Contacts of the helix formed by residues 78 - 101 (chain C) 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 MET 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.5 32.5 - - + -
20B GLY 5.2 2.7 - - - +
22B LEU* 3.3 36.8 - - + +
126B THR* 5.3 1.6 - - + -
157B ALA 6.1 0.9 - - - +
27C ALA* 4.2 10.8 - - + +
75C TYR* 3.8 2.6 - - - -
77C GLY* 1.3 74.2 - - - -
79C GLY* 1.3 66.3 + - - +
80C PRO* 3.5 9.6 - - + -
81C ASP* 3.7 17.3 + - - +
82C TYR 3.3 2.6 + - - -
127C ARG* 4.4 5.4 - - - +
130C GLY* 2.9 20.5 + - - +
131C VAL* 3.1 20.8 - - - +
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Residues in contact with GLY 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 6.1 2.2 - - - -
75C TYR* 3.9 21.5 - - - -
77C GLY 3.7 2.4 + - - -
78C MET* 1.3 73.5 - - - +
80C PRO* 1.3 68.1 - - - +
82C TYR* 2.9 21.7 + - - +
83C ARG* 3.0 13.9 + - - +
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Residues in contact with PRO 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLN* 3.0 26.4 - - + +
126B THR* 5.5 2.0 - - + -
157B ALA* 2.9 28.5 - - + +
158B GLY* 3.8 13.9 - - - -
159B TYR* 4.1 15.3 - - + +
78C MET* 3.8 9.2 - - + -
79C GLY* 1.3 89.6 - - - +
81C ASP* 1.3 64.8 + - - +
83C ARG* 3.1 22.4 + - - +
84C VAL* 3.0 25.6 + - - +
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Residues in contact with ASP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLN* 2.6 35.3 + - - +
78C MET* 3.7 10.2 + - - +
79C GLY 3.2 0.2 - - - -
80C PRO* 1.3 76.9 - - - +
82C TYR* 1.3 57.9 + - - +
84C VAL* 3.2 5.4 + - - +
85C LEU* 2.9 32.8 + - - +
127C ARG* 2.9 37.0 + - - -
129C PHE* 3.5 17.4 - - + -
130C GLY* 3.0 16.7 + - - -
131C VAL* 3.5 20.0 - - + -
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Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS 4.5 4.0 - - - -
63C LYS* 2.9 27.4 + - - -
65C GLU* 3.5 22.2 - - + +
73C LEU* 3.2 23.4 + - + +
74C VAL* 4.1 4.5 - - - -
75C TYR* 3.3 61.9 - + + -
78C MET 3.3 3.6 + - - +
79C GLY 2.9 12.4 + - - +
81C ASP* 1.3 78.9 - - - +
83C ARG* 1.3 60.7 + - - +
85C LEU* 3.2 4.6 + - - +
86C VAL* 2.8 49.5 + - + +
131C VAL* 3.8 5.3 - - + +
133C LEU* 3.6 19.7 - - + -
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Residues in contact with ARG 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 3.3 31.2 + - - +
119B ALA* 3.3 16.2 + - - +
120B ASP* 2.0 65.7 + - - +
123B GLN* 4.0 4.2 - - - +
158B GLY 2.8 28.7 + - - -
160B TYR* 3.5 30.2 - - - -
79C GLY 3.0 6.1 + - - +
80C PRO* 3.3 30.8 - - - +
82C TYR* 1.3 84.6 - - + +
84C VAL* 1.3 63.6 + - - +
86C VAL* 3.1 6.6 + - - +
87C HIS* 3.0 22.2 + - - +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ASP* 4.6 14.8 - - + +
123B GLN* 3.1 32.3 - - + +
124B VAL* 5.9 1.6 - - + -
127B GLN* 5.1 1.3 - - - +
80C PRO 3.0 12.1 + - - +
81C ASP* 3.4 8.5 - - - +
83C ARG* 1.3 76.0 - - - +
85C LEU* 1.3 65.9 + - + +
86C VAL 3.2 0.5 + - - -
87C HIS* 3.2 6.5 + - - +
88C ARG* 3.0 35.5 + - + +
120C TYR* 6.0 1.1 - - - +
129C PHE* 4.0 23.8 - - + -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 4.9 1.7 - - - +
81C ASP 2.9 21.3 + - - +
82C TYR* 3.7 4.3 - - - +
84C VAL* 1.3 78.0 - - + +
86C VAL* 1.3 57.7 + - - +
88C ARG* 3.7 3.8 - - + +
89C ALA* 2.9 30.3 + - - +
113C VAL* 5.2 6.2 - - + +
116C VAL* 4.1 15.5 - - + -
117C MET* 3.9 43.3 - - + -
129C PHE* 4.0 34.8 - - + -
131C VAL* 4.3 12.8 - - + -
133C LEU* 4.0 25.9 - - + +
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 5.9 1.6 - - - +
65C GLU* 4.2 10.8 - - + +
67C ILE* 4.1 7.4 - - + -
73C LEU* 3.8 13.2 - - + -
82C TYR* 2.8 58.0 + - + +
83C ARG* 3.1 8.7 + - - +
85C LEU* 1.3 75.2 - - - +
87C HIS* 1.3 66.8 + - - +
89C ALA* 3.2 2.1 + - - +
90C ARG* 2.9 61.5 + - - +
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 6.5 0.7 - - - -
117B ARG* 6.3 0.9 - - - -
120B ASP* 5.4 10.5 - - - +
83C ARG 3.0 11.8 + - - +
84C VAL* 3.5 10.5 - - - +
86C VAL* 1.3 77.4 - - - +
88C ARG* 1.3 66.2 + - - +
90C ARG* 3.1 12.2 + - - +
91C LYS* 2.9 60.5 + - + +
65b LEU* 4.5 11.9 - - + +
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C VAL* 3.0 30.0 + - + +
85C LEU* 3.7 8.5 - - + +
87C HIS* 1.3 82.1 - - - +
89C ALA* 1.3 57.3 + - - +
91C LYS* 3.2 14.5 + - - +
92C LEU* 2.9 34.3 + - + +
116C VAL* 3.8 49.1 - - + +
119C GLU* 4.1 18.0 + - - -
120C TYR* 4.1 21.4 + - - -
129C PHE* 5.2 0.2 - - - -
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 3.8 23.3 - - + -
73C LEU* 4.8 5.6 - - + -
85C LEU 2.9 19.3 + - - +
86C VAL* 3.7 3.4 - - - +
88C ARG* 1.3 75.6 - - - +
90C ARG* 1.3 59.0 + - - +
92C LEU* 3.3 3.4 + - - +
93C ALA* 2.9 25.6 + - - +
109C LEU* 3.5 12.3 - - + +
113C VAL* 3.7 30.3 - - + +
133C LEU* 6.6 0.2 - - + -
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 4.4 14.8 - - - +
65C GLU* 3.1 27.1 + - - +
66C PRO* 2.8 31.1 + - - +
67C ILE* 3.5 31.4 - - + +
86C VAL* 2.9 37.2 + - - +
87C HIS* 3.5 10.3 - - - +
89C ALA* 1.3 77.6 - - - +
91C LYS* 1.3 63.0 + - - +
93C ALA* 3.3 3.6 + - - +
94C GLN* 3.0 26.0 + - - +
64b GLU* 5.2 0.2 - - - +
65b LEU* 3.5 21.5 - - + -
68b LEU* 3.5 41.5 + - + +
69b SER* 4.3 9.0 - - - +
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Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C HIS* 2.9 43.1 + - + +
88C ARG* 3.2 18.8 + - - +
90C ARG* 1.3 75.5 - - - +
92C LEU* 1.3 64.8 + - + +
94C GLN* 3.1 6.8 + - + +
95C GLN* 2.9 38.8 + - + +
65b LEU* 4.3 18.5 - - + +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 2.9 25.4 + - + +
89C ALA* 3.5 6.1 - - - +
91C LYS* 1.3 76.4 - - + +
93C ALA* 1.3 64.6 + - - +
95C GLN* 3.2 22.6 + - - +
96C TYR* 3.0 23.6 + - - +
104C ILE* 4.5 2.0 - - - +
109C LEU* 4.4 6.3 - - + -
112C ARG* 4.0 32.2 - - + +
113C VAL* 4.0 37.9 - - + +
116C VAL* 4.2 15.9 - - + -
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 4.2 6.7 - - + -
68C THR* 3.6 30.1 - - + -
89C ALA 2.9 14.4 + - - +
90C ARG 3.4 9.9 - - - +
92C LEU* 1.3 77.8 - - - +
94C GLN* 1.3 60.6 + - - +
96C TYR* 3.3 3.6 + - - +
97C TYR* 2.9 27.0 + - - +
104C ILE* 3.8 26.8 + - + +
109C LEU* 4.1 2.1 - - + +
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C THR* 4.7 4.8 - - - +
90C ARG 3.0 19.8 + - - +
91C LYS* 3.6 7.0 - - + +
93C ALA* 1.3 77.2 - - - +
95C GLN* 1.3 59.5 + - - +
97C TYR* 3.7 16.7 - - - +
98C LEU* 2.8 35.5 + - + +
61b SER* 2.8 48.3 + - - +
64b GLU* 2.6 42.9 + - - +
65b LEU* 3.6 21.1 - - + -
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LYS* 2.9 33.1 + - + +
92C LEU* 3.2 22.8 + - + +
94C GLN* 1.3 71.6 - - - +
96C TYR* 1.3 67.9 - - - +
98C LEU* 3.2 15.5 + - + +
99C VAL* 3.1 28.8 + - + +
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU 3.0 9.4 + - - +
93C ALA 3.4 8.1 - - - +
95C GLN* 1.3 81.7 - - - +
97C TYR* 1.3 56.6 + - - +
99C VAL* 3.3 0.4 + - - -
100C TYR* 2.9 63.6 + + + +
102C GLU* 3.5 27.7 + - - -
103C PRO 4.2 0.7 - - - -
104C ILE* 3.5 30.1 - - + -
105C PRO* 3.4 25.9 - - + +
108C GLN* 4.7 2.0 - - + -
112C ARG* 4.0 26.0 - - - +
74c TYR* 3.5 15.2 + + - -
78c GLU* 2.7 29.3 + - - -
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Residues in contact with TYR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LYS* 4.4 21.3 + - - -
93C ALA 2.9 16.5 + - - +
94C GLN* 3.7 24.2 - - - +
95C GLN 3.2 0.4 - - - -
96C TYR* 1.3 74.8 - - - +
98C LEU* 1.3 61.7 + - - +
101C GLN* 2.7 61.3 + - - +
102C GLU 3.5 41.3 - - - +
103C PRO* 3.8 16.4 - - + -
104C ILE 5.6 0.7 - - - +
57b GLN 6.0 2.0 - - - -
60b SER* 5.5 8.7 - - - -
61b SER* 5.5 8.5 - - - -
64b GLU* 4.9 2.9 - - - -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 2.8 19.3 + - + +
95C GLN* 3.4 17.5 - - + +
97C TYR* 1.3 77.9 - - + +
99C VAL* 1.3 67.3 + - + +
101C GLN* 4.2 7.4 + - - +
54b MET* 5.6 2.9 - - - +
57b GLN* 4.0 24.7 - - + +
58b LEU* 4.0 34.8 - - + +
61b SER* 3.9 28.3 - - - +
93c ASN* 4.8 4.4 - - - +
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLN* 3.1 17.3 + - + +
96C TYR* 4.0 2.2 - - - +
98C LEU* 1.3 86.6 - - + +
100C TYR* 1.3 90.2 + - + +
101C GLN* 5.3 0.2 - - - +
70c ARG* 5.7 1.6 - - - +
89c SER* 3.7 24.2 - - - +
90c MET* 4.1 4.2 + - + -
93c ASN* 4.0 35.4 - - + +
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Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 2.9 65.5 + + + +
99C VAL* 1.3 100.4 - - + +
101C GLN* 1.3 72.3 + - - +
102C GLU* 3.0 21.0 + - - +
112C ARG* 5.0 7.8 + - - -
70c ARG* 5.5 2.1 + - - +
74c TYR* 4.0 19.2 - + - +
85c TYR 5.5 0.2 - - - -
86c THR* 3.8 25.6 - - + -
89c SER* 3.8 11.7 + - - -
90c MET* 3.2 36.5 - - + +
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Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TYR* 2.7 72.9 + - - +
98C LEU* 4.2 7.8 + - - +
100C TYR* 1.3 74.0 - - - +
102C GLU* 1.3 55.5 - - - +
103C PRO* 4.7 0.5 - - - +
57b GLN* 3.4 52.5 + - - +
89c SER* 3.7 21.8 - - - +
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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