Contacts of the helix formed by residues 134 - 157 (chain P) in PDB entry 5XS0
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 134 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P PHE* 3.8 1.1 - - - -
132P LEU* 3.4 2.4 - - - +
133P LYS* 1.3 76.2 - - - +
135P LYS* 1.3 62.8 + - - +
136P ALA 3.6 0.7 + - - -
137P LEU* 3.4 30.5 + - - +
138P SER* 3.0 24.8 + - - -
130Q GLU* 2.7 37.1 + - - -
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Residues in contact with LYS 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P VAL* 3.6 22.4 - - + +
103P PHE* 3.4 50.0 - - + -
105P VAL* 5.6 0.7 - - + -
134P SER* 1.3 72.3 + - - +
136P ALA* 1.3 62.2 + - - +
138P SER* 3.3 3.5 + - - -
139P LEU* 2.9 31.6 + - + +
95Q PHE* 3.7 34.3 - - + +
97Q ASP* 3.1 31.8 + - - -
130Q GLU* 4.9 1.0 + - - -
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Residues in contact with ALA 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P SER* 3.3 6.3 + - - +
135P LYS* 1.3 80.3 - - - +
137P LEU* 1.3 59.5 + - - +
139P LEU* 3.8 0.2 - - - +
140P GLU* 2.9 24.9 + - - +
95Q PHE* 3.4 26.8 - - + -
105Q VAL 4.1 8.7 - - - +
106Q GLY* 4.2 3.1 - - - -
126Q TYR* 3.3 13.1 - - - -
128Q VAL* 3.6 32.3 - - + -
130Q GLU* 4.2 5.5 + - + +
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Residues in contact with LEU 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P LEU* 4.4 20.4 - - + +
134P SER* 3.4 25.8 + - - +
136P ALA* 1.3 76.0 - - - +
138P SER* 1.3 61.0 + - - +
140P GLU* 3.6 16.5 - - - +
141P LYS* 2.9 31.2 + - - +
58Q GLY* 5.8 9.6 - - - +
128Q VAL* 4.0 22.0 - - + -
130Q GLU* 4.0 11.9 - - - +
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Residues in contact with SER 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P PHE* 3.8 17.2 + - - +
105P VAL* 3.9 21.1 - - - -
129P SER* 3.2 28.0 + - - -
132P LEU* 3.4 20.1 + - - +
134P SER 3.0 17.8 + - - -
135P LYS 3.6 5.2 - - - -
137P LEU* 1.3 76.8 - - - +
139P LEU* 1.3 57.1 + - - +
142P ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P VAL* 4.2 20.9 - - + -
96P VAL* 4.0 17.0 - - + -
105P VAL* 3.6 30.3 - - + -
107P VAL* 4.5 1.6 - - + -
135P LYS* 2.9 21.0 + - + +
136P ALA 3.8 0.2 - - - +
138P SER* 1.3 75.7 - - - +
140P GLU* 1.3 62.4 + - - +
142P ALA* 3.3 0.3 + - - +
143P ARG* 2.9 33.3 + - + +
94Q ASP* 3.7 19.1 - - + +
95Q PHE* 3.7 23.8 - - + -
126Q TYR* 3.4 28.0 - - + +
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Residues in contact with GLU 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P ALA 2.9 17.1 + - - +
137P LEU* 3.6 21.5 - - - +
139P LEU* 1.3 76.1 - - - +
141P LYS* 1.3 64.9 + - - +
143P ARG* 4.0 1.0 - - - +
144P LYS* 2.6 65.9 + - + +
126Q TYR* 3.5 31.9 - - + +
128Q VAL* 4.2 10.9 - - - +
149Q ASP* 5.3 0.2 - - - -
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Residues in contact with LYS 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P VAL* 3.0 30.3 + - - +
129P SER* 3.6 16.2 - - - +
130P GLU 5.4 0.8 - - - +
132P LEU* 5.6 5.2 - - + -
137P LEU 2.9 17.2 + - - +
138P SER 3.8 2.9 - - - +
140P GLU* 1.3 78.0 - - + +
142P ALA* 1.3 57.9 - - - +
144P LYS* 4.1 3.9 - - - +
145P GLU* 2.9 56.6 + - + +
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Residues in contact with ALA 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P VAL* 3.8 16.6 - - + +
107P VAL* 3.8 19.3 - - + -
127P GLY* 3.2 35.0 - - - +
128P VAL 4.0 7.0 - - - +
129P SER* 4.2 0.6 - - - +
138P SER 2.9 16.3 + - - +
139P LEU 3.9 1.8 - - - +
141P LYS* 1.3 77.4 - - - +
143P ARG* 1.3 56.8 + - - +
146P ALA* 2.9 27.7 + - - +
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Residues in contact with ARG 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P GLN* 2.5 60.2 + - - +
93P VAL* 3.3 29.7 - - - +
107P VAL* 3.9 13.9 - - + -
139P LEU* 2.9 23.9 + - - +
140P GLU* 4.0 3.1 - - - +
142P ALA* 1.3 76.1 - - - +
144P LYS* 1.3 63.1 + - - +
146P ALA* 3.2 1.4 + - - +
147P VAL* 3.0 21.7 + - - +
92Q ASN* 5.0 4.8 + - - +
94Q ASP* 2.8 33.7 + - - -
108Q CYS* 3.5 37.8 - - - +
110Q PHE* 4.4 4.8 - - - -
124Q VAL* 4.1 10.3 - - + -
126Q TYR* 3.9 10.5 - - + -
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Residues in contact with LYS 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P GLU* 2.6 56.8 + - + +
141P LYS* 4.1 3.6 - - - +
143P ARG* 1.3 75.5 - - - +
145P GLU* 1.3 62.4 + - - +
147P VAL* 3.2 6.4 + - - +
148P THR* 3.0 27.8 + - - -
124Q VAL* 4.2 12.3 - - + +
126Q TYR* 4.2 10.3 - - + +
149Q ASP* 2.9 32.5 + - - -
153Q ARG* 3.4 42.8 + - - +
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Residues in contact with GLU 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P TYR 3.8 5.1 - - - +
127P GLY* 3.8 9.2 - - - -
128P VAL* 3.4 26.5 + - - +
141P LYS* 2.9 48.4 + - + +
144P LYS* 1.3 76.9 - - - +
146P ALA* 1.3 58.8 + - - +
148P THR* 3.8 5.9 - - - +
149P ASP* 2.9 34.6 + - + +
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Residues in contact with ALA 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P GLN* 4.2 0.2 - - - +
107P VAL* 3.3 35.2 - - + +
109P ALA* 3.7 22.0 - - + +
125P GLY* 3.5 8.3 - - - -
126P TYR 3.4 13.0 - - - -
127P GLY* 3.5 1.3 - - - +
142P ALA 2.9 16.2 + - - +
143P ARG 3.2 4.7 + - - +
145P GLU* 1.3 76.9 - - - +
147P VAL* 1.3 61.8 + - - +
150P GLY 2.9 19.1 + - - -
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Residues in contact with VAL 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P HIS* 5.3 5.4 - - + +
88P ILE* 3.6 32.5 - - + -
91P GLN* 3.5 17.3 - - - +
109P ALA* 4.0 9.6 - - + -
111P VAL* 3.6 7.9 - - + +
143P ARG 3.0 16.7 + - - +
144P LYS* 3.2 8.3 + - - +
146P ALA* 1.3 76.6 - - - +
148P THR* 1.3 65.1 + - - +
150P GLY 3.3 1.2 + - - -
151P LEU* 2.9 23.0 + - + +
122Q GLU 5.0 1.6 - - - +
123Q ASP* 3.3 32.3 - - - +
124Q VAL* 3.7 11.0 - - + -
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Residues in contact with THR 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P GLY* 4.4 20.4 - - - +
144P LYS 3.0 17.7 + - - -
145P GLU* 3.9 6.3 - - - -
147P VAL* 1.3 77.6 - - - +
149P ASP* 1.3 63.2 + - - +
151P LEU* 3.2 11.0 + - + +
152P LYS* 3.0 37.8 + - + +
123Q ASP* 5.4 1.7 + - - -
153Q ARG* 4.1 12.1 + - - -
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Residues in contact with ASP 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O GLU* 5.5 0.2 - - - -
144O LYS* 2.9 33.4 + - - -
125P GLY* 3.5 3.2 - - - -
126P TYR 3.1 27.4 + - - +
145P GLU* 2.9 19.1 + - + +
148P THR* 1.3 76.6 - - - +
150P GLY* 1.3 58.7 + - - +
152P LYS* 3.3 20.7 + - - +
153P ARG* 2.9 37.6 + - - +
156P ARG* 5.6 2.1 + - - -
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Residues in contact with GLY 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P VAL* 3.7 16.7 - - - +
123P ASP* 4.5 2.8 - - - +
124P VAL 3.9 4.5 - - - -
125P GLY* 3.2 24.1 - - - -
146P ALA 2.9 13.0 + - - -
147P VAL 3.7 3.1 - - - -
149P ASP* 1.3 76.0 - - - +
151P LEU* 1.3 57.6 + - - +
153P ARG* 4.0 0.5 - - - +
154P ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P VAL* 5.9 1.1 - - + -
72P ILE* 4.6 18.6 - - + -
84P TRP* 4.1 14.4 - - + -
86P HIS* 3.8 39.5 - - + +
111P VAL* 3.7 10.9 - - + +
113P VAL* 3.6 24.7 - - + -
147P VAL* 2.9 14.4 + - + +
148P THR* 3.2 13.0 + - + +
150P GLY* 1.3 76.6 - - - +
152P LYS* 1.3 59.8 + - + +
154P ALA* 3.3 1.1 + - - +
155P LEU* 2.9 42.3 + - + +
123Q ASP* 5.6 3.6 - - - +
157Q SER* 5.2 0.9 - - - +
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Residues in contact with LYS 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P TYR* 4.6 14.8 - - - +
66P ILE* 3.2 29.6 + - + +
67P GLU* 5.2 0.2 - - - +
68P GLY* 4.4 12.5 - - - +
71P VAL* 4.1 28.2 - - + +
148P THR* 3.0 31.0 + - + +
149P ASP* 3.3 24.3 + - - +
151P LEU* 1.3 78.8 - - + +
153P ARG* 1.3 57.8 - - + +
155P LEU* 3.3 6.7 + - - +
156P ARG* 2.9 37.2 + - - +
162P LEU 4.9 1.9 - - - +
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Residues in contact with ARG 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O LYS* 3.5 48.3 + - - +
148O THR* 3.8 19.4 + - - -
123P ASP* 3.1 39.3 + - + +
124P VAL 2.7 26.1 + - - +
149P ASP* 2.9 38.0 + - - +
150P GLY 4.0 0.9 - - - +
152P LYS* 1.3 77.3 - - + +
154P ALA* 1.3 62.3 + - - +
156P ARG* 3.4 53.0 - - - +
157P SER* 3.9 4.3 + - - -
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Residues in contact with ALA 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O HIS* 5.9 0.2 - - - -
111P VAL 3.8 14.6 - - - +
113P VAL* 3.7 17.9 - - + -
121P HIS* 3.6 30.7 - - - +
122P GLU 4.9 0.7 - - - -
123P ASP* 3.7 12.0 - - - +
150P GLY 2.9 18.3 + - - +
151P LEU* 3.8 1.1 - - - +
153P ARG* 1.3 77.2 - - - +
155P LEU* 1.3 63.5 + - - +
157P SER* 3.3 19.8 + - - -
158P PHE* 4.5 2.4 - - - -
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Residues in contact with LEU 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P VAL* 3.6 31.6 - - + +
72P ILE* 5.6 0.4 - - + -
75P ALA* 4.3 11.7 - - + -
79P PHE* 5.1 2.5 - - + -
84P TRP* 4.1 20.0 - - + -
113P VAL* 3.7 31.6 - - + -
151P LEU* 2.9 35.8 + - + +
152P LYS 3.3 3.8 + - - +
154P ALA* 1.3 70.4 - - - +
156P ARG* 1.3 66.1 + - - +
157P SER 3.1 4.0 + - - -
158P PHE* 3.2 27.6 + - + -
162P LEU* 3.5 32.0 - - + +
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Residues in contact with ARG 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O ILE* 4.8 7.9 - - + -
149P ASP* 5.6 2.4 + - - -
152P LYS* 2.9 22.1 + - - +
153P ARG* 3.4 50.8 - - - +
154P ALA 3.2 0.2 - - - -
155P LEU* 1.3 76.6 - - - +
157P SER* 1.3 57.0 + - - +
158P PHE 3.0 6.3 + - - -
159P GLY 3.3 16.8 + - - +
162P LEU 4.2 6.9 + - - +
163P GLY* 3.6 24.4 + - - +
164P ASN* 3.6 16.3 - - + +
166P ILE* 4.1 22.2 - - - +
167P LEU* 3.7 34.8 - - - +
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Residues in contact with SER 157 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O ILE* 3.8 21.6 - - - +
76O ASN* 3.3 15.8 + - - +
84O TRP* 3.3 22.0 - - - -
86O HIS* 3.8 15.9 + - - -
151O LEU* 4.9 1.2 - - - +
121P HIS* 3.4 33.4 + - - -
123P ASP* 4.6 3.1 + - - -
153P ARG 3.9 7.8 + - - -
154P ALA 3.6 8.3 + - - -
155P LEU 3.1 2.2 - - - -
156P ARG* 1.3 76.1 - - - +
158P PHE* 1.3 58.5 + - - +
159P GLY 3.5 0.4 - - - -
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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