Contacts of the helix formed by residues 52 - 81 (chain Z) in PDB entry 6L49
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 52 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-224J C 3.3 23.3 + - - -
77Y ARG* 4.5 4.3 - - - +
78Y ILE 2.5 30.4 + - - -
79Y ILE* 3.7 12.6 - - - +
80Y PRO* 4.6 4.7 - - - +
39Z TYR* 6.1 0.4 - - - -
51Z ILE* 1.3 78.7 - - - +
53Z SER* 1.3 55.9 + - - +
54Z LYS* 3.4 4.5 - - - -
55Z ALA* 4.1 10.1 - - - -
56Z MET* 2.6 33.5 + - - +
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Residues in contact with SER 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-224J C 2.9 47.7 + - - -
39Z TYR* 5.3 3.4 + - - -
52Z SER* 1.3 71.1 - - - +
54Z LYS* 1.3 62.4 + - - +
56Z MET* 3.4 9.4 - - - +
57Z GLY* 2.9 23.2 + - - -
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Residues in contact with LYS 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99T GLY* 4.7 5.0 - - - -
80Y PRO* 4.1 18.2 - - + -
104Y GLN* 4.7 23.4 - - + +
52Z SER* 3.4 3.0 - - - -
53Z SER* 1.3 78.3 - - - +
55Z ALA* 1.3 58.8 + - - +
57Z GLY* 3.2 2.8 + - - -
58Z ILE* 2.9 35.2 + - + +
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Residues in contact with ALA 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Y ILE* 3.7 22.7 - - + +
79Y ILE 4.5 0.7 - - - -
80Y PRO* 4.1 11.5 - - + +
83Y LEU* 3.7 20.1 - - + +
51Z ILE* 3.7 13.2 - - + -
52Z SER* 3.4 12.8 + - - +
53Z SER 3.3 0.4 - - - -
54Z LYS* 1.3 76.9 - - - +
56Z MET* 1.3 58.4 + - - +
58Z ILE* 3.4 7.8 + - - +
59Z MET* 2.9 33.1 + - - +
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Residues in contact with MET 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Z SER* 6.3 0.4 - - - -
34Z TYR 3.3 26.7 - - - +
35Z SER* 3.7 30.1 - - - +
38Z VAL* 3.7 30.5 - - + -
39Z TYR* 4.2 18.8 - - + +
51Z ILE* 4.3 5.6 - - + +
52Z SER 2.6 21.1 + - - +
53Z SER* 3.4 12.8 - - - +
54Z LYS 3.2 0.4 - - - -
55Z ALA* 1.3 70.7 - - - +
57Z GLY* 1.3 58.3 + - - +
59Z MET* 4.2 6.5 - - + -
60Z ASN* 2.9 36.8 + - + +
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Residues in contact with GLY 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99T GLY* 4.1 16.0 + - - -
101T GLY 5.6 0.9 + - - -
53Z SER 2.9 14.4 + - - -
54Z LYS* 3.2 4.2 + - - -
56Z MET* 1.3 73.2 - - - +
58Z ILE* 1.3 52.5 + - - +
60Z ASN* 3.4 6.2 + - - +
61Z SER* 2.7 38.2 + - - -
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Residues in contact with ILE 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98T TYR* 3.9 17.4 - - + +
99T GLY* 3.8 19.1 - - - +
62Y ILE* 6.3 1.8 - - + -
80Y PRO* 3.8 22.2 - - + -
83Y LEU* 3.8 16.6 - - + -
87Y ILE* 5.6 0.9 - - + -
102Y ILE* 3.8 26.5 - - + -
103Y ALA* 3.5 26.0 - - + +
54Z LYS* 2.9 23.2 + - + +
55Z ALA* 3.6 7.0 - - - +
56Z MET 3.3 0.2 - - - -
57Z GLY* 1.3 76.4 - - - +
59Z MET* 1.3 57.8 + - - +
61Z SER* 2.8 18.3 + - - -
62Z PHE* 2.9 18.5 + - + +
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Residues in contact with MET 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Y THR* 3.8 29.6 - - + -
62Y ILE* 3.7 32.8 - - + -
63Y LEU* 3.8 30.7 - - + -
83Y LEU* 3.9 17.9 - - + -
38Z VAL* 4.0 10.1 - - + -
51Z ILE* 3.9 12.1 - - + -
55Z ALA 2.9 21.6 + - - +
56Z MET* 3.8 16.6 - - + +
58Z ILE* 1.3 75.7 - - - +
60Z ASN* 1.3 57.7 + - - +
62Z PHE* 3.3 9.3 + - + +
63Z VAL* 2.9 33.4 + - - +
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Residues in contact with ASN 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102T GLY* 4.8 1.7 - - - +
33Z SER* 3.8 14.3 - - - +
34Z TYR* 3.1 46.9 - - - +
56Z MET* 2.9 25.9 + - + +
57Z GLY* 3.9 7.0 - - - +
59Z MET* 1.3 74.5 - - - +
61Z SER* 1.3 58.6 + - - +
63Z VAL* 3.3 4.8 + - - +
64Z ASN* 2.5 55.2 + - - +
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Residues in contact with SER 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98T TYR* 3.3 24.8 - - - +
99T GLY 3.4 5.2 + - - -
101T GLY* 4.0 15.3 - - - -
102T GLY* 3.4 21.9 - - - +
57Z GLY 2.7 24.4 + - - -
58Z ILE* 2.8 16.6 + - - -
60Z ASN* 1.3 73.0 + - - +
62Z PHE* 1.3 58.2 + - - +
64Z ASN* 4.0 0.5 - - - +
65Z ASP* 2.9 32.2 + - - +
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Residues in contact with PHE 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98T TYR* 3.6 25.3 - - + -
55Y LEU* 5.8 0.2 - - + -
58Y LEU* 4.1 34.8 - - + -
59Y THR* 4.7 4.7 - - + -
62Y ILE* 4.5 22.0 - - + -
87Y ILE* 6.1 0.2 - - + -
93Y LEU* 5.0 8.1 - - + -
96Y LEU* 4.3 7.4 - - + -
97Y LEU* 3.9 30.5 - - + -
58Z ILE* 2.9 20.1 + - + +
59Z MET* 3.5 16.4 - - - +
60Z ASN 3.3 0.2 - - - -
61Z SER* 1.3 74.1 - - - +
63Z VAL* 1.3 67.7 + - + +
65Z ASP* 3.9 0.5 - - - +
66Z ILE* 2.5 71.6 + - + +
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Residues in contact with VAL 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y PHE* 3.9 13.2 - - + -
55Y LEU* 3.5 31.9 - - + +
59Y THR* 3.7 29.6 - - + -
34Z TYR* 3.7 33.0 - - + -
38Z VAL* 5.1 5.4 - - + -
59Z MET 2.9 20.6 + - - +
60Z ASN* 3.7 6.5 - - - +
62Z PHE* 1.3 78.2 - - + +
64Z ASN* 1.3 57.9 + - - +
66Z ILE 3.5 0.2 + - - -
67Z PHE* 2.9 30.5 + - + +
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Residues in contact with ASN 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102T GLY* 3.4 27.1 + - - +
33Y LEU* 5.1 9.5 - - - +
34Z TYR* 4.5 13.9 - - - -
60Z ASN* 2.5 56.7 + - - +
63Z VAL* 1.3 77.3 - - - +
65Z ASP* 1.3 56.5 + - - +
67Z PHE* 3.5 8.9 + - - +
68Z GLU* 2.9 40.3 + - - +
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Residues in contact with ASP 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96T THR* 4.9 10.8 - - + +
98T TYR* 2.8 30.6 + - + +
102T GLY 4.4 3.3 + - - +
97Y LEU* 4.6 0.3 - - - +
100Y VAL* 4.9 4.4 - - - +
61Z SER 2.9 19.4 + - - +
64Z ASN* 1.3 72.7 - - - +
66Z ILE* 1.3 60.9 + - - +
68Z GLU* 3.5 10.3 + - - +
69Z ARG* 2.9 66.3 + - - +
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Residues in contact with ILE 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y LEU* 6.2 0.4 - - + -
54Y VAL* 4.8 1.8 - - + -
55Y LEU* 4.0 14.8 - - + -
58Y LEU* 3.5 26.5 - - + -
96Y LEU* 4.1 6.1 - - + -
62Z PHE* 2.5 73.8 + - + +
63Z VAL 3.9 3.1 - - - +
65Z ASP* 1.3 75.5 - - - +
67Z PHE* 1.3 59.2 + - - +
69Z ARG* 3.4 20.4 + - - +
70Z ILE* 3.0 49.9 + - + +
98Z LEU* 5.8 1.6 - - + -
99Z LEU* 6.0 0.2 - - + -
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Residues in contact with PHE 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Y VAL* 3.7 25.4 - - + -
33Y LEU* 3.6 46.9 - - + -
34Y LEU* 3.8 19.1 - - + -
39Y TYR* 4.1 16.6 - - - -
51Y LEU* 3.7 33.2 - - + -
55Y LEU* 4.1 17.0 - - + +
34Z TYR* 5.8 3.1 - - - +
63Z VAL* 2.9 19.5 + - + +
64Z ASN* 3.9 10.5 - - - +
66Z ILE* 1.3 78.3 - - - +
68Z GLU* 1.3 65.2 + - + +
70Z ILE* 4.1 0.7 - - - +
71Z ALA* 2.9 33.4 + - + +
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Residues in contact with GLU 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102T GLY 3.7 18.7 - - - +
80V TYR* 5.0 15.3 + - - -
39Y TYR* 4.2 16.3 - - - +
64Z ASN* 2.9 26.3 + - - +
65Z ASP* 3.9 7.3 - - - +
67Z PHE* 1.3 84.8 - - + +
69Z ARG* 1.3 58.0 - - + +
71Z ALA* 3.9 4.1 - - - +
72Z GLY* 2.9 26.2 + - - -
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Residues in contact with ARG 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Y LEU* 3.1 56.7 + - - +
97Y LEU* 3.7 9.1 - - - +
100Y VAL* 5.3 4.5 - - - +
65Z ASP* 2.9 49.9 + - - +
66Z ILE* 3.8 15.4 - - - +
68Z GLU* 1.3 78.3 - - + +
70Z ILE* 1.3 58.3 + - - +
72Z GLY* 3.4 1.1 + - - -
73Z GLU* 3.0 29.8 + - - +
98Z LEU* 4.5 21.5 - - + +
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Residues in contact with ILE 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y LEU* 4.1 11.7 - - + -
54Y VAL* 3.9 14.1 - - + -
66Z ILE* 3.0 34.9 + - + +
69Z ARG* 1.3 75.1 - - - +
71Z ALA* 1.3 57.5 + - - +
73Z GLU* 3.4 5.3 + - - +
74Z ALA* 2.9 29.3 + - - +
91Z ILE* 3.7 27.8 - - + -
94Z ALA* 3.9 14.8 - - + +
95Z VAL* 3.9 25.4 - - + +
98Z LEU* 3.7 26.0 - - + -
99Z LEU* 5.3 5.4 - - + -
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Residues in contact with ALA 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Y LEU* 4.1 19.7 - - + -
39Y TYR* 3.7 28.4 - - + +
51Y LEU* 4.8 2.8 - - + +
67Z PHE* 2.9 25.1 + - + +
68Z GLU 3.9 1.8 - - - +
70Z ILE* 1.3 77.5 - - - +
72Z GLY* 1.3 52.4 + - - +
74Z ALA* 3.5 4.9 + - - +
75Z SER* 2.5 38.9 + - - -
86Z ILE* 5.2 1.0 - - - +
91Z ILE* 5.1 5.6 - - - -
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Residues in contact with GLY 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Y TYR* 4.4 6.0 - - - -
68Z GLU 2.9 18.1 + - - -
69Z ARG 3.9 0.9 - - - -
71Z ALA* 1.3 73.4 - - - +
73Z GLU* 1.3 60.2 + - - +
75Z SER* 3.4 6.8 + - - -
76Z ARG* 2.9 38.5 + - - +
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Residues in contact with GLU 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X TYR* 4.3 13.3 + - - -
92X ARG* 4.5 16.9 + - - +
69Z ARG 3.0 18.5 + - - +
70Z ILE* 3.8 4.9 - - - +
72Z GLY* 1.3 77.2 - - - +
74Z ALA* 1.3 57.8 + - - +
76Z ARG* 3.1 32.6 + - - +
77Z LEU* 2.9 41.6 + - + +
80Z TYR* 5.9 0.7 - - - -
94Z ALA* 3.7 26.5 - - + +
97Z LEU* 5.2 7.6 - - + +
98Z LEU* 5.7 5.2 - - + -
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Residues in contact with ALA 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Z ILE 2.9 18.5 + - - +
71Z ALA 4.0 2.7 - - - +
73Z GLU* 1.3 73.7 - - - +
75Z SER* 1.3 61.1 + - - +
77Z LEU* 3.4 7.2 + - - +
78Z ALA* 2.9 29.5 + - - +
86Z ILE* 4.4 7.0 - - + +
90Z GLU* 3.7 29.0 - - + +
91Z ILE* 3.7 28.0 - - + -
94Z ALA* 3.9 1.3 - - + +
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Residues in contact with SER 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Y TYR* 3.4 43.2 - - - +
40Y SER* 6.1 0.4 - - - -
71Z ALA 2.5 23.4 + - - -
72Z GLY* 3.7 6.7 - - - -
73Z GLU 3.3 0.2 - - - -
74Z ALA* 1.3 77.0 - - - +
76Z ARG* 1.3 55.7 + - - +
78Z ALA* 3.4 5.3 + - - +
79Z HIS* 2.7 41.7 + - - -
86Z ILE* 3.9 8.6 - - - +
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Residues in contact with ARG 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91X LYS* 5.7 7.3 - - - +
92X ARG* 6.3 2.0 - - - +
72Z GLY* 2.9 26.7 + - - +
73Z GLU* 3.1 42.3 + - - +
75Z SER* 1.3 77.7 - - - +
77Z LEU* 1.3 56.0 + - - +
79Z HIS* 3.3 6.2 + - + +
80Z TYR* 2.9 72.4 + - + +
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Residues in contact with LEU 77 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X TYR* 3.6 33.7 - - + -
75X HIS* 3.4 30.7 - - + +
73Z GLU* 2.9 30.0 + - - +
74Z ALA* 3.7 5.6 - - - +
75Z SER 3.3 0.4 - - - -
76Z ARG* 1.3 76.1 - - - +
78Z ALA* 1.3 57.6 + - - +
80Z TYR* 3.4 8.1 + - + +
81Z ASN* 2.4 38.8 + - - +
90Z GLU* 4.2 2.0 - - + +
93Z THR* 3.7 21.8 - - + -
94Z ALA* 4.0 16.4 - - + +
97Z LEU* 4.0 16.2 - - + -
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Residues in contact with ALA 78 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Y SER* 5.7 2.5 - - - -
74Z ALA 2.9 17.9 + - - +
75Z SER* 3.8 6.7 - - - +
77Z LEU* 1.3 75.6 - - - +
79Z HIS* 1.3 65.4 + - - +
81Z ASN* 3.3 9.2 + - - +
83Z ARG* 2.9 45.2 + - + +
84Z SER* 5.5 0.7 - - - -
85Z THR 3.8 15.7 - - - +
86Z ILE* 4.5 7.6 - - + -
90Z GLU* 4.3 11.4 - - + +
----------------------------------------------------------
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Residues in contact with HIS 79 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U LYS 4.5 1.3 + - - -
37U GLY* 3.2 30.8 + - - -
38U ASN* 3.5 22.8 + - + -
39Y TYR 3.8 18.2 - - - -
40Y SER* 5.3 3.1 - - - -
75Z SER* 2.7 32.1 + - - +
76Z ARG* 3.3 7.8 + - + +
78Z ALA* 1.3 77.7 - - + +
80Z TYR* 1.3 67.9 + - + +
81Z ASN 3.7 0.2 + - - -
82Z LYS* 3.8 9.8 + - - +
83Z ARG 4.9 0.9 - - - +
84Z SER* 6.6 0.2 - - - -
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Residues in contact with TYR 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68V GLU* 5.3 9.8 + - - -
72X TYR* 5.5 4.3 - + - -
88X TYR* 3.4 72.4 + + + -
91X LYS* 4.7 15.1 + - - +
73Z GLU* 5.9 1.1 - - - -
76Z ARG* 2.9 57.5 + - + +
77Z LEU* 3.8 14.8 - - + +
78Z ALA 3.2 0.4 - - - -
79Z HIS* 1.3 83.1 - - + +
81Z ASN* 1.3 64.0 + - - +
82Z LYS* 3.3 10.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 81 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X TYR 5.7 0.4 + - - -
75X HIS* 2.9 50.3 + - + +
76X ALA* 3.3 18.7 - - - +
77Z LEU* 2.4 32.1 + - - +
78Z ALA* 3.3 6.4 + - - +
80Z TYR* 1.3 81.8 - - - +
82Z LYS* 1.3 77.8 + - - +
83Z ARG* 3.2 22.0 + - + +
89Z ARG* 4.8 0.3 + - - -
90Z GLU* 5.5 2.0 - - - +
----------------------------------------------------------
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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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