Contacts of the helix formed by residues 55 - 86 (chain E) in PDB entry 4KNF
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 55 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL* 1.3 74.9 - - - +
56E ALA* 1.3 65.1 + - - +
57E LYS* 3.6 20.8 + - - +
58E TRP* 2.8 23.4 + - - -
59E LYS* 3.2 13.8 + - - +
246E GLU* 4.7 0.9 + - - -
247E SER* 3.0 22.7 + - - -
251E LYS* 5.0 11.6 - - - +
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Residues in contact with ALA 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLN* 3.1 43.0 + - - +
248D SER* 6.5 0.7 - - - -
55E SER* 1.3 72.6 - - - +
57E LYS* 1.3 64.0 - - - +
58E TRP 2.9 1.4 + - - -
59E LYS* 3.3 9.0 + - + +
60E THR* 4.5 0.5 + - - -
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E SER* 3.6 14.1 + - - +
56E ALA* 1.3 78.1 - - - +
58E TRP* 1.3 72.9 + - + +
60E THR* 5.2 2.4 + - - -
61E SER* 5.4 2.1 + - - -
182E VAL* 6.3 3.1 - - + -
246E GLU* 2.7 44.3 + - - -
250E ALA* 5.3 4.9 - - - +
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Residues in contact with TRP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL* 3.6 12.8 - - + -
55E SER* 2.8 16.2 + - - -
57E LYS* 1.3 87.0 - - + +
59E LYS* 1.3 68.7 + - - +
60E THR 3.4 2.2 - - - -
61E SER* 3.2 35.6 - - - -
62E LEU* 3.3 8.5 + - + +
112E ILE* 6.2 1.8 - - + -
181E ALA* 4.0 30.5 - - + -
182E VAL* 4.7 11.2 - - + -
185E ALA* 4.4 16.2 - - + -
239E ILE* 4.7 12.3 - - + -
242E VAL* 4.0 21.1 - - + -
243E ALA* 3.5 31.6 - - + -
246E GLU* 3.0 26.0 + - + +
247E SER* 3.7 20.4 - - - -
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Residues in contact with LYS 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ASP* 3.7 25.8 - - - +
53D GLN* 3.2 29.8 - - + +
51E ARG* 3.1 51.9 + - + +
52E ASP* 4.3 6.8 - - - +
54E VAL* 2.7 31.7 + - - +
55E SER* 3.2 13.2 + - - +
56E ALA* 3.3 9.6 + - + +
58E TRP* 1.3 75.9 - - - +
60E THR* 1.3 64.3 + - - +
62E LEU* 3.0 13.7 + - - +
63E THR* 2.9 14.2 + - - -
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Residues in contact with THR 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PHE* 3.9 15.5 - - + -
50D GLU* 2.8 26.1 + - - +
53D GLN* 3.2 13.8 + - - +
240D TRP* 3.6 32.5 - - + -
51E ARG* 3.9 0.2 - - - +
56E ALA 4.5 0.6 + - - -
57E LYS 5.2 1.8 + - - -
58E TRP 3.4 0.6 - - - -
59E LYS* 1.3 75.2 - - - +
61E SER* 1.3 53.6 + - - +
63E THR* 3.0 3.1 + - - -
64E VAL* 2.8 39.2 + - + +
111E LEU* 4.5 17.0 - - + -
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Residues in contact with SER 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E LYS 5.4 2.2 + - - -
58E TRP* 3.2 26.6 + - - -
60E THR* 1.3 78.1 - - - +
62E LEU* 1.3 58.2 + - - -
64E VAL* 3.4 2.8 + - - +
65E SER* 3.0 30.0 + - - -
108E GLU* 2.7 29.8 + - - +
111E LEU* 4.5 14.2 - - - +
112E ILE* 5.8 1.7 - - - +
239E ILE* 4.2 18.0 - - - +
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PHE* 3.6 34.1 - - + +
50E GLU* 3.7 26.7 - - + +
51E ARG* 3.6 14.8 - - + -
54E VAL* 4.1 13.5 - - + -
58E TRP 3.3 9.4 + - - +
59E LYS 3.0 9.3 + - - +
61E SER* 1.3 77.6 - - - +
63E THR* 1.3 61.3 + - - +
65E SER* 3.4 7.4 + - - +
66E GLY* 2.9 24.1 + - - -
236E GLY 5.1 0.4 - - - +
239E ILE* 4.4 9.9 - - + -
240E TRP* 3.8 46.4 - - + +
243E ALA* 5.2 3.1 - - + -
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Residues in contact with THR 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PHE* 4.1 26.0 - - + -
49D VAL* 4.0 13.0 - - + -
50D GLU* 2.7 28.7 + - + +
48E PHE* 3.7 24.5 - - + -
51E ARG* 2.8 22.2 + - - +
59E LYS 2.9 2.9 + - - -
60E THR* 3.3 7.4 - - - -
62E LEU* 1.3 73.4 - - - +
64E VAL* 1.3 60.1 + - - +
66E GLY* 3.3 1.7 + - - -
67E LEU* 2.8 34.5 + - + +
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Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PHE* 4.9 9.9 - - + -
60E THR* 2.8 34.4 + - + +
61E SER* 3.8 5.6 - - - +
63E THR* 1.3 71.1 - - - +
65E SER* 1.3 52.5 + - - +
67E LEU* 3.0 10.5 + - + +
68E ILE* 2.8 44.2 + - + +
104E LEU* 3.6 40.8 - - + +
107E VAL* 4.6 15.0 - - + -
108E GLU* 4.4 13.2 - - + +
111E LEU* 4.8 7.2 - - + -
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PHE* 3.7 27.6 - - - -
61E SER 3.0 16.6 + - - -
62E LEU* 3.5 13.8 - - - +
64E VAL* 1.3 76.3 - - - +
66E GLY* 1.3 56.8 + - - +
68E ILE* 3.4 13.1 + - - +
69E THR* 3.0 29.8 + - - +
108E GLU* 3.4 12.3 + - - -
232E LYS 5.3 1.8 - - - +
235E PHE* 6.0 0.7 - - - -
236E GLY* 4.0 15.7 + - - -
239E ILE* 5.1 3.6 - - - +
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E THR* 3.5 6.5 - - - +
47E PHE* 3.8 13.0 - - - -
48E PHE* 3.8 21.4 - - - -
62E LEU 2.9 17.7 + - - -
63E THR 3.7 2.7 - - - -
65E SER* 1.3 70.0 - - - +
67E LEU* 1.3 55.4 + - - +
69E THR* 3.1 8.1 + - - -
70E GLY* 2.7 34.1 + - - -
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Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ALA* 3.7 38.6 - - + +
45D VAL* 3.9 25.4 - - + -
46D PHE* 4.0 33.0 - - + +
48E PHE* 3.8 4.4 - - + -
63E THR* 2.8 19.1 + - + +
64E VAL* 3.0 12.5 + - + +
66E GLY* 1.3 75.9 - - - +
68E ILE* 1.3 56.7 + - - +
70E GLY* 5.0 0.7 - - - -
71E ILE* 2.9 40.2 + - + +
104E LEU* 4.3 22.9 - - + -
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Residues in contact with ILE 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 2.8 35.9 + - + +
65E SER* 3.6 11.9 - - - +
66E GLY 3.3 0.2 - - - -
67E LEU* 1.3 72.0 - - - +
69E THR* 1.3 57.2 + - + +
71E ILE 3.5 0.2 + - - -
72E ALA* 2.9 27.7 + - - +
101E THR* 3.7 19.1 - - + +
104E LEU* 3.7 19.5 - - + +
105E LEU* 3.9 41.1 - - + +
108E GLU* 5.3 1.6 - - - +
232E LYS* 3.5 45.8 - - + +
301E RET 4.6 1.1 - - + -
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Residues in contact with THR 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E MET* 3.6 24.1 - - - +
43E ALA* 3.9 19.3 - - + -
44E THR* 3.0 28.4 + - - -
47E PHE* 3.9 5.4 - - + -
65E SER 3.0 19.1 + - - +
66E GLY* 3.1 10.6 + - - -
68E ILE* 1.3 76.1 - - + +
70E GLY* 1.3 50.7 + - - +
72E ALA* 3.4 7.4 + - - +
73E PHE* 2.9 32.2 + - - +
232E LYS* 4.1 24.5 - - + +
233E ILE* 4.2 2.9 - - + -
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Residues in contact with GLY 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E THR* 3.0 17.8 + - - -
66E GLY 2.7 20.7 + - - -
67E LEU* 3.7 1.6 - - - -
69E THR* 1.3 70.0 - - - +
71E ILE* 1.3 66.6 + - - +
73E PHE* 3.4 6.7 + - - +
74E TRP* 3.3 30.7 + - - -
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Residues in contact with ILE 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA* 5.1 10.3 - - + +
41D LEU* 6.1 4.9 - - + -
42D ALA* 4.0 25.4 - - + -
67E LEU* 2.9 24.9 + - + +
68E ILE 4.0 2.7 - - - +
70E GLY* 1.3 72.5 - - - +
72E ALA* 1.3 64.2 + - - +
73E PHE 3.2 0.3 + - - -
74E TRP* 3.3 5.5 + - - +
75E HIS* 3.0 49.0 + - + +
97E ASN* 3.5 11.4 - - - +
100E LEU* 4.0 26.2 - - + +
101E THR* 4.0 8.7 - - + -
104E LEU* 3.9 23.8 - - + -
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Residues in contact with ALA 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E MET* 3.6 24.0 - - + -
68E ILE 2.9 18.3 + - - +
69E THR 3.4 5.6 - - - +
71E ILE* 1.3 77.2 - - - +
73E PHE* 1.4 51.6 + - - +
75E HIS* 3.2 2.9 + - - +
76E TYR* 2.6 43.5 + - + -
97E ASN* 3.4 20.3 + - - +
101E THR* 5.0 0.2 - - + -
232E LYS* 3.9 15.9 - - + -
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Residues in contact with PHE 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E THR* 3.6 32.8 - - + +
38E ALA* 5.9 0.2 - - - -
40E MET* 3.8 15.6 - - + +
41E LEU* 3.8 45.5 - - + +
44E THR* 4.8 0.4 - - - +
69E THR 2.9 19.7 + - - +
70E GLY* 3.5 7.9 - - - +
71E ILE 3.3 0.2 - - - -
72E ALA* 1.4 67.7 - - - +
74E TRP* 1.3 118.9 + + - +
76E TYR* 3.1 5.7 + - - +
77E LEU* 3.0 40.3 + - + +
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Residues in contact with TRP 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TRP* 6.1 0.9 - - + -
41D LEU* 4.2 27.2 - - + +
70E GLY* 3.3 23.0 + - - -
71E ILE* 3.3 9.0 + - - +
73E PHE* 1.3 99.0 - + - +
75E HIS* 1.3 67.6 + - + +
77E LEU* 3.3 35.5 + - + +
78E TYR* 3.2 35.7 - + + -
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Residues in contact with HIS 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TRP* 2.8 43.2 + + - -
38D ALA* 4.8 6.1 - - + -
71E ILE* 3.0 34.3 + - + +
72E ALA 3.6 5.8 - - - +
74E TRP* 1.3 81.4 - - + +
76E TYR* 1.3 49.4 - - - +
78E TYR* 3.2 7.0 + - - +
79E MET* 2.8 40.1 + - + +
93E PHE* 3.8 18.5 - + - +
96E ILE* 3.3 19.0 - - + +
97E ASN* 3.6 24.9 - - + +
100E LEU* 3.7 21.1 - - + -
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Residues in contact with TYR 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 3.8 18.3 - + - -
36E VAL* 2.9 33.0 - - + -
37E THR* 3.6 26.1 + - - +
40E MET* 4.3 9.4 - - + -
72E ALA* 2.6 35.3 + - + +
73E PHE* 3.1 6.0 + - - +
75E HIS* 1.3 69.5 - - - +
77E LEU* 1.3 64.8 + - - +
79E MET* 3.5 24.7 - - + +
80E ARG* 3.1 24.4 + - - +
94E ARG* 3.1 7.9 + - - -
97E ASN* 4.3 6.3 - - - -
225E ASN* 3.4 24.2 - - - -
228E ASP* 2.5 45.6 + - + +
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E THR* 4.0 21.1 - - + -
73E PHE* 3.0 25.0 + - + +
74E TRP* 3.3 40.2 - - + +
75E HIS 3.2 0.2 - - - -
76E TYR* 1.3 77.0 - - - +
78E TYR* 1.3 67.9 + - + +
80E ARG* 3.4 5.0 + - + +
81E GLY* 3.2 18.2 + - - -
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Residues in contact with TYR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TRP* 3.8 28.9 - + - -
74E TRP* 3.2 37.6 + + + -
75E HIS* 3.2 7.6 + - - +
77E LEU* 1.3 81.5 - - + +
79E MET* 1.3 62.0 + - - +
81E GLY* 3.3 2.7 + - - +
82E VAL* 3.1 27.4 + - - +
93E PHE* 3.7 38.4 - + + -
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Residues in contact with MET 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 3.8 11.5 - - + -
75E HIS* 2.8 17.6 + - + +
76E TYR* 3.5 59.0 - - + +
77E LEU 3.3 0.2 - - - -
78E TYR* 1.3 75.3 - - - +
80E ARG* 1.3 60.5 + - - +
82E VAL 3.5 0.7 + - - -
83E TRP* 3.2 18.7 + - - +
90E PRO* 3.4 29.8 - - + +
93E PHE* 3.6 19.5 - - + -
94E ARG* 3.6 49.4 - - - +
97E ASN* 4.5 9.0 - - - +
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Residues in contact with ARG 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 2.6 41.5 - - - +
30E GLY* 3.0 28.1 + - - +
33E PHE* 3.4 31.6 - - + -
34E TRP* 3.8 31.7 - - - +
37E THR* 5.1 3.1 - - - +
76E TYR 3.1 16.8 + - - +
77E LEU* 3.9 5.2 - - + +
79E MET* 1.3 74.1 - - - +
81E GLY* 1.3 67.6 + - - +
83E TRP* 3.0 10.7 + - - +
84E ILE* 3.0 51.0 + - + +
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Residues in contact with GLY 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLY* 4.3 4.9 - - - -
77E LEU 3.2 10.7 + - - -
78E TYR* 3.3 4.7 + - - -
80E ARG* 1.3 79.3 - - - +
82E VAL* 1.3 60.8 + - - +
84E ILE* 3.3 3.4 + - - +
85E ASP* 3.1 35.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLY 3.5 10.1 - - - +
21D GLY 3.1 34.8 - - - +
22D ASP* 3.5 15.5 - - + +
78E TYR 3.1 18.8 + - - +
79E MET 3.8 4.0 - - - +
80E ARG 3.2 0.2 - - - -
81E GLY* 1.3 76.6 - - - +
83E TRP* 1.3 59.2 + - - +
86E THR* 2.9 39.0 + - - +
88E ASP* 3.8 13.4 - - + +
89E THR 4.6 1.1 - - - +
90E PRO* 3.5 26.0 - - + -
93E PHE* 3.9 9.2 - - + -
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Residues in contact with TRP 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASP* 2.8 33.5 + - - +
29E VAL* 2.9 37.0 - - + +
30E GLY* 3.5 21.3 - - - -
33E PHE* 3.6 22.2 - + + -
79E MET 3.2 5.1 + - - +
80E ARG 3.0 9.1 + - - +
82E VAL* 1.3 77.1 - - - +
84E ILE* 1.3 61.0 + - + +
87E GLY* 3.1 44.1 + - - +
88E ASP 3.2 29.8 - - - -
89E THR* 4.1 4.5 - - - -
90E PRO* 4.7 1.5 - - + +
217E ALA* 4.4 18.4 - - + -
218E SER* 4.5 5.4 - - - -
221E ASN* 3.7 22.9 - - - -
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Residues in contact with ILE 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASP* 3.9 20.6 - - - +
30E GLY* 4.5 1.8 - - - -
80E ARG* 3.0 54.2 + - + +
81E GLY* 3.9 2.2 - - - +
83E TRP* 1.3 85.5 - - + +
85E ASP* 1.3 74.9 + - - +
86E THR 3.3 1.6 + - - -
87E GLY* 4.0 2.3 + - - -
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Residues in contact with ASP 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLY* 3.8 31.0 - - - +
81E GLY* 3.1 22.0 + - - +
84E ILE* 1.3 84.5 - - - +
86E THR* 1.3 62.9 + - + +
----------------------------------------------------------
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Residues in contact with THR 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLY 4.2 10.8 - - - +
21D GLY* 4.4 12.6 - - - -
22D ASP 5.6 0.2 - - - +
82E VAL* 2.9 21.7 + - + +
84E ILE 4.4 0.9 - - - -
85E ASP* 1.3 88.6 - - + +
87E GLY* 1.3 58.8 + - - +
88E ASP* 2.9 40.7 + - - +
----------------------------------------------------------
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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