Contacts of the helix formed by residues 118 - 140 (chain B) in PDB entry 5HJS
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 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLN 3.9 0.8 + - - -
117B LEU* 1.3 75.0 - - - +
119B ARG* 1.3 64.7 + - - +
120B GLU* 3.6 10.5 + - - +
121B ASP* 3.0 32.4 + - - +
122B GLN* 2.9 19.4 + - - +
209B GLN* 4.6 9.9 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.9 10.9 - - - +
117B LEU 3.6 1.6 + - - -
118B SER* 1.3 70.5 - - - +
120B GLU* 1.3 56.0 + - - +
122B GLN* 2.9 39.1 + - - +
123B ILE* 3.0 35.5 + - + +
-1D THR* 4.6 6.1 - - + +
6D HIS* 3.9 19.5 - - + +
9D LEU* 3.8 38.2 + - - +
10D GLN* 4.0 12.5 + - - +
101D SO4 2.9 45.8 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER* 3.0 9.8 - - - +
119B ARG* 1.3 79.0 - - - +
121B ASP* 1.3 57.1 + - - +
123B ILE* 3.4 4.8 + - - +
124B ALA* 2.9 26.6 + - - +
207B ASN* 5.3 6.5 - - - +
209B GLN* 6.4 2.2 - - + -
-3D SER* 3.5 14.9 - - - -
-2D LEU* 2.8 37.0 + - + +
-1D THR* 2.7 45.9 + - - +
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.2 19.0 - - + +
118B SER* 3.0 25.3 + - - +
120B GLU* 1.3 74.6 - - - +
122B GLN* 1.4 60.9 + - - +
124B ALA* 3.2 4.1 + - - +
125B LEU* 2.9 39.2 + - + +
207B ASN 4.1 2.3 - - - +
208B VAL* 3.5 13.5 - - + -
209B GLN* 2.7 35.4 + - - +
210B ASP* 3.0 31.9 + - - +
214B VAL* 5.2 1.8 - - + -
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.5 43.5 + - + +
115B LEU* 3.5 24.8 + - - +
117B LEU* 2.9 24.9 + - + +
118B SER 2.9 11.0 + - - +
119B ARG* 2.9 51.4 + - - +
121B ASP* 1.4 75.4 - - - +
123B ILE* 1.3 58.2 + - - +
125B LEU* 3.5 0.8 + - - +
126B LEU* 3.1 35.5 + - - +
9D LEU* 3.7 13.5 - - + +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG* 3.0 22.6 + - + +
120B GLU* 3.7 4.9 - - - +
122B GLN* 1.3 75.2 - - - +
124B ALA* 1.3 65.5 + - - +
126B LEU* 4.2 0.4 - - - +
127B LYS* 2.9 29.2 + - + +
-2D LEU* 4.0 16.6 - - + -
-1D THR* 3.8 33.0 - - + +
2D HIS* 3.8 33.0 - - + +
5D LEU* 3.9 15.8 - - + +
6D HIS* 4.0 27.8 - - + +
9D LEU* 3.8 15.9 - - + -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU 2.9 17.7 + - - +
121B ASP* 3.2 8.7 + - - +
123B ILE* 1.3 76.6 - - - +
125B LEU* 1.3 63.6 + - - +
127B LYS* 4.0 4.5 - - - +
128B THR* 3.8 20.8 + - - -
205B ARG* 4.4 4.9 - - - +
206B PRO 3.9 13.6 - - - +
207B ASN 3.7 19.7 - - - +
208B VAL* 4.2 7.4 - - + -
-2D LEU* 3.6 21.9 - - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 4.4 4.7 - - + -
117B LEU* 3.7 29.6 - - + -
121B ASP 2.9 19.3 + - - +
122B GLN 3.8 4.0 - - - +
124B ALA* 1.3 75.7 - - - +
126B LEU* 1.3 55.5 + - - +
128B THR* 4.6 0.7 - - - -
129B SER* 2.7 37.9 + - - -
200B ILE* 3.5 33.9 - - + +
201B PHE* 3.9 15.9 - - + -
202B SER 3.8 15.0 - - - +
205B ARG* 4.2 6.9 + - + -
208B VAL* 3.7 25.6 - - + -
214B VAL* 4.1 13.7 - - + -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 4.2 20.9 - - + +
105B VAL* 4.1 11.2 - - + -
108B ALA* 3.7 25.8 - - + -
114B PHE* 3.7 24.7 - - + -
122B GLN 3.1 16.5 + - - +
123B ILE 4.2 1.8 - - - +
125B LEU* 1.3 75.3 - - - +
127B LYS* 1.3 67.0 + - - +
129B SER* 3.6 8.1 - - - +
130B ALA* 2.9 29.3 + - - +
200B ILE* 4.6 7.0 - - + -
278B ILE* 5.7 0.2 - - - -
5D LEU* 4.1 26.5 - - + -
9D LEU* 3.8 20.9 - - + -
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ILE* 2.9 20.0 + - + +
124B ALA* 4.0 4.7 - - - +
125B LEU 3.3 0.4 - - - -
126B LEU* 1.3 79.0 - - - +
128B THR* 1.3 66.5 + - - +
130B ALA* 4.2 8.3 + - - +
131B ILE* 5.2 0.7 + - - +
207B ASN* 5.8 3.1 - - - +
277B GLU 3.4 6.7 + - - -
278B ILE* 2.9 48.6 + - + +
279B TRP* 4.6 7.6 + - - -
280B ASP 4.8 6.7 + - - -
282B HIS* 5.9 1.2 - - - -
-2D LEU* 4.7 16.6 - - + -
1D ARG* 5.6 1.3 - - - +
2D HIS* 2.8 42.8 + - + +
5D LEU* 4.5 5.3 - - + +
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ALA 3.8 13.5 + - - -
126B LEU 3.3 0.2 - - - -
127B LYS* 1.3 84.6 - - - +
129B SER* 1.3 61.7 + - - +
130B ALA 3.4 0.7 - - - -
131B ILE* 4.1 16.1 - - - +
132B GLU* 4.3 4.5 - - - +
205B ARG* 3.5 39.9 + - - +
206B PRO* 4.0 23.9 + - + +
254B SER* 4.6 7.1 + - - +
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 5.5 0.5 - - - +
125B LEU 2.7 26.7 + - - -
126B LEU* 3.6 6.8 - - - +
128B THR* 1.3 75.6 - - - +
130B ALA* 1.4 66.9 + - - +
131B ILE 3.3 1.3 - - - -
132B GLU* 3.2 5.5 + - - +
133B VAL* 3.0 23.2 + - - +
199B SER* 3.8 14.8 - - - -
200B ILE* 3.7 22.7 - - - +
205B ARG* 3.5 24.8 - - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.8 9.9 - - + -
104B ILE* 3.6 18.3 - - + +
126B LEU 2.9 20.9 + - - +
127B LYS 4.2 3.8 - - - +
128B THR 3.4 1.4 - - - -
129B SER* 1.4 76.0 + - - +
131B ILE* 1.3 57.1 + - - +
133B VAL* 3.3 1.0 + - - -
134B MET* 2.9 39.3 + - - +
278B ILE* 3.9 27.1 - - + -
279B TRP* 4.8 0.4 - - - +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LYS 6.0 0.2 - - - +
128B THR 4.1 10.3 - - - +
130B ALA* 1.3 74.3 - - - +
132B GLU* 1.3 62.7 + - - +
134B MET* 3.3 8.5 + - + +
135B LEU* 2.9 45.2 + - + +
171B PHE* 4.5 1.3 - - + -
254B SER* 3.6 32.5 - - - +
257B HIS* 3.5 50.3 - - + +
279B TRP* 3.9 17.3 - - + +
301B 668 3.7 25.8 - - + -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B THR 4.3 4.6 - - - +
129B SER 3.2 6.8 + - - +
131B ILE* 1.3 76.0 - - - +
133B VAL* 1.4 57.6 + - - +
135B LEU* 3.3 2.7 + - - -
136B LEU* 3.0 27.8 + - - +
199B SER* 3.1 15.6 + - - +
205B ARG* 2.8 44.7 + - - +
247B LEU* 4.9 4.2 - - - +
250B LEU* 3.4 53.4 - - + +
251B ARG* 3.3 18.4 + - - -
254B SER* 4.1 16.3 + - - -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN* 5.9 0.2 - - - +
104B ILE* 3.6 31.2 - - + -
107B PHE* 6.0 0.7 - - + -
129B SER 3.0 20.8 + - - +
130B ALA 3.8 3.6 - - - +
132B GLU* 1.4 72.4 - - - +
134B MET* 1.3 59.8 + - - +
136B LEU* 3.4 7.9 + - + +
137B GLU* 2.9 32.7 + - + +
196B ILE* 3.7 42.6 - - + +
199B SER* 4.1 13.9 - - - +
200B ILE* 4.0 20.4 - - + -
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 3.7 30.1 - - + +
100B SER* 3.4 22.0 - - - +
101B VAL* 4.1 14.6 - - + -
104B ILE* 3.6 8.3 - - + -
130B ALA* 2.9 27.6 + - - +
131B ILE* 3.3 9.8 + - + +
133B VAL* 1.3 76.6 - - - +
135B LEU* 1.4 51.2 + - - +
137B GLU* 3.4 5.2 + - - +
138B THR* 2.7 36.0 + - - -
279B TRP* 3.6 26.0 - - + -
301B 668 3.5 43.2 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 2.9 42.4 + - + +
132B GLU* 3.8 4.7 - - - +
134B MET* 1.4 74.6 - - - +
136B LEU* 1.4 59.4 + - - +
138B THR* 3.4 9.0 + - + +
139B SER* 2.9 29.3 + - - -
171B PHE* 4.5 9.0 - - + -
175B ILE* 3.9 32.8 - - + -
178B PHE* 3.9 11.9 - - + -
179B SER* 5.0 0.7 + - - -
250B LEU* 4.0 11.7 - - + +
253B LEU* 3.7 42.2 - - + +
254B SER 5.1 0.2 - - - +
301B 668 4.7 8.1 - - + -
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLU 3.0 16.7 + - - +
133B VAL* 3.4 11.2 + - - +
135B LEU* 1.4 75.1 - - - +
137B GLU* 1.4 61.9 + - - +
139B SER* 2.9 19.2 + - - -
140B ARG* 3.1 11.6 + - - +
178B PHE* 4.1 9.2 - - + -
182B MET* 3.8 28.3 - - + -
192B PHE* 3.5 12.7 - - + -
195B LEU* 4.3 20.4 - - + +
196B ILE* 3.9 39.0 - - + +
199B SER* 4.7 3.6 - - - -
246B LYS* 5.7 1.3 - - + -
247B LEU* 5.0 0.9 - - + -
250B LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN* 2.8 31.4 + - - -
100B SER* 5.0 5.6 - - - +
104B ILE* 5.4 3.0 - - + +
133B VAL* 2.9 30.2 + - + +
134B MET* 3.4 8.3 + - - +
136B LEU* 1.4 74.4 - - - +
138B THR* 1.3 60.0 + - - +
140B ARG* 3.2 29.1 + - - +
141B ARG* 2.7 58.6 + - - +
196B ILE* 3.4 8.7 - - + +
301B 668 4.1 19.5 - - + -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B MET 2.7 20.9 + - - -
135B LEU* 3.5 10.8 - - + +
137B GLU* 1.3 74.0 - - - +
139B SER* 1.4 59.7 + - - +
141B ARG* 3.0 21.1 + - - +
142B TYR 3.4 7.3 + - - -
149B ILE* 3.6 41.4 - - + +
151B PHE* 4.0 5.7 - - + -
162B PHE* 5.0 1.8 - - + -
175B ILE* 4.0 19.1 - - + -
179B SER* 4.2 2.0 - - - +
301B 668 3.3 29.3 + - + +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 2.9 14.8 + - - -
136B LEU* 2.9 16.1 + - - -
138B THR* 1.4 74.9 - - - +
140B ARG* 1.3 59.0 + - - +
142B TYR* 3.4 16.6 - - - +
178B PHE* 3.9 4.7 - - - -
179B SER* 3.5 28.3 - - - +
182B MET* 3.4 37.8 - - - +
183B ASN* 4.9 5.7 + - - +
192B PHE* 3.7 10.0 - - - -
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN* 3.2 29.6 + - - +
136B LEU 3.1 8.3 + - - +
137B GLU* 3.2 40.8 + - - +
138B THR 3.2 0.2 - - - -
139B SER* 1.3 78.3 + - - +
141B ARG* 1.3 73.4 + - + +
142B TYR 3.4 3.2 + - - +
189B ASP* 3.3 35.4 + - - +
192B PHE* 3.5 55.2 - - + +
196B ILE* 4.0 2.6 - - - +
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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