Contacts of the helix formed by residues 44 - 78 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LYS 2.7 11.9 + - - +
41C ALA* 2.9 17.1 + - - +
43C SER* 1.3 72.7 - - - +
45C PRO* 1.3 61.2 - - - +
46C ALA* 2.8 25.2 + - - +
47C VAL* 2.9 28.8 + - + +
48C TRP* 3.5 6.8 - - - -
220C ARG* 2.8 33.6 + - - -
203E GLU* 4.3 1.0 - - - +
204E ARG* 3.3 14.5 + - - +
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Residues in contact with PRO 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER 2.8 16.1 - - - +
44C ASP* 1.3 79.5 - - - +
46C ALA* 1.3 64.2 + - - +
47C VAL 3.2 0.2 - - - -
48C TRP* 3.8 13.7 - - + +
49C LYS* 3.0 36.5 + - + +
204E ARG* 4.2 19.5 - - - +
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ASP* 2.8 20.2 + - - +
45C PRO* 1.3 80.0 - - - +
47C VAL* 1.3 62.5 + - - +
49C LYS* 3.2 20.5 + - - +
50C VAL* 3.2 19.7 + - - +
216C LEU* 5.2 4.0 - - + -
220C ARG* 4.7 1.1 - - - +
203E GLU* 4.5 22.7 - - + +
204E ARG* 4.2 19.0 - - - +
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA 4.1 10.8 - - - +
44C ASP* 2.9 25.2 + - + +
46C ALA* 1.3 76.9 - - - +
48C TRP* 1.3 72.5 + - + +
50C VAL* 2.9 6.2 + - + +
51C VAL* 2.8 42.5 + - + +
216C LEU* 3.8 27.4 - - + -
220C ARG* 4.2 9.2 - - - +
232C VAL* 4.4 21.1 - - + -
235C ILE* 4.8 14.4 - - + -
236C LEU* 5.4 1.3 - - + -
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Residues in contact with TRP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ALA 4.8 0.6 + - - -
42C ALA* 2.5 36.5 + - + -
43C SER* 4.1 4.4 - - - +
44C ASP 3.5 23.5 + - - -
45C PRO* 3.7 10.7 + - + +
46C ALA 3.4 0.2 - - - -
47C VAL* 1.3 81.1 - - + +
49C LYS* 1.3 61.3 + - - +
51C VAL* 4.2 15.9 - - + -
52C LEU* 3.1 40.1 + - + +
235C ILE* 4.6 16.2 - - + -
239C LEU* 3.7 35.0 - - + -
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PRO* 3.0 29.5 + - + +
46C ALA* 3.3 13.9 - - - +
47C VAL 3.1 0.8 - - - -
48C TRP* 1.3 75.5 - - - +
50C VAL* 1.3 58.0 + - + +
52C LEU* 3.6 5.3 + - - +
53C THR* 2.6 33.2 + - - -
204E ARG* 5.9 4.3 - - - +
206E GLU* 6.0 2.8 + - - -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ALA 3.2 15.3 - - - +
47C VAL* 2.9 7.3 + - - +
49C LYS* 1.3 75.0 - - + +
51C VAL* 1.3 68.5 + - + +
53C THR* 2.8 6.0 + - - -
54C THR* 2.7 23.7 + - - -
211C MET* 3.2 27.4 - - + +
212C ILE 2.9 12.1 - - - +
213C ALA* 2.7 40.8 - - - +
216C LEU* 4.3 25.8 - - + -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 2.8 34.9 + - + +
48C TRP* 3.8 18.4 - - + +
50C VAL* 1.3 72.5 - - + +
52C LEU* 1.3 71.8 + - + +
54C THR* 3.2 8.3 - - - -
55C TYR* 3.0 42.2 + - + +
213C ALA* 4.8 3.8 - - + -
236C LEU* 3.8 18.8 - - + -
239C LEU* 3.6 34.3 - - + -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C TRP* 3.1 26.9 + - + +
49C LYS* 3.9 6.1 - - - +
51C VAL* 1.3 84.0 - - + +
53C THR* 1.3 67.7 + - - +
55C TYR* 4.6 7.6 - - + -
56C TYR* 2.8 31.2 + - + +
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Residues in contact with THR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS 2.6 22.2 + - - -
50C VAL* 2.8 10.5 + - - -
52C LEU* 1.3 73.5 - - - +
54C THR* 1.3 58.6 + - - +
56C TYR* 4.1 5.5 - - + +
57C ALA* 2.8 33.8 + - - +
128C LEU* 4.2 20.3 - - + +
131C ILE* 4.5 5.6 - - + -
210C PRO* 4.3 19.0 - - + +
211C MET 3.9 16.2 + - - +
212C ILE* 5.5 0.9 - - + -
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL 2.7 14.6 + - - -
51C VAL* 3.2 10.3 - - - -
53C THR* 1.3 74.7 - - - +
55C TYR* 1.3 79.2 + - + +
57C ALA* 2.8 17.1 + - - +
58C ALA* 2.9 14.7 + - - +
135C MET* 4.2 4.1 - - + +
197C ILE* 3.9 29.6 - - + +
212C ILE* 3.3 22.7 - - + +
213C ALA* 2.9 32.5 + - + +
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 3.0 30.8 + - + +
52C LEU* 4.0 8.1 - - + +
54C THR* 1.3 83.5 - - + +
56C TYR* 1.3 56.7 + - - +
58C ALA 3.5 0.2 + - - -
59C LEU* 2.9 27.5 + - - +
193C TRP* 3.1 39.5 + + + +
197C ILE* 3.1 34.4 - - + +
213C ALA* 6.1 1.3 - - + -
236C LEU* 5.5 4.5 - - + +
239C LEU* 3.3 40.6 + - + +
240C SER* 3.7 19.1 + - - -
243C VAL* 3.9 13.2 - - + +
244C PHE* 5.5 0.2 - - - -
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Residues in contact with TYR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 2.8 24.8 + - + +
53C THR* 4.1 4.0 - - + +
55C TYR* 1.3 70.8 - - - +
57C ALA* 1.3 67.5 + - - +
59C LEU* 3.3 14.7 + - + +
60C ILE* 3.3 45.3 + - + +
128C LEU* 3.4 33.9 - - + +
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C THR 2.8 19.8 + - - +
54C THR* 2.8 7.2 + - - +
56C TYR* 1.3 73.4 - - - +
58C ALA* 1.3 63.7 + - - +
60C ILE* 3.1 15.3 + - - +
61C SER* 3.3 9.4 + - - -
128C LEU* 3.6 26.0 - - + -
131C ILE* 3.7 27.1 - - + -
132C VAL* 3.8 12.5 - - + +
135C MET* 3.8 4.8 - - + +
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C THR 2.9 14.7 + - - +
55C TYR 3.8 3.6 - - - +
57C ALA* 1.3 75.6 - - - +
59C LEU* 1.3 64.2 + - - +
61C SER* 2.9 22.1 + - - -
62C THR* 3.2 12.1 + - - -
135C MET* 3.4 19.9 - - + -
193C TRP* 3.6 17.2 - - + +
196C GLY* 4.1 2.9 - - - -
197C ILE* 3.8 25.8 - - + +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TYR 2.9 17.8 + - - +
56C TYR* 3.5 17.9 - - + +
57C ALA 3.1 0.4 - - - -
58C ALA* 1.3 77.7 - - - +
60C ILE* 1.3 66.3 + - + +
62C THR* 3.6 4.4 + - - -
63C LEU* 3.2 43.6 + - + +
193C TRP* 3.5 23.3 - - + +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 3.3 51.1 - - + +
57C ALA* 3.1 7.7 + - - +
59C LEU* 1.3 80.3 - - + +
61C SER* 1.3 66.1 + - - +
63C LEU* 3.3 9.9 + - + +
64C ILE* 3.0 46.1 + - + +
128C LEU* 4.5 10.3 - - + -
132C VAL* 4.0 17.0 - - + -
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA 3.3 6.5 + - - -
58C ALA* 2.9 14.7 + - - +
60C ILE* 1.3 77.7 - - - +
62C THR* 1.3 62.1 + - - +
64C ILE* 3.2 7.8 + - - -
65C ALA* 2.8 25.1 + - - +
132C VAL* 4.3 6.4 - - - +
135C MET* 4.1 11.5 - - - +
136C LEU* 3.1 46.9 - - - +
139C SER* 3.8 13.4 + - - -
192C SER 4.7 2.4 + - - -
196C GLY* 5.2 0.3 - - - -
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Residues in contact with THR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ALA 3.2 10.8 + - - -
59C LEU* 3.7 11.9 - - - +
60C ILE 3.1 0.4 - - - -
61C SER* 1.3 79.5 + - - +
63C LEU* 1.3 73.1 + - + +
65C ALA* 2.7 15.7 + - + +
66C VAL* 2.8 18.8 + - + +
189C ALA* 3.7 30.3 - - + +
192C SER* 2.7 29.3 + - - +
193C TRP* 3.5 18.4 + - + +
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 3.2 34.1 + - + +
60C ILE* 3.3 10.3 + - + +
62C THR* 1.3 85.2 - - + +
64C ILE* 1.3 65.7 + - + +
66C VAL* 3.3 7.2 + - + +
67C ILE* 2.9 41.5 + - + +
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.0 26.7 + - + +
61C SER* 3.4 7.9 - - - +
63C LEU* 1.3 76.4 - - + +
65C ALA* 1.3 63.1 + - - +
67C ILE* 4.5 5.6 - - - -
68C PHE* 3.0 43.6 + - + +
132C VAL* 3.8 27.6 - - + -
136C LEU* 3.9 23.8 - - + -
16D ILE* 6.0 2.7 - - + -
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C SER 2.8 13.2 + - - +
62C THR* 2.7 14.2 + - - +
64C ILE* 1.3 73.1 - - - +
66C VAL* 1.3 60.7 + - - +
68C PHE* 3.0 0.4 + - - -
69C GLY* 2.3 40.5 + - - +
136C LEU* 4.1 11.0 - - + +
139C SER* 5.9 1.1 - - - +
140C VAL* 4.9 13.9 - - + +
143C TYR* 3.9 26.0 - - + -
144C ILE* 6.4 0.2 - - + -
192C SER* 4.9 3.1 - - - +
16D ILE* 5.8 2.5 - - - -
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C THR* 2.8 22.3 + - + +
63C LEU* 3.7 11.4 - - + +
65C ALA* 1.3 74.6 - - - +
67C ILE* 1.3 64.6 + - + +
70C THR* 2.9 32.9 + - - +
71C PRO* 3.9 0.3 - - - +
143C TYR* 3.3 40.3 - - + +
185C ILE* 4.5 11.0 - - + -
189C ALA* 4.2 16.6 - - + -
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 2.9 37.4 + - + +
64C ILE* 3.9 4.3 - - - +
66C VAL* 1.3 78.4 - - + +
68C PHE* 1.3 78.8 + - + +
71C PRO* 3.7 5.8 - - - +
12D LEU* 3.6 25.2 - - + +
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE* 3.0 34.6 + - + +
67C ILE* 1.3 96.4 - - + +
69C GLY* 1.3 64.1 + - - +
70C THR 3.5 0.9 - - - -
71C PRO* 3.1 18.9 - - - +
72C LEU 3.9 3.5 + - - -
12D LEU* 3.3 39.4 - - + +
13D SER* 4.0 0.2 - - - -
15D ILE* 3.5 36.3 - - + -
16D ILE* 3.0 35.8 - - + +
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Residues in contact with GLY 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ALA* 2.3 30.3 + - - +
68C PHE* 1.3 67.3 - - - +
70C THR* 1.3 64.6 + - - -
72C LEU* 3.1 6.4 + - - +
73C ALA* 2.9 20.9 + - - +
140C VAL* 5.9 0.4 - - - -
143C TYR* 4.1 6.3 - - - -
144C ILE* 3.9 26.9 - - - +
16D ILE* 4.0 5.8 - - - +
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 2.9 20.5 + - - +
69C GLY* 1.3 73.5 - - - +
71C PRO* 1.3 75.5 - - + +
73C ALA* 2.6 20.0 + - - +
74C TYR* 2.9 10.0 + - - +
143C TYR* 2.5 33.9 + - - -
147C ALA* 4.7 0.4 - - - -
151C PHE* 3.4 30.7 - - + -
173C PHE* 4.3 12.6 - - + -
178C LEU* 4.4 6.1 - - + -
185C ILE* 4.5 6.8 - - + +
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Residues in contact with PRO 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL 3.9 0.4 - - - +
67C ILE* 3.7 18.6 - - - +
68C PHE 3.1 20.9 - - - +
70C THR* 1.3 95.3 - - + +
72C LEU* 1.3 59.4 + - - +
74C TYR* 3.4 6.9 + - + +
75C ILE* 3.1 27.8 + - - +
173C PHE* 5.4 2.7 - - + -
9D LEU* 3.8 44.7 - - + +
12D LEU* 3.8 16.2 - - + -
13D SER* 4.2 2.7 - - - -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C PHE 4.3 2.9 - - - +
69C GLY 3.1 8.8 + - - +
70C THR 2.9 2.0 + - - -
71C PRO* 1.3 76.0 - - - +
73C ALA* 1.3 61.0 + - - +
75C ILE* 3.2 11.5 + - + +
76C LEU* 2.8 47.6 + - + +
87C VAL* 3.9 23.1 - - + -
91C VAL* 3.6 18.8 - - + -
144C ILE* 3.6 26.7 - - + -
13D SER* 3.5 30.3 - - - +
16D ILE* 4.7 4.0 - - + -
17D LEU* 4.0 21.3 - - + +
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Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY 2.9 9.7 + - - +
70C THR 2.6 14.2 + - - +
72C LEU* 1.3 72.6 - - - +
74C TYR* 1.3 60.2 + - - +
76C LEU* 3.3 2.4 + - - +
77C ALA* 3.1 20.3 + - - +
144C ILE* 3.5 15.7 - - + +
147C ALA* 3.5 33.4 - - + -
148C LYS* 3.5 25.7 - - - +
151C PHE* 3.9 3.6 - - + -
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Residues in contact with TYR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C THR 2.9 9.0 + - - +
71C PRO* 3.6 9.0 - - + +
73C ALA* 1.3 76.0 - - - +
75C ILE* 1.3 70.9 + - + +
77C ALA* 2.9 15.4 + - - +
78C ARG* 2.9 44.6 + - + +
79C LYS* 5.9 6.5 - - - -
151C PHE* 3.5 37.8 - + + -
159C GLU* 3.1 19.0 + - - -
169C PRO 5.7 0.9 + - - -
172C VAL* 5.5 2.1 - - - +
173C PHE* 3.8 26.5 + + + +
177C SER* 3.8 20.8 + - - -
5D PHE* 5.5 3.1 - + - -
9D LEU* 4.2 19.7 - - + -
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO 3.1 10.9 + - - +
72C LEU* 3.2 14.6 + - + +
74C TYR* 1.3 88.0 - - + +
76C LEU* 1.3 62.6 + - + +
78C ARG* 4.1 1.1 - - - +
79C LYS* 3.3 50.6 + - + +
81C PHE* 3.8 27.4 - - + -
6D SER 5.6 1.1 - - - +
9D LEU* 4.3 17.0 - - + +
10D ALA* 4.3 13.7 - - + +
13D SER* 3.7 22.0 - - - +
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 2.8 38.1 + - + +
73C ALA* 3.8 4.5 - - - +
74C TYR 3.0 0.2 - - - -
75C ILE* 1.3 79.2 - - + +
77C ALA* 1.3 61.7 + - - +
81C PHE* 4.5 5.4 - - + -
84C LYS* 2.7 44.8 + - + +
87C VAL* 4.1 21.3 - - + -
88C GLU* 4.2 25.0 - - + +
91C VAL* 4.5 12.6 - - + -
144C ILE* 4.4 13.2 - - + -
148C LYS* 4.1 29.1 - - + +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ALA 3.1 14.4 + - - +
74C TYR 2.9 4.3 + - - +
76C LEU* 1.3 78.2 - - - +
78C ARG* 1.3 73.9 + - + +
84C LYS* 5.2 0.7 + - - -
148C LYS* 3.9 17.2 - - + +
151C PHE* 3.9 8.3 - - + -
152C ALA* 3.8 33.9 - - + +
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C TYR* 2.9 44.5 + - + +
75C ILE 5.0 0.2 - - - -
77C ALA* 1.3 95.0 + - + +
79C LYS* 1.3 75.9 + - + +
80C SER* 3.7 3.6 + - - -
84C LYS* 4.8 1.4 + - - -
151C PHE* 2.7 33.3 + - - +
152C ALA* 4.5 6.3 + - - +
154C VAL* 2.9 22.8 + - - +
156C VAL* 4.0 28.8 - - - +
159C GLU* 3.1 38.9 + - - -
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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