Contacts of the helix formed by residues 55 - 87 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 1.3 75.0 - - - +
56D ALA* 1.3 55.2 + - - +
57D LYS* 3.3 14.6 + - - +
58D TRP* 2.8 43.8 + - - -
59D LYS* 3.1 13.9 + - - +
246D GLU* 4.2 3.8 + - - -
247D SER* 2.9 21.1 + - - -
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLN* 3.0 42.7 - - - +
251C LYS* 4.2 21.3 - - + +
55D SER* 1.3 72.6 - - - +
57D LYS* 1.3 62.4 + - - +
58D TRP 3.1 1.0 + - - -
59D LYS* 3.6 6.9 + - - +
60D THR* 4.7 0.5 + - - -
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D SER* 3.1 12.2 + - - +
56D ALA* 1.3 76.7 - - - +
58D TRP* 1.3 80.6 + - + +
60D THR 5.5 0.2 - - - -
61D SER* 4.8 3.3 + - - -
179D SER* 4.5 14.3 + - - -
182D VAL* 5.3 8.7 - - + +
246D GLU* 2.7 30.5 + - - +
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Residues in contact with TRP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 3.7 8.3 - - + -
55D SER* 2.8 35.9 + - - +
57D LYS* 1.3 92.6 - - + +
59D LYS* 1.3 62.4 + - - +
60D THR 3.3 3.1 - - - -
61D SER* 3.0 34.8 + - - -
62D LEU* 3.3 7.4 + - + +
112D ILE* 5.7 6.3 - - + -
181D ALA* 3.8 29.6 - - + -
182D VAL* 4.6 10.5 - - + -
185D ALA* 4.6 13.0 - - + -
239D ILE* 4.7 12.8 - - + -
242D VAL* 3.6 25.6 - - + -
243D ALA* 3.3 31.6 - - + -
246D GLU* 3.3 25.2 + - + +
247D SER* 3.6 14.8 - - - -
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Residues in contact with LYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASP* 3.8 20.9 - - - +
53C GLN* 3.5 27.6 - - - +
51D ARG* 2.9 65.7 + - - +
52D ASP* 4.4 8.3 + - - +
54D VAL* 2.8 30.0 + - + -
55D SER* 3.1 18.0 + - - +
56D ALA* 3.6 3.9 + - - +
58D TRP* 1.3 77.8 - - - +
60D THR* 1.3 61.7 + - - +
62D LEU* 3.1 4.9 + - - +
63D THR 3.0 13.7 + - - -
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 4.0 15.5 - - + -
50C GLU* 2.7 26.3 + - - +
53C GLN* 3.0 11.9 + - - -
240C TRP* 3.8 30.8 - - + -
244C VAL* 5.7 1.4 - - - +
56D ALA 4.7 0.4 + - - -
58D TRP 3.3 0.8 - - - -
59D LYS* 1.3 73.7 - - - +
61D SER* 1.3 65.1 + - - +
63D THR* 3.3 1.6 + - - -
64D VAL* 3.0 26.7 + - + +
111D LEU* 4.1 22.2 - - + -
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LYS 4.8 2.6 + - - -
58D TRP* 3.0 26.2 + - - -
60D THR* 1.3 78.4 - - - +
62D LEU* 1.3 59.1 + - - +
64D VAL 3.1 1.9 + - - -
65D SER* 2.8 29.7 + - - -
108D GLU* 3.4 26.6 + - - +
111D LEU* 4.3 13.5 - - - +
112D ILE* 5.6 4.2 - - - +
239D ILE* 4.1 21.4 - - - +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 3.7 31.2 - - + +
48D PHE* 4.8 0.2 - - - -
50D GLU* 3.9 8.1 - - + +
51D ARG* 3.6 37.7 - - + +
54D VAL* 3.9 21.8 - - + -
58D TRP* 3.3 15.0 - - + +
59D LYS 3.1 2.7 + - - +
61D SER* 1.3 81.6 - - - +
63D THR* 1.3 59.4 + - - +
65D SER* 3.4 8.6 - - - -
66D GLY* 2.8 26.5 + - - -
239D ILE* 4.9 4.3 - - + -
240D TRP* 4.0 30.5 - - + +
243D ALA* 4.3 11.2 - - + -
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Residues in contact with THR 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 3.6 38.1 - - + -
49C VAL* 3.9 3.8 - - + +
50C GLU* 2.6 28.0 + - + +
48D PHE* 3.7 24.5 - - + -
51D ARG* 2.7 19.9 + - - +
59D LYS 3.0 4.3 + - - -
60D THR* 3.5 8.3 - - - -
61D SER 3.2 0.2 - - - -
62D LEU* 1.3 73.8 - - - +
64D VAL* 1.3 53.7 + - - +
66D GLY* 2.9 5.0 + - - -
67D LEU* 2.8 39.3 + - + +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 4.8 11.0 - - + -
60D THR* 3.0 28.9 + - + +
61D SER 3.6 2.7 - - - +
63D THR* 1.3 71.9 - - - +
65D SER* 1.3 68.3 + - - +
67D LEU* 3.2 13.2 + - + +
68D ILE* 2.9 34.1 + - + +
104D LEU* 3.5 35.6 - - + +
107D VAL* 4.2 18.6 - - + -
108D GLU* 4.0 17.7 - - + +
111D LEU* 4.7 2.2 - - + -
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Residues in contact with SER 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 3.6 18.5 - - - -
61D SER 2.8 13.7 + - - -
62D LEU* 3.4 14.4 - - - -
64D VAL* 1.3 79.7 - - - +
66D GLY* 1.4 55.2 + - - -
68D ILE* 3.5 13.5 + - - +
69D THR* 3.2 26.3 + - - +
108D GLU* 4.1 11.2 + - - -
232D LYS 5.0 1.6 + - - +
235D PHE* 5.8 1.0 - - - -
236D GLY* 3.2 30.6 + - - -
239D ILE* 5.4 1.6 - - - +
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D THR* 3.4 9.4 - - - +
47D PHE* 3.8 13.7 - - - -
48D PHE* 3.7 18.3 - - - -
62D LEU 2.8 17.5 + - - -
63D THR 2.9 5.0 + - - -
65D SER* 1.4 68.7 - - - +
67D LEU* 1.3 55.0 + - - +
69D THR* 2.9 10.5 + - - -
70D GLY* 2.8 29.8 + - - -
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 3.6 33.7 - - + +
45C VAL* 3.8 26.5 - - + -
46C PHE* 3.9 34.3 - - + +
48D PHE* 3.8 5.1 - - + -
63D THR* 2.8 20.0 + - + +
64D VAL* 3.6 14.1 - - + +
66D GLY* 1.3 70.6 - - - +
68D ILE* 1.3 64.8 + - - +
70D GLY* 4.4 1.8 - - - +
71D ILE* 3.1 35.4 + - + +
104D LEU* 4.0 21.5 - - + -
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Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D VAL* 2.9 35.5 + - + +
65D SER* 3.5 11.9 - - - +
67D LEU* 1.3 76.4 - - - +
69D THR* 1.3 64.8 + - + +
72D ALA* 3.0 21.8 + - - +
101D THR* 3.7 18.4 - - + +
104D LEU* 3.7 20.4 - - + +
105D LEU* 3.9 36.3 - - + +
108D GLU* 5.5 1.6 - - + +
232D LYS* 3.6 42.4 - - + +
301D RET 4.9 1.3 - - + -
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 3.2 37.2 - - + +
43D ALA* 3.8 11.0 - - + -
44D THR* 3.0 26.5 + - - -
47D PHE* 3.6 25.0 - - + -
65D SER 3.2 7.0 + - - +
66D GLY* 2.9 15.9 + - - -
68D ILE* 1.3 77.3 - - + +
70D GLY* 1.3 55.7 + - - +
73D PHE* 2.9 22.2 + - - +
232D LYS* 3.9 17.7 - - + +
233D ILE* 4.5 0.2 - - + -
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Residues in contact with GLY 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D THR* 3.4 17.9 - - - -
48D PHE* 6.0 0.2 - - - -
66D GLY 2.8 18.6 + - - -
67D LEU* 3.4 2.7 + - - -
68D ILE 3.3 0.2 - - - -
69D THR* 1.3 70.3 + - - +
71D ILE* 1.3 65.2 + - - +
73D PHE* 3.2 14.0 + - - +
74D TRP* 3.1 28.1 + - - -
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Residues in contact with ILE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA* 4.8 12.3 - - + +
41C LEU* 6.2 3.4 - - + -
42C ALA* 3.8 30.1 - - + -
67D LEU* 3.1 19.6 + - + +
68D ILE 4.0 1.6 - - - +
70D GLY* 1.3 73.5 - - - +
72D ALA* 1.3 64.9 + - - +
74D TRP* 3.5 8.6 + - + +
75D HIS* 2.8 49.7 + - + +
97D ASN* 3.8 6.7 - - - +
100D LEU* 4.1 22.4 - - + +
101D THR* 4.0 10.3 - - + -
104D LEU* 4.1 18.2 - - + -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 2.5 41.7 - - + -
68D ILE 3.0 10.5 + - - +
71D ILE* 1.3 77.2 - - - +
73D PHE* 1.3 50.1 - - - +
75D HIS* 3.1 3.1 + - - +
76D TYR* 2.7 43.5 + - + -
97D ASN* 3.4 23.5 + - - +
101D THR* 4.4 0.2 - - - +
232D LYS* 4.1 8.1 - - + -
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Residues in contact with PHE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR* 3.4 35.7 - - + -
38D ALA* 5.7 0.4 - - - -
40D MET* 3.8 14.3 - - + +
41D LEU* 3.6 44.0 - - + +
44D THR* 4.8 0.7 - - - +
69D THR 2.9 15.0 + - - +
70D GLY* 3.2 11.0 + - - +
72D ALA* 1.3 74.1 - - - +
74D TRP* 1.3 98.5 + + - +
76D TYR* 3.1 7.1 + - - +
77D LEU* 3.1 44.4 + - + +
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Residues in contact with TRP 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TRP* 6.2 2.2 - - + -
41C LEU* 4.2 26.6 - - + +
70D GLY* 3.1 28.1 + - - -
71D ILE* 4.0 8.3 - - + +
72D ALA 3.3 0.2 - - - -
73D PHE* 1.3 95.5 - + - +
75D HIS* 1.3 62.6 + - + +
77D LEU* 3.1 39.3 + - + +
78D TYR* 3.2 34.3 - + + -
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Residues in contact with HIS 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TRP* 2.8 44.1 + + - -
38C ALA* 4.7 5.8 - - + -
71D ILE* 2.8 29.5 + - + -
72D ALA 3.1 6.5 + - - +
74D TRP* 1.3 76.5 - - + +
76D TYR* 1.3 59.8 + - - +
78D TYR* 3.2 5.4 + - - +
79D MET* 2.7 37.9 + - + +
93D PHE* 4.1 24.2 - + + +
96D ILE* 3.8 7.4 - - + +
97D ASN* 3.2 30.5 + - + +
100D LEU* 3.6 24.9 - - + -
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Residues in contact with TYR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 3.9 22.4 - + - -
36D VAL* 3.3 33.4 - - + +
37D THR* 3.4 29.5 + - - +
40D MET* 4.5 2.7 - - + -
72D ALA* 2.7 39.3 + - + +
73D PHE* 3.6 6.1 - - - +
75D HIS* 1.3 74.1 - - - +
77D LEU* 1.3 60.0 + - - +
79D MET* 3.5 16.8 - - + +
80D ARG* 3.1 26.0 + - - +
94D ARG* 2.9 14.0 + - - -
97D ASN* 4.3 6.3 - - - -
225D ASN* 3.4 22.3 - - - -
228D ASP* 2.6 43.3 + - + +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR* 4.1 16.3 - - + +
73D PHE* 3.1 34.8 + - + +
74D TRP* 3.1 39.0 + - + +
76D TYR* 1.3 76.8 - - - +
78D TYR* 1.3 66.0 + - + +
80D ARG* 4.0 3.6 - - - +
81D GLY* 3.2 18.5 + - - -
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Residues in contact with TYR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TRP* 3.7 30.2 - + - -
74D TRP* 3.2 39.4 + + + -
75D HIS 3.2 6.8 + - - +
77D LEU* 1.3 82.0 - - + +
79D MET* 1.3 65.4 + - - +
81D GLY* 3.3 2.4 + - - -
82D VAL* 3.0 28.3 + - + +
93D PHE* 3.6 37.2 - + + -
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Residues in contact with MET 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PHE* 4.1 10.1 - - + -
75D HIS* 2.7 29.0 + - + +
76D TYR* 3.5 46.4 - - + +
78D TYR* 1.3 73.1 - - - +
80D ARG* 1.3 64.0 + - - +
82D VAL* 3.0 6.6 + - - +
83D TRP* 3.0 21.8 + - - +
90D PRO* 3.7 24.9 - - + +
93D PHE* 3.5 21.3 - - + -
94D ARG* 3.8 48.5 - - - +
97D ASN* 4.4 10.8 - - - +
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.3 27.5 - - - +
30D GLY* 2.8 40.6 + - - -
33D PHE* 3.5 29.1 - - + -
34D TRP* 3.6 45.5 - - - +
37D THR* 4.9 3.1 - - - +
76D TYR 3.1 16.6 + - - +
77D LEU* 4.0 3.8 - - - +
79D MET* 1.3 78.1 - - - +
81D GLY* 1.3 56.8 + - - +
83D TRP* 3.5 0.9 + - - +
84D ILE* 3.1 53.5 + - + +
93E PHE* 6.0 0.2 - - - -
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Residues in contact with GLY 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 5.2 0.8 + - - -
77D LEU 3.2 13.5 + - - -
78D TYR* 3.3 3.3 + - - -
79D MET 3.2 0.8 - - - -
80D ARG* 1.3 73.4 - - - +
82D VAL* 1.3 61.1 + - - +
84D ILE* 4.0 10.1 - - - -
85D ASP* 3.1 38.7 + - - +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 3.4 41.3 - - - +
22C ASP* 3.5 13.9 - - + +
78D TYR* 3.0 16.3 + - + +
79D MET 3.0 8.4 + - - +
81D GLY* 1.3 76.5 - - - +
83D TRP* 1.3 63.4 + - - +
85D ASP* 5.1 0.2 - - - -
86D THR* 3.1 37.0 + - - +
88D ASP* 3.9 18.6 - - + +
89D THR 4.8 0.2 - - - -
90D PRO* 4.0 20.4 - - + -
93D PHE* 3.8 13.7 - - + -
----------------------------------------------------------
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Residues in contact with TRP 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASP* 2.9 37.2 + - - -
29D VAL* 3.3 36.3 - - + +
30D GLY* 3.8 15.0 - - - -
33D PHE* 3.7 21.5 - + + -
79D MET 3.0 6.9 + - - +
80D ARG 3.6 7.2 - - - +
82D VAL* 1.3 77.5 - - - +
84D ILE* 1.3 60.5 + - + +
87D GLY* 2.7 54.9 + - - -
88D ASP 3.5 24.2 - - - +
89D THR* 4.5 2.5 - - - -
90D PRO* 4.8 2.0 - - + +
217D ALA* 4.5 14.1 - - + -
218D SER* 4.5 9.2 - - - -
221D ASN* 3.9 21.8 - - - -
----------------------------------------------------------
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Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASP* 4.2 17.3 - - - +
80D ARG* 3.1 54.5 + - + +
81D GLY* 3.7 7.6 - - - +
83D TRP* 1.3 83.4 - - + +
85D ASP* 1.3 78.9 + - - +
86D THR 3.7 0.2 + - - -
87D GLY 4.8 0.5 + - - -
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Residues in contact with ASP 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 5.4 3.8 - - - +
81D GLY* 3.1 23.1 + - - +
82D VAL* 4.5 0.4 - - - +
84D ILE* 1.3 97.2 - - - +
86D THR* 1.3 69.6 + - + +
----------------------------------------------------------
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY* 4.3 18.8 - - - +
82D VAL* 3.1 20.8 + - - +
85D ASP* 1.3 87.9 - - + +
87D GLY* 1.3 59.8 + - - +
88D ASP* 2.9 39.2 + - - +
----------------------------------------------------------
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D VAL 3.6 0.2 + - - -
83D TRP* 2.7 54.7 + - - -
84D ILE 4.6 0.6 - - - -
86D THR* 1.3 71.1 + - - +
88D ASP* 1.3 61.0 + - - +
89D THR 4.1 0.2 + - - -
217D ALA* 5.7 1.4 - - - +
----------------------------------------------------------
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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