Contacts of the helix formed by residues 79 - 102 (chain P) in PDB entry 5M32
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 ILE 79 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O PHE* 3.7 30.3 - - + -
16O GLY 5.5 0.4 - - - +
17O LYS* 5.9 2.5 - - - -
18O LEU* 4.3 24.7 - - + +
151O SER* 6.1 1.3 - - - -
27P ALA* 3.8 22.2 - - + -
77P ALA 4.0 5.2 - - - +
78P GLY* 1.3 70.5 - - - -
80P THR* 1.3 62.5 + - - +
81P SER* 3.3 27.1 - - - +
82P ASP* 3.8 17.6 + - - +
83P ALA* 3.9 15.9 + - - +
131P GLY* 3.0 26.4 + - - +
132P VAL* 4.2 0.5 - - - +
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Residues in contact with THR 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O SER* 5.6 0.9 - - - +
152O GLY 5.4 0.5 - - - +
153O ALA* 3.8 27.5 - - + +
155O PHE* 5.6 5.6 - - + -
63P GLU* 4.7 15.3 + - - +
66P TYR* 4.9 5.5 + - - -
76P VAL* 5.0 12.9 - - - +
78P GLY 3.3 7.0 + - - +
79P ILE* 1.3 72.3 - - + +
81P SER* 1.3 66.4 + - - +
82P ASP 3.4 0.2 - - - -
83P ALA* 4.2 1.2 - - - +
84P ASN* 3.8 20.1 + - - +
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Residues in contact with SER 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O LEU* 5.1 2.9 - - - +
114O ALA 5.5 0.5 - - - +
118O GLN* 3.2 18.7 - - - +
121O THR* 4.9 1.9 + - - +
151O SER* 3.3 44.6 + - - -
152O GLY* 3.8 17.4 - - - +
153O ALA 4.3 0.2 - - - -
79P ILE* 3.3 15.3 - - - +
80P THR* 1.3 82.1 - - - +
82P ASP* 1.3 73.8 + - - +
84P ASN* 4.0 10.0 - - - +
85P VAL* 4.1 2.8 - - - +
128P ARG* 4.7 2.4 + - - -
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Residues in contact with ASP 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O GLN* 2.8 17.5 - - - +
122O GLN* 4.1 3.8 - - - -
79P ILE* 3.8 19.9 + - + +
80P THR 3.4 0.2 - - - -
81P SER* 1.3 85.8 + - - +
83P ALA* 1.3 58.9 + - - +
85P VAL* 3.0 29.5 + - - +
86P LEU* 3.2 7.0 + - - +
128P ARG* 2.4 50.3 + - - -
130P PHE* 4.6 16.3 - - + -
131P GLY* 3.6 16.9 + - - +
132P VAL* 4.9 2.2 - - + -
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Residues in contact with ALA 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P TYR* 5.5 2.0 - - + -
76P VAL* 3.6 31.6 - - + -
79P ILE 3.9 6.4 + - - +
80P THR 4.0 1.7 + - - +
81P SER 3.5 0.4 - - - -
82P ASP* 1.3 75.9 - - - +
84P ASN* 1.3 55.2 + - - +
86P LEU* 3.0 17.4 + - + +
87P THR* 2.6 38.7 + - - -
132P VAL* 3.7 23.3 - - + -
134P LEU* 5.6 2.5 - - + -
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Residues in contact with ASN 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111O GLN* 4.0 14.7 + - - +
114O ALA* 5.4 2.3 - - - +
152O GLY 4.9 6.0 - - - +
154O TYR* 3.3 31.4 + - - -
66P TYR* 4.6 21.0 + - - +
80P THR 3.8 17.1 + - - +
81P SER* 4.0 6.3 - - - +
83P ALA* 1.3 75.2 - - - +
85P VAL* 1.3 62.6 + - + +
87P THR* 3.2 14.3 + - - +
88P ASN* 3.0 24.0 + - - +
91P ARG* 6.0 0.8 - - - +
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Residues in contact with VAL 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O ALA 5.1 0.2 - - - +
115O SER* 4.4 23.8 - - - +
118O GLN* 3.3 47.8 - - + +
81P SER 4.1 2.0 - - - +
82P ASP 3.0 11.0 + - - +
84P ASN* 1.3 75.2 - - + +
86P LEU* 1.3 60.9 + - + +
88P ASN* 3.1 10.0 + - - +
89P GLU* 2.8 36.4 + - + +
130P PHE* 5.6 8.3 - - + -
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Residues in contact with LEU 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82P ASP 3.2 3.8 + - - +
83P ALA* 3.0 19.9 + - + +
85P VAL* 1.3 79.1 - - - +
87P THR* 1.3 53.4 + - - +
89P GLU* 3.0 11.7 - - + +
90P LEU* 2.6 46.8 + - + +
114P LEU* 3.8 22.0 - - + +
117P ILE* 5.4 0.7 - - + -
118P LYS* 4.8 5.2 - - + -
130P PHE* 3.5 42.2 - - + -
132P VAL* 3.6 26.7 - - + -
134P LEU* 3.8 31.4 - - + -
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Residues in contact with THR 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P TYR* 3.6 28.0 - - + -
68P LEU* 3.6 9.7 - - - +
74P CYS* 3.2 26.7 - - - -
83P ALA* 2.6 18.8 + - - +
84P ASN* 3.2 23.8 - - - +
86P LEU* 1.3 74.3 - - - +
88P ASN* 1.3 51.2 + - - +
90P LEU* 3.1 14.6 + - - +
91P ARG* 2.7 48.5 + - - +
134P LEU* 5.1 3.1 - - - -
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Residues in contact with ASN 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115O SER* 5.8 2.8 + - - -
84P ASN* 3.0 14.9 + - - +
85P VAL* 3.5 9.6 - - - +
87P THR* 1.3 75.3 - - - +
89P GLU* 1.3 63.5 + - - +
91P ARG* 3.1 25.9 + - - +
92P LEU* 3.0 22.3 + - - +
72W LEU* 5.5 4.2 - - - +
76W LYS* 3.7 34.8 - - - +
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Residues in contact with GLU 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P VAL* 2.8 26.7 + - + +
86P LEU* 3.0 20.0 - - + +
88P ASN* 1.3 74.7 - - - +
90P LEU* 1.3 59.2 + - - +
92P LEU* 3.1 27.8 + - - +
93P ILE* 3.3 13.5 + - + +
114P LEU* 5.4 3.8 - - + -
117P ILE* 5.4 10.5 - - + +
121P TYR* 6.1 0.7 - - - -
130P PHE* 6.3 2.5 - - + -
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Residues in contact with LEU 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P LEU* 3.7 33.2 - - + -
86P LEU* 2.6 26.4 + - + +
87P THR* 3.3 16.6 - - - +
89P GLU* 1.3 71.5 - - - +
91P ARG* 1.3 65.2 + - - +
93P ILE* 3.0 18.8 + - + +
94P ALA* 3.0 20.4 + - - +
110P LEU* 3.7 28.7 - - + +
114P LEU* 3.7 25.4 - - + -
134P LEU* 4.1 3.8 - - + -
136P TYR* 3.4 29.8 - - + +
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Residues in contact with ARG 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P TYR* 4.3 18.4 - - - +
67P LYS 3.2 26.9 + - - +
68P LEU* 4.2 20.2 - - + +
84P ASN* 6.0 0.6 - - - +
87P THR* 2.7 24.7 + - - +
88P ASN* 3.1 47.4 + - - +
90P LEU* 1.3 79.7 - - - +
92P LEU* 1.3 62.0 + - - +
94P ALA* 3.1 17.0 + - - +
95P GLN* 3.2 20.4 + - + +
72W LEU* 4.8 7.0 - - + -
75W LEU* 3.8 36.9 + - + +
76W LYS* 4.6 11.9 - - - +
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Residues in contact with LEU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ASN* 3.0 11.8 + - - +
89P GLU* 3.1 19.5 - - - +
91P ARG* 1.3 75.0 - - - +
93P ILE* 1.3 61.5 + - + +
95P GLN* 3.1 5.5 + - - +
96P ARG* 2.9 62.6 + - - +
68W PHE* 4.0 17.7 - - + -
72W LEU* 3.8 26.4 - - + +
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Residues in contact with ILE 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P GLU* 3.7 12.3 - - + +
90P LEU* 3.0 25.7 + - + +
92P LEU* 1.3 76.3 - - + +
94P ALA* 1.3 64.8 + - - +
96P ARG* 3.1 34.9 + - + +
97P TYR* 3.0 22.1 + - + +
105P ILE* 4.7 11.0 - - + -
109P GLN 6.1 0.2 - - - -
110P LEU* 5.0 5.8 - - + +
113P ALA* 3.9 33.9 - - + +
114P LEU* 4.5 12.6 - - + +
117P ILE* 5.1 10.3 - - + -
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Residues in contact with ALA 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P LEU* 4.3 17.5 - - + +
69P ASN* 4.8 4.7 - - + +
90P LEU 3.0 7.3 + - - +
91P ARG* 3.1 11.4 + - - +
93P ILE* 1.3 74.5 - - - +
95P GLN* 1.3 66.4 + - + +
97P TYR* 3.1 15.6 + - - +
98P LEU* 3.3 10.0 + - - +
105P ILE* 3.8 28.5 - - + +
110P LEU* 3.7 22.2 - - + +
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Residues in contact with GLN 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P LEU 4.1 13.1 + - - -
69P ASN* 4.0 16.8 - - - +
91P ARG* 3.2 12.7 + - + +
92P LEU 3.1 6.6 + - - +
94P ALA* 1.3 77.3 - - - +
96P ARG* 1.3 58.6 + - - +
98P LEU* 3.0 19.0 + - - +
99P LEU 3.0 21.3 + - - -
67W LYS 4.4 0.7 - - - +
68W PHE* 3.6 29.4 - - + +
71W ASN* 2.9 48.3 + - - +
72W LEU* 4.0 25.4 - - + -
75W LEU* 4.6 7.3 - - - +
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Residues in contact with ARG 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P LEU* 2.9 40.0 + - - +
93P ILE* 3.2 35.9 - - + +
95P GLN* 1.3 75.1 - - - +
97P TYR* 1.3 60.5 + - - +
99P LEU* 3.1 11.3 + - + +
100P GLN* 2.8 30.0 + - - +
117P ILE* 6.3 0.6 - - - +
68W PHE* 3.7 15.9 - - + -
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Residues in contact with TYR 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P ILE* 3.0 8.8 + - + +
94P ALA 3.1 9.6 + - - +
96P ARG* 1.3 78.4 - - - +
98P LEU* 1.3 51.7 + - - +
100P GLN* 3.0 5.1 + - - +
101P TYR* 2.7 67.7 + + + +
103P GLU* 3.0 42.4 + - + -
105P ILE* 3.6 46.0 - - + -
106P PRO* 4.0 6.5 - - + +
109P GLN* 4.4 21.3 - - + -
67X TYR* 3.1 26.2 + + - -
75X LEU* 4.8 0.2 - - - +
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Residues in contact with LEU 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P ASN* 5.8 2.7 - - - +
94P ALA 3.3 5.3 + - - +
95P GLN* 3.0 34.5 + - - +
97P TYR* 1.3 79.0 - - - +
99P LEU* 1.3 58.2 + - - +
102P GLN* 2.7 64.7 + - - +
103P GLU 3.3 26.6 + - - +
104P PRO* 5.0 2.7 - - + -
105P ILE* 6.4 0.2 - - + -
67W LYS* 4.6 20.6 - - + +
68W PHE* 5.6 2.2 - - + -
71W ASN* 3.9 13.5 - - - +
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Residues in contact with LEU 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P GLN 3.0 12.0 + - - +
96P ARG* 3.1 14.1 + - + +
98P LEU* 1.3 76.2 - - - +
100P GLN* 1.3 61.1 + - - +
102P GLN* 4.4 3.9 - - - +
64W GLN* 3.8 24.5 - - - +
65W ARG* 3.9 34.1 - - - +
68W PHE* 4.2 27.1 - - + +
86X ARG* 3.0 54.3 + - - +
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Residues in contact with GLN 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P ARG 2.8 15.2 + - - +
97P TYR* 3.0 1.3 + - - -
99P LEU* 1.3 81.7 - - - +
101P TYR* 1.3 86.8 + - + +
102P GLN* 5.9 0.2 - - - -
82X ASN 4.0 4.7 - - - +
83X PHE* 3.4 50.3 + - + -
86X ARG* 3.8 25.7 - - - +
87X ASN* 5.0 6.3 - - - +
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Residues in contact with TYR 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P TYR* 2.7 63.1 + + + +
98P LEU 3.1 0.2 + - - -
100P GLN* 1.3 97.8 - - + +
102P GLN* 1.3 70.1 + - - +
103P GLU* 3.3 3.7 + - + +
63X ASN* 5.6 1.7 + - - +
67X TYR* 4.6 16.7 - + + +
70X ARG* 5.5 2.6 + - - -
75X LEU* 4.3 20.9 - - + -
78X THR* 5.6 0.5 - - - +
79X ALA* 3.6 48.3 - - + +
82X ASN* 4.0 5.5 + - - +
83X PHE* 3.5 34.1 - + + -
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Residues in contact with GLN 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P LEU* 2.7 54.2 + - - +
99P LEU* 4.4 2.8 - - - +
100P GLN 5.9 0.2 - - - -
101P TYR* 1.3 73.8 - - - +
103P GLU* 1.3 59.4 + - - +
104P PRO* 4.7 1.0 - - - +
64W GLN* 3.3 56.1 - - - +
67W LYS* 6.0 3.6 - - - +
78X THR* 5.4 5.6 - - + +
82X ASN* 3.6 25.4 - - + +
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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