Contacts of the helix formed by residues 44 - 78 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LYS 2.7 11.8 + - - +
41D ALA* 3.0 18.2 + - - +
43D SER* 1.3 71.8 - - - +
45D PRO* 1.3 65.4 - - - +
46D ALA* 2.8 28.2 + - - +
47D VAL* 2.9 29.8 + - + +
48D TRP* 3.5 6.5 - - - -
220D ARG* 3.0 27.8 + - - -
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Residues in contact with PRO 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D SER 2.7 15.6 - - - +
44D ASP* 1.3 79.4 - - - +
46D ALA* 1.3 64.0 + - - +
47D VAL 3.2 0.2 - - - -
48D TRP* 3.8 14.7 - - + +
49D LYS* 3.0 35.4 + - + +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ASP* 2.8 20.7 + - - +
45D PRO* 1.3 80.2 - - - +
47D VAL* 1.3 61.5 + - - +
49D LYS* 3.2 20.4 + - - +
50D VAL* 3.2 20.5 + - - +
216D LEU* 5.4 5.4 - - + -
220D ARG* 4.6 7.9 - - - +
51E LYS* 6.3 3.6 - - - -
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 4.0 10.3 - - - +
44D ASP* 2.9 25.5 + - + +
46D ALA* 1.3 77.3 - - - +
48D TRP* 1.3 72.2 + - + +
50D VAL* 2.9 10.9 + - - +
51D VAL* 2.8 42.0 + - + +
216D LEU* 4.0 22.4 - - + -
220D ARG* 4.1 10.1 - - - +
232D VAL* 4.5 20.6 - - + -
235D ILE* 4.9 15.7 - - + -
236D LEU* 5.6 1.3 - - + -
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Residues in contact with TRP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 4.8 0.4 + - - -
42D ALA* 2.5 39.3 + - + -
43D SER* 4.1 3.7 - - - +
44D ASP 3.5 24.4 + - - -
45D PRO* 4.0 10.1 - - + +
46D ALA 3.4 0.2 - - - -
47D VAL* 1.3 79.7 - - + +
49D LYS* 1.3 61.6 + - - +
51D VAL* 4.2 16.4 - - + -
52D LEU* 3.1 39.5 + - + +
235D ILE* 4.7 13.0 - - + -
239D LEU* 3.9 32.3 - - + -
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PRO* 3.0 30.4 + - - +
46D ALA* 3.3 13.7 - - - +
47D VAL 3.1 0.6 - - - -
48D TRP* 1.3 77.5 - - - +
50D VAL* 1.3 57.9 + - + +
52D LEU* 3.9 6.1 - - - +
53D THR* 2.6 32.0 + - - -
55E GLU* 5.6 0.6 + - - -
62E GLU* 2.9 41.0 + - - +
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Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA 3.2 15.7 - - - +
47D VAL* 2.9 7.1 + - - +
49D LYS* 1.3 75.8 - - + +
51D VAL* 1.3 67.0 + - + +
53D THR* 2.8 5.5 + - - -
54D THR* 2.7 23.7 + - - -
211D MET* 3.1 32.3 - - + +
212D ILE 3.3 4.5 - - - +
213D ALA* 3.1 35.2 - - + +
216D LEU* 4.1 29.2 - - + -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 2.8 38.5 + - + +
48D TRP* 3.8 18.8 - - + +
50D VAL* 1.3 73.3 - - + +
52D LEU* 1.3 70.4 + - + +
54D THR* 3.2 8.7 - - - -
55D TYR* 3.0 41.5 + - + -
213D ALA* 4.9 4.0 - - + -
236D LEU* 3.9 14.8 - - + -
239D LEU* 3.6 34.3 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D TRP* 3.1 26.1 + - + +
49D LYS* 3.9 5.8 - - - +
51D VAL* 1.3 84.1 - - + +
53D THR* 1.3 68.4 + - - +
55D TYR* 4.6 7.2 - - + -
56D TYR* 2.8 31.6 + - + +
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LYS 2.6 24.0 + - - -
50D VAL* 2.8 10.9 + - - -
52D LEU* 1.3 72.2 - - - +
54D THR* 1.3 65.7 + - - +
56D TYR* 4.1 5.4 - - + +
57D ALA* 2.8 26.0 + - - +
128D LEU* 4.6 12.8 - - + -
131D ILE* 4.6 11.7 - - + -
210D PRO* 4.6 18.8 - - + +
211D MET 3.7 16.7 + - - +
212D ILE* 4.2 0.9 - - + -
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL 2.7 12.6 + - - -
51D VAL* 3.2 10.5 - - - -
53D THR* 1.3 75.6 - - - +
55D TYR* 1.3 79.0 + - + +
57D ALA* 2.8 15.2 + - - +
58D ALA* 2.9 14.2 + - - +
135D MET* 4.2 0.7 - - + +
197D ILE* 3.8 26.9 - - + +
212D ILE* 3.3 29.9 - - + +
213D ALA* 2.8 35.5 + - + +
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Residues in contact with TYR 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 3.0 31.7 + - + +
52D LEU* 4.0 8.3 - - + +
54D THR* 1.3 83.9 - - + +
56D TYR* 1.3 59.2 + - - +
58D ALA 3.5 0.3 + - - -
59D LEU* 2.9 27.1 + - - +
193D TRP* 3.2 36.9 + + + -
197D ILE* 3.2 34.7 - - + +
213D ALA* 6.1 1.1 - - + -
236D LEU* 5.1 5.5 + - + +
239D LEU* 3.2 43.8 + - + +
240D SER* 3.9 14.0 + - - -
243D VAL* 4.1 12.1 - - + +
244D PHE* 5.7 0.5 - - - -
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Residues in contact with TYR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 2.8 24.8 + - + +
53D THR* 4.1 3.8 - - + +
55D TYR* 1.3 71.7 - - - +
57D ALA* 1.3 67.1 + - - +
59D LEU* 3.3 16.3 + - + +
60D ILE* 3.3 51.6 + - + +
128D LEU* 4.1 22.9 - - + +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D THR 2.8 19.4 + - - +
54D THR 2.8 6.8 + - - +
56D TYR* 1.3 77.8 - - - +
58D ALA* 1.3 63.0 + - - +
60D ILE* 3.1 17.3 + - - +
61D SER* 3.3 8.7 + - - -
128D LEU* 4.2 16.8 - - + -
131D ILE* 3.6 31.6 - - + -
132D VAL* 3.9 9.8 - - + +
135D MET* 3.7 4.5 - - - +
212D ILE* 3.8 3.1 - - + -
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D THR 2.9 14.2 + - - +
55D TYR 3.8 3.6 - - - +
57D ALA* 1.3 76.1 - - - +
59D LEU* 1.3 63.1 + - - +
61D SER* 2.9 21.0 + - - -
62D THR* 3.2 12.1 + - - -
135D MET* 3.3 16.7 - - + -
193D TRP* 3.5 16.3 - - + +
196D GLY* 4.0 2.7 - - - -
197D ILE* 3.6 32.8 - - + +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D TYR 2.9 17.9 + - - +
56D TYR* 3.5 19.3 - - + +
57D ALA 3.2 0.2 - - - -
58D ALA* 1.3 76.9 - - - +
60D ILE* 1.3 65.3 + - + +
62D THR* 3.6 3.6 + - - -
63D LEU* 3.2 44.7 + - + +
193D TRP* 3.4 25.5 - - + +
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 3.3 52.5 - - + +
57D ALA* 3.1 8.8 + - - +
59D LEU* 1.3 81.8 - - + +
61D SER* 1.3 67.3 + - - +
63D LEU* 3.3 8.8 + - + +
64D ILE* 3.0 43.3 + - + +
128D LEU* 4.4 13.2 - - + -
132D VAL* 3.8 19.5 - - + -
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ALA 3.3 6.1 + - - -
58D ALA* 2.9 13.2 + - - +
60D ILE* 1.3 78.3 - - - +
62D THR* 1.3 62.5 + - - +
64D ILE* 3.2 2.6 + - - +
65D ALA* 2.8 24.8 + - - +
132D VAL* 4.2 12.7 - - - +
135D MET* 3.9 14.2 - - - +
136D LEU* 3.3 45.5 - - - +
139D SER* 3.9 12.4 + - - -
192D SER 4.7 2.9 + - - -
196D GLY* 5.0 0.3 - - - -
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Residues in contact with THR 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ALA 3.2 10.8 + - - -
59D LEU* 3.7 11.0 - - - -
60D ILE 3.1 0.2 - - - -
61D SER* 1.3 79.2 + - - +
63D LEU* 1.3 74.5 + - + +
65D ALA* 2.7 15.1 + - + +
66D VAL* 2.8 18.3 + - + +
139D SER* 6.0 0.2 - - - -
189D ALA* 3.9 29.2 - - + +
192D SER* 2.8 29.2 + - - +
193D TRP* 3.4 19.4 - - + +
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 3.2 33.2 + - + +
60D ILE* 3.3 10.7 + - + +
62D THR* 1.3 84.4 - - + +
64D ILE* 1.3 64.8 + - + +
66D VAL* 3.3 8.5 + - + +
67D ILE* 2.9 41.9 + - + +
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 6.1 2.0 - - + -
60D ILE* 3.0 23.2 + - + +
61D SER* 3.4 6.7 - - - +
63D LEU* 1.3 76.4 - - + +
65D ALA* 1.3 63.1 + - - +
67D ILE* 4.5 5.6 - - - -
68D PHE* 3.0 43.6 + - + +
132D VAL* 3.5 31.6 - - + -
136D LEU* 3.9 23.8 - - + -
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 5.9 1.8 - - - -
61D SER 2.8 14.1 + - - +
62D THR* 2.7 14.2 + - - +
64D ILE* 1.3 73.6 - - - +
66D VAL* 1.3 60.6 + - + +
68D PHE* 3.0 0.6 + - - -
69D GLY* 2.3 42.8 + - - +
136D LEU* 4.1 12.3 - - + +
139D SER* 5.9 1.6 - - - +
140D VAL* 5.0 12.6 - - + +
143D TYR* 4.1 23.6 - - + -
192D SER* 4.7 4.5 - - - +
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D THR* 2.8 23.5 + - + +
63D LEU* 3.7 10.8 - - + +
65D ALA* 1.3 76.1 - - - +
67D ILE* 1.3 66.4 + - + +
70D THR* 2.8 38.9 + - - +
71D PRO* 3.9 0.2 - - - +
143D TYR* 3.6 32.8 - - + +
185D ILE* 4.7 9.0 - - + -
189D ALA* 4.1 17.3 - - + -
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.6 24.4 - - + +
63D LEU* 2.9 37.2 + - + +
64D ILE* 3.9 4.9 - - - +
66D VAL* 1.3 78.2 - - + +
68D PHE* 1.3 75.6 + - + +
71D PRO* 3.7 6.8 - - - +
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Residues in contact with PHE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.3 42.6 - - + +
13C SER* 4.1 0.3 - - - -
15C ILE* 3.6 32.3 - - + -
16C ILE* 3.1 35.3 - - + +
64D ILE* 3.0 35.0 + - + +
67D ILE* 1.3 96.6 - - + +
69D GLY* 1.3 65.2 + - - +
70D THR 3.5 0.7 - - - -
71D PRO* 3.2 16.7 - - - +
72D LEU 3.8 3.5 + - - -
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Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 4.2 6.4 - - - +
65D ALA* 2.3 30.3 + - - +
68D PHE* 1.3 67.5 - - - +
70D THR* 1.3 64.8 + - - -
72D LEU* 3.1 6.3 + - - +
73D ALA* 2.9 20.4 + - - +
140D VAL* 6.0 1.1 - - - -
143D TYR* 4.0 7.9 - - - -
144D ILE* 4.1 22.8 - - - +
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL* 2.8 25.6 + - - +
69D GLY* 1.3 73.1 - - - +
71D PRO* 1.3 72.1 - - + +
73D ALA* 2.7 19.4 + - - +
74D TYR* 2.9 10.7 + - - +
143D TYR* 2.5 33.3 + - - -
147D ALA* 4.9 0.4 - - + -
151D PHE* 3.8 24.9 - - + -
173D PHE* 4.4 13.5 - - + -
178D LEU* 4.4 6.3 - - + -
185D ILE* 4.5 7.9 - - + +
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Residues in contact with PRO 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 3.7 45.4 - - + +
12C LEU* 3.9 15.9 - - + -
13C SER* 4.4 2.2 - - - -
66D VAL 3.9 0.4 - - - +
67D ILE 3.7 17.3 - - - +
68D PHE 3.2 20.6 - - - +
70D THR* 1.3 95.5 - - + +
72D LEU* 1.3 59.5 + - - +
74D TYR* 3.4 6.8 + - + +
75D ILE* 3.1 27.3 + - - +
173D PHE* 5.3 2.2 - - + -
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 3.5 30.6 - - - +
16C ILE* 4.8 5.4 - - + -
17C LEU* 4.1 20.2 - - + -
68D PHE 4.3 3.1 - - - +
69D GLY* 3.1 8.8 + - - +
70D THR 2.9 2.0 + - - -
71D PRO* 1.3 77.0 - - - +
73D ALA* 1.3 60.5 + - - +
75D ILE* 3.3 10.6 + - + +
76D LEU* 2.9 47.3 + - + +
81D PHE* 6.3 0.2 - - + -
87D VAL* 3.9 22.4 - - + -
91D VAL* 3.6 17.7 - - + -
144D ILE* 3.5 26.7 - - + -
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLY 2.9 10.4 + - - +
70D THR 2.7 14.3 + - - +
72D LEU* 1.3 72.7 - - - +
74D TYR* 1.3 60.4 + - - +
76D LEU* 3.3 5.4 + - - +
77D ALA* 3.1 23.6 + - - +
144D ILE* 3.7 22.2 - - + +
147D ALA* 3.4 34.5 - - + -
148D LYS* 3.7 9.5 - - - +
151D PHE* 3.8 5.5 - - + -
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Residues in contact with TYR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 5.5 3.1 - + - -
9C LEU* 4.2 19.3 - - + -
70D THR 2.9 9.2 + - - +
71D PRO* 3.6 7.9 - - + +
73D ALA* 1.3 76.3 - - - +
75D ILE* 1.3 69.8 + - + +
77D ALA* 2.9 15.1 + - - +
78D ARG* 2.9 42.7 + - + +
79D LYS* 5.9 7.0 - - - -
151D PHE* 3.5 31.3 - + + -
159D GLU* 3.5 14.7 + - - -
169D PRO 5.2 2.8 + - - -
172D VAL* 5.3 2.3 - - - +
173D PHE* 3.4 41.6 + + + +
177D SER* 3.6 21.3 + - - -
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER 5.6 1.1 - - - +
9C LEU* 4.3 24.7 - - + +
10C ALA* 4.3 7.2 - - + +
13C SER* 3.8 21.8 - - - +
71D PRO 3.1 12.2 + - - +
72D LEU* 3.3 13.4 + - + +
74D TYR* 1.3 86.3 - - + +
76D LEU* 1.3 64.2 + - + +
78D ARG* 4.8 1.3 - - - +
79D LYS* 3.3 49.9 + - + +
81D PHE* 3.8 26.7 - - + -
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LEU* 2.9 39.0 + - + +
73D ALA 3.8 4.3 - - - +
74D TYR 2.9 0.4 + - - -
75D ILE* 1.3 80.8 - - + +
77D ALA* 1.3 62.3 + - - +
78D ARG 3.6 0.2 + - - -
81D PHE* 4.5 5.2 - - + -
84D LYS* 2.7 44.1 + - + +
87D VAL* 4.1 21.5 - - + -
88D GLU* 4.2 24.9 - - + +
91D VAL* 4.5 11.9 - - + -
144D ILE* 4.3 18.2 - - + -
148D LYS* 4.2 24.2 - - + +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ALA 3.1 14.4 + - - +
74D TYR 2.9 2.3 + - - +
76D LEU* 1.3 77.4 - - - +
78D ARG* 1.3 74.7 + - - +
84D LYS* 5.1 0.7 + - - -
148D LYS* 3.9 15.2 - - + +
151D PHE* 3.6 28.7 - - + -
152D ALA* 3.9 18.7 - - + +
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Residues in contact with ARG 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D TYR* 2.9 45.3 + - + +
75D ILE* 5.0 0.4 - - - -
76D LEU 4.7 0.2 - - - +
77D ALA* 1.3 93.4 + - + +
79D LYS* 1.3 75.6 + - + +
80D SER* 3.7 3.6 + - - -
84D LYS* 4.8 1.2 + - - -
151D PHE* 2.9 35.7 + - - +
152D ALA* 4.7 4.4 + - - +
154D VAL* 3.2 24.5 + - - +
156D VAL* 4.3 23.3 - - - +
159D GLU* 2.7 42.8 + - - -
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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