Contacts of the helix formed by residues 22 - 54 (chain D) in PDB entry 1F33
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 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ASP 3.6 3.4 + - - -
21D VAL* 1.3 75.4 - - - +
23D ASP* 1.3 60.5 + - - +
24D SER* 3.7 10.5 - - - -
25D GLU* 3.0 32.9 + - - +
26D LYS* 2.8 25.8 + - - +
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Residues in contact with ASP 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 4.3 15.7 - - + +
21D VAL 3.4 3.5 + - - +
22D SER* 1.3 73.2 - - - +
24D SER* 1.3 57.2 + - - +
26D LYS* 3.6 14.5 + - - +
27D LYS* 2.9 37.1 + - + +
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Residues in contact with SER 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER* 3.7 11.6 - - - -
23D ASP* 1.3 79.8 - - - +
25D GLU* 1.3 63.7 + - - +
27D LYS* 3.8 3.5 - - - +
28D ALA* 3.1 23.0 + - - +
140D LYS* 4.3 11.6 + - - -
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D VAL* 3.7 18.5 - - + +
22D SER* 3.0 19.5 + - - +
24D SER* 1.3 78.3 - - - +
26D LYS* 1.3 58.7 + - - +
28D ALA* 4.2 6.1 - - - -
29D THR* 2.6 44.2 + - - +
140D LYS* 3.1 43.9 - - + +
141D ASP* 3.4 15.6 + - + +
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Residues in contact with LYS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 3.7 15.7 - - + -
15D LEU 5.2 2.2 + - - +
17D THR* 3.4 23.6 + - - +
19D ASN* 2.8 30.6 + - - -
20D ASP* 4.9 0.2 - - - +
21D VAL* 2.9 36.6 + - + +
22D SER 2.8 21.8 + - - +
23D ASP* 3.6 11.9 + - - +
25D GLU* 1.3 72.0 - - - +
27D LYS* 1.3 58.0 + - - +
29D THR* 3.7 0.7 - - - -
30D VAL* 2.8 37.5 + - - +
87D LEU* 3.1 39.9 - - + +
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR* 3.0 53.4 - - + +
13D ASN* 3.7 11.3 - - - +
14D LEU* 3.8 21.3 - - + +
23D ASP* 2.9 15.3 + - + +
24D SER* 3.8 4.5 - - - +
26D LYS* 1.3 76.6 - - - +
28D ALA* 1.3 62.5 + - - +
30D VAL* 3.5 4.1 + - - +
31D GLU* 3.1 24.4 + - - +
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D SER 3.1 17.3 + - - +
25D GLU* 3.6 3.8 - - - +
27D LYS* 1.3 77.1 - - - +
29D THR* 1.3 56.8 + - - +
31D GLU* 3.2 10.1 + - - +
32D LEU* 3.0 26.7 + - - +
140D LYS* 3.9 30.1 - - + +
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Residues in contact with THR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D VAL* 5.7 0.2 - - - +
25D GLU* 2.6 30.6 + - - +
28D ALA* 1.3 69.7 - - - +
30D VAL* 1.3 67.6 + - - +
32D LEU* 3.0 8.5 + - - +
33D LEU* 2.8 33.3 + - + +
87D LEU* 3.3 24.6 - - + +
140D LYS* 5.3 4.2 + - - +
141D ASP* 3.8 18.8 + - - +
144D THR* 3.2 35.2 - - + +
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR* 5.0 12.3 - - + +
14D LEU* 4.3 4.7 - - + -
26D LYS 2.8 29.0 + - - +
27D LYS* 3.8 6.3 - - - +
29D THR* 1.3 72.7 - - - +
31D GLU* 1.3 57.6 + - - +
33D LEU* 3.9 0.7 - - - +
34D ASN* 3.0 45.8 + - - +
84D ALA* 3.6 33.4 - - + +
87D LEU* 4.2 9.4 - - + -
89D GLY* 3.7 27.8 - - - +
90D VAL 4.2 2.9 - - - +
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Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D THR* 4.7 17.3 - - + +
27D LYS 3.1 15.2 + - - +
28D ALA* 3.5 11.6 - - - +
29D THR 3.1 0.6 - - - -
30D VAL* 1.3 77.3 - - - +
32D LEU* 1.3 64.7 + - - +
34D ASN* 3.6 4.7 + - - +
35D ARG* 3.2 27.0 + - - +
101D LYS* 6.3 0.9 - - - +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ALA 3.0 13.4 + - - +
29D THR* 3.5 10.5 - - + +
31D GLU* 1.3 76.5 - - - +
33D LEU* 1.3 61.5 + - + +
35D ARG* 3.2 40.7 - - - +
36D GLN* 3.2 20.3 + - + +
135D ALA* 3.9 32.1 - - + +
138D GLU* 3.6 20.4 - - + +
139D ALA* 4.1 23.6 - - + +
144D THR* 5.0 4.7 - - + -
148D LEU* 4.3 11.0 - - + -
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D THR* 2.8 28.7 + - + +
30D VAL 3.9 3.6 - - - +
32D LEU* 1.3 72.4 - - + +
34D ASN* 1.3 60.4 + - - +
35D ARG 3.0 1.6 - - - -
36D GLN* 2.8 9.6 + - - +
37D VAL* 2.7 31.1 + - - +
80D MET* 3.6 34.0 - - + +
83D ARG* 3.5 20.9 - - + -
84D ALA* 3.4 36.1 - - + +
144D THR* 3.5 24.5 - - + -
147D ILE* 5.2 2.7 - - + -
148D LEU* 4.6 10.5 - - + -
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 3.0 37.4 + - - +
31D GLU* 4.1 5.1 - - - +
32D LEU 3.5 0.2 - - - -
33D LEU* 1.3 76.2 - - - +
35D ARG* 1.3 61.1 + - - +
37D VAL* 3.7 8.8 - - - +
38D ILE* 3.1 34.4 + - + +
84D ALA* 4.6 4.8 - - - +
90D VAL 2.9 21.9 + - - -
91D ALA* 3.3 5.9 - - - +
92D LEU* 2.6 50.9 + - + +
101D LYS* 5.8 2.9 - - - +
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLU* 3.2 18.2 + - - +
32D LEU* 3.2 38.8 - - - +
33D LEU 3.0 0.2 - - - -
34D ASN* 1.3 77.1 - - - +
36D GLN* 1.3 71.0 + - - +
38D ILE* 3.6 8.4 + - - +
39D GLN* 3.4 24.4 + - - +
101D LYS* 6.0 1.8 - - - +
103D PRO* 5.7 1.2 - - - +
131D ASP* 2.8 40.8 + - - -
135D ALA* 4.3 4.2 - - - +
138D GLU* 3.8 14.5 + - - -
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Residues in contact with GLN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.5 16.4 - - + +
33D LEU* 2.8 8.1 + - - +
35D ARG* 1.3 83.6 + - - +
37D VAL* 1.3 66.2 + - - +
39D GLN* 2.9 26.9 + - - +
40D PHE* 2.8 48.4 + - - -
80D MET* 3.6 19.3 - - + -
131D ASP* 3.6 10.4 - - - +
132D VAL* 3.6 21.5 - - - +
135D ALA* 3.6 20.5 - - - +
148D LEU* 4.0 17.5 - - + -
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU 2.7 24.3 + - - +
34D ASN* 3.7 15.0 - - - +
36D GLN* 1.3 73.0 - - - +
38D ILE* 1.3 57.3 + - - +
40D PHE* 3.8 2.3 - - - +
41D ILE* 2.9 52.8 + - + +
77D LEU* 4.1 12.8 - - + +
80D MET* 4.0 13.2 - - + -
81D ALA* 3.8 35.9 - - + +
84D ALA* 6.1 0.2 - - + -
91D ALA* 5.7 0.7 - - + -
92D LEU 3.6 22.0 - - - +
93D GLY* 4.8 0.2 - - - -
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ASN* 3.1 20.7 + - + +
35D ARG* 3.8 7.4 - - - +
37D VAL* 1.3 75.6 - - - +
39D GLN* 1.3 62.3 + - - +
41D ILE 3.5 0.2 + - - -
42D ASP* 3.1 23.9 + - - +
92D LEU* 4.0 17.7 - - + +
97D VAL* 3.6 15.3 - - + -
98D ILE* 3.5 38.1 - - + +
101D LYS* 3.4 40.4 - - + +
102D THR* 4.0 23.3 - - - +
103D PRO* 5.1 1.1 - - + -
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Residues in contact with GLN 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 3.4 10.7 + - - +
36D GLN* 2.9 33.5 + - - +
38D ILE* 1.3 80.9 - - - +
40D PHE* 1.3 58.0 + - + +
42D ASP* 3.5 3.9 + - - +
43D LEU* 2.9 29.7 + - - +
103D PRO* 3.3 39.2 - - + +
104D LEU* 4.0 3.5 - - + +
127D ILE* 4.2 6.5 - - - +
128D VAL* 3.3 37.2 - - + +
131D ASP* 3.1 34.5 + - - +
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLN* 2.8 50.6 + - - +
37D VAL 3.8 2.5 - - - +
39D GLN* 1.3 70.9 - - - +
41D ILE* 1.3 62.1 + - - +
43D LEU* 3.2 6.5 + - + +
44D SER* 2.8 30.8 + - - -
73D LEU* 3.9 30.1 - - + +
76D HIS* 4.0 15.7 - - + -
77D LEU* 4.1 16.6 - - + -
80D MET* 3.6 21.3 - - + -
128D VAL* 3.6 18.2 - - + -
132D VAL* 4.3 9.9 - - + -
151D ALA* 3.9 13.7 - - + -
155D LEU* 3.3 35.0 - - + -
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Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 2.9 33.2 + - + +
38D ILE 3.9 3.6 - - - +
40D PHE* 1.3 75.8 - - - +
42D ASP* 1.3 61.1 + - - +
44D SER* 2.7 21.7 + - - +
45D LEU* 3.1 23.1 + - + +
77D LEU* 3.3 30.1 - - + -
93D GLY* 3.7 36.1 - - - +
98D ILE* 4.0 16.6 - - + -
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ILE 3.1 18.7 + - - +
39D GLN 3.8 3.6 - - - +
41D ILE* 1.3 75.8 - - - +
43D LEU* 1.3 59.7 + - - +
45D LEU* 3.2 12.0 + - - +
46D ILE* 2.9 43.8 + - - +
98D ILE* 3.7 18.8 - - + +
102D THR* 2.6 33.3 + - - +
104D LEU* 3.4 20.2 - - + +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLN 2.9 18.4 + - - +
40D PHE* 3.2 6.5 + - - +
42D ASP* 1.3 76.1 - - - +
44D SER* 1.3 58.1 + - - +
46D ILE* 3.3 7.4 + - + +
47D THR* 2.7 32.1 + - - -
73D LEU* 4.1 11.2 - - + -
104D LEU* 3.9 10.9 - - + +
124D ARG* 3.8 25.6 - - + +
125D TYR* 3.5 56.1 - - + +
128D VAL* 4.0 12.1 - - + -
155D LEU* 3.9 22.9 - - + -
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Residues in contact with SER 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE 2.8 13.5 + - - -
41D ILE* 2.7 25.2 + - - +
43D LEU* 1.3 75.2 - - - +
45D LEU* 1.3 69.4 + - - +
47D THR* 3.2 5.9 + - - -
48D LYS* 3.2 21.3 + - - +
70D ARG* 4.1 18.7 + - - +
73D LEU* 3.8 26.4 - - - +
74D ILE* 4.6 13.9 - - - +
77D LEU* 4.7 1.7 - - - +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE* 3.1 28.1 + - + +
42D ASP* 3.2 19.5 + - - +
44D SER* 1.3 85.1 + - - +
46D ILE* 1.3 63.8 + - + +
48D LYS* 3.2 8.9 + - + +
49D GLN* 3.0 23.1 + - - +
52D TRP* 5.3 1.0 - - - -
98D ILE* 5.2 7.0 - - + -
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ASP* 2.9 34.5 + - - +
43D LEU* 3.6 7.4 - - + +
45D LEU* 1.3 75.0 - - + +
47D THR* 1.3 66.5 + - - +
49D GLN* 3.0 17.5 + - - +
50D ALA* 3.1 12.8 + - - +
104D LEU* 3.7 31.2 - - + -
105D LYS 4.8 2.0 - - - +
106D SER* 6.2 0.2 - - - -
107D TYR* 3.3 41.7 - - + +
121D LEU* 3.8 10.3 - - + -
124D ARG* 4.2 23.1 - - + +
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Residues in contact with THR 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU 2.7 22.0 + - - -
44D SER* 3.4 11.9 - - - -
46D ILE* 1.3 75.7 - - - +
48D LYS* 1.3 59.4 + - + +
50D ALA* 3.9 2.4 - - - +
51D HIS* 3.0 28.3 + - + +
66D LEU* 3.3 44.9 - - + +
70D ARG* 4.4 9.4 - - + +
73D LEU* 3.8 3.1 - - - +
121D LEU* 4.2 9.2 - - - -
125D TYR* 2.6 32.9 + - - +
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Residues in contact with LYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D SER 3.2 9.4 + - - +
45D LEU* 3.6 10.3 - - - +
46D ILE 3.2 0.8 - - - -
47D THR* 1.3 79.1 - - + +
49D GLN* 1.3 58.4 + - - +
51D HIS* 3.1 34.2 + - + +
52D TRP* 2.8 71.3 + - + +
67D ASP* 2.8 24.1 + - - +
70D ARG* 3.0 53.2 - - + +
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU 3.0 13.4 + - - +
46D ILE* 3.0 13.8 + - - +
48D LYS* 1.3 77.9 - - - +
50D ALA* 1.3 63.2 + - - +
52D TRP* 4.0 15.5 - - + -
53D ASN* 3.0 53.9 + - - +
107D TYR* 4.2 21.3 - - + -
108D PRO 4.5 3.6 + - - -
109D LEU* 4.1 31.0 - - + +
117D HIS* 5.4 1.6 - - - -
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE 3.1 4.0 + - - +
47D THR 3.9 1.3 - - - +
49D GLN* 1.3 79.0 - - - +
51D HIS* 1.3 64.4 + - - +
53D ASN 3.4 1.4 + - - -
54D MET* 3.2 32.1 + - + +
107D TYR* 3.3 23.6 - - - +
117D HIS* 3.4 17.9 - - + +
121D LEU* 3.6 35.7 - - + -
----------------------------------------------------------
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Residues in contact with HIS 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 3.0 21.2 + - + +
48D LYS* 3.1 41.0 + - + +
50D ALA* 1.3 77.8 - - - +
52D TRP* 1.3 75.4 + + - +
54D MET* 3.5 9.6 - - - +
59D PHE* 4.6 1.0 - - - -
63D HIS* 2.6 82.4 + + - -
64D GLU* 5.0 0.4 - - - -
66D LEU* 4.0 19.0 - - + +
67D ASP* 3.9 20.1 + - + -
----------------------------------------------------------
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Residues in contact with TRP 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TRP* 3.9 25.1 + + - -
45D LEU 5.3 1.3 - - - -
48D LYS* 2.8 60.1 + - + +
49D GLN* 4.0 20.9 - - + +
51D HIS* 1.3 95.4 - + - +
53D ASN* 1.3 71.5 + - - +
54D MET 3.8 2.3 + - - +
63D HIS* 4.6 4.9 - + - -
70D ARG* 5.5 3.1 - - - -
----------------------------------------------------------
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Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLN* 3.0 45.8 + - - +
50D ALA 3.4 2.8 + - - -
52D TRP* 1.3 89.1 - - - +
54D MET* 1.3 61.0 + - - +
55D ARG* 4.7 1.9 - - - +
111D ILE 4.6 1.3 - - - +
112D HIS* 3.0 38.4 + - + +
117D HIS* 3.4 18.2 + - + +
----------------------------------------------------------
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Residues in contact with MET 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TRP* 5.1 1.6 + - - -
164A SER* 4.4 1.0 + - - -
50D ALA* 3.2 17.4 + - + +
51D HIS 3.5 11.2 - - - +
52D TRP 3.6 2.5 - - - +
53D ASN* 1.3 79.5 - - - +
55D ARG* 1.3 69.4 + - - +
59D PHE* 3.4 31.8 - - + +
62D VAL* 3.4 28.9 - - + -
63D HIS* 4.1 13.5 - - - -
66D LEU* 3.4 30.1 - - + -
112D HIS 3.2 6.1 - - - +
114D VAL* 4.4 16.8 - - + +
117D HIS* 3.7 29.6 - - + -
118D LEU* 5.1 0.7 - - + -
121D LEU* 4.7 2.2 - - + -
----------------------------------------------------------
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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