Contacts of the helix formed by residues 31 - 60 (chain I) in PDB entry 4E45
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 31 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H THR* 3.7 12.6 - - - +
77H ILE 3.0 19.5 + - - -
78H ASN* 4.2 8.5 - - - +
79H THR 4.7 0.7 + - - -
30I VAL* 1.3 77.8 - - - +
32I GLY* 1.3 65.4 + - - +
33I ASP* 3.4 8.8 + - - +
34I ALA* 3.0 23.0 + - - +
35I LEU* 2.9 20.3 + - - +
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Residues in contact with GLY 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LYS* 6.2 0.2 - - - +
30I VAL 3.7 2.0 + - - -
31I SER* 1.3 72.4 - - - +
33I ASP* 1.3 62.1 + - - +
35I LEU* 3.2 12.3 + - - +
36I GLN* 3.1 22.2 + - - +
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Residues in contact with ASP 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H THR* 4.1 18.4 - - + +
103H ILE* 3.4 31.8 - - + +
104H ALA* 5.2 8.5 - - - +
31I SER* 3.8 7.4 - - - +
32I GLY* 1.3 75.0 - - - +
34I ALA* 1.3 64.0 + - - +
36I GLN* 3.4 4.8 + - - +
37I LEU* 3.2 23.9 + - - +
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Residues in contact with ALA 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H ILE* 3.8 11.2 - - + +
78H ASN 3.7 26.0 - - - +
79H THR* 4.2 4.8 - - - +
82H VAL* 4.0 12.8 - - + -
30I VAL* 3.8 11.0 - - + -
31I SER* 3.0 21.0 + - - +
33I ASP* 1.3 75.1 - - - +
35I LEU* 1.3 56.9 + - - +
37I LEU* 3.2 5.6 + - - +
38I MET* 2.9 32.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770E HIS* 3.7 31.2 - - + +
12I LYS* 3.6 34.8 - - + +
15I VAL* 3.8 14.4 - - + -
16I SER* 3.6 30.5 - - - +
19I LEU* 4.2 9.4 - - + -
30I VAL* 3.8 12.9 - - + +
31I SER 2.9 12.9 + - - +
32I GLY* 3.2 14.1 + - - +
34I ALA* 1.3 75.7 - - - +
36I GLN* 1.3 58.5 + - - +
38I MET* 3.2 5.3 + - - +
39I VAL* 3.0 27.8 + - - +
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Residues in contact with GLN 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ILE* 3.8 25.1 - - + +
12I LYS* 5.7 6.5 - - + +
32I GLY 3.1 12.8 + - - +
33I ASP* 4.0 4.9 - - - +
34I ALA 3.4 0.2 - - - -
35I LEU* 1.3 76.7 - - - +
37I LEU* 1.3 61.6 + - - +
39I VAL* 3.4 10.4 + - - +
40I GLU* 3.3 26.3 + - - +
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Residues in contact with LEU 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H THR* 3.7 30.5 - - + +
82H VAL* 3.8 29.8 - - + -
83H LYS* 5.1 0.9 - - + -
96H ILE* 3.6 25.6 - - + +
99H LYS* 3.9 10.1 - - + -
100H SER* 3.5 34.3 - - - +
103H ILE* 3.7 13.0 - - + -
33I ASP 3.2 14.2 + - - +
34I ALA 3.2 9.1 + - - +
36I GLN* 1.3 78.7 - - - +
38I MET* 1.3 58.1 + - - +
40I GLU* 3.2 6.8 + - + +
41I LEU* 2.9 28.4 + - - +
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Residues in contact with MET 38 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H CYS* 5.4 1.1 - - - -
61H PHE* 3.6 41.7 - - + -
65H LEU* 3.8 20.6 - - + -
82H VAL* 3.9 14.8 - - + -
85H LEU* 3.7 18.8 - - + -
15I VAL* 3.9 16.8 - - + -
19I LEU* 4.1 19.3 - - + -
30I VAL* 5.7 0.4 - - + -
34I ALA* 2.9 21.4 + - + +
35I LEU 3.2 4.9 + - - +
37I LEU* 1.3 73.0 - - - +
39I VAL* 1.3 65.9 + - - +
41I LEU* 3.8 13.2 - - + +
42I LEU* 3.0 33.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 39 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLY* 5.8 1.1 - - - -
10I PHE* 3.4 27.2 - - - +
12I LYS* 3.7 35.0 - - + +
15I VAL* 3.7 21.5 - - + -
35I LEU 3.0 18.0 + - - +
36I GLN* 3.6 11.2 - - - +
37I LEU 3.2 0.2 - - - -
38I MET* 1.3 79.1 - - - +
40I GLU* 1.3 74.7 + - - +
42I LEU* 3.7 2.4 + - - +
43I LYS* 3.4 19.6 + - + +
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Residues in contact with GLU 40 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H TYR* 5.0 6.5 + - + -
96H ILE* 5.0 5.6 - - + -
99H LYS* 4.1 46.7 + - + -
103H ILE* 5.8 2.2 - - + -
36I GLN 3.3 11.6 + - - +
37I LEU* 3.2 10.8 + - + +
39I VAL* 1.3 87.2 - - - +
41I LEU* 1.3 60.7 + - - +
43I LYS* 3.2 20.7 + - - +
44I VAL* 2.9 33.8 + - - +
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Residues in contact with LEU 41 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H PHE* 3.6 32.3 - - + -
82H VAL* 4.9 5.8 - - + +
85H LEU* 3.7 29.8 - - + -
86H ALA* 5.4 3.1 - - + +
92H LEU* 4.1 35.7 - - + -
96H ILE* 4.3 17.4 - - + +
37I LEU 2.9 16.0 + - - +
38I MET* 3.3 16.1 + - + +
40I GLU* 1.3 77.0 - - - +
42I LEU* 1.3 63.0 + - - +
44I VAL* 3.3 4.5 + - - +
45I PHE* 3.0 21.0 + - - +
81I PHE* 4.4 8.5 - - + -
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Residues in contact with LEU 42 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H THR* 4.3 18.8 - - + +
57H GLN* 5.2 2.0 - - + -
58H CYS* 3.9 37.0 - - + +
61H PHE* 4.0 25.4 - - + -
10I PHE* 3.8 24.5 - - + -
15I VAL* 3.9 29.6 - - + -
18I LEU* 4.5 8.7 - - + -
38I MET* 3.0 19.0 + - + +
39I VAL 4.0 1.1 - - - +
41I LEU* 1.3 75.7 - - - +
43I LYS* 1.3 62.7 + - - +
45I PHE* 3.2 8.4 + - + +
46I VAL* 3.1 25.5 + - - +
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Residues in contact with LYS 43 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU* 4.1 18.4 - - + -
33H GLU* 5.2 5.8 + - - -
95H TYR* 6.1 0.9 - - - +
8I SER 3.3 25.9 + - - +
9I GLY* 4.7 6.1 - - - -
10I PHE* 4.0 14.7 - - + -
39I VAL* 3.4 12.0 + - + +
40I GLU* 3.2 25.5 + - - +
42I LEU* 1.3 76.5 - - - +
44I VAL* 1.3 67.8 + - + +
46I VAL* 3.1 2.3 + - - +
47I VAL* 2.9 37.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 44 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H LEU* 3.9 15.7 - - + -
95H TYR* 3.6 44.0 - - + +
96H ILE* 5.7 1.3 - - + -
40I GLU* 2.9 20.5 + - + +
41I LEU* 3.5 9.9 - - - +
43I LYS* 1.3 78.1 - - + +
45I PHE* 1.3 58.0 + - - +
47I VAL* 3.5 4.7 + - - +
48I GLU* 2.9 29.0 + - + +
81I PHE* 4.2 2.0 - - + -
748J GLN* 4.5 13.9 + - + +
749J VAL* 3.6 28.9 - - + -
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Residues in contact with PHE 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 4.9 0.9 - - + -
53H LEU* 4.1 13.9 - - + -
54H THR* 3.7 42.0 - - + -
57H GLN* 3.8 37.0 - - + -
61H PHE* 5.3 3.6 - - + -
41I LEU 3.0 12.7 + - - +
42I LEU* 3.5 11.7 - - + +
43I LYS 3.2 0.2 - - - -
44I VAL* 1.3 77.0 - - - +
46I VAL* 1.3 65.3 + - - +
48I GLU* 3.3 2.6 + - - +
49I ALA* 3.0 25.5 + - + +
77I LEU* 4.3 18.6 - - + +
78I LEU* 4.2 15.5 - - + -
81I PHE* 3.7 45.7 - + + -
----------------------------------------------------------
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Residues in contact with VAL 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H VAL* 3.9 24.9 - - + +
30H LEU* 3.8 29.8 - - + -
31H CYS* 4.6 5.4 - - - -
50H ILE* 4.2 8.9 - - + +
54H THR* 3.5 23.3 - - + +
10I PHE* 3.8 24.5 - - + -
42I LEU 3.1 14.4 + - - +
43I LYS 3.7 5.2 - - - +
45I PHE* 1.3 79.1 - - - +
47I VAL* 1.3 63.2 + - - +
49I ALA* 3.3 2.4 + - - +
50I ALA* 3.0 21.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU* 4.7 16.8 - - + -
34H VAL* 4.3 16.2 - - + -
43I LYS* 2.9 38.1 + - + +
44I VAL* 4.1 4.3 - - - +
46I VAL* 1.3 76.8 - - - +
48I GLU* 1.3 52.7 + - - +
50I ALA* 4.2 5.2 - - - -
51I VAL* 2.8 42.1 + - + +
747J HIS* 3.8 26.0 - - + +
748J GLN* 4.5 8.3 - - - +
----------------------------------------------------------
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Residues in contact with GLU 48 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I VAL* 2.9 19.4 + - - +
45I PHE 3.6 3.6 - - - +
47I VAL* 1.3 76.3 - - - +
49I ALA* 1.3 56.4 + - - +
52I ARG* 2.7 74.1 + - - +
77I LEU* 3.6 14.4 - - + -
81I PHE* 4.2 7.2 - - + -
747J HIS* 2.8 32.2 + - - +
748J GLN* 2.9 25.4 + - - +
749J VAL* 3.3 24.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 4.2 26.2 - - + +
53H LEU* 5.5 2.7 - - + -
45I PHE* 3.0 15.6 + - + +
46I VAL* 3.7 6.7 - - - +
48I GLU* 1.3 75.9 - - - +
50I ALA* 1.3 54.4 + - - +
52I ARG* 3.8 2.8 - - - +
53I GLY* 2.9 29.8 + - - -
70I LEU* 4.0 15.1 - - + +
73I VAL* 4.7 0.7 - - - +
77I LEU* 3.6 29.0 - - + +
----------------------------------------------------------
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Residues in contact with ALA 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU 5.8 0.2 - - - -
31H CYS* 4.1 16.6 - - - -
34H VAL* 4.1 18.2 - - + -
42H PHE* 3.5 28.7 - - + -
50H ILE* 4.0 4.2 - - - +
46I VAL* 3.0 17.3 + - + +
47I VAL* 3.5 5.8 - - - +
49I ALA* 1.3 75.8 - - - +
51I VAL* 1.3 57.9 + - - +
53I GLY* 3.0 3.3 + - - -
54I VAL* 2.9 29.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H VAL* 3.9 19.7 - - + -
38H LYS* 4.6 11.4 - - + +
47I VAL* 2.8 30.8 + - + +
50I ALA* 1.3 67.7 - - - +
52I ARG* 1.3 65.1 + - - +
54I VAL* 3.1 7.7 + - + +
55I ARG* 2.8 49.5 + - + +
746J THR 5.6 0.2 - - - +
747J HIS* 3.4 52.0 - - + +
----------------------------------------------------------
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Residues in contact with ARG 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I GLU* 2.7 51.6 + - - +
49I ALA* 4.0 1.3 - - - +
51I VAL* 1.3 76.4 - - - +
53I GLY* 1.3 63.4 + - - +
55I ARG* 3.5 9.2 + - + +
56I GLN 3.1 16.8 + - - -
73I VAL* 3.6 34.3 + - + +
76I GLN* 3.5 5.9 + - - +
77I LEU* 3.4 34.1 - - - +
80I ASP* 2.7 33.7 + - - +
744J LEU* 6.1 0.9 - - - +
745J PRO* 3.6 18.7 - - - +
746J THR* 3.7 17.0 - - - +
747J HIS* 5.2 0.2 - - + -
749J VAL* 2.8 27.5 + - - +
751J HIS* 3.6 8.7 - - - -
----------------------------------------------------------
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Residues in contact with GLY 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H PHE* 5.4 0.2 - - - -
49I ALA 2.9 17.2 + - - -
50I ALA 3.0 4.4 + - - -
52I ARG* 1.3 74.0 - - - +
54I VAL* 1.3 66.0 + - - +
56I GLN* 3.2 6.6 + - - +
57I ALA* 3.0 22.3 + - - +
65I VAL* 3.7 24.6 - - - +
69I GLN* 4.3 4.9 - - - +
70I LEU* 5.0 3.6 - - - -
73I VAL* 4.5 8.7 - - - +
----------------------------------------------------------
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Residues in contact with VAL 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H VAL* 3.9 15.3 - - + -
38H LYS* 3.8 21.8 - - + -
40H MET* 4.1 15.5 - - + +
42H PHE* 3.5 23.3 - - + -
50I ALA 2.9 18.3 + - - +
51I VAL* 3.4 9.0 - - - +
53I GLY* 1.3 75.6 - - - +
55I ARG* 1.3 55.3 + - - +
57I ALA* 2.8 5.1 + - - +
58I GLN* 2.7 62.3 + - + +
65I VAL* 3.9 11.2 - - + -
----------------------------------------------------------
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Residues in contact with ARG 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LYS* 3.5 36.8 - - - +
51I VAL* 2.8 36.6 + - + +
52I ARG* 3.8 6.5 - - - +
54I VAL* 1.3 71.0 - - - +
56I GLN* 1.3 57.5 + - - +
58I GLN* 2.7 44.8 + - - +
59I ALA* 3.0 27.4 + - - +
745J PRO* 4.1 34.2 - - + +
746J THR 5.3 6.5 + - - +
747J HIS* 5.1 3.2 + - - -
----------------------------------------------------------
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Residues in contact with GLN 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ARG 3.1 16.7 + - - +
53I GLY 3.6 4.3 - - - +
54I VAL 3.1 0.8 - - - -
55I ARG* 1.3 75.5 - - - +
57I ALA* 1.3 63.9 + - - +
59I ALA* 3.3 9.8 + - - +
60I GLU* 3.0 55.2 + - - +
69I GLN* 3.8 24.2 - - + +
72I LYS* 3.5 18.8 - - + +
73I VAL* 3.9 12.4 - - + +
739J TRP* 4.2 12.1 - - - +
744J LEU* 4.0 21.7 - - - +
745J PRO* 5.2 5.1 - - + +
----------------------------------------------------------
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Residues in contact with ALA 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H MET* 3.9 23.8 - - - -
53I GLY 3.0 12.0 + - - +
54I VAL 2.8 9.5 + - - +
56I GLN* 1.3 72.4 - - - +
58I GLN* 1.3 63.5 + - - +
60I GLU* 3.1 11.2 + - - +
62I ALA* 3.1 27.3 + - + -
64I ARG 4.1 13.5 - - - +
65I VAL* 4.2 6.3 - - + -
69I GLN* 3.9 18.6 - - + +
----------------------------------------------------------
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Residues in contact with GLN 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LYS 3.4 24.0 + - - -
39H GLU 5.2 0.2 + - - -
40H MET* 4.0 19.1 - - + +
54I VAL* 2.7 23.8 + - + +
55I ARG* 2.7 52.1 + - - +
57I ALA* 1.3 72.8 - - - +
59I ALA* 1.3 59.3 + - - +
61I ASP* 3.4 19.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ARG 3.0 15.4 + - - +
56I GLN* 3.7 16.8 - - - +
57I ALA 3.1 0.4 - - - -
58I GLN* 1.3 77.1 - - - +
60I GLU* 1.3 59.6 + - + +
61I ASP* 3.3 5.3 - - - +
745J PRO* 6.4 1.6 - - + -
----------------------------------------------------------
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Residues in contact with GLU 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLN* 3.0 37.9 + - - +
57I ALA 3.1 4.7 + - - +
59I ALA* 1.3 78.5 - - - +
61I ASP* 1.3 72.2 + - - +
62I ALA* 3.2 9.2 + - + +
69I GLN* 3.3 26.9 + - - +
72I LYS* 3.0 27.9 + - - +
739J TRP* 5.6 1.3 - - - +
----------------------------------------------------------
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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).
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