Contacts of the helix formed by residues 22 - 54 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP 3.6 2.8 + - - -
21B VAL* 1.3 75.8 - - - +
23B ASP* 1.3 61.6 + - - +
24B SER* 3.6 11.1 - - - -
25B GLU* 3.0 32.5 + - - +
26B LYS* 2.8 25.6 + - - +
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Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.7 28.0 - - + +
21B VAL 4.2 4.3 - - - +
22B SER* 1.3 73.3 - - - +
24B SER* 1.3 63.4 + - - +
26B LYS* 3.7 4.3 + - - +
27B LYS* 2.9 36.0 + - + +
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Residues in contact with SER 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 3.6 11.4 - - - -
23B ASP* 1.3 80.2 - - - +
25B GLU* 1.3 58.8 + - - +
27B LYS* 3.7 4.5 - - - +
28B ALA* 3.0 27.5 + - - +
140B LYS* 4.2 12.3 + - - -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 3.7 18.0 - - + +
22B SER* 3.0 19.2 + - - +
24B SER* 1.3 77.6 - - - +
26B LYS* 1.3 56.8 + - - +
28B ALA* 4.1 6.1 - - - -
29B THR* 2.6 46.0 + - - +
140B LYS* 3.2 43.9 - - + +
141B ASP* 3.4 15.9 + - - +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.5 25.2 - - + +
15B LEU 5.2 2.6 + - - -
17B THR* 3.4 24.4 + - - +
19B ASN* 2.8 31.6 + - - -
21B VAL* 2.9 37.1 + - + +
22B SER 2.8 20.5 + - - +
23B ASP* 3.7 5.0 + - - +
25B GLU* 1.3 72.0 - - - +
27B LYS* 1.3 53.3 + - - +
29B THR* 3.7 2.0 - - - -
30B VAL* 2.8 42.3 + - - +
87B LEU* 3.1 37.5 - - + +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 3.8 25.5 - - + +
13B ASN* 3.5 38.0 - - - +
14B LEU* 4.1 24.2 - - + +
23B ASP* 2.9 24.5 + - - +
24B SER* 3.7 4.7 - - - +
26B LYS* 1.3 76.1 - - - +
28B ALA* 1.3 63.0 + - - +
30B VAL* 3.9 4.3 - - - +
31B GLU* 3.2 23.6 + - - +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER 3.0 17.5 + - - +
25B GLU* 3.6 3.6 - - - +
27B LYS* 1.3 76.6 - - - +
29B THR* 1.3 57.7 + - - +
31B GLU* 3.2 11.1 + - - +
32B LEU* 3.0 27.3 + - - +
140B LYS* 3.8 31.0 - - + +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 5.7 0.2 - - - +
25B GLU* 2.6 31.3 + - - +
26B LYS 3.7 0.2 - - - -
28B ALA* 1.3 71.2 - - - +
30B VAL* 1.3 57.9 + - - -
32B LEU* 3.0 9.2 + - + +
33B LEU* 2.8 38.7 + - + +
87B LEU* 3.3 24.9 - - + +
140B LYS* 5.3 4.0 + - - +
141B ASP* 3.8 18.1 + - + +
144B THR* 3.1 34.5 - - + +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR 6.1 2.7 - - - +
14B LEU* 4.6 3.1 - - + -
26B LYS 2.8 31.3 + - - +
27B LYS* 3.9 5.8 - - - +
29B THR* 1.3 72.6 - - - +
31B GLU* 1.3 58.0 + - - +
33B LEU* 3.9 0.9 - - - +
34B ASN* 3.0 46.0 + - - +
84B ALA* 3.6 33.8 - - + +
87B LEU* 4.2 10.5 - - + +
89B GLY* 3.7 28.9 - - - +
90B VAL 4.2 1.8 - - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS 3.2 12.1 + - - +
28B ALA* 3.4 11.4 - - - +
29B THR 3.1 0.2 - - - -
30B VAL* 1.3 79.5 - - - +
32B LEU* 1.3 65.1 + - - +
34B ASN* 4.1 4.9 - - - +
35B ARG* 3.2 26.8 + - + +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA 3.0 13.0 + - - +
29B THR* 3.0 11.6 + - + +
31B GLU* 1.3 77.4 - - - +
33B LEU* 1.3 64.2 + - - +
35B ARG* 3.2 40.5 + - - +
36B GLN* 3.2 20.8 + - + +
135B ALA* 3.9 31.2 - - + +
138B GLU* 3.6 20.4 - - + +
139B ALA* 4.0 23.1 - - + +
144B THR* 5.1 5.4 - - + -
148B LEU* 4.3 11.2 - - + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR* 2.8 29.5 + - + +
30B VAL 3.9 3.1 - - - +
32B LEU* 1.3 77.0 - - + +
34B ASN* 1.3 57.3 + - - +
36B GLN* 2.8 23.1 + - - +
37B VAL* 2.8 17.3 + - - +
80B MET* 3.6 34.0 - - + +
83B ARG* 3.5 21.8 - - + -
84B ALA* 3.4 36.3 - - + +
144B THR* 3.5 25.6 - - + -
147B ILE* 5.2 2.9 - - + -
148B LEU* 4.6 9.2 - - + -
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Residues in contact with ASN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.0 38.7 + - - +
31B GLU* 4.1 5.6 - - - +
33B LEU* 1.3 76.4 - - - +
35B ARG* 1.3 60.9 + - - +
37B VAL* 3.7 8.7 - - - +
38B ILE* 3.1 34.2 + - + +
84B ALA* 4.5 4.4 - - - +
90B VAL 3.0 21.2 + - - -
91B ALA* 3.3 7.1 - - - +
92B LEU* 2.7 49.6 + - + +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLU* 3.2 17.8 + - - +
32B LEU* 3.2 38.4 - - - +
33B LEU 3.0 0.6 - - - -
34B ASN* 1.3 78.3 - - - +
36B GLN* 1.3 68.6 + - - +
38B ILE* 3.6 9.7 + - - +
39B GLN* 3.4 23.2 + - - +
131B ASP* 2.8 41.4 + - - -
135B ALA* 4.3 3.6 - - - +
138B GLU* 3.8 14.1 + - - -
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.2 16.6 + - + +
33B LEU* 2.8 8.5 + - - +
35B ARG* 1.3 83.7 + - - +
37B VAL* 1.3 56.0 + - - +
39B GLN* 2.9 28.2 + - - +
40B PHE* 2.8 58.4 + - - -
80B MET* 3.6 18.8 - - + -
131B ASP* 3.7 10.2 - - - +
132B VAL* 3.6 19.9 - - - +
135B ALA* 3.5 21.4 - - - +
148B LEU* 3.9 17.9 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TRP* 4.5 7.2 - - + -
33B LEU* 2.8 20.0 + - + +
34B ASN* 3.7 14.6 - - - +
36B GLN* 1.3 75.8 - - - +
38B ILE* 1.3 58.2 + - - +
40B PHE* 3.8 1.9 - - - +
41B ILE* 2.8 55.0 + - + +
77B LEU* 4.0 16.4 - - + +
80B MET* 4.0 11.9 - - + +
81B ALA* 3.8 31.9 - - + +
84B ALA* 6.2 0.2 - - + -
91B ALA* 5.8 0.2 - - + -
92B LEU 3.5 22.4 - - - +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASN* 3.1 21.0 + - + +
35B ARG* 3.8 8.5 - - - +
36B GLN 3.2 0.2 - - - -
37B VAL* 1.3 75.9 - - - +
39B GLN* 1.3 63.6 + - - +
42B ASP* 3.1 24.3 + - - +
92B LEU* 4.1 15.0 - - + +
97B VAL* 3.6 24.0 - - + -
98B ILE* 3.4 40.5 - - + +
101B LYS* 4.0 26.0 - - + +
102B THR* 4.0 23.3 - - - +
103B PRO* 5.0 1.1 - - + -
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 3.4 11.3 + - - +
36B GLN* 2.9 33.5 + - - +
38B ILE* 1.3 80.7 - - - +
40B PHE* 1.3 58.1 + - + +
42B ASP* 3.4 4.7 + - - +
43B LEU* 2.9 29.5 + - - +
103B PRO* 3.3 38.1 - - + +
104B LEU* 4.1 3.4 - - + +
127B ILE* 4.3 6.3 - - - +
128B VAL* 3.3 37.8 - - + +
131B ASP* 3.1 34.0 + - - +
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLN* 2.8 51.7 + - - +
37B VAL 3.8 2.9 - - - +
39B GLN* 1.3 71.4 - - - +
41B ILE* 1.3 65.6 - - - +
43B LEU* 3.1 6.8 + - - +
44B SER* 2.9 25.3 + - - -
73B LEU* 3.8 29.6 - - + +
76B HIS* 4.0 19.3 - - + -
77B LEU* 4.0 16.2 - - + -
80B MET* 3.6 18.4 - - + -
128B VAL* 3.6 17.9 - - + -
132B VAL* 4.3 9.2 - - + -
151B ALA* 3.9 13.0 - - + -
155B LEU* 3.2 34.5 - - + -
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.6 28.9 - - + -
52A TRP* 4.3 11.7 - - + -
37B VAL* 2.8 35.5 + - + +
40B PHE* 1.3 71.6 - - - +
42B ASP* 1.3 60.7 + - - +
44B SER* 2.6 22.5 + - - +
45B LEU* 3.0 17.5 + - + +
77B LEU* 3.3 25.1 - - + +
93B GLY* 3.7 34.1 - - - +
98B ILE* 3.9 19.5 - - + -
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 3.0 37.8 + - - +
96A GLN* 5.2 1.4 - - - +
38B ILE 3.1 15.6 + - - +
39B GLN 3.7 3.8 - - - +
41B ILE* 1.3 81.2 - - - +
43B LEU* 1.3 56.9 + - - +
45B LEU* 3.2 6.5 + - - +
46B ILE* 2.9 42.9 + - - +
98B ILE* 3.7 9.4 - - + +
102B THR* 2.7 29.0 + - - +
104B LEU* 3.4 20.5 - - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN 2.9 17.5 + - - +
40B PHE* 3.1 7.6 + - + +
42B ASP* 1.3 76.0 - - - +
44B SER* 1.3 53.2 + - - +
46B ILE* 3.4 7.2 + - + +
47B THR* 2.6 37.1 + - - -
73B LEU* 4.2 11.0 - - + -
104B LEU* 3.9 11.4 - - + +
124B ARG* 3.8 28.9 - - + +
125B TYR* 3.5 46.2 - - + -
128B VAL* 4.0 11.7 - - + -
155B LEU* 3.8 28.9 - - + -
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE 2.9 12.9 + - - -
41B ILE* 2.6 25.5 + - - +
43B LEU* 1.3 75.8 - - - +
45B LEU* 1.3 67.4 + - - +
47B THR* 3.2 5.2 + - - -
48B LYS* 3.2 24.4 + - - +
70B ARG* 4.1 16.1 + - - +
73B LEU* 3.9 26.4 - - - +
74B ILE* 4.6 13.3 - - - +
77B LEU* 4.7 1.8 - - - +
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Residues in contact with LEU 45 (chain B).
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* 3.6 32.5 - - + -
45A LEU* 4.7 18.8 - - + -
93A GLY 3.8 18.9 - - - +
94A THR* 5.0 1.1 - - - -
95A THR* 4.1 34.1 - - - +
98A ILE* 5.3 2.0 - - + -
41B ILE* 3.0 25.4 + - + +
42B ASP* 3.2 11.6 + - - +
44B SER* 1.3 85.2 + - - +
46B ILE* 1.3 63.1 + - - +
48B LYS* 3.2 9.1 + - - +
49B GLN* 3.0 20.4 + - - +
52B TRP* 5.3 0.5 - - - -
98B ILE* 5.2 1.8 - - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 5.3 6.3 - - + -
96A GLN* 5.9 2.5 - - - +
42B ASP* 2.9 35.0 + - - +
43B LEU* 3.6 6.5 - - + +
45B LEU* 1.3 75.6 - - + +
47B THR* 1.3 64.7 + - - +
49B GLN* 3.1 8.4 + - - +
50B ALA* 3.0 22.9 + - - +
104B LEU* 3.7 32.1 - - + -
105B LYS 4.8 2.0 - - - +
106B SER* 6.2 0.2 - - - -
107B TYR* 3.4 41.1 - - + +
121B LEU* 3.9 11.2 - - + -
124B ARG* 4.2 23.3 - - + +
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU 2.6 23.6 + - - -
44B SER* 3.4 11.4 - - - -
45B LEU 3.2 0.2 - - - -
46B ILE* 1.3 76.0 - - - +
48B LYS* 1.3 57.7 - - + +
50B ALA* 3.9 2.1 - - - +
51B HIS* 3.0 28.0 + - + +
66B LEU* 3.3 44.4 - - + +
67B ASP* 5.4 0.2 - - - -
70B ARG* 4.5 9.9 - - + +
73B LEU* 3.8 3.5 - - - +
121B LEU* 4.2 9.4 - - - -
125B TYR* 2.7 31.4 + - - +
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 2.7 26.0 + - - +
82A GLU* 5.4 1.0 + - - -
44B SER 3.2 8.8 + - - +
45B LEU* 3.2 11.1 + - - +
46B ILE 3.2 0.2 - - - -
47B THR* 1.3 78.9 - - + +
49B GLN* 1.3 64.6 + - - +
51B HIS* 3.2 33.6 + - + +
52B TRP* 2.8 60.2 + - + +
67B ASP* 2.9 22.1 + - - +
70B ARG* 2.9 49.4 - - + +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 5.2 0.6 - - - +
91A ALA 2.6 24.1 + - - +
92A LEU* 3.2 2.9 - - - -
93A GLY 3.0 19.8 + - - +
94A THR* 3.2 36.6 - - + +
45B LEU 3.0 10.5 + - - +
46B ILE* 3.3 12.8 - - - +
48B LYS* 1.3 78.2 - - - +
50B ALA* 1.3 61.9 + - - +
52B TRP* 4.0 6.0 - - - -
53B ASN* 2.9 47.4 + - - +
107B TYR* 4.2 17.0 - - + -
108B PRO 4.4 3.8 + - - -
109B LEU* 4.0 20.4 - - - +
117B HIS* 4.6 1.5 - - - -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE 3.0 4.6 + - - +
47B THR 3.9 1.6 - - - +
49B GLN* 1.3 79.8 - - - +
51B HIS* 1.3 65.5 + - - +
53B ASN 3.3 2.3 + - - -
54B MET* 3.2 30.8 + - + +
107B TYR* 3.4 23.5 - - - +
117B HIS* 3.4 17.7 + - + +
121B LEU* 3.6 35.2 - - + -
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 4.5 5.6 + - - -
47B THR* 3.0 21.4 + - + +
48B LYS* 3.2 35.9 + - + +
50B ALA* 1.3 77.6 - - - +
52B TRP* 1.3 80.3 + + - +
54B MET* 3.5 10.3 - - - +
59B PHE* 4.5 0.9 - - - -
63B HIS* 2.6 82.3 + + - -
64B GLU* 5.0 0.2 - - - -
66B LEU* 3.9 17.2 - - + +
67B ASP* 3.9 21.3 + - + -
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Residues in contact with TRP 52 (chain B).
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* 4.5 2.7 - - + -
41A ILE* 4.3 10.5 - - + -
77A LEU* 3.5 20.6 - - + -
78A ASP* 3.3 31.6 + - - +
81A ALA* 3.3 27.0 - - + +
82A GLU* 4.2 15.7 - - + +
85A VAL* 3.5 26.4 - - + +
91A ALA* 3.7 29.2 - - + -
92A LEU 4.7 0.7 - - - -
93A GLY* 4.1 24.2 - - - -
45B LEU 5.3 0.2 - - - -
48B LYS* 2.8 52.0 + - + +
49B GLN* 4.0 7.0 - - - -
51B HIS* 1.3 95.7 + + - +
53B ASN* 1.3 62.0 + - - +
54B MET 3.7 3.3 + - - +
59B PHE* 5.5 1.9 - - - -
63B HIS* 4.6 4.2 - + - -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.3 15.0 - - - +
89A GLY 4.3 0.7 - - - +
90A VAL* 3.4 15.2 - - + +
91A ALA 2.9 45.8 + - - +
49B GLN* 2.9 33.0 + - - +
50B ALA 3.3 5.0 + - - -
52B TRP* 1.3 80.9 - - - +
54B MET* 1.3 59.6 + - - +
55B ARG* 4.7 2.6 - - - +
111B ILE 4.6 0.9 - - - +
112B HIS* 3.1 33.7 + - + +
117B HIS* 3.4 16.1 + - + +
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 6.0 0.7 - - - +
50B ALA 3.2 18.5 + - - +
51B HIS 3.5 10.8 - - - +
52B TRP 3.5 2.7 - - - +
53B ASN* 1.3 78.3 - - - +
55B ARG* 1.3 67.7 + - - +
59B PHE* 3.3 33.8 - - + +
62B VAL* 3.5 28.5 - - + -
63B HIS* 4.1 15.7 - - - -
66B LEU* 3.3 29.2 - - + -
112B HIS 3.2 5.8 - - - +
114B VAL* 4.3 15.3 - - + +
117B HIS* 3.6 28.0 - - + -
118B LEU* 5.0 0.7 - - + -
121B LEU* 4.7 2.0 - - + -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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