Contacts of the helix formed by residues 137 - 171 (chain B) in PDB entry 4DAJ
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 ASN 137 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 3.9 0.8 + - - +
136B GLY* 1.3 70.4 - - - -
138B LEU* 1.3 73.7 + - - +
139B ALA 3.2 1.6 - - - -
140B CYS* 2.7 36.3 + - - +
141B ASP* 3.3 7.3 + - - +
213B ARG* 3.1 42.3 - - - +
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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
----------------------------------------------------------
135B LEU 5.1 0.6 + - - -
137B ASN* 1.3 86.4 + - - +
139B ALA* 1.3 59.0 + - + +
141B ASP* 2.7 37.7 + - + +
142B LEU* 2.9 41.0 + - + -
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Residues in contact with ALA 139 (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 LEU* 5.3 1.6 - - - +
133B TRP* 3.4 3.2 - - - -
135B LEU* 3.4 54.6 + - + +
137B ASN 3.2 0.6 - - - -
138B LEU* 1.3 84.5 - - + +
140B CYS* 1.3 56.9 + - - +
142B LEU* 3.5 8.1 + - - +
143B TRP* 2.9 31.2 + - - +
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Residues in contact with CYS 140 (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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133B TRP* 3.1 30.5 - - + +
136B GLY 3.7 2.7 - - - +
137B ASN* 2.7 21.1 + - - +
139B ALA* 1.3 72.0 - - - +
141B ASP* 1.3 59.1 + - - -
143B TRP* 3.9 0.4 - - - +
144B LEU* 3.1 36.5 + - - +
213B ARG* 5.5 3.8 - - - +
215B VAL* 5.4 4.9 - - - -
219B GLU 5.1 0.2 - - - -
220B CYS* 2.0 53.2 - - + -
221B PHE 4.2 2.9 - - - -
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Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN* 3.6 7.7 - - - +
138B LEU* 2.7 31.8 + - + +
140B CYS* 1.3 75.7 - - - +
142B LEU* 1.3 54.8 + - + +
143B TRP 3.3 0.2 - - - -
144B LEU* 3.8 6.1 - - - +
145B SER* 2.7 40.3 + - - -
203B ILE* 4.1 9.7 - - + +
204B LEU* 3.6 25.5 - - + +
207B GLN* 3.7 22.2 + - - +
213B ARG* 3.7 15.2 + - - -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 2.9 37.1 + - + +
139B ALA* 3.8 9.2 - - - +
141B ASP* 1.3 76.4 - - + +
143B TRP* 1.3 58.0 + - - +
145B SER* 3.1 6.8 + - - +
146B ILE* 2.9 49.0 + - + +
204B LEU* 4.9 12.1 - - + -
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 4.1 6.5 - - + -
120B SER* 3.3 32.8 + - - +
123B LEU* 3.7 34.6 - - + +
124B PHE* 3.7 46.7 - + + -
127B TYR* 5.6 7.4 - + + -
133B TRP* 4.2 13.5 - + + -
139B ALA 2.9 18.8 + - - +
140B CYS 3.9 1.3 - - - +
142B LEU* 1.3 77.2 - - - +
144B LEU* 1.3 94.4 + - + +
146B ILE* 3.8 4.7 - - - +
147B ASP* 3.0 38.6 + - - +
220B CYS* 4.0 25.8 - - + -
529B TYR* 5.0 7.4 - + - -
533B TYR* 4.3 0.4 - - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B CYS* 3.1 25.1 + - - +
141B ASP* 3.4 5.6 + - - +
143B TRP* 1.3 106.9 - - + +
145B SER* 1.3 57.0 + - - +
147B ASP* 3.6 2.2 - - + +
148B TYR* 3.0 53.5 + - + +
203B ILE* 4.0 15.5 - - + -
220B CYS* 4.2 0.4 - - - -
221B PHE* 3.2 46.2 - - - +
222B ILE* 3.7 13.7 - - + +
529B TYR* 4.8 4.3 - - - +
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP 2.7 24.9 + - - -
142B LEU* 3.1 14.0 + - - +
144B LEU* 1.3 74.1 - - - +
146B ILE* 1.3 59.0 + - - +
149B VAL* 2.9 37.4 + - - +
200B ALA* 4.4 16.8 - - - -
203B ILE* 3.4 28.4 - - - +
204B LEU* 4.3 11.7 - - - +
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Residues in contact with ILE 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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115B ILE* 4.6 23.6 - - + +
116B ILE* 6.2 0.2 - - - -
119B ILE* 4.2 33.7 - - + -
120B SER* 4.4 9.2 - - - +
142B LEU* 2.9 38.5 + - + +
143B TRP* 3.8 4.5 - - - +
145B SER* 1.3 76.5 + - - +
147B ASP* 1.3 68.2 + - - +
149B VAL* 4.1 2.3 - - - +
150B ALA* 3.0 27.5 + - + +
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.9 8.5 - - - +
120B SER* 3.5 21.2 + - - +
143B TRP* 3.0 25.6 + - + +
144B LEU* 3.6 5.4 - - + +
146B ILE* 1.3 78.4 - - - +
148B TYR* 1.3 62.6 + - + +
150B ALA* 3.4 4.3 - - - +
151B SER* 2.9 25.5 + - - -
529B TYR* 3.5 7.1 + - - -
533B TYR* 2.5 33.3 + - - -
2000B 0HK 2.8 32.0 - - - -
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.0 33.6 + - + +
147B ASP* 1.3 77.8 - - + +
149B VAL* 1.3 66.7 + - - +
151B SER* 2.8 19.4 + - - -
152B ASN* 2.9 15.4 + - - +
199B TRP* 3.8 41.5 - + + -
203B ILE* 4.2 6.7 - - + -
222B ILE* 3.6 28.9 - - + +
225B LEU* 4.8 5.9 - - + +
506B TYR* 4.5 7.8 + - - -
529B TYR* 3.3 23.5 + - - -
2000B 0HK 2.7 58.0 + + + +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER 2.9 33.5 + - - +
146B ILE* 4.2 2.9 - - - +
148B TYR* 1.3 71.8 - - - +
150B ALA* 1.3 58.0 + - - +
153B ALA* 2.9 32.7 + - - +
192B TRP* 4.6 17.3 - - + +
195B SER* 3.9 3.8 - - - -
196B PHE* 3.7 43.1 - - + +
199B TRP* 3.8 27.4 - - + -
200B ALA* 4.1 10.1 - - + +
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Residues in contact with ALA 150 (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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112B ALA* 4.0 12.7 - - - +
115B ILE* 4.0 27.8 - - + -
116B ILE* 4.8 10.3 - - + +
146B ILE* 3.0 21.1 + - + +
147B ASP* 3.4 6.1 - - - +
149B VAL* 1.3 78.9 - - - +
151B SER* 1.3 56.8 + - - +
153B ALA* 3.5 5.5 - - - +
154B SER* 2.9 27.1 + - - -
192B TRP* 4.8 9.0 - - + -
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Residues in contact with SER 151 (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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116B ILE* 5.4 6.9 - - - +
147B ASP* 2.9 14.3 + - - -
148B TYR* 2.8 18.5 + - - -
150B ALA* 1.3 73.1 - - - +
152B ASN* 1.3 58.2 + - - +
154B SER* 2.8 28.3 + - - -
155B VAL* 2.9 12.1 + - - +
503B TRP* 3.5 17.5 - - - -
2000B 0HK 3.1 41.6 - - - +
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Residues in contact with ASN 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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148B TYR 2.9 9.0 + - - +
149B VAL 4.4 0.2 - - - +
151B SER* 1.3 71.9 + - - +
153B ALA* 1.3 67.0 + - - +
154B SER 2.9 2.0 + - - -
155B VAL* 3.1 15.0 + - - +
156B MET* 2.9 37.6 + - - +
195B SER* 2.8 30.7 + - - +
198B LEU* 5.0 7.7 - - - +
199B TRP* 3.2 31.4 + - + +
238B ALA* 3.7 14.7 - - - +
2000B 0HK 3.3 23.3 - - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 5.5 0.9 - - - -
149B VAL 2.9 23.3 + - - +
150B ALA* 3.5 5.4 - - - +
152B ASN* 1.3 74.7 - - - +
154B SER* 1.3 57.9 + - - +
156B MET* 3.9 3.8 - - - +
157B ASN* 2.9 30.8 + - - +
191B ALA* 5.3 2.3 - - - +
192B TRP* 3.9 42.3 + - + +
195B SER* 3.1 19.4 + - - +
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.6 17.8 - - - +
112B ALA* 4.3 12.2 - - - +
113B ASP* 4.5 10.3 + - - -
150B ALA 2.9 13.3 + - - -
151B SER* 2.8 19.3 + - - -
153B ALA* 1.3 75.0 - - - +
155B VAL* 1.3 65.5 + - - -
157B ASN* 2.8 25.7 + - - +
158B LEU* 3.0 12.9 + - - +
499B PHE* 5.6 1.0 - - - -
503B TRP* 5.1 6.2 - - - -
535B ASN* 5.1 5.9 + - - -
539B ASN* 5.4 1.4 + - - -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B SER 2.9 4.3 + - - +
152B ASN* 3.1 24.9 + - - +
154B SER* 1.3 73.5 - - - +
156B MET* 1.3 71.5 + - + +
158B LEU* 3.0 14.4 + - - +
159B LEU* 2.9 25.3 + - + +
238B ALA 3.8 24.0 - - - +
239B PHE* 5.3 0.2 - - + -
242B PRO* 4.9 11.4 - - + -
246B MET* 4.5 1.8 - - + +
499B PHE* 3.5 20.2 - - + -
503B TRP* 3.2 40.6 - - + -
2000B 0HK 4.6 0.2 - - - -
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Residues in contact with MET 156 (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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152B ASN* 2.9 34.7 + - - +
153B ALA* 3.9 4.7 - - - +
155B VAL* 1.3 85.3 - - + +
157B ASN* 1.3 64.2 + - - +
159B LEU* 3.1 18.1 + - + +
160B VAL* 2.9 30.9 + - + +
191B ALA* 4.0 24.2 - - + +
194B ILE* 3.9 42.2 - - + -
195B SER* 3.5 9.6 - - - -
198B LEU* 5.3 2.9 - - - -
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Residues in contact with ASN 157 (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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105B PHE* 3.0 34.4 + - - +
108B SER* 2.7 26.0 + - - -
109B LEU* 3.2 23.9 - - + +
153B ALA 2.9 14.7 + - - +
154B SER* 2.8 17.6 + - - +
156B MET* 1.3 76.6 - - - +
158B LEU* 1.3 60.5 + - - +
160B VAL* 3.1 8.6 + - - +
161B ILE* 3.0 26.7 + - - +
188B ILE* 5.0 6.1 - - - +
191B ALA* 5.3 5.5 - - - +
192B TRP* 4.2 6.2 + - - -
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Residues in contact with LEU 158 (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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109B LEU* 3.6 34.1 - - + -
154B SER* 3.0 15.9 + - - +
155B VAL* 3.0 8.7 + - - +
157B ASN* 1.3 74.8 - - - +
159B LEU* 1.3 63.7 + - - +
161B ILE* 2.9 11.3 + - + +
162B SER* 2.9 23.7 + - - -
246B MET* 3.5 14.6 - - - -
495B ILE* 3.7 20.2 - - + +
496B LEU* 5.1 6.5 - - + +
499B PHE* 3.5 51.6 - - + -
535B ASN* 5.7 0.4 - - - +
539B ASN* 5.9 1.6 - - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 2.9 17.9 + - + +
156B MET* 3.1 22.0 + - + +
158B LEU* 1.3 74.9 - - - +
160B VAL* 1.3 64.7 + - + +
162B SER* 3.0 5.0 + - - -
163B PHE* 2.9 37.1 + - + -
241B MET* 5.7 2.7 - - - -
242B PRO* 3.4 43.1 - - + +
245B ILE* 4.2 15.3 - - + -
246B MET* 3.2 29.1 - - + -
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Residues in contact with VAL 160 (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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105B PHE* 4.0 26.7 - - + -
156B MET* 2.9 21.7 + - + +
157B ASN* 3.5 10.8 - - - +
159B LEU* 1.3 73.6 - - + +
161B ILE* 1.3 57.8 + - - +
163B PHE* 4.3 5.7 - - - +
164B ASP* 2.9 30.2 + - + +
187B MET* 3.9 38.6 - - + +
188B ILE* 6.0 1.8 - - + +
191B ALA* 5.0 13.9 - - + -
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Residues in contact with ILE 161 (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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105B PHE* 3.6 36.1 - - + -
106B LEU* 4.4 11.2 - - + -
109B LEU* 3.5 31.4 - - + -
157B ASN* 3.2 15.5 - - - +
158B LEU* 2.9 14.5 + - + +
160B VAL* 1.3 75.4 - - - +
162B SER* 1.3 66.9 + - - +
164B ASP* 3.0 7.0 + - + +
165B ARG* 3.0 49.2 + - - +
492B LEU* 5.2 13.7 - - + -
495B ILE* 5.9 0.7 - - + -
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU 2.9 8.3 + - - -
159B LEU 3.4 5.4 - - - -
161B ILE* 1.3 78.1 - - - +
163B PHE* 1.3 63.7 + - - +
165B ARG 3.4 0.3 + - - -
166B TYR* 3.0 23.6 + - - +
246B MET* 3.1 39.6 + - - +
249B LEU* 4.0 19.7 - - - -
250B TYR* 5.8 0.4 - - - +
253B ILE* 3.5 15.0 - - - +
492B LEU* 5.0 11.3 - - - +
496B LEU* 5.0 3.6 - - - +
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Residues in contact with PHE 163 (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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229A THR* 3.2 27.6 - - - -
230A ILE* 4.2 23.8 - - + -
159B LEU* 2.9 35.4 + - + +
160B VAL* 4.3 4.9 - - - +
162B SER* 1.3 71.3 - - - +
164B ASP* 1.3 65.8 + - - +
166B TYR* 4.4 4.9 - + - -
167B PHE* 2.9 59.7 + + + +
245B ILE* 3.8 27.1 - - + -
249B LEU* 3.2 25.4 - - + -
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Residues in contact with ASP 164 (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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101B VAL* 3.8 2.4 - - - +
102B ASN* 4.0 2.6 - - - +
105B PHE* 3.1 27.3 - - + -
160B VAL* 2.9 23.4 + - + +
161B ILE* 3.0 6.2 + - - +
163B PHE* 1.3 78.6 - - - +
165B ARG* 1.3 74.1 + - - +
168B SER* 2.8 26.0 + - - -
175B TYR* 3.0 29.9 + - - +
179B ARG* 2.8 37.1 + - - -
187B MET* 6.4 0.4 - - - -
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Residues in contact with ARG 165 (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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102B ASN* 3.1 46.1 + - - +
105B PHE* 5.8 0.2 - - - -
106B LEU* 5.9 4.6 - - - +
161B ILE* 3.0 31.6 + - - +
162B SER* 4.1 2.9 - - - +
164B ASP* 1.3 89.0 + - - +
166B TYR* 1.3 57.3 + - - +
168B SER* 3.2 7.0 - - - -
169B ILE* 2.9 38.5 + - + +
179B ARG* 5.3 2.7 - - - +
253B ILE* 4.3 18.6 - - + -
489B ALA 5.7 2.2 - - - +
490B GLN* 3.4 47.3 + - - +
491B THR* 5.3 1.6 - - - +
492B LEU* 4.7 23.4 - - + +
1001B MET* 6.1 2.9 - - + -
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Residues in contact with TYR 166 (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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227A GLU* 4.0 26.0 + - - -
229A THR* 5.4 4.1 - - + +
162B SER 3.0 17.9 + - - +
163B PHE* 4.0 8.3 - + - +
165B ARG* 1.3 77.7 - - - +
167B PHE* 1.3 67.8 + + - +
169B ILE* 3.3 8.1 + - + +
170B THR* 2.9 60.1 + - + +
249B LEU* 3.9 28.5 - - + -
252B ARG* 3.6 32.7 - - + +
253B ILE* 3.9 20.6 - - + +
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLU* 3.5 38.8 - - + -
230A ILE* 5.8 2.7 - - + -
163B PHE* 2.9 44.9 + + + +
164B ASP 3.7 1.6 - - - +
166B TYR* 1.3 81.1 - + - +
168B SER* 1.3 62.1 + - - +
170B THR* 3.7 11.4 - - - -
171B ARG* 2.8 39.2 + - + +
175B TYR* 3.7 35.7 - + + -
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASP 2.8 18.2 + - - -
165B ARG* 3.2 12.1 - - - -
167B PHE* 1.3 77.6 - - - +
169B ILE* 1.3 67.6 + - - +
172B PRO* 3.9 6.2 - - - +
175B TYR* 3.6 11.5 - - - -
176B ARG* 3.0 40.9 - - - +
179B ARG* 2.7 32.2 + - - -
1001B MET* 4.6 6.7 - - - -
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ARG* 2.9 36.1 + - + +
166B TYR* 3.6 11.2 - - + +
167B PHE 3.2 0.2 - - - -
168B SER* 1.3 80.0 - - - +
170B THR* 1.3 73.0 + - + +
172B PRO* 3.9 10.4 - - - +
252B ARG 5.8 1.6 - - - +
253B ILE* 4.7 17.5 - - + -
256B GLU* 3.9 26.7 - - + +
257B THR* 4.8 5.8 - - + -
259B LYS* 4.8 25.2 - - + +
1001B MET* 3.3 41.8 - - + +
1068B ASN* 4.6 5.3 - - - +
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 4.7 5.0 + - - +
166B TYR* 2.9 61.1 + - + +
167B PHE* 3.7 13.0 - - - -
169B ILE* 1.3 79.3 - - + +
171B ARG* 1.3 62.2 + - - +
172B PRO* 3.0 11.1 - - - +
1064B GLU* 4.3 3.1 - - - +
1068B ASN* 3.3 25.2 + - - +
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 2.8 24.2 + - + +
170B THR* 1.3 77.6 + - - +
172B PRO* 1.3 57.8 - - - +
174B THR* 4.1 11.4 - - + -
175B TYR* 2.8 35.0 + - + +
176B ARG 3.3 1.0 + - - -
1064B GLU* 3.2 22.2 - - - +
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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