Contacts of the helix formed by residues 37 - 68 (chain C) in PDB entry 1IB1
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 37 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU 3.8 1.6 + - - -
36C LEU* 1.3 78.2 - - - +
38C ASN* 1.3 65.9 + - - +
39C GLU* 3.7 9.4 + - - +
40C GLU* 3.2 38.3 + - - +
41C ARG* 2.9 20.7 + - - +
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Residues in contact with ASN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU 5.5 0.3 - - - +
37C SER* 1.3 73.9 - - - +
39C GLU* 1.3 57.3 + - - +
41C ARG* 3.1 41.2 + - - +
42C ASN* 2.9 28.9 + - - +
113C GLU* 4.6 6.9 + - - +
129G SER* 6.2 1.0 - - - +
130G PHE* 6.0 6.7 - - + -
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 4.9 8.2 - - + +
11C LYS* 3.2 37.6 + - - +
37C SER* 3.1 9.5 + - - +
38C ASN* 1.3 76.2 - - - +
40C GLU* 1.3 65.6 + - + +
42C ASN* 3.1 7.3 + - + +
43C LEU* 2.9 35.9 + - + +
130G PHE* 6.6 0.2 - - - -
133G GLN* 3.6 45.9 + - - +
135G LYS* 3.8 4.8 - - - +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LYS* 3.7 25.0 + - - +
4C ASN* 5.9 0.5 + - - -
7C VAL* 4.0 31.2 - - + +
26C MET* 3.3 19.7 - - + +
29C VAL* 4.0 8.7 - - - +
35C GLU 4.5 0.3 - - - +
36C LEU* 3.5 29.0 - - + +
37C SER* 3.2 32.2 + - - +
39C GLU* 1.3 81.2 - - + +
41C ARG* 1.3 57.6 - - - +
43C LEU* 3.4 3.0 + - - -
44C LEU* 2.9 26.3 + - - +
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 4.1 12.1 - - + +
37C SER 2.9 13.5 + - - +
38C ASN* 3.1 39.5 + - - +
40C GLU* 1.3 74.4 - - - +
42C ASN* 1.3 60.1 + - - +
44C LEU* 3.3 4.8 + - - +
45C SER* 3.0 27.2 + - - -
113C GLU* 3.6 21.0 + - - -
114C SER* 3.5 33.9 + - - +
117C PHE* 3.6 42.6 - - + +
118C TYR* 3.2 34.1 - - + +
166C ILE* 4.1 9.7 - - - +
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Residues in contact with ASN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN 2.9 13.6 + - - +
39C GLU* 3.5 10.0 - - - +
41C ARG* 1.3 76.5 - - - +
43C LEU* 1.3 68.4 + - - +
45C SER* 3.2 1.2 + - - -
46C VAL* 2.8 37.7 + - - +
117C PHE* 5.2 0.9 - - - -
35G ASN* 3.0 39.2 + - - +
84G TRP* 5.6 0.3 - - - -
86G VAL* 3.2 28.3 - - + +
87G GLU* 3.3 22.2 + - - +
130G PHE* 6.5 0.4 - - + -
135G LYS* 5.5 1.9 + - - -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.7 32.8 - - + +
10C ALA* 4.5 2.5 - - + -
11C LYS* 3.8 24.0 - - + -
14C GLU* 4.7 6.1 - - - +
22C MET* 3.7 26.8 - - + +
26C MET* 3.9 21.0 - - + +
39C GLU* 2.9 22.3 + - + +
40C GLU* 3.4 10.8 - - - +
41C ARG 3.3 0.2 - - - -
42C ASN* 1.3 88.5 - - - +
44C LEU* 1.3 56.0 + - - +
46C VAL* 4.6 0.4 - - - -
47C ALA* 2.9 31.0 + - - +
35G ASN* 5.5 1.6 - - - +
135G LYS* 4.2 14.4 - - - +
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C MET* 3.5 38.6 - - + +
27C LYS 4.3 0.2 - - - +
30C THR* 3.9 7.2 - - - +
36C LEU* 3.8 21.5 - - + -
40C GLU 2.9 16.8 + - - +
41C ARG 3.6 5.2 - - - +
42C ASN 3.2 0.2 - - - -
43C LEU* 1.3 73.6 - - - +
45C SER* 1.3 65.3 + - - +
47C ALA* 3.5 0.8 + - - +
48C TYR* 3.2 58.7 + - + +
100C LEU* 4.6 6.5 - - + -
105C LEU* 3.9 25.4 - - + -
118C TYR* 5.0 5.2 - - + -
121C MET* 4.7 11.9 - - + -
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ARG 3.0 16.2 + - - -
42C ASN 3.5 4.5 - - - -
44C LEU* 1.3 76.5 - - - +
46C VAL* 1.3 58.7 + - - +
48C TYR* 4.0 0.9 - - - +
49C LYS* 2.8 35.4 + - - +
117C PHE* 3.7 18.7 - - - -
121C MET* 4.0 17.2 - - - +
125C TYR* 4.4 1.9 + - - -
87G GLU* 2.8 33.5 + - - -
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 4.0 20.4 - - - +
19C TYR* 4.6 2.5 - - + -
22C MET* 4.1 13.2 - - + -
42C ASN* 2.8 29.5 + - - +
43C LEU* 4.0 3.1 - - - +
45C SER* 1.3 70.6 - - - +
47C ALA* 1.3 66.1 + - - +
49C LYS* 4.0 0.2 - - - +
50C ASN* 2.9 42.8 + - - +
34G ALA* 3.9 23.6 - - + +
35G ASN* 3.3 34.1 - - + +
87G GLU* 4.4 3.4 - - + -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 4.1 3.3 - - - +
22C MET* 3.7 22.9 - - + +
23C ALA* 3.6 33.0 - - - +
26C MET* 4.8 0.2 - - + -
43C LEU 2.9 19.9 + - - +
44C LEU* 3.7 6.3 - - - +
46C VAL* 1.3 79.0 - - - +
48C TYR* 1.3 59.1 + - + +
50C ASN* 3.2 3.5 + - - +
51C VAL* 2.9 32.1 + - - +
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Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ALA* 4.0 28.5 + - + +
27C LYS* 3.5 21.1 - - - +
44C LEU* 3.2 48.2 + - + +
45C SER 4.2 0.7 - - - +
47C ALA* 1.3 76.8 - - + +
49C LYS* 1.3 65.8 + - - +
50C ASN 3.1 2.0 - - - -
51C VAL* 3.8 6.9 - - + +
52C VAL* 2.9 28.8 + - - +
93C ILE* 4.0 20.2 - - + -
96C ASP* 3.5 23.8 + - + -
97C VAL* 3.6 29.8 - - + -
100C LEU* 3.9 13.7 - - + +
121C MET* 4.7 4.3 - - + -
125C TYR* 3.2 18.2 - - + +
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C SER* 2.8 26.6 + - - +
46C VAL 4.0 0.4 - - - +
48C TYR* 1.3 71.3 - - - +
50C ASN* 1.3 57.1 + - - +
52C VAL* 3.6 3.1 - - + +
53C GLY* 3.0 25.8 + - - -
56C ARG* 5.5 1.6 - - - +
120C LYS* 4.6 2.0 - - - +
124C ASP* 3.8 16.4 + - - -
125C TYR* 3.3 11.8 + - + +
128C TYR* 3.0 33.3 + - + +
173C ASN* 4.3 0.2 - - - +
31G TPO 3.6 13.3 + - - +
32G LEU* 3.4 40.7 + - - +
33G PRO 4.5 4.0 + - - -
34G ALA* 3.6 28.7 - - + +
87G GLU* 4.9 5.0 + - - +
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Residues in contact with ASN 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.4 52.0 + - + -
46C VAL* 2.9 36.3 + - - +
47C ALA 3.4 3.1 - - - +
48C TYR 3.1 0.4 - - - -
49C LYS* 1.3 77.1 - - - +
51C VAL* 1.3 65.0 + - - +
53C GLY* 3.9 0.6 - - - -
54C ALA* 3.1 24.1 + - - +
34G ALA* 4.1 14.6 + - - +
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.2 37.7 - - + +
20C ASP* 3.6 24.9 - - - +
23C ALA* 4.0 10.3 - - + -
47C ALA 2.9 16.5 + - - +
48C TYR* 3.2 11.6 + - + +
50C ASN* 1.3 75.7 - - - +
52C VAL* 1.3 61.1 + - - +
54C ALA* 3.7 3.1 - - - +
55C ARG* 3.1 31.7 + - - +
93C ILE* 3.4 32.5 - - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR 2.9 19.5 + - - +
49C LYS* 3.6 9.2 - - + +
51C VAL* 1.3 75.3 - - - +
53C GLY* 1.3 72.0 + - - +
54C ALA 3.1 1.8 - - - -
55C ARG* 3.0 4.7 + - - +
56C ARG* 2.9 34.0 + - + +
90C LEU* 3.4 24.2 - - + -
93C ILE* 4.1 24.5 - - + -
94C CYS* 4.3 11.0 - - - -
125C TYR* 4.1 6.1 - - + -
128C TYR* 4.0 33.7 - - + -
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Residues in contact with GLY 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS 3.0 14.8 + - - -
50C ASN* 3.4 1.3 + - - -
52C VAL* 1.3 84.5 - - - +
54C ALA* 1.3 62.3 + - - +
56C ARG* 3.2 18.1 + - - +
57C SER* 2.9 26.2 + - - -
60C ARG* 4.2 3.2 + - - -
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASN 3.1 16.8 + - - +
51C VAL* 3.7 7.9 - - - +
52C VAL 3.1 0.4 - - - -
53C GLY* 1.3 76.7 - - - +
55C ARG* 1.3 71.9 + - - +
57C SER* 3.4 6.0 + - - -
58C SER* 3.1 26.6 + - - -
18D ARG* 5.9 0.2 - - - -
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Residues in contact with ARG 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASP* 3.1 36.5 + - - -
51C VAL* 3.1 24.0 + - - +
52C VAL* 3.0 3.4 + - - +
54C ALA* 1.3 85.7 - - - +
56C ARG* 1.3 67.7 + - - +
58C SER* 3.2 7.5 + - - -
59C TRP* 2.8 24.4 + - - +
86C ILE* 3.7 10.2 - - + +
89C GLU* 3.0 45.0 + - + +
90C LEU* 3.5 23.6 - - + +
93C ILE* 3.8 19.2 - - + +
18D ARG* 4.3 10.9 - - - +
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 5.4 2.2 - - - +
52C VAL* 2.9 25.8 + - - +
53C GLY* 3.6 15.6 - - - +
55C ARG* 1.3 75.3 - - - +
57C SER* 1.3 58.4 + - - +
59C TRP* 3.1 9.5 + - - +
60C ARG* 3.0 54.7 + - - +
90C LEU* 3.8 18.4 - - + -
128C TYR* 3.6 34.2 - - + -
131C GLU* 2.9 40.5 + - - +
28G ARG* 3.7 17.6 - - - +
29G ARG* 4.3 0.2 - - - +
31G TPO 2.8 40.4 + - - -
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLY 2.9 17.1 + - - -
54C ALA* 3.5 7.2 - - - -
56C ARG* 1.3 76.5 - - - +
58C SER* 1.3 61.8 + - - +
60C ARG* 3.3 26.9 + - - +
61C VAL* 3.2 23.4 + - - +
21G PRO* 5.7 0.5 - - - +
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Residues in contact with SER 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ALA 3.1 13.5 + - - -
55C ARG* 3.2 10.1 + - - -
57C SER* 1.3 77.2 - - - +
59C TRP* 1.3 57.5 + - - +
61C VAL* 3.0 25.4 - - - +
62C VAL* 3.0 18.3 - - - +
86C ILE* 4.2 6.8 - - - +
16D ALA* 2.9 24.7 + - - +
17D GLU 5.2 0.2 - - - -
18D ARG* 3.6 28.2 + - - +
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Residues in contact with TRP 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ARG 2.8 13.6 + - - +
56C ARG* 3.1 13.7 + - - +
58C SER* 1.3 74.5 - - - +
60C ARG* 1.3 88.8 + - + +
62C VAL* 3.1 7.5 - - - +
63C SER* 2.7 50.2 + - - -
83C ARG* 3.4 20.9 - - + +
86C ILE* 4.3 8.0 - - + +
87C GLU* 3.0 43.7 + - + +
90C LEU* 4.3 7.6 - - + -
131C GLU* 3.5 26.0 - - + -
132C VAL* 3.4 24.2 - - + +
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Residues in contact with ARG 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLY* 4.2 4.8 + - - -
56C ARG* 3.0 45.8 + - - +
57C SER* 3.3 32.3 + - - +
59C TRP* 1.3 92.1 - - + +
61C VAL* 1.3 56.9 + - - +
63C SER* 3.5 3.6 + - - -
64C SER* 3.0 28.2 + - - -
131C GLU* 5.8 1.0 + - - -
19G GLY 4.6 6.1 + - - -
21G PRO* 4.3 22.6 - - + +
28G ARG* 3.3 52.7 - - - +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER 3.2 12.4 + - - +
58C SER* 3.0 27.4 - - - +
60C ARG* 1.3 76.5 - - - +
62C VAL* 1.3 57.4 + - - +
64C SER* 3.2 4.6 + - - -
65C ILE* 2.9 45.9 + - + +
15D GLN* 4.0 18.8 - - + +
16D ALA* 3.7 18.8 - - + +
21G PRO* 4.4 15.7 - - + +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C SER 3.0 25.3 + - - +
59C TRP* 3.1 18.2 - - - +
61C VAL* 1.3 77.4 - - + +
63C SER* 1.3 56.4 + - - +
65C ILE* 3.8 10.0 - - - +
66C GLU* 3.0 26.3 + - - +
79C ALA* 3.7 25.0 - - + +
82C TYR* 4.1 16.4 - - + -
83C ARG* 4.0 20.6 - - + +
86C ILE* 3.9 16.6 - - + -
12D LEU* 4.3 14.1 - - + -
16D ALA* 5.1 4.5 - - + -
----------------------------------------------------------
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C TRP* 2.7 53.4 + - - -
60C ARG* 3.6 6.7 - - - -
62C VAL* 1.3 75.0 - - - +
64C SER* 1.3 67.3 + - - +
66C GLU* 3.1 10.4 + - - +
67C GLN* 2.9 43.2 + - - +
83C ARG* 3.8 8.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ARG 3.0 17.9 + - - -
61C VAL* 3.5 4.3 - - - -
63C SER* 1.3 76.4 - - - +
65C ILE* 1.3 66.4 + - - +
67C GLN* 3.4 7.6 + - - +
68C LYS* 3.1 44.1 + - - +
21G PRO* 3.9 33.3 + - - +
22G GLY* 4.1 2.6 + - - -
----------------------------------------------------------
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 2.9 31.1 + - + +
62C VAL* 3.8 5.4 - - - +
64C SER* 1.3 79.2 - - - +
66C GLU* 1.3 60.5 - - - +
68C LYS* 3.4 5.5 + - - +
69C THR* 2.8 28.3 + - - +
79C ALA* 4.9 3.6 - - + -
12D LEU* 3.6 29.6 - - + +
15D GLN* 3.6 44.9 - - + +
16D ALA 5.8 0.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL 3.0 18.3 + - - +
63C SER* 3.1 6.6 + - - +
65C ILE* 1.3 73.3 - - - +
67C GLN* 1.3 79.3 + - - +
69C THR* 3.0 24.8 + - - -
76C GLN* 3.4 27.9 + - + +
79C ALA* 4.0 17.7 - - + -
80C ARG* 3.4 27.0 + - - +
83C ARG* 3.0 44.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C SER* 2.9 44.6 + - - +
64C SER* 3.8 7.2 - - - +
66C GLU* 1.3 84.6 - - - +
68C LYS* 1.3 65.1 + - + +
69C THR 2.9 11.8 + - - +
76C GLN* 4.3 10.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 3.1 30.5 + - - +
65C ILE* 3.7 6.5 - - - +
66C GLU 3.2 0.2 - - - -
67C GLN* 1.3 77.8 - - + +
69C THR* 1.3 55.6 + - - +
70C GLU* 3.0 27.6 + - - +
22G GLY* 3.3 32.5 + - - -
141H TRP* 3.3 32.5 - - + +
170H ARG 5.0 5.8 + - - +
----------------------------------------------------------
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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