Contacts of the helix formed by residues 130 - 153 (chain B) in PDB entry 2YVE
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 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP* 3.0 26.7 + - - +
127B LEU 3.5 2.5 + - - +
129B ASN* 1.3 79.0 - - - +
131B ALA* 1.3 62.3 + - - +
132B HIS* 3.0 22.8 + - - +
133B LYS* 3.1 34.0 + - + +
134B ARG* 3.1 25.8 + - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASN 4.0 1.6 + - - -
130B ASP* 1.3 72.7 + - - +
132B HIS* 1.3 57.0 + - - +
134B ARG* 3.3 32.0 + - - +
135B ALA* 3.0 28.1 + - - +
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 5.4 8.0 - - + +
130B ASP* 3.0 10.1 + - - +
131B ALA* 1.3 75.8 - - - +
133B LYS* 1.3 75.7 + - + +
135B ALA* 3.2 6.1 + - - +
136B VAL* 3.1 44.6 + - + +
174B PRO* 4.4 20.7 - - + +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 5.8 0.7 - - - +
123B ASP* 2.9 46.2 + - - +
124B THR 5.2 0.2 - - - -
125B ASP* 2.8 32.1 + - - +
126B ASP* 4.9 2.9 - - + +
127B LEU* 3.5 14.5 - - + +
130B ASP* 3.1 36.1 + - + +
132B HIS* 1.3 85.6 - - + +
134B ARG* 1.3 57.7 + - - +
136B VAL* 3.5 6.3 + - - +
137B TYR* 2.9 29.3 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.9 21.0 + - - +
165A MET* 3.4 16.3 - - - +
168A THR* 3.2 31.6 + - + +
171A GLU* 5.3 8.3 + - - -
127B LEU* 3.0 43.1 + - + +
128B GLU 3.2 17.8 + - - -
129B ASN 3.9 1.8 - - - -
130B ASP 3.1 20.1 + - - +
131B ALA* 3.6 31.9 - - - +
132B HIS 3.1 0.2 - - - -
133B LYS* 1.3 75.9 - - - +
135B ALA* 1.3 59.8 + - - +
137B TYR 3.3 0.2 + - - -
138B LEU* 2.8 30.5 + - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 5.0 2.9 - - - +
131B ALA 3.0 13.6 + - - +
132B HIS* 3.2 11.9 + - - +
134B ARG* 1.3 76.5 - - - +
136B VAL* 1.3 61.6 + - - +
138B LEU* 3.5 22.1 + - - +
139B VAL* 3.5 13.7 + - - +
172B LEU* 4.8 2.5 - - - +
174B PRO* 4.1 20.1 - - + +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.4 12.6 - - + -
81B LEU* 3.9 18.5 - - + +
122B PRO* 3.5 28.0 - - + +
132B HIS* 3.1 40.8 + - + +
133B LYS* 3.8 5.8 - - - +
135B ALA* 1.3 74.8 - - - +
137B TYR* 1.3 65.3 + - - +
139B VAL* 3.2 20.1 + - - +
140B GLN* 3.4 9.9 + - - +
174B PRO* 4.3 14.8 - - + -
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A HIS* 2.8 31.3 + + - -
153A HIS* 4.8 2.1 + - - -
155A ASP* 4.7 0.9 + - - -
157A LEU* 4.2 16.2 - - + +
165A MET* 4.0 10.3 - - + -
121B ILE* 4.2 14.7 - - + +
122B PRO* 3.6 35.7 - - + -
123B ASP 4.6 3.6 - - - +
124B THR* 3.6 22.7 - - + +
127B LEU* 3.9 24.5 - - + -
133B LYS 2.9 18.7 + - - +
134B ARG 3.9 3.1 - - - +
136B VAL* 1.3 75.6 - - - +
138B LEU* 1.3 61.0 + - - +
140B GLN* 3.1 14.3 + - + +
141B LEU* 2.9 52.4 + - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 3.9 13.9 - - + -
165A MET* 3.6 9.6 - - + +
168A THR* 4.2 16.8 - - + -
169A ILE* 3.7 32.3 - - + -
172A LEU* 3.9 30.7 - - + -
134B ARG 2.8 17.7 + - - +
135B ALA* 3.5 10.5 - - - +
136B VAL 3.2 0.4 - - - -
137B TYR* 1.3 75.4 - - - +
139B VAL* 1.3 63.2 + - - +
141B LEU* 3.3 4.2 + - + +
142B ALA* 3.0 22.0 + - - +
172B LEU* 4.1 24.7 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.0 11.7 - - + -
85B VAL* 3.5 26.5 - - + -
135B ALA 3.6 14.8 - - - +
136B VAL 3.2 9.1 + - - +
138B LEU* 1.3 77.4 - - - +
140B GLN* 1.3 62.6 + - - +
142B ALA* 3.2 3.2 + - - +
143B ALA* 3.0 21.8 + - - +
169B ILE* 3.8 13.2 - - + +
172B LEU* 3.7 41.7 - - + +
173B ILE* 3.9 20.6 - - + +
174B PRO* 4.6 0.9 - - + -
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A HIS* 3.7 4.3 - - - +
81B LEU* 4.5 5.0 - - + +
84B VAL* 3.5 12.1 - - - +
85B VAL* 5.7 0.4 - - - -
88B LEU* 3.6 13.3 - - - +
121B ILE* 3.3 40.9 - - + +
122B PRO* 3.2 34.7 - - + +
136B VAL 3.4 2.4 + - - -
137B TYR* 3.1 21.7 + - + +
139B VAL* 1.3 80.6 - - - +
141B LEU* 1.3 57.0 + - - +
143B ALA* 3.3 4.4 + - - +
144B ASP* 2.9 65.5 + - - +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU 3.5 1.4 - - - +
142A ALA* 3.7 16.6 - - + +
145A GLY* 3.4 32.6 - - - +
146A LEU* 3.9 16.4 - - + +
149A HIS* 4.5 10.3 - - + -
165A MET* 3.8 41.3 - - + -
169A ILE* 4.3 13.9 - - + -
137B TYR* 2.9 33.8 + - + +
138B LEU* 3.3 7.4 + - - +
140B GLN* 1.3 75.2 - - - +
142B ALA* 1.3 62.8 + - - +
144B ASP* 3.2 7.9 + - - +
145B GLY 3.0 18.4 + - - -
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Residues in contact with ALA 142 (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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138A LEU* 3.9 17.7 - - + +
141A LEU* 3.7 5.2 - - + +
142A ALA* 3.8 22.3 - - + +
138B LEU 3.0 15.8 + - - +
139B VAL* 3.2 5.6 + - - +
141B LEU* 1.3 76.2 - - - +
143B ALA* 1.3 58.1 + - - +
145B GLY* 3.1 2.4 + - - -
146B LEU 2.9 23.7 + - - -
169B ILE* 3.6 30.1 - - + +
172B LEU* 4.8 2.0 - - + -
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Residues in contact with ALA 143 (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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84B VAL* 5.5 0.2 - - + -
85B VAL* 4.1 30.5 - - + +
88B LEU* 3.7 26.4 - - + +
139B VAL 3.0 16.6 + - - +
140B GLN* 3.5 7.0 - - - +
142B ALA* 1.3 76.4 - - - +
144B ASP* 1.3 58.9 + - - +
146B LEU* 3.2 5.7 + - - +
147B PHE* 3.0 27.0 + - - +
169B ILE* 3.9 9.8 - - + +
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY* 4.0 11.8 - - - +
152A ILE* 3.6 20.3 - - + +
153A HIS* 2.7 34.4 + - - -
88B LEU* 3.4 10.9 - - - +
140B GLN* 2.9 40.7 + - - +
141B LEU* 3.2 15.9 + - - +
143B ALA* 1.3 76.7 - - - +
145B GLY* 1.3 62.7 - - - +
147B PHE* 3.2 9.0 + - - +
148B VAL* 3.1 27.4 + - - +
1002B MBT 4.6 1.0 - - - -
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.4 29.6 - - - +
144A ASP* 4.1 10.5 - - - +
145A GLY* 4.0 7.4 - - - -
141B LEU 3.0 11.5 + - - -
142B ALA 3.1 1.9 + - - -
144B ASP* 1.3 77.3 - - - +
146B LEU* 1.3 56.5 + - - +
148B VAL* 3.7 4.4 - - - +
149B HIS* 2.9 31.4 + - - +
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Residues in contact with LEU 146 (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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141A LEU* 3.9 12.2 - - + +
85B VAL* 5.9 0.4 - - + +
88B LEU 4.5 0.9 - - - +
89B ALA* 3.9 22.7 - - + +
142B ALA 2.9 12.4 + - - +
143B ALA* 3.2 8.3 + - - +
145B GLY* 1.3 75.8 - - - +
147B PHE* 1.3 63.7 + - - +
148B VAL 3.3 0.5 + - - -
149B HIS* 3.4 10.8 + - - +
157B LEU* 3.6 31.4 - - + -
162B ARG* 3.0 44.4 + - + +
165B MET* 4.3 11.2 - - + -
166B LEU* 3.9 29.6 - - + +
169B ILE* 4.0 16.8 - - + -
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Residues in contact with PHE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 4.5 10.1 - - + -
88B LEU* 3.2 38.3 + - + +
90B GLU 3.5 18.4 - - - -
91B ASN* 3.5 7.3 + - - -
92B VAL* 3.0 68.4 + - + +
96B GLU* 4.3 3.4 - - - -
100B LEU* 4.4 8.7 - - + -
143B ALA 3.0 11.1 + - - +
144B ASP 3.3 9.0 - - - +
146B LEU* 1.3 77.7 - - - +
148B VAL* 1.3 68.1 + - + +
1002B MBT 3.3 54.7 - + - -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 6.6 0.2 - - + -
144A ASP 5.0 0.2 - - - +
148A VAL* 3.9 23.1 - - + -
152A ILE* 4.0 27.1 - - + -
92B VAL* 4.4 13.0 - - + -
97B LEU* 4.7 7.4 - - + -
144B ASP 3.1 16.5 + - - +
145B GLY* 3.7 8.1 - - - +
147B PHE* 1.3 86.3 - - + +
149B HIS* 1.3 68.4 + - - +
150B ASP 3.3 2.5 - - - -
151B TYR* 2.9 23.4 + - + +
152B ILE* 3.4 31.3 + - + -
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Residues in contact with HIS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR* 5.5 0.2 - - + -
137A TYR* 2.6 42.8 + + - -
141A LEU* 4.0 7.9 - - + -
145B GLY 2.9 16.8 + - - +
146B LEU* 3.4 15.5 + - - +
147B PHE 3.5 0.4 + - - -
148B VAL* 1.3 75.8 - - - +
150B ASP* 1.3 78.1 + - - +
151B TYR 3.0 0.7 + - - -
152B ILE* 3.2 3.5 + - - -
153B HIS* 3.0 62.7 + + + +
155B ASP* 3.2 27.1 - - + -
157B LEU* 3.4 24.8 - - + +
162B ARG* 4.3 3.1 - - - +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 5.6 5.4 - - - +
91B ASN* 3.5 27.5 - - - +
148B VAL 3.1 1.4 + - - -
149B HIS* 1.3 96.3 + - - +
151B TYR* 1.3 61.8 + - + +
153B HIS 3.5 13.7 - - - +
156B VAL* 3.5 33.5 - - + +
157B LEU 3.2 16.7 + - - +
162B ARG* 3.2 20.0 + - - -
2001B GOL 5.5 0.5 + - - -
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Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 5.8 0.4 - - + -
100A LEU 3.5 19.4 - - - +
101A ILE* 4.0 31.9 - - + +
104A PRO* 6.0 1.3 - - - +
91B ASN* 3.3 26.0 + - - -
92B VAL* 2.7 40.2 + - + -
93B SER* 4.0 0.2 - - - -
94B ARG* 3.3 32.1 + - + +
97B LEU* 3.5 31.0 - - + -
148B VAL* 2.9 14.0 + - + +
150B ASP* 1.3 81.2 - - + +
152B ILE* 1.3 64.7 + - + +
153B HIS 3.6 0.9 - - - -
2001B GOL 3.0 13.8 + - - -
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Residues in contact with ILE 152 (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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97A LEU* 3.9 27.8 - - + -
100A LEU* 4.0 15.7 - - + -
117A ASN* 4.9 0.5 - - - +
144A ASP* 3.7 38.1 - - + +
147A PHE* 4.6 8.5 - - + -
148A VAL* 4.2 14.4 - - + -
1001A MBT 3.7 16.7 - - - -
148B VAL* 3.4 28.7 + - + +
149B HIS* 3.9 4.5 - - - +
151B TYR* 1.3 81.7 - - + +
153B HIS* 1.3 69.9 + - + +
2001B GOL 2.8 26.9 + - - -
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Residues in contact with HIS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 4.6 5.5 + - - -
121A ILE* 3.6 33.2 - - + +
137A TYR* 3.9 8.4 + - - +
140A GLN* 3.9 16.9 - - + +
144A ASP* 2.6 31.6 + - - -
1001A MBT 5.9 3.6 - - - -
149B HIS* 3.0 51.5 + + + +
150B ASP* 3.5 18.9 - - - +
151B TYR 4.5 0.2 - - - -
152B ILE* 1.3 90.4 + - + +
154B ASP* 1.3 58.6 + - - +
155B ASP* 3.3 8.8 + - + +
156B VAL* 6.0 0.3 - - - +
2001B GOL 3.9 9.5 + - - -
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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