Contacts of the helix formed by residues 133 - 157 (chain A) in PDB entry 5VLR
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 ASP 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PHE 5.4 0.6 + - - -
131A LEU* 4.2 14.1 - - + +
132A CYS* 1.3 77.2 - - - +
134A PRO* 1.4 71.1 - - - +
135A GLU* 3.0 22.2 + - - +
136A VAL* 3.3 31.1 + - + +
137A ASN* 2.9 27.1 + - - +
428A TYR* 5.0 0.9 - - - -
460A ARG* 3.8 16.8 + - - -
662A LEU* 5.6 0.7 - - - +
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Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A CYS 4.0 6.5 - - - +
133A ASP* 1.4 85.4 - - - +
135A GLU* 1.3 56.6 + - - +
137A ASN* 2.9 12.2 + - + +
138A ASP* 2.7 43.6 + - - +
428A TYR* 3.2 20.6 - - + +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASP* 3.0 15.8 + - - +
134A PRO* 1.3 77.8 - - - +
136A VAL* 1.3 55.6 + - - +
138A ASP* 4.0 1.0 - - - +
139A PHE* 3.1 29.3 + - - +
428A TYR* 3.3 49.2 + - + +
460A ARG* 3.2 30.9 + - - -
624A TYR* 3.2 34.4 - - - +
625A LEU* 3.3 18.6 + - + +
626A ASP* 4.9 2.1 + - + +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 4.0 29.2 - - + +
131A LEU* 4.1 13.9 - - + -
133A ASP* 3.3 35.2 + - + +
134A PRO 3.2 0.4 - - - -
135A GLU* 1.3 73.5 - - - +
137A ASN* 1.3 60.1 + - - +
139A PHE* 3.4 3.0 + - - +
140A ARG* 3.1 36.0 + - - +
625A LEU* 3.8 19.7 - - + -
662A LEU* 4.3 12.1 - - + -
666A LEU* 3.8 24.2 - - + -
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Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE 4.4 12.3 - - - +
129A ASP* 4.9 7.7 + - - +
132A CYS* 4.6 5.9 - - - +
133A ASP 2.9 29.0 + - - +
134A PRO* 2.9 11.3 + - + +
136A VAL* 1.3 76.6 - - - +
138A ASP* 1.3 60.2 + - - +
140A ARG* 3.5 15.9 + - - +
141A ALA* 3.0 28.9 + - - +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PRO* 2.7 22.4 + - - +
135A GLU 4.0 3.4 - - - +
137A ASN* 1.3 71.0 - - - +
139A PHE* 1.4 66.9 + - - +
141A ALA* 3.9 5.1 - - - +
142A LYS* 3.0 26.4 + - - +
428A TYR* 2.6 40.3 + - + -
626A ASP* 6.0 0.4 - - - -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU 3.1 18.7 + - - +
136A VAL* 3.6 6.7 - - - +
138A ASP* 1.4 76.2 - - - +
140A ARG* 1.4 60.6 + - + +
142A LYS* 3.7 2.0 - - - -
143A MET* 2.8 66.1 + - + +
625A LEU* 3.2 48.5 - - + -
626A ASP* 3.6 16.4 - - + +
630A THR* 3.8 23.1 - - + -
634A LEU* 4.9 0.9 - - + -
663A ARG* 5.3 0.9 - - + -
666A LEU* 3.3 41.3 - - + -
667A ILE* 4.1 13.9 - - + -
670A ALA* 4.8 0.4 - - + -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ASN* 5.2 2.4 - - - +
125A LEU* 3.5 25.7 + - - +
128A PHE* 3.8 19.9 - - - +
129A ASP* 3.0 33.9 + - - +
136A VAL* 3.1 19.9 + - - +
137A ASN* 3.7 12.0 + - - +
139A PHE* 1.4 83.0 - - + +
141A ALA* 1.3 61.6 + - - +
143A MET* 5.1 0.2 - - - -
144A CYS* 3.0 36.8 + - - +
666A LEU* 3.7 26.9 - - + +
669A GLU* 2.9 36.1 + - - +
673A ARG* 4.6 2.0 - - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN 3.0 17.6 + - - +
138A ASP* 3.9 5.8 - - - +
139A PHE 3.4 0.2 - - - -
140A ARG* 1.3 75.0 - - - +
142A LYS* 1.4 62.9 + - - +
144A CYS* 4.2 1.5 - - - +
145A GLN* 3.1 26.6 + - - +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASP 3.0 18.2 + - - +
139A PHE* 3.8 1.6 - - - +
141A ALA* 1.4 76.1 - - - +
143A MET* 1.3 75.2 + - + +
145A GLN* 3.6 6.2 + - + +
146A PHE* 3.0 28.4 + - + +
626A ASP* 2.8 32.5 + - - +
631A LYS* 6.3 0.7 - - - -
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Residues in contact with MET 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 2.8 60.9 + - + +
140A ARG* 4.7 0.7 - - - +
142A LYS* 1.3 111.8 - - + +
144A CYS* 1.3 64.2 + - - +
146A PHE* 3.5 10.6 + - + +
147A CYS* 3.1 32.2 + - - -
626A ASP* 4.2 12.6 - - - +
630A THR* 4.9 2.0 - - - -
631A LYS* 4.7 24.7 - - + -
634A LEU* 4.2 18.6 - - + -
670A ALA* 3.9 12.3 - - + -
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Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 3.0 32.1 + - - +
141A ALA* 4.3 1.3 - - - +
143A MET* 1.3 73.2 - - - +
145A GLN* 1.4 52.6 + - - +
147A CYS* 3.7 5.1 - - - +
148A GLU* 2.8 45.3 + - - +
666A LEU 5.8 0.4 - - - -
669A GLU* 3.4 32.8 - - - -
670A ALA* 4.3 10.3 - - - +
673A ARG* 3.4 30.0 - - - +
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ALA 3.1 21.4 + - - +
142A LYS* 3.8 6.5 - - - +
144A CYS* 1.4 72.2 - - - +
146A PHE* 1.4 57.9 + - + +
148A GLU* 3.2 8.3 + - - +
149A GLU* 2.8 71.5 + - - +
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LYS* 3.0 18.9 + - + +
143A MET* 3.5 16.6 + - + +
145A GLN* 1.4 75.2 - - - +
147A CYS* 1.3 59.3 + - - +
149A GLU* 3.6 13.4 - - - +
150A ALA* 3.1 27.9 + - - +
153A ARG* 5.0 1.6 + - - -
631A LYS* 6.3 2.9 - - + -
638A LEU* 5.0 0.9 - - - -
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Residues in contact with CYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A MET* 3.1 26.3 + - - +
144A CYS* 3.7 3.6 - - - +
146A PHE* 1.3 77.3 - - - +
148A GLU* 1.4 64.5 + - - +
150A ALA* 3.2 4.5 + - - +
151A ALA* 3.0 23.7 + - - +
634A LEU* 4.5 15.5 - - - -
638A LEU* 3.8 23.7 - - + +
670A ALA* 3.3 40.6 - - - +
671A TYR 4.3 0.9 - - - -
674A GLY* 3.7 15.0 - - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A CYS* 2.8 28.9 + - - +
145A GLN* 3.7 6.5 - - - +
147A CYS* 1.4 69.2 - - - +
149A GLU* 1.4 56.5 + - + +
151A ALA* 3.3 5.6 + - - +
152A ALA* 3.0 28.3 + - - +
673A ARG* 3.5 45.7 + - + +
674A GLY* 4.5 0.4 - - - -
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLN* 2.8 58.3 + - - +
146A PHE* 3.6 13.3 - - - +
148A GLU* 1.4 68.8 - - + +
150A ALA* 1.4 53.9 - - - +
152A ALA* 3.0 9.3 + - - +
153A ARG* 2.8 48.5 + - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE 3.1 14.9 + - - +
147A CYS 3.5 5.2 - - - +
149A GLU* 1.4 77.7 - - - +
151A ALA* 1.4 52.9 + - - +
153A ARG* 3.5 30.3 + - - +
154A ARG* 2.8 35.2 + - - +
638A LEU* 3.9 25.6 - - + -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A CYS 3.0 10.3 + - - +
148A GLU* 3.4 11.0 - - - +
149A GLU 3.2 0.2 - - - -
150A ALA* 1.4 72.8 - - - +
152A ALA* 1.4 60.5 + - - +
154A ARG* 3.1 22.1 + - - +
155A GLN* 3.0 27.5 + - - +
638A LEU* 5.6 0.2 - - - +
673A ARG 4.6 2.9 - - - +
674A GLY* 3.4 29.1 + - - +
676A THR* 5.7 3.6 - - - +
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU 3.0 13.6 + - - +
149A GLU* 3.4 11.7 - - - +
151A ALA* 1.4 70.5 - - - +
153A ARG* 1.3 63.8 + - - +
155A GLN* 3.2 19.2 + - - +
156A GLN* 3.3 14.5 + - - +
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE 5.0 1.2 + - - -
149A GLU* 2.8 30.9 + - - +
150A ALA* 3.5 39.0 + - - +
152A ALA* 1.3 71.8 - - - +
154A ARG* 1.4 62.8 + - - +
156A GLN* 3.2 23.0 + - - +
157A LEU* 3.8 7.8 + - - +
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA 2.8 15.5 + - - +
151A ALA* 3.1 27.6 + - - +
153A ARG* 1.4 75.3 - - - +
155A GLN* 1.3 64.5 + - - +
156A GLN 3.4 0.7 + - - -
157A LEU* 3.7 17.9 + - - +
161A ALA* 6.0 0.3 - - - +
162A TRP* 3.9 26.2 - - + +
165A TYR* 3.3 55.5 + - + -
638A LEU* 3.3 35.7 + - - +
674A GLY 2.8 30.5 + - - -
675A SER* 4.0 4.2 + - - +
676A THR* 5.4 1.8 + - - +
677A HIS* 5.5 11.0 - - - +
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Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA 3.0 11.7 + - - +
152A ALA* 3.2 13.2 + - - +
154A ARG* 1.3 79.6 - - - +
156A GLN* 1.4 60.4 + - - +
157A LEU 3.6 0.7 - - - +
162A TRP* 4.6 3.8 + - - +
286A ARG* 3.0 70.7 + - - +
287A ASP* 4.4 12.9 + - - +
677A HIS* 3.6 17.0 + - - -
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Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ALA 3.3 12.6 + - - +
153A ARG* 3.2 16.4 + - + +
155A GLN* 1.4 76.2 - - - +
157A LEU* 1.4 64.3 + - + +
286A ARG* 3.8 5.4 + - - -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ARG 3.8 6.4 + - - +
154A ARG* 3.7 13.0 + - - +
155A GLN 3.6 3.4 - - - +
156A GLN* 1.4 83.4 - - + +
158A GLY* 1.3 61.3 + - - +
161A ALA* 3.8 25.4 - - + -
162A TRP* 5.4 2.2 - - - +
286A ARG* 3.0 20.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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