Contacts of the helix formed by residues 44 - 78 (chain I) in PDB entry 2ONK
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 44 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LYS 2.7 11.2 + - - +
41I ALA* 3.0 18.9 + - - +
43I SER* 1.3 72.9 - - - +
45I PRO* 1.3 64.9 - - - +
46I ALA* 2.8 31.8 + - - +
47I VAL* 2.9 29.5 + - + +
48I TRP* 3.5 6.1 - - - -
220I ARG* 2.9 32.3 + - - -
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Residues in contact with PRO 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I SER 2.7 15.4 - - - +
44I ASP* 1.3 79.1 - - - +
46I ALA* 1.3 64.4 + - - +
47I VAL 3.2 0.2 - - - -
48I TRP* 3.8 13.2 - - + +
49I LYS* 3.0 35.0 + - + +
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Residues in contact with ALA 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I ASP* 2.8 21.1 + - - +
45I PRO* 1.3 80.2 - - + +
47I VAL* 1.3 62.9 + - - +
49I LYS* 3.2 20.7 + - - +
50I VAL* 3.2 20.7 + - + +
216I LEU* 5.4 5.4 - - + -
220I ARG* 4.4 8.5 - - - +
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Residues in contact with VAL 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ALA 4.0 10.1 - - - +
44I ASP* 2.9 25.0 + - + +
46I ALA* 1.3 79.6 - - - +
48I TRP* 1.3 69.2 + - + +
50I VAL* 2.9 6.8 + - - +
51I VAL* 2.8 42.6 + - + +
216I LEU* 4.0 25.4 - - + -
220I ARG* 4.1 9.8 - - - +
232I VAL* 4.3 22.7 - - + -
235I ILE* 4.7 17.0 - - + -
236I LEU* 5.5 0.4 - - + -
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Residues in contact with TRP 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I ALA 4.8 0.2 + - - -
42I ALA* 2.5 37.2 + - + -
43I SER* 4.1 3.5 - - - +
44I ASP 3.5 24.2 + - - -
45I PRO* 4.1 10.3 - - + +
46I ALA 3.4 0.4 - - - -
47I VAL* 1.3 80.7 - - + +
49I LYS* 1.3 63.0 + - - +
51I VAL* 3.8 15.4 - - + +
52I LEU* 3.1 40.4 + - + +
235I ILE* 4.5 16.4 - - + -
239I LEU* 3.8 32.8 - - + -
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Residues in contact with LYS 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I PRO* 3.0 29.2 + - - +
46I ALA* 3.3 14.4 - - - +
47I VAL 3.1 0.8 - - - -
48I TRP* 1.3 75.8 - - - +
50I VAL* 1.3 55.9 + - + +
52I LEU* 3.6 5.6 + - - +
53I THR* 2.6 32.4 + - - -
62J GLU* 3.8 29.1 + - - +
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Residues in contact with VAL 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ALA 3.2 15.5 - - - +
47I VAL* 2.9 6.7 + - - +
49I LYS* 1.3 75.0 - - + +
51I VAL* 1.3 67.0 + - - +
53I THR* 2.8 10.0 + - - -
54I THR* 2.7 24.6 + - - -
211I MET* 3.3 21.5 - - + +
212I ILE 3.2 10.8 - - - +
213I ALA* 2.9 40.2 - - + +
216I LEU* 4.0 29.6 - - + -
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Residues in contact with VAL 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I VAL* 2.8 35.6 + - + +
48I TRP* 3.8 18.2 - - + +
50I VAL* 1.3 72.3 - - + +
52I LEU* 1.3 66.6 + - + +
54I THR* 3.2 8.8 - - - -
55I TYR* 3.0 46.6 + - + -
213I ALA* 4.7 4.3 - - + -
236I LEU* 3.8 17.7 - - + -
239I LEU* 3.4 35.4 - - + -
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Residues in contact with LEU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I TRP* 3.1 26.5 + - + +
49I LYS* 3.9 5.8 - - - +
51I VAL* 1.3 83.2 - - + +
53I THR* 1.3 68.0 + - - +
55I TYR* 4.0 7.4 - - + +
56I TYR* 2.8 31.2 + - + +
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Residues in contact with THR 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I LYS 2.6 24.4 + - - -
50I VAL* 2.8 11.7 + - - -
52I LEU* 1.3 71.7 - - - +
54I THR* 1.3 65.8 + - - +
56I TYR* 4.1 6.0 - - + +
57I ALA* 2.9 25.1 + - - +
128I LEU* 4.6 17.0 - - + -
131I ILE* 4.7 2.9 - - + -
210I PRO* 4.6 16.4 - - + +
211I MET 3.6 16.0 + - - +
212I ILE* 4.2 7.6 - - + -
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Residues in contact with THR 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I VAL 2.7 11.4 + - - -
51I VAL* 3.2 9.9 - - - -
53I THR* 1.3 80.6 - - - +
55I TYR* 1.3 80.1 + - + +
57I ALA* 2.9 9.5 + - - +
58I ALA* 2.9 14.1 + - - +
135I MET* 4.2 1.4 - - + +
197I ILE* 3.8 28.3 - - + +
212I ILE* 3.3 26.8 - - + +
213I ALA* 2.8 36.1 + - + +
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Residues in contact with TYR 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I VAL* 3.0 28.4 + - + +
52I LEU* 4.0 7.6 - - + +
54I THR* 1.3 83.8 - - + +
56I TYR* 1.3 57.9 + - - +
58I ALA 3.5 0.2 + - - -
59I LEU* 2.9 26.2 + - - +
193I TRP* 3.1 39.0 + + + -
197I ILE* 3.1 35.2 - - + +
213I ALA* 6.1 0.4 - - + -
236I LEU* 4.9 6.2 + - + +
239I LEU* 3.2 43.2 + - + +
240I SER* 3.7 19.2 + - - -
243I VAL* 3.9 11.2 - - + +
244I PHE* 5.6 0.5 - - - -
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Residues in contact with TYR 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I LEU* 2.8 25.0 + - + +
53I THR* 4.1 4.3 - - - +
55I TYR* 1.3 72.7 - - - +
57I ALA* 1.3 67.3 + - - +
59I LEU* 3.3 16.2 + - + +
60I ILE* 3.3 52.5 + - + +
128I LEU* 4.1 23.3 - - + +
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Residues in contact with ALA 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I THR 2.9 20.3 + - - +
54I THR 2.9 6.8 + - - +
56I TYR* 1.3 77.6 - - - +
58I ALA* 1.3 62.6 + - - +
60I ILE* 3.1 17.0 + - - +
61I SER* 3.3 9.2 + - - -
128I LEU* 4.2 16.8 - - + -
131I ILE* 3.6 30.5 - - + -
132I VAL* 3.9 10.0 - - + +
135I MET* 3.7 4.1 - - - +
212I ILE* 3.7 2.9 - - + -
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Residues in contact with ALA 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I THR 2.9 13.5 + - - +
55I TYR 3.8 3.8 - - - +
57I ALA* 1.3 77.3 - - - +
59I LEU* 1.3 62.0 + - - +
61I SER* 2.9 21.0 + - - -
62I THR* 3.2 12.1 + - - -
135I MET* 3.3 21.5 - - + -
193I TRP* 3.6 16.6 - - + +
196I GLY* 3.9 3.1 - - - -
197I ILE* 3.6 26.9 - - + +
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Residues in contact with LEU 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I TYR 2.9 17.0 + - - +
56I TYR* 3.5 18.4 - - + +
57I ALA 3.2 0.2 - - - -
58I ALA* 1.3 77.1 - - - +
60I ILE* 1.3 65.3 + - + +
62I THR* 3.6 4.0 + - - -
63I LEU* 3.2 44.5 + - + +
193I TRP* 3.4 25.8 - - + +
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Residues in contact with ILE 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I TYR* 3.3 51.8 - - + +
57I ALA* 3.1 8.8 + - - +
59I LEU* 1.3 80.2 - - + +
61I SER* 1.3 65.8 + - - +
63I LEU* 3.3 10.1 + - + +
64I ILE* 2.9 42.7 + - + +
128I LEU* 4.3 13.9 - - + -
132I VAL* 3.8 17.9 - - + -
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Residues in contact with SER 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I ALA 3.3 7.5 + - - -
58I ALA* 2.9 13.4 + - - -
60I ILE* 1.3 78.1 - - - +
62I THR* 1.3 62.1 + - - +
64I ILE* 3.2 2.6 + - - -
65I ALA* 2.8 25.1 + - - +
132I VAL* 4.1 12.1 - - - +
135I MET* 3.9 13.0 - - - +
136I LEU* 3.2 45.0 - - - +
139I SER* 3.9 12.6 + - - -
192I SER 4.7 2.6 + - - -
196I GLY* 5.0 0.5 - - - -
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Residues in contact with THR 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I ALA 3.2 10.9 + - - -
59I LEU* 3.7 11.0 - - + -
60I ILE 3.1 0.4 - - - -
61I SER* 1.3 78.7 + - - +
63I LEU* 1.3 74.1 + - + +
65I ALA* 2.7 15.5 + - + +
66I VAL* 2.8 18.6 + - + +
139I SER* 5.9 0.2 - - - -
143I TYR* 5.8 0.2 - - + -
189I ALA* 3.9 29.4 - - + +
192I SER* 2.8 28.9 + - - +
193I TRP* 3.4 19.1 - - + +
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Residues in contact with LEU 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I LEU* 3.2 34.6 + - + +
60I ILE* 3.7 9.6 - - + +
62I THR* 1.3 85.3 - - + +
64I ILE* 1.3 65.1 + - + +
66I VAL* 3.3 8.4 + - + +
67I ILE* 2.9 42.4 + - + +
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Residues in contact with ILE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 6.0 1.6 - - + -
60I ILE* 2.9 24.7 + - + +
61I SER* 3.4 6.5 - - - +
63I LEU* 1.3 75.8 - - + +
65I ALA* 1.3 64.1 + - - +
67I ILE* 4.5 5.8 - - - -
68I PHE* 3.0 42.2 + - + +
132I VAL* 3.4 32.8 - - + -
136I LEU* 3.8 23.3 - - + -
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Residues in contact with ALA 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 5.8 2.0 - - - -
61I SER 2.8 12.6 + - - +
62I THR* 2.7 14.4 + - - +
64I ILE* 1.3 72.5 - - - +
66I VAL* 1.3 61.0 + - - +
68I PHE* 3.0 0.4 + - - -
69I GLY* 2.3 41.8 + - - +
136I LEU* 3.9 12.5 - - + +
139I SER* 5.8 1.3 - - - +
140I VAL* 4.8 12.6 - - + -
143I TYR* 4.2 23.6 - - + -
192I SER* 4.8 4.0 - - - +
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Residues in contact with VAL 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I THR* 2.8 23.0 + - + +
63I LEU* 3.7 11.4 - - + +
65I ALA* 1.3 76.2 - - - +
67I ILE* 1.3 65.5 + - + +
70I THR* 2.9 32.8 + - - +
143I TYR* 3.5 40.1 - - + +
185I ILE* 4.7 8.7 - - + -
189I ALA* 4.2 16.2 - - + -
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Residues in contact with ILE 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 3.5 24.5 - - + +
63I LEU* 2.9 36.5 + - + +
64I ILE* 3.9 4.3 - - - +
66I VAL* 1.3 79.1 - - + +
68I PHE* 1.3 78.2 + - + +
71I PRO* 3.7 5.9 - - - +
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Residues in contact with PHE 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 3.2 42.7 - - + +
13H SER* 4.0 0.3 - - - -
15H ILE* 3.5 34.3 - - + -
16H ILE* 3.1 36.0 - - + +
64I ILE* 3.0 35.1 + - + +
67I ILE* 1.3 97.0 - - + +
69I GLY* 1.3 63.6 + - - +
70I THR 3.5 0.7 - - - -
71I PRO* 3.1 18.6 - - - +
72I LEU 3.8 3.5 + - - -
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Residues in contact with GLY 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 4.0 7.1 - - - +
65I ALA* 2.3 29.9 + - - +
68I PHE* 1.3 68.1 - - - +
70I THR* 1.3 64.4 + - - -
72I LEU* 3.1 6.9 + - - +
73I ALA* 2.9 20.1 + - - +
140I VAL* 5.8 0.9 - - - -
143I TYR* 4.2 6.1 - - - -
144I ILE* 4.0 24.8 - - - +
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Residues in contact with THR 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I ALA 3.6 0.6 + - - -
66I VAL* 2.9 25.8 + - - +
69I GLY* 1.3 73.9 - - - +
71I PRO* 1.3 72.4 - - + +
73I ALA* 2.7 19.4 + - - +
74I TYR* 2.9 10.6 + - - +
143I TYR* 2.6 33.9 + - - +
147I ALA* 5.0 0.7 - - - -
151I PHE* 3.8 26.2 - - + -
173I PHE* 4.4 13.9 - - + -
178I LEU* 4.6 5.6 - - + -
185I ILE* 4.7 5.6 - - + +
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Residues in contact with PRO 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LEU* 3.7 45.8 - - + +
12H LEU* 3.8 15.3 - - + -
13H SER* 4.3 2.5 - - - +
66I VAL 3.9 0.7 - - - +
67I ILE 3.7 17.5 - - - +
68I PHE 3.1 21.8 - - - +
70I THR* 1.3 95.7 - - + +
72I LEU* 1.3 58.8 + - - +
74I TYR* 3.4 6.4 + - + +
75I ILE* 3.1 27.6 + - - +
173I PHE* 5.6 1.3 - - + -
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Residues in contact with LEU 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H SER* 3.4 31.0 - - - +
16H ILE* 4.7 6.1 - - + -
17H LEU* 4.0 20.6 - - + +
68I PHE 4.3 2.5 - - - +
69I GLY 3.1 8.6 + - - +
70I THR 2.9 2.0 + - - -
71I PRO* 1.3 75.8 - - - +
73I ALA* 1.3 60.4 + - - +
75I ILE* 3.3 10.6 + - + +
76I LEU* 2.9 47.2 + - + +
81I PHE* 6.3 0.2 - - + -
87I VAL* 3.9 22.9 - - + -
91I VAL* 3.6 28.3 - - + -
144I ILE* 3.6 15.5 - - + -
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Residues in contact with ALA 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I GLY 2.9 10.4 + - - +
70I THR* 2.7 14.8 + - - +
72I LEU* 1.3 72.8 - - - +
74I TYR* 1.3 61.1 + - - +
76I LEU* 3.3 5.0 + - - +
77I ALA* 3.1 23.4 + - - +
144I ILE* 3.6 24.4 - - + +
147I ALA* 3.6 31.9 - - + -
148I LYS* 3.8 11.0 - - - +
151I PHE* 4.2 4.2 - - + -
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Residues in contact with TYR 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PHE* 5.4 4.3 - + - -
9H LEU* 4.1 22.0 - - + -
70I THR 2.9 8.8 + - - +
71I PRO* 3.6 9.4 - - + +
73I ALA* 1.3 76.3 - - - +
75I ILE* 1.3 68.8 + - + +
77I ALA* 2.9 15.4 + - - +
78I ARG* 2.9 45.5 + - + +
79I LYS* 5.9 7.4 - - - -
151I PHE* 3.7 27.7 - + + -
159I GLU* 3.7 13.5 + - - -
169I PRO 5.4 2.3 + - - -
172I VAL* 5.7 1.9 - - - +
173I PHE* 3.6 45.2 + + + +
177I SER* 4.0 13.5 + - - -
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Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H SER 5.5 1.1 - - - +
9H LEU* 4.2 12.6 - - + -
10H ALA* 4.2 21.1 - - + +
13H SER* 3.8 21.8 - - - +
71I PRO 3.1 11.8 + - - +
72I LEU* 3.6 13.5 - - + +
74I TYR* 1.3 86.7 - - + +
76I LEU* 1.3 62.8 + - + +
78I ARG* 4.1 1.6 - - - +
79I LYS* 3.3 50.0 + - + +
81I PHE* 3.8 27.4 - - + -
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Residues in contact with LEU 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 2.9 38.8 + - + +
73I ALA* 3.8 4.5 - - - +
74I TYR 2.9 0.4 + - - -
75I ILE* 1.3 79.9 - - - +
77I ALA* 1.3 62.3 + - - +
78I ARG 3.6 0.3 + - - -
81I PHE* 4.5 4.9 - - + -
84I LYS* 2.7 43.9 + - + +
87I VAL* 4.1 21.8 - - + -
88I GLU* 4.2 25.2 - - + +
91I VAL* 4.5 12.6 - - + -
144I ILE* 4.4 17.3 - - + -
148I LYS* 4.5 22.3 - - - +
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Residues in contact with ALA 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I ALA 3.1 15.1 + - - +
74I TYR 2.9 4.5 + - - +
76I LEU* 1.3 78.6 - - - +
78I ARG* 1.3 73.6 + - + +
84I LYS* 5.1 0.9 + - - -
148I LYS* 3.8 22.8 - - + +
151I PHE* 4.0 22.7 - - + -
152I ALA* 4.2 11.5 - - + +
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Residues in contact with ARG 78 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I TYR* 2.9 45.5 + - + +
75I ILE* 5.0 0.2 - - - -
76I LEU 3.3 0.4 - - - +
77I ALA* 1.3 94.2 + - + +
79I LYS* 1.3 75.9 + - + +
80I SER* 3.7 3.6 + - - -
84I LYS* 4.8 1.2 + - - -
151I PHE* 2.9 35.8 + - - +
152I ALA* 4.8 5.1 + - - +
154I VAL* 3.4 17.1 + - - +
156I VAL* 4.4 24.8 - - - +
159I GLU* 2.9 40.9 + - - -
----------------------------------------------------------
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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