - + +
22A SER* 3.0 18.4 + - - +
24A SER* 1.3 76.8 - - - +
26A LYS* 1.3 58.7 + - - +
28A ALA* 4.1 6.5 - - - -
29A THR* 2.6 43.8 + - - +
140A LYS* 3.1 44.9 - - + +
141A ASP* 3.4 15.9 + - - +
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Residues in contact with LYS 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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14A LEU* 3.6 24.1 - - + +
15A LEU 5.2 2.0 + - - -
17A THR* 3.3 24.4 + - - +
19A ASN* 2.7 31.6 + - - -
20A ASP* 4.8 0.2 - - - +
21A VAL* 2.8 45.0 + - + +
22A SER 2.8 13.7 + - - +
23A ASP* 3.7 6.1 + - - +
25A GLU* 1.3 72.3 - - - +
27A LYS* 1.3 53.5 + - - +
29A THR* 3.7 2.4 - - - -
30A VAL* 2.8 42.2 + - - +
87A LEU* 3.2 36.3 - - + +
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Residues in contact with LYS 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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12A THR 3.5 7.0 + - - -
13A ASN* 2.8 50.7 - - - +
14A LEU* 3.6 29.8 - - + -
23A ASP* 3.0 28.2 + - + +
24A SER* 3.8 3.8 - - - +
26A LYS* 1.3 75.8 - - - +
28A ALA* 1.3 64.4 + - - +
30A VAL* 3.7 3.9 - - - +
31A GLU* 3.1 24.2 + - - +
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Residues in contact with ALA 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 SER 3.0 18.5 + - - +
25A GLU* 3.6 4.0 - - - +
27A LYS* 1.3 75.1 - - - +
29A THR* 1.3 63.5 + - - +
31A GLU* 3.2 10.5 + - - +
32A LEU* 3.0 21.5 + - - +
140A LYS* 3.9 30.3 - - + +
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Residues in contact with THR 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 GLU* 2.6 30.0 + - - +
28A ALA* 1.3 69.4 - - - +
30A VAL* 1.3 67.5 + - - +
32A LEU* 2.9 9.5 + - + +
33A LEU* 2.8 32.3 + - + +
87A LEU* 3.3 24.3 - - + +
140A LYS* 5.3 4.0 + - - +
141A ASP* 3.8 18.7 + - + +
144A THR* 3.2 35.7 - - + +
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Residues in contact with VAL 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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14A LEU* 4.6 4.5 - - + -
26A LYS 2.8 28.5 + - - +
27A LYS* 3.7 6.5 - - - +
29A THR* 1.3 73.0 - - - +
31A GLU* 1.3 58.2 + - - +
33A LEU* 3.9 0.6 - - - +
34A ASN* 3.0 46.8 + - - +
84A ALA* 3.6 32.7 - - + +
87A LEU* 4.2 10.5 - - + +
89A GLY* 3.6 27.8 - - - +
90A VAL 4.2 2.7 - - - +
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Residues in contact with GLU 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 LYS 3.1 13.5 + - - +
28A ALA* 3.4 11.8 - - - +
29A THR 3.0 0.6 - - - -
30A VAL* 1.3 77.1 - - - +
32A LEU* 1.3 65.7 + - - +
34A ASN* 3.6 4.9 + - - +
35A ARG* 3.2 27.6 + - - +
101A LYS* 6.0 3.8 - - - +
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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 ALA 3.0 11.7 + - - +
29A THR* 2.9 12.4 + - + +
31A GLU* 1.3 76.5 - - - +
33A LEU* 1.3 63.3 + - + +
35A ARG* 3.3 40.3 + - - +
36A GLN* 3.2 19.9 + - + +
135A ALA* 3.9 30.3 - - + +
138A GLU* 3.6 20.4 - - + +
139A ALA* 4.0 23.3 - - + +
144A THR* 5.0 4.7 - - + -
148A LEU* 4.2 12.8 - - + -
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Residues in contact with LEU 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 THR* 2.8 29.4 + - + +
30A VAL 3.9 2.5 - - - +
32A LEU* 1.3 74.6 - - - +
34A ASN* 1.3 58.9 + - - +
36A GLN* 2.7 26.7 + - - +
37A VAL* 2.8 16.4 + - + +
80A MET* 3.6 35.6 - - + +
83A ARG* 3.6 19.7 - - + -
84A ALA* 3.4 36.8 - - + +
144A THR* 3.6 25.4 - - + -
147A ILE* 5.2 2.5 - - + -
148A LEU* 4.6 9.9 - - + -
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Residues in contact with ASN 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 VAL* 3.0 38.5 + - - +
31A GLU* 4.0 5.1 - - - +
33A LEU* 1.3 76.2 - - - +
35A ARG* 1.3 63.0 + - - +
37A VAL* 3.6 8.9 - - - +
38A ILE* 3.0 33.6 + - + +
84A ALA* 4.5 5.4 - - - +
90A VAL 3.0 20.9 + - - -
91A ALA* 3.4 5.9 - - - +
92A LEU* 2.6 50.4 + - + +
101A LYS* 5.9 2.9 - - - +
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Residues in contact with ARG 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 GLU* 3.2 18.7 + - - +
32A LEU* 3.3 38.6 - - - +
33A LEU 3.0 0.4 - - - -
34A ASN* 1.3 79.0 - - - +
36A GLN* 1.3 71.7 + - - +
38A ILE* 3.8 9.4 - - - +
39A GLN* 3.4 21.9 + - - +
101A LYS* 5.8 5.6 - - - +
131A ASP* 2.8 40.6 + - - -
135A ALA* 4.4 4.2 - - - +
138A GLU* 3.9 14.3 + - - -
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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
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32A LEU* 3.5 15.7 - - + +
33A LEU* 2.7 9.1 + - - +
35A ARG* 1.3 84.8 + - - +
37A VAL* 1.3 58.8 + - - +
39A GLN* 2.9 27.4 + - - +
40A PHE* 2.8 54.6 + - - -
80A MET* 3.6 19.7 - - - -
131A ASP* 3.7 10.9 - - - +
132A VAL* 3.7 20.5 - - - +
135A ALA* 3.6 19.6 - - - +
148A LEU* 3.9 18.2 - - + -
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Residues in contact with VAL 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU 2.8 22.8 + - - +
34A ASN* 3.3 15.5 + - - +
36A GLN* 1.3 71.7 - - - +
38A ILE* 1.3 56.8 + - - +
40A PHE* 3.8 1.8 - - - +
41A ILE* 2.9 53.0 + - + +
77A LEU* 3.9 16.8 - - + +
80A MET* 4.0 11.2 - - + -
81A ALA* 3.8 32.5 - - + +
92A LEU 3.6 22.2 - - - +
52B TRP* 4.5 7.9 - - + -
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Residues in contact with ILE 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 ASN* 3.0 22.2 + - + +
35A ARG* 3.8 8.3 - - - +
37A VAL* 1.3 74.8 - - - +
39A GLN* 1.3 62.5 + - - +
42A ASP* 3.1 24.3 + - - +
92A LEU* 4.0 18.4 - - + +
97A VAL* 3.6 17.0 - - + -
98A ILE* 3.5 37.6 - - + +
101A LYS* 3.5 56.5 - - + +
102A THR* 4.0 6.7 - - - +
103A PRO* 5.0 0.7 - - + -
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Residues in contact with GLN 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 ARG* 3.4 10.9 + - - +
36A GLN* 2.9 37.0 + - - +
38A ILE* 1.3 80.7 - - - +
40A PHE* 1.3 57.2 + - + +
42A ASP* 3.4 4.6 + - - +
43A LEU* 2.9 28.5 + - - +
103A PRO* 3.4 39.0 - - + +
104A LEU* 4.0 4.2 - - + +
127A ILE* 4.3 6.7 - - - +
128A VAL* 3.3 37.5 - - + +
131A ASP* 3.0 34.7 + - - +
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Residues in contact with PHE 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* 2.8 51.1 + - - +
37A VAL 3.9 2.7 - - - +
39A GLN* 1.3 70.0 - - - +
41A ILE* 1.3 67.2 + - - +
43A LEU* 3.1 7.5 + - + +
44A SER* 2.9 25.1 + - - -
73A LEU* 3.8 30.5 - - + +
76A HIS* 4.0 15.5 - - + -
77A LEU* 4.0 16.1 - - + +
80A MET* 3.6 22.9 - - + -
128A VAL* 3.6 17.3 - - + -
132A VAL* 4.3 9.0 - - + -
151A ALA* 3.9 14.1 - - + -
155A LEU* 3.2 35.2 - - + -
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Residues in contact with ILE 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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37A VAL* 2.9 36.8 + - + +
38A ILE 3.9 3.4 - - - +
40A PHE* 1.3 75.1 - - - +
42A ASP* 1.3 61.8 + - - +
44A SER* 2.7 22.1 + - - +
45A LEU* 3.0 17.8 + - + +
77A LEU* 3.3 25.8 - - + -
93A GLY* 3.7 34.1 - - - +
98A ILE* 3.9 16.6 - - + -
45B LEU* 3.6 28.0 - - + -
52B TRP* 4.3 11.2 - - + -
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Residues in contact with ASP 42 (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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38A ILE 3.1 17.9 + - - +
39A GLN 3.8 3.4 - - - +
41A ILE* 1.3 79.5 - - - +
43A LEU* 1.3 57.6 + - - +
45A LEU* 3.3 6.3 + - - +
46A ILE* 2.9 43.6 + - - +
98A ILE* 3.7 9.6 - - + +
102A THR* 2.7 31.1 + - - +
104A LEU* 3.4 19.8 - - + +
95B THR* 3.1 35.9 + - - +
96B GLN* 4.8 1.7 - - - +
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Residues in contact with LEU 43 (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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39A GLN 2.9 17.6 + - - +
40A PHE* 3.1 6.9 + - + +
42A ASP* 1.3 76.9 - - - +
44A SER* 1.3 52.9 + - - +
46A ILE* 3.3 7.6 + - + +
47A THR* 2.7 36.8 + - - -
73A LEU* 4.1 10.5 - - + -
104A LEU* 3.9 11.8 - - + +
124A ARG* 3.8 28.0 - - + +
125A TYR* 3.6 52.0 - - + -
128A VAL* 4.0 11.7 - - + -
155A LEU* 3.8 23.6 - - + -
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Residues in contact with SER 44 (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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40A PHE 2.9 12.7 + - - -
41A ILE* 2.7 24.7 + - - +
43A LEU* 1.3 75.0 - - - +
45A LEU* 1.3 67.7 + - - +
47A THR* 3.3 6.1 + - - -
48A LYS* 3.2 24.3 + - - +
70A ARG* 4.1 17.1 + - - +
73A LEU* 3.9 25.3 - - - +
74A ILE* 4.7 12.3 - - - +
77A LEU* 4.7 4.1 - - - +
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Residues in contact with LEU 45 (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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41A ILE* 3.0 25.9 + - + +
42A ASP* 3.6 10.3 - - - +
44A SER* 1.3 84.1 + - - +
46A ILE* 1.3 63.3 + - + +
48A LYS* 3.2 9.4 + - + +
49A GLN* 3.1 22.3 + - - +
52A TRP* 5.3 0.5 - - - -
98A ILE* 5.2 2.5 - - + -
41B ILE* 3.6 33.0 - - + -
45B LEU* 4.7 18.2 - - + -
93B GLY 3.8 17.5 - - - +
94B THR* 5.0 0.9 - - - -
95B THR* 4.1 33.7 - - - +
98B ILE* 5.3 1.3 - - + -
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Residues in contact with ILE 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 2.9 34.4 + - - +
43A LEU* 3.6 7.4 - - + +
45A LEU* 1.3 76.0 - - + +
47A THR* 1.3 65.9 + - - +
49A GLN* 3.1 9.2 + - - +
50A ALA* 3.0 21.8 + - - +
104A LEU* 3.7 31.6 - - + -
105A LYS 4.8 1.8 - - - +
106A SER* 6.2 0.2 - - - -
107A TYR* 3.3 42.2 - - + +
121A LEU* 3.9 10.1 - - + -
124A ARG* 4.2 22.4 - - + +
94B THR* 5.3 6.1 - - + -
96B GLN* 5.9 3.4 - - - +
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Residues in contact with THR 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU 2.7 25.0 + - - -
44A SER* 3.5 8.7 - - - -
45A LEU 3.3 0.2 - - - -
46A ILE* 1.3 76.0 - - - +
48A LYS* 1.3 58.7 + - + +
50A ALA* 3.5 2.4 + - - +
51A HIS* 2.9 29.0 + - + +
66A LEU* 3.3 44.7 - - + +
70A ARG* 4.4 9.4 - - + +
73A LEU* 3.9 2.8 - - - +
121A LEU* 4.2 9.2 - - - -
125A TYR* 2.6 32.7 + - + +
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Residues in contact with LYS 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER 3.2 10.5 + - - +
45A LEU* 3.2 10.4 + - + +
46A ILE 3.2 0.6 - - - -
47A THR* 1.3 79.5 - - + +
49A GLN* 1.3 59.1 + - - +
51A HIS* 3.0 34.8 + - + +
52A TRP* 2.8 64.7 + - + +
67A ASP* 2.8 24.5 + - - +
70A ARG* 2.9 48.0 - - + +
78B ASP* 2.8 23.0 + - - +
82B GLU* 5.4 1.0 + - - -
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Residues in contact with GLN 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU 3.1 9.8 + - - +
46A ILE* 3.1 13.4 + - - +
48A LYS* 1.3 77.5 - - - +
50A ALA* 1.3 62.0 + - - +
52A TRP* 4.0 6.2 - - - -
53A ASN* 2.9 48.4 + - - +
107A TYR* 4.3 14.6 - - + -
108A PRO 4.5 3.6 + - - -
109A LEU* 4.0 19.1 - - - +
117A HIS* 4.5 1.4 - - - -
90B VAL* 5.2 0.4 - - - +
91B ALA 2.6 24.5 + - - +
92B LEU* 3.2 3.6 - - - +
93B GLY 3.0 19.5 + - - +
94B THR* 3.3 37.5 - - + +
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Residues in contact with ALA 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE 3.0 4.6 + - - +
47A THR 3.8 1.3 - - - +
49A GLN* 1.3 77.7 - - - +
51A HIS* 1.3 64.7 + - - +
53A ASN 3.3 1.7 + - - -
54A MET* 3.2 32.2 + - + +
107A TYR* 3.4 23.5 - - - +
117A HIS* 3.4 18.5 - - + +
121A LEU* 3.6 35.0 - - + -
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Residues in contact with HIS 51 (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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47A THR* 2.9 20.6 + - + +
48A LYS* 3.0 41.9 + - + +
50A ALA* 1.3 77.5 - - - +
52A TRP* 1.3 76.6 + + - +
54A MET* 3.6 10.0 - - - +
59A PHE* 4.6 0.7 - - - -
63A HIS* 2.7 82.1 + + - -
64A GLU* 5.0 0.2 - - - -
66A LEU* 4.0 17.9 - - + +
67A ASP* 3.8 20.1 + - + -
82B GLU* 4.6 6.0 + - - -
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Residues in contact with TRP 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 2.8 50.8 + - + +
49A GLN* 4.0 7.0 - - - -
51A HIS* 1.3 96.3 - + - +
53A ASN* 1.3 62.4 + - - +
54A MET 3.6 2.3 + - - +
63A HIS* 4.7 3.1 - + - -
37B VAL* 4.5 2.7 - - + -
41B ILE* 4.3 11.4 - - + -
77B LEU* 3.5 20.9 - - + -
78B ASP* 3.3 31.5 + - - +
81B ALA* 3.3 26.3 - - + +
82B GLU* 4.2 16.4 - - + +
85B VAL* 3.4 25.9 - - + +
91B ALA* 3.7 30.3 - - + -
92B LEU 4.7 0.9 - - - -
93B GLY* 4.1 23.8 - - - -
160E TRP* 3.9 10.0 - - - -
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Residues in contact with ASN 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN* 2.9 32.9 + - - +
50A ALA 3.3 4.6 + - - -
52A TRP* 1.3 81.0 - - - +
54A MET* 1.3 60.8 + - - +
55A ARG* 4.8 2.5 - - - +
111A ILE 4.6 1.3 - - - +
112A HIS* 3.0 33.3 + - + +
117A HIS* 3.4 16.0 + - + +
85B VAL* 3.4 14.2 - - - +
89B GLY 4.3 1.0 - - - +
90B VAL* 3.4 15.1 - - + +
91B ALA 2.9 46.4 + - - +
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Residues in contact with MET 54 (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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50A ALA* 3.2 17.2 + - + +
51A HIS 3.6 10.8 - - - +
52A TRP 3.6 2.9 - - - +
53A ASN* 1.3 78.9 - - - +
55A ARG* 1.3 69.4 + - - +
59A PHE* 3.3 31.2 - - + +
62A VAL* 3.4 30.3 - - + -
63A HIS* 4.1 11.2 - - - -
66A LEU* 3.3 30.3 - - + -
112A HIS 3.2 5.6 - - - +
114A VAL* 4.3 17.3 - - + +
117A HIS* 3.6 30.1 - - + -
118A LEU* 5.0 0.7 - - + -
121A LEU* 4.6 2.0 - - + -
85B VAL* 6.0 0.5 - - - +
160E TRP* 5.2 1.6 + - - -
164E SER* 4.4 0.9 + - - -
----------------------------------------------------------
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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