Contacts of the helix formed by residues 140 - 165 (chain J) in PDB entry 5D3E
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 GLY 140 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J THR* 1.3 74.5 - - - +
141J GLU* 1.3 63.0 + - - -
142J LYS* 3.4 1.1 - - - -
143J ARG* 3.6 7.7 + - - +
144J ALA* 3.2 22.2 + - - +
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Residues in contact with GLU 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J THR 3.6 0.6 + - - -
140J GLY* 1.3 73.5 - - - -
142J LYS* 1.3 65.0 + - + +
143J ARG 3.3 0.2 - - - -
144J ALA* 3.7 11.8 - - + +
145J THR* 3.2 26.7 + - - +
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Residues in contact with LYS 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E GLU* 5.2 13.9 + - - +
138J ALA* 4.5 12.1 - - + -
139J THR* 3.2 23.3 + - - +
140J GLY* 5.7 0.6 - - - -
141J GLU* 1.3 81.4 - - + +
143J ARG* 1.3 61.6 + - - +
145J THR* 3.1 23.1 - - - +
146J VAL* 3.1 16.0 + - - +
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Residues in contact with ARG 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J ALA* 4.1 17.8 + - - +
138J ALA* 3.3 33.1 - - - +
139J THR* 3.8 8.9 + - - +
140J GLY 3.6 12.7 + - - +
141J GLU 3.3 0.2 - - - -
142J LYS* 1.3 80.9 - - - +
144J ALA* 1.3 60.4 - - - +
146J VAL* 3.4 6.2 - - - +
147J VAL* 3.0 59.3 + - + +
185J GLU 4.7 3.4 + - - -
186J ILE* 2.7 36.0 + - - +
187J GLN* 5.6 0.4 + - - -
188J ASN* 5.9 0.8 - - - +
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Residues in contact with ALA 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J GLY 3.2 17.0 + - - +
141J GLU* 4.0 12.3 - - + +
142J LYS 3.3 0.4 - - - -
143J ARG* 1.3 84.6 - - - +
145J THR* 1.3 59.6 + - - +
147J VAL* 4.2 4.6 - - - +
148J GLU* 3.3 26.2 + - - +
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Residues in contact with THR 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J GLU 3.2 15.5 + - - +
142J LYS* 3.1 21.1 - - - +
144J ALA* 1.3 79.6 - - - +
146J VAL* 1.3 59.6 + - + +
148J GLU* 3.6 10.3 + - - +
149J SER* 3.0 28.8 + - - -
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Residues in contact with VAL 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J TYR* 3.5 32.7 - - + +
134J LEU* 3.5 29.8 - - + +
135J ALA* 3.9 22.2 - - + +
138J ALA* 4.8 1.6 - - + -
142J LYS 3.1 21.5 + - - +
143J ARG* 3.4 13.5 - - - +
145J THR* 1.3 78.1 - - + +
147J VAL* 1.3 63.3 + - - +
148J GLU 3.3 0.2 - - - -
149J SER* 3.5 4.5 + - - -
150J SER* 3.1 25.5 + - - -
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Residues in contact with VAL 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J ALA* 3.6 24.7 - - + -
143J ARG* 3.0 46.3 + - - +
144J ALA* 4.2 3.6 - - - +
146J VAL* 1.3 73.8 - - - +
148J GLU* 1.3 67.8 + - - +
150J SER* 3.3 7.8 + - - -
151J GLU* 3.1 21.0 + - - +
182J PHE* 3.2 20.8 - - + -
186J ILE* 3.9 11.4 - - + +
187J GLN* 3.5 21.8 - - - +
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Residues in contact with GLU 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J ALA 3.3 19.1 + - - +
145J THR* 3.7 10.0 - - - +
147J VAL* 1.3 80.8 - - - +
149J SER* 1.3 62.9 + - - +
151J GLU* 3.7 3.5 + - - +
152J LYS* 3.2 22.8 + - + +
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Residues in contact with SER 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J LYS* 5.3 2.0 + - - -
131J TYR* 3.9 34.7 - - - -
145J THR* 3.0 15.2 + - - -
146J VAL* 3.7 8.6 - - - -
147J VAL 3.3 0.4 - - - -
148J GLU* 1.3 77.2 - - - +
150J SER* 1.3 64.8 + - - +
152J LYS* 3.3 12.8 + - - +
153J ALA* 3.1 21.7 + - - +
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Residues in contact with SER 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J GLY* 3.0 24.6 + - - -
131J TYR* 3.7 18.5 - - - +
132J ARG* 3.9 9.6 + - - +
146J VAL 3.1 15.2 + - - -
147J VAL* 3.4 11.0 - - - -
149J SER* 1.3 76.9 - - - +
151J GLU* 1.3 58.2 + - - +
153J ALA* 3.0 6.4 + - - +
154J TYR* 3.0 36.5 + - - +
182J PHE* 4.0 12.8 - - - -
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Residues in contact with GLU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J VAL 3.1 10.0 + - - +
148J GLU* 4.4 3.8 - - - +
150J SER* 1.3 79.9 + - - +
152J LYS* 1.3 57.7 + - - +
154J TYR* 4.2 4.9 - - - -
155J SER* 2.9 39.3 + - - -
179J TYR* 3.7 26.2 + - + +
182J PHE* 3.7 21.7 - - + -
183J TYR* 4.5 12.0 + - + -
187J GLN* 3.2 23.9 + - - +
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Residues in contact with LYS 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J LYS* 5.4 9.9 - - - +
148J GLU* 3.2 15.7 + - + +
149J SER* 3.4 14.6 - - - +
150J SER 3.2 0.4 - - - -
151J GLU* 1.3 76.8 - - - +
153J ALA* 1.3 58.3 + - - +
155J SER* 4.6 1.7 - - - -
156J GLU* 3.1 41.5 + - - +
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Residues in contact with ALA 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J LEU* 3.4 29.0 - - - +
127J LYS* 3.8 22.9 - - + +
128J GLY* 3.5 13.0 - - - +
149J SER 3.1 10.3 + - - +
150J SER 3.0 9.3 + - - +
152J LYS* 1.3 76.0 - - - +
154J TYR* 1.3 66.3 + - - +
156J GLU* 3.3 7.1 + - - +
157J ALA* 3.0 23.9 + - - +
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Residues in contact with TYR 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J LYS* 3.7 27.4 - - + -
128J GLY* 3.4 23.4 - - - -
129J ASP* 2.9 22.2 + - - -
132J ARG* 3.0 16.2 + - - -
150J SER* 3.0 27.7 + - - +
151J GLU* 4.0 2.7 - - - +
153J ALA* 1.3 75.6 - - - +
155J SER* 1.3 50.9 + - - +
157J ALA* 3.1 6.9 + - - +
158J HIS* 2.7 33.8 + - - +
175J LEU* 4.5 15.4 - - + +
178J ASN* 3.6 15.7 - - + +
179J TYR* 3.6 38.0 - + + -
182J PHE* 3.9 31.0 - + + -
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Residues in contact with SER 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J GLU* 2.9 28.9 + - - -
152J LYS* 4.6 2.7 - - - -
154J TYR* 1.3 73.6 - - - +
156J GLU* 1.3 58.0 + - - +
158J HIS* 3.0 7.2 + - - +
159J GLU* 2.8 49.7 + - - +
179J TYR* 3.6 16.5 + - - -
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Residues in contact with GLU 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J LYS* 5.2 6.9 + - - -
124J LEU* 4.1 23.6 - - + +
127J LYS* 5.8 2.3 + - - -
152J LYS* 3.1 36.8 + - - +
153J ALA* 3.3 8.0 + - - +
155J SER* 1.3 77.3 - - - +
157J ALA* 1.3 56.9 + - - +
159J GLU* 3.5 16.2 + - - +
160J ILE* 3.4 24.7 + - + +
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Residues in contact with ALA 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J VAL* 4.0 13.5 - - - +
124J LEU* 3.8 23.3 - - + +
125J LYS 4.6 0.9 - - - +
153J ALA 3.0 16.7 + - - +
154J TYR* 3.5 4.0 - - - +
156J GLU* 1.3 78.2 - - - +
158J HIS* 1.3 59.3 + - - +
159J GLU 3.2 0.7 - - - -
160J ILE* 3.3 5.2 + - - +
161J SER* 2.8 30.1 + - - -
175J LEU* 3.5 25.3 - - + +
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Residues in contact with HIS 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J TYR 2.7 16.3 + - - +
155J SER* 3.4 14.8 - - - +
157J ALA* 1.3 74.5 - - - +
159J GLU* 1.3 56.5 + - + +
160J ILE 3.1 0.4 - - - -
161J SER* 2.9 20.2 + - - -
162J LYS* 2.9 63.8 + - + +
175J LEU* 3.7 8.9 - - + +
176J ALA* 4.6 14.5 - - + -
179J TYR* 3.2 30.8 - + + -
196J LEU* 4.1 24.7 - - + +
199J THR* 5.7 1.4 + - - -
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Residues in contact with GLU 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J SER* 2.8 32.1 + - - +
156J GLU* 3.5 19.1 + - - +
157J ALA 3.2 0.4 - - - -
158J HIS* 1.3 75.8 - - + +
160J ILE* 1.3 65.7 + - + +
162J LYS* 5.1 2.5 - - - -
163J GLU* 3.1 22.4 - - - +
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Residues in contact with ILE 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J GLU* 5.3 9.2 - - - +
117J TYR* 3.9 37.7 - - + +
120J LYS* 5.3 10.1 - - + -
121J VAL* 4.3 17.6 - - + +
124J LEU* 5.8 2.7 - - + -
156J GLU* 3.4 18.6 - - + +
157J ALA* 3.3 7.0 + - - +
159J GLU* 1.3 82.9 - - + +
161J SER* 1.3 61.4 + - - +
162J LYS 3.4 1.3 - - - -
163J GLU* 3.7 7.0 - - + -
164J HIS* 3.0 33.3 + - + +
165J MET* 3.8 4.7 + - - +
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Residues in contact with SER 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J VAL* 4.1 10.1 - - - +
157J ALA 2.8 13.1 + - - -
158J HIS* 2.9 30.1 + - - -
160J ILE* 1.3 77.1 - - - +
162J LYS* 1.3 59.8 + - - +
165J MET* 2.7 42.5 - - - +
172J ARG* 3.3 24.8 - - - +
175J LEU* 3.3 17.8 - - - +
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Residues in contact with LYS 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J HIS* 2.9 49.2 + - + +
159J GLU* 5.1 3.1 - - - -
161J SER* 1.3 79.5 - - - +
163J GLU* 1.3 64.8 + - - +
165J MET 4.5 4.0 + - - +
172J ARG* 2.9 40.7 + - + +
199J THR* 5.2 9.3 + - - -
200J ALA* 5.9 0.6 - - - +
203J ASP* 3.2 11.5 + - - -
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Residues in contact with GLU 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J GLU 3.1 24.0 + - - +
160J ILE* 3.7 8.5 - - + -
161J SER 3.3 0.6 - - - -
162J LYS* 1.3 80.9 - - - +
164J HIS* 1.3 97.2 + - + +
165J MET 3.7 0.2 - - - -
166J GLN* 5.4 1.7 + - - -
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Residues in contact with HIS 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J TYR* 3.2 59.5 - + + +
160J ILE* 3.0 17.0 + - + +
163J GLU* 1.3 110.1 + - + +
165J MET* 1.3 64.5 + - + +
166J GLN* 3.8 13.9 + - - +
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Residues in contact with MET 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J TYR* 4.8 3.8 - - + +
118J GLU* 4.6 15.0 - - + +
121J VAL* 3.6 39.3 - - + -
160J ILE 4.8 1.3 - - - +
161J SER* 2.7 32.7 + - - +
162J LYS 4.5 3.0 - - - +
163J GLU 3.7 1.2 - - - -
164J HIS* 1.3 84.1 - - + +
166J GLN* 1.3 65.4 + - - +
169J HIS* 4.0 30.5 - - + -
171J ILE* 4.3 5.6 - - + -
172J ARG* 2.9 53.8 + - + +
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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) + - + + + + + -
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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