Contacts of the helix formed by residues 57 - 80 (chain t) in PDB entry 5GJQ
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 PHE 57 (chain t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4t PRO 3.5 21.5 - - - -
5t TYR* 4.1 7.4 - + - -
6t VAL* 3.3 45.5 - - + +
8t ASN* 3.4 3.6 - - - -
55t SER 4.3 0.2 - - - -
56t GLY* 1.3 72.5 - - - -
58t HIS* 1.3 65.2 + - - +
59t GLY* 3.3 7.9 + - - -
60t ASP* 3.3 46.1 + - - +
61t CYS* 3.0 21.9 + - - -
105t TYR* 2.9 32.5 + - + +
97u TYR* 4.9 0.2 - + - -
100u ARG* 4.3 7.0 - - - -
128u LEU* 3.8 24.7 - - + -
130u VAL* 3.5 15.0 - - + -
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Residues in contact with HIS 58 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8t ASN* 2.7 26.2 + - + +
29t LEU* 3.7 27.2 - - + +
40t SER* 3.9 19.6 + - - -
41t PRO 5.9 0.7 - - - -
42t LYS* 5.6 9.0 - - + +
44t TYR* 4.6 9.9 - - - -
56t GLY 3.5 2.4 + - - -
57t PHE* 1.3 71.9 - - - +
59t GLY* 1.3 58.1 + - - +
61t CYS* 3.1 10.4 + - + +
62t LEU* 2.9 53.7 + - + +
130u VAL* 4.4 6.7 - - + -
131u ALA 3.4 36.1 + - - -
132u TYR* 5.3 0.6 - - - +
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Residues in contact with GLY 59 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57t PHE* 3.3 20.6 - - - -
58t HIS* 1.3 77.5 - - - +
60t ASP* 1.3 58.6 + - - +
62t LEU* 3.4 3.6 + - - +
63t THR* 2.9 32.6 + - - -
94u ARG* 4.0 1.2 + - - -
97u TYR* 3.7 9.2 - - - -
128u LEU 4.5 2.0 - - - -
129u GLY 3.5 24.5 - - - -
130u VAL* 4.2 1.8 - - - +
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Residues in contact with ASP 60 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5t TYR* 3.8 9.4 - - - -
57t PHE* 3.3 28.6 + - + +
59t GLY* 1.3 74.6 - - - +
61t CYS* 1.3 61.5 + - - +
63t THR* 3.9 0.8 - - - -
64t LEU* 2.8 32.7 + - - +
99t ARG* 4.6 0.3 + - - -
103t PRO 3.9 0.5 - - - +
104t TYR* 3.2 16.6 - - + -
105t TYR 2.8 23.7 + - - +
106t VAL* 3.7 16.6 - - + -
97u TYR* 3.2 24.2 + - - -
100u ARG* 3.2 15.1 + - - -
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Residues in contact with CYS 61 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44t TYR* 4.7 8.7 - - - +
54t CYS* 3.7 42.0 - - + +
55t SER* 4.0 13.5 - - - -
56t GLY 4.3 0.7 - - - -
57t PHE 3.0 20.1 + - - +
58t HIS* 3.1 20.1 + - + +
60t ASP* 1.3 76.5 - - - +
62t LEU* 1.3 58.4 + - - +
64t LEU* 3.8 2.5 - - - +
65t THR* 2.9 33.1 + - - -
106t VAL* 4.0 15.5 - - - -
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Residues in contact with LEU 62 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44t TYR* 4.4 17.9 - - + +
58t HIS* 2.9 51.7 + - + +
59t GLY* 3.8 3.1 - - - +
61t CYS* 1.3 75.1 - - - +
63t THR* 1.3 65.5 + - - +
65t THR* 3.1 6.4 + - + -
66t LYS* 3.0 40.2 + - - +
93u THR* 4.6 1.1 - - + -
94u ARG* 3.8 18.6 - - - +
129u GLY 4.4 7.0 - - - +
131u ALA* 4.2 22.2 - - + +
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Residues in contact with THR 63 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m PHE* 4.4 11.6 - - + -
59t GLY 2.9 15.1 + - - -
60t ASP 3.9 2.2 - - - -
62t LEU* 1.3 76.2 - - - +
64t LEU* 1.3 63.8 + - - +
66t LYS* 3.1 6.1 + - - +
67t ILE* 3.0 40.1 + - + +
104t TYR* 4.3 4.9 - - - +
94u ARG* 2.2 37.4 + - - +
97u TYR* 3.0 37.9 - - + +
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Residues in contact with LEU 64 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54t CYS* 5.2 2.5 - - - -
60t ASP 2.8 19.8 + - - +
61t CYS* 3.8 3.4 - - - +
63t THR* 1.3 76.1 - - - +
65t THR* 1.3 63.1 + - - +
67t ILE* 3.2 6.2 + - + +
68t ILE* 2.9 36.1 + - + +
92t LEU* 4.2 11.2 - - + -
95t ILE* 4.0 26.7 - - + -
96t LEU* 4.0 19.7 - - + -
104t TYR* 4.1 21.9 - - + -
106t VAL* 3.8 15.7 - - + -
108t ASN* 3.6 35.7 - - - +
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Residues in contact with THR 65 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44t TYR* 3.7 49.3 - - + +
46t LEU* 5.7 0.3 - - - +
52t ILE* 5.3 1.9 - - - +
54t CYS* 4.1 9.4 - - - -
61t CYS 2.9 19.4 + - - -
62t LEU* 3.1 9.6 + - + +
64t LEU* 1.3 77.5 - - - +
66t LYS* 1.3 69.0 + - + +
68t ILE* 3.2 10.5 + - - +
69t GLU* 3.0 40.7 + - + +
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Residues in contact with LYS 66 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96m ARG 5.1 3.4 - - - +
97m PHE* 4.0 37.1 - - + +
100m ASP* 5.2 12.5 - - - +
62t LEU* 3.0 29.3 + - - +
63t THR 3.9 4.0 - - - +
65t THR* 1.3 83.4 - - + +
67t ILE* 1.3 63.2 + - - +
69t GLU* 3.3 12.2 + - - +
70t ALA* 3.0 23.9 + - - +
90u SER* 4.1 17.0 + - - +
93u THR* 5.2 2.0 - - - +
94u ARG* 3.2 38.6 - - - +
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Residues in contact with ILE 67 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m PHE* 3.6 23.8 - - + -
63t THR* 3.0 26.5 + - + +
64t LEU* 3.2 9.2 + - + +
66t LYS* 1.3 77.6 - - - +
68t ILE* 1.3 63.4 + - + +
70t ALA* 3.4 3.8 + - - +
71t ARG* 3.0 30.1 + - + +
95t ILE* 4.0 33.7 - - + -
104t TYR* 3.3 27.4 - - + +
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Residues in contact with ILE 68 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46t LEU* 3.8 33.4 - - + -
52t ILE* 3.8 26.9 - - + -
54t CYS* 5.7 0.9 - - - -
64t LEU* 2.9 30.7 + - + +
65t THR* 3.5 9.4 - - - +
67t ILE* 1.3 77.7 - - - +
69t GLU* 1.3 63.9 + - - +
71t ARG* 3.3 2.1 + - - +
72t LEU* 3.0 27.9 + - + +
88t ILE* 5.2 3.8 - - + -
91t MET* 4.4 22.6 - - + +
92t LEU* 3.8 28.5 - - + -
95t ILE* 4.9 4.3 - - + -
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Residues in contact with GLU 69 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44t TYR* 5.0 9.5 - - - +
45t LYS 5.0 8.0 + - - +
46t LEU* 4.7 14.8 - - + -
65t THR* 3.0 32.3 + - + +
66t LYS* 3.3 16.2 + - - +
68t ILE* 1.3 76.1 - - - +
70t ALA* 1.3 63.6 + - - +
72t LEU* 3.0 19.0 + - + +
73t LYS* 3.1 24.2 + - - +
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Residues in contact with ALA 70 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93m LEU* 4.0 30.3 - - + +
97m PHE* 5.2 11.0 - - + -
66t LYS 3.0 17.1 + - - +
67t ILE* 3.6 6.3 - - - +
69t GLU* 1.3 75.7 - - - +
71t ARG* 1.3 59.9 + - + +
73t LYS* 3.2 10.8 + - - +
74t MET* 3.0 34.6 + - - +
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Residues in contact with ARG 71 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102l THR* 4.0 7.3 - - - +
103l TYR* 2.1 41.5 + - - -
67t ILE* 3.0 25.2 + - + +
68t ILE 3.9 2.0 - - - +
70t ALA* 1.3 75.7 - - + +
72t LEU* 1.3 65.7 + - - +
74t MET* 3.4 21.2 + - - +
75t TYR* 3.0 23.9 + - - +
91t MET* 3.6 37.4 - - + +
94t THR* 4.4 6.1 + - - -
95t ILE* 3.9 25.4 - - + +
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Residues in contact with LEU 72 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46t LEU* 3.7 50.9 - - + +
47t THR* 4.4 5.4 - - + -
68t ILE* 3.0 23.5 + - + +
69t GLU* 3.0 10.1 + - + +
71t ARG* 1.3 78.7 - - - +
73t LYS* 1.3 64.7 + - + +
75t TYR* 3.2 6.1 + - - +
76t LYS* 2.9 21.1 + - - +
82t ALA* 6.1 0.3 - - - -
83t MET* 3.3 35.9 + - + +
88t ILE* 3.6 22.7 - - + -
91t MET* 5.1 3.6 - - + -
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Residues in contact with LYS 73 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66m VAL 5.9 0.2 - - - +
67m ASP* 3.9 14.8 - - - +
68m ASN* 4.8 10.8 - - - +
93m LEU* 4.2 22.7 - - + +
96m ARG* 3.5 40.0 - - - +
69t GLU* 3.1 20.0 + - - +
70t ALA* 3.6 10.9 - - - +
72t LEU* 1.3 81.1 - - + +
74t MET* 1.3 62.9 + - - +
76t LYS* 3.1 11.7 + - + +
77t HIS* 2.9 39.9 + - + +
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Residues in contact with MET 74 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90m GLN* 4.5 13.5 - - - +
93m LEU* 3.3 33.9 - - + -
70t ALA* 3.0 25.9 + - - +
71t ARG* 3.6 23.8 - - + +
72t LEU 3.2 0.2 - - - -
73t LYS* 1.3 75.0 - - - +
75t TYR* 1.3 62.5 + - - +
77t HIS* 3.2 8.0 + - - +
78t SER* 3.0 25.3 + - - -
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Residues in contact with TYR 75 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99l HIS* 3.6 22.8 - + - -
103l TYR* 3.7 38.4 - + + +
105l GLU* 2.7 28.6 + - - -
108l THR* 5.8 1.2 - - - +
71t ARG 3.0 13.8 + - - +
72t LEU 3.6 7.4 - - - +
74t MET* 1.3 76.0 - - - +
76t LYS* 1.3 64.0 + - - +
78t SER* 4.7 0.9 - - - -
79t ASN* 2.8 52.5 + - + +
81t LYS* 3.8 25.0 - - + -
82t ALA 4.0 4.7 + - - -
83t MET* 3.3 43.9 - - + -
87t ALA* 5.7 0.9 - - + -
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Residues in contact with LYS 76 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65m HIS* 4.8 16.7 + - + +
72t LEU 2.9 13.4 + - - +
73t LYS* 3.1 12.8 + - + +
75t TYR* 1.3 79.4 - - - +
77t HIS* 1.3 72.2 + - + +
80t ASN* 2.8 44.1 + - - +
81t LYS* 3.3 26.0 - - - +
82t ALA* 4.8 6.1 - - + +
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Residues in contact with HIS 77 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114l GLN* 5.4 2.1 - - - +
65m HIS* 3.4 47.8 + + + +
66m VAL 3.0 26.4 + - - -
67m ASP* 4.7 1.2 - - - -
89m ARG* 3.8 49.3 + - + +
93m LEU* 6.3 1.8 - - + -
73t LYS* 2.9 31.3 + - + +
74t MET* 3.2 7.8 + - - +
76t LYS* 1.3 92.5 + - + +
78t SER* 1.3 60.2 + - - +
79t ASN 3.7 0.3 + - - -
80t ASN* 4.3 11.1 + - - +
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Residues in contact with SER 78 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110l GLU* 4.6 0.7 - - - +
111l SER* 3.4 15.9 + - - +
114l GLN* 3.8 20.9 - - - +
89m ARG* 5.6 1.1 - - - +
74t MET 3.0 16.2 + - - -
75t TYR* 4.7 0.7 - - - -
77t HIS* 1.3 77.6 - - - +
79t ASN* 1.3 71.0 + - - +
80t ASN* 3.8 2.4 + - - -
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Residues in contact with ASN 79 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99l HIS* 3.8 18.0 + - - -
108l THR* 4.4 10.9 + - + +
110l GLU* 4.3 5.7 - - - +
111l SER* 2.8 26.0 - - - +
75t TYR* 2.8 57.2 + - + +
78t SER* 1.3 91.3 + - - +
80t ASN* 1.3 73.2 + - - +
81t LYS* 3.1 25.8 - - + +
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Residues in contact with ASN 80 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110l GLU* 3.2 33.7 + - - +
114l GLN* 4.8 3.8 - - - -
149l LYS* 6.2 1.6 - - - +
61m LYS* 5.0 6.5 + - - +
76t LYS* 2.8 29.0 + - - +
77t HIS 4.4 11.7 + - - +
78t SER 4.5 2.0 + - - -
79t ASN* 1.3 79.4 - - - +
81t LYS* 1.3 56.9 + - - +
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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