Contacts of the helix formed by residues 126 - 160 (chain A) in PDB entry 1Z0X
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 126 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 4.1 3.4 - - - +
124A GLY 3.5 4.8 + - - -
125A PHE* 1.3 77.7 - - - +
127A PRO* 1.3 75.4 - - - +
128A GLU* 4.1 9.6 + - - +
129A MSE 3.2 25.3 + - - +
130A THR* 2.8 21.5 + - - -
215A ASN* 4.1 8.0 + - - +
218A SER* 3.6 26.1 + - - -
219A SER* 4.5 2.1 - - - +
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Residues in contact with PRO 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MSE 5.6 0.3 - - - +
121A ARG* 3.0 41.1 - - - +
126A SER* 1.3 90.0 - - - +
128A GLU* 1.3 60.9 + - - +
130A THR* 3.5 2.9 + - - +
131A HIS* 3.2 22.9 + - - +
186B GLU* 3.9 16.1 - - + +
190B PHE* 3.8 18.8 - - + -
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 3.3 8.7 - - - +
127A PRO* 1.3 79.1 - - - +
129A MSE 1.3 65.6 + - + +
131A HIS* 3.8 4.3 - - - +
132A LEU* 3.0 30.6 + - - +
218A SER* 5.7 3.9 + - - -
190B PHE* 3.4 29.4 - - + -
202B GLN* 4.6 17.8 + - - +
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Residues in contact with MSE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 5.0 0.2 - - - -
125A PHE* 4.4 5.2 - - + -
126A SER* 3.2 21.3 + - - +
128A GLU* 1.3 80.2 - - + +
130A THR* 1.3 62.2 + - - +
132A LEU* 3.3 32.3 - - + -
133A ALA* 2.8 37.2 + - + +
207A TYR* 3.5 17.3 - - - +
211A LEU* 3.8 21.8 - - + -
214A ASP 4.8 1.3 - - - +
215A ASN* 2.7 40.2 - - + +
202B GLN* 3.4 22.7 - - - -
206B THR* 4.2 10.5 - - - +
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MSE 3.3 49.8 - - + +
120A LEU* 3.5 26.6 - - + +
121A ARG* 3.6 11.2 - - + +
125A PHE* 3.2 13.5 + - - +
126A SER 2.8 21.6 + - - -
127A PRO* 3.7 5.2 - - - -
129A MSE 1.3 77.6 - - - +
131A HIS* 1.3 57.3 + - - +
133A ALA 3.4 0.3 + - - -
134A VAL* 2.9 36.6 + - - +
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Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MSE 3.6 14.3 - - + +
127A PRO 3.2 14.5 + - - +
128A GLU 3.8 5.2 - - - +
130A THR* 1.3 78.2 - - - +
132A LEU* 1.3 66.4 + - + +
134A VAL 4.0 0.2 - - - -
135A THR* 2.9 52.7 + - + +
187B SER* 3.0 39.5 + - - -
190B PHE* 3.9 39.2 + + + +
194B ILE* 5.3 5.1 - - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.0 20.6 + - - +
129A MSE 3.3 28.3 - - + -
131A HIS* 1.3 84.7 - - + +
133A ALA* 1.3 58.0 + - - +
135A THR* 3.4 6.0 + - - +
136A SER* 2.8 50.7 + - - +
207A TYR* 4.1 2.0 - - - +
199B ALA* 3.7 29.8 - - + +
202B GLN* 3.2 41.5 - - + +
203B ALA* 4.2 2.2 - - + -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 5.5 0.2 - - + -
120A LEU* 3.8 15.5 - - + -
129A MSE 2.8 22.0 + - + +
130A THR 3.8 3.1 - - - +
132A LEU* 1.3 76.0 - - - +
134A VAL* 1.3 64.4 + - - +
136A SER* 3.3 1.0 + - - -
137A LEU* 3.0 33.9 + - + +
207A TYR* 3.5 15.7 - - + +
211A LEU* 3.9 24.9 - - + -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 5.0 5.2 - - + -
82A MSE 5.4 0.5 - - - +
113A LEU* 4.4 11.9 - - + -
116A MSE 4.3 33.7 - - + +
117A MSE 3.8 41.1 - - + +
120A LEU* 3.8 15.9 - - + -
130A THR 2.9 22.5 + - - +
131A HIS 4.2 1.6 - - - +
133A ALA* 1.3 74.9 - - - +
135A THR* 1.3 64.6 + - + +
137A LEU* 3.6 8.7 + - - +
138A GLN* 3.2 24.5 + - + +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MSE 5.5 2.7 - - + -
131A HIS* 2.9 48.2 + - + +
132A LEU* 3.4 10.6 + - - +
134A VAL* 1.3 79.3 - - + +
136A SER* 1.3 62.5 + - - +
138A GLN* 3.3 7.2 + - - +
139A HIS* 2.9 51.6 + - - -
147B ASP* 5.5 0.9 - - - -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 2.8 41.3 + - - +
133A ALA 3.3 1.5 + - - -
135A THR* 1.3 74.2 + - - +
137A LEU* 1.3 61.3 + - - +
139A HIS* 3.6 12.5 + - - +
140A LEU* 3.0 27.7 + - - +
207A TYR* 3.7 24.1 - - - -
140B LEU* 3.6 14.1 - - - +
203B ALA* 3.3 12.6 - - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.4 35.0 - - + -
82A MSE 3.8 31.1 - - + +
116A MSE 6.4 0.2 - - - -
133A ALA* 3.0 23.6 + - + +
134A VAL* 3.9 6.3 - - - +
136A SER* 1.3 74.3 - - - +
138A GLN* 1.3 67.0 + - - +
140A LEU* 3.3 10.1 + - + +
141A LEU* 3.1 22.9 + - - +
200A PHE* 4.6 4.2 - - - -
204A VAL* 3.9 30.3 - - + -
207A TYR* 3.9 31.4 - - + -
208A LEU* 4.4 4.3 - - + -
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Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MSE 4.0 9.6 - - - +
85A TYR* 3.7 28.5 - - - -
89A TYR* 4.0 9.9 + - - -
109A ARG* 3.5 20.5 + - - +
113A LEU* 5.1 3.4 - - + -
116A MSE 3.8 12.1 - - - +
134A VAL* 3.2 21.8 + - + +
135A THR* 3.7 10.1 - - - +
136A SER 3.3 0.2 - - - -
137A LEU* 1.3 78.0 - - - +
139A HIS* 1.3 56.8 + - + +
141A LEU* 3.3 7.5 + - - +
142A PHE* 2.8 73.8 + - + -
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 2.9 46.8 + - - +
136A SER* 3.6 11.9 + - - +
137A LEU 3.2 0.2 - - - -
138A GLN* 1.3 77.0 - - + +
140A LEU* 1.3 64.1 + - - +
142A PHE* 4.3 5.4 - + - -
143A GLY 3.1 18.7 + - - -
139B HIS 3.3 10.1 - - - +
140B LEU* 3.8 19.9 - - + +
143B GLY* 3.4 16.6 - - - -
144B MSE 3.2 37.4 - - + +
147B ASP* 2.7 31.5 + - - +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER 3.0 14.1 + - - +
137A LEU* 3.4 16.6 - - + +
138A GLN 3.3 0.2 - - - -
139A HIS* 1.3 77.6 - - - +
141A LEU* 1.3 56.8 + - - +
144A MSE 2.9 31.3 + - + +
200A PHE* 3.9 11.4 - - + -
203A ALA* 3.9 40.6 - - + +
204A VAL* 4.2 14.4 - - + +
207A TYR* 5.3 6.1 - - + -
136B SER* 3.7 29.2 - - - +
139B HIS* 3.7 11.9 - - + +
140B LEU* 4.2 14.3 - - + +
207B TYR* 5.1 6.5 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MSE 5.5 3.6 - - - -
85A TYR* 3.9 22.4 - - + +
86A TYR* 3.7 26.9 - - + +
89A TYR* 3.4 31.6 - - + -
137A LEU 3.1 8.0 + - - +
138A GLN* 3.7 13.7 - - - +
140A LEU* 1.3 80.1 - - - +
142A PHE* 1.3 53.0 + - + +
144A MSE 3.2 3.6 + - + +
145A ILE* 2.8 69.9 + - + +
200A PHE* 3.6 27.8 - - + -
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Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.7 22.4 - + - -
96A VAL* 3.6 32.4 - - + +
99A GLU* 3.8 26.0 - - + -
100A ILE* 3.7 23.8 - - + -
109A ARG* 4.4 2.9 - - - -
138A GLN* 2.8 64.5 + - + +
139A HIS* 3.8 10.3 - + - +
141A LEU* 1.3 74.5 - - + +
143A GLY* 1.3 61.4 + - - +
145A ILE* 3.8 0.5 - - - -
146A MSE 3.0 31.8 + - + +
143B GLY* 4.2 14.6 - - - -
147B ASP* 4.4 9.9 - - - -
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS 3.1 8.5 + - - -
142A PHE* 1.3 79.5 - - - +
144A MSE 1.3 61.4 - - - +
146A MSE 3.3 18.3 - - - +
147A ASP* 2.9 28.4 + - - +
139B HIS* 3.6 26.0 - - - -
142B PHE* 4.0 6.8 - - - -
143B GLY* 3.9 2.2 - - - -
----------------------------------------------------------
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Residues in contact with MSE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 3.9 22.9 - - + -
140A LEU* 2.9 22.6 + - + +
141A LEU* 3.3 9.9 - - - +
143A GLY* 1.3 77.4 - - - +
145A ILE* 1.3 59.2 + - - +
147A ASP* 3.8 2.4 - - - +
148A ALA* 3.2 31.1 + - - +
194A ILE 4.4 5.4 - - - +
195A HIS* 4.1 22.9 - - - +
196A GLN 3.8 10.5 - - - +
199A ALA* 4.2 6.5 - - + -
200A PHE* 3.6 43.3 - - + +
139B HIS* 3.2 31.2 + - + +
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 4.8 1.3 - - + +
89A TYR* 3.1 47.3 - - + +
90A GLN* 4.0 18.2 - - - +
95A ALA* 6.3 0.9 - - + +
96A VAL* 3.8 19.1 - - + +
141A LEU* 2.8 45.9 + - + +
144A MSE 1.3 79.0 - - + +
146A MSE 1.3 57.2 + - - +
147A ASP 3.3 0.2 - - - -
148A ALA* 3.9 4.9 - - - +
149A THR* 2.7 45.5 + - - +
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Residues in contact with MSE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 3.9 22.4 - - + -
97A ALA* 5.6 3.4 - - + +
100A ILE* 4.9 4.5 - - + -
142A PHE* 3.0 16.7 + - + +
143A GLY* 3.3 32.8 - - - +
145A ILE* 1.3 74.1 - - - +
147A ASP* 1.3 66.5 + - - +
149A THR* 3.3 5.8 + - - -
150A GLU* 3.2 33.0 + - - +
100B ILE* 4.8 11.7 - - + -
142B PHE* 4.2 2.9 - - + +
143B GLY* 3.9 16.2 - - - +
146B MSE 3.2 44.6 - - + +
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Residues in contact with ASP 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY 2.9 19.4 + - - +
144A MSE 3.8 0.4 - - - +
146A MSE 1.3 79.1 - - - +
148A ALA* 1.3 62.0 + - - +
150A GLU* 3.5 3.6 + - - +
151A GLU* 3.1 28.7 + - - +
100B ILE* 4.7 16.8 - - - +
135B THR* 5.8 0.7 - - - -
139B HIS* 3.1 29.6 + - + +
142B PHE* 4.8 16.1 - - + -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A MSE 3.2 18.5 + - - +
145A ILE* 4.0 6.3 - - + +
147A ASP* 1.3 80.7 - - - +
149A THR* 1.3 60.2 - - - +
151A GLU* 3.1 9.6 - - - +
152A LYS* 3.1 24.7 + - - +
195A HIS* 4.8 24.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 4.8 25.8 - - + +
94A CYS* 6.2 3.4 - - - +
145A ILE* 2.7 31.6 + - - +
146A MSE 3.3 8.2 + - - -
148A ALA* 1.3 73.7 - - - +
150A GLU* 1.3 75.1 + - - +
152A LYS* 3.2 25.5 - - + +
153A GLN* 3.2 10.5 + - - +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO 5.2 4.9 - - - +
146A MSE 3.2 14.4 + - - +
147A ASP 4.0 3.1 - - - +
149A THR* 1.3 83.4 - - - +
151A GLU* 1.3 58.3 + - - +
153A GLN* 2.8 18.9 + - - +
154A LEU* 2.6 45.3 + - + +
100B ILE* 3.0 49.7 - - + +
101B GLN* 3.8 18.5 + - - +
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Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 3.1 18.6 + - - +
148A ALA* 3.1 15.9 - - - +
150A GLU* 1.3 78.4 - - - +
152A LYS* 1.3 58.3 + - - +
154A LEU* 3.2 11.3 + - - +
155A VAL* 2.8 46.9 + - + +
195A HIS* 6.3 3.4 - - + -
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 3.1 11.0 + - - +
149A THR* 3.2 24.0 - - + +
151A GLU* 1.3 79.3 - - - +
153A GLN* 1.3 67.4 + - + +
155A VAL* 3.7 10.2 - - - +
156A SER* 3.1 30.8 + - - -
----------------------------------------------------------
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 5.7 1.4 - - - -
22A PRO* 3.6 36.4 + - - +
23A THR* 5.1 8.0 + - - -
149A THR* 3.2 13.8 + - - +
150A GLU* 2.8 22.9 + - - +
152A LYS* 1.3 85.8 - - + +
154A LEU* 1.3 61.1 + - + +
156A SER* 3.2 6.3 + - - -
157A GLN* 2.9 56.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 2.6 30.8 + - + +
151A GLU* 3.7 10.1 - - - +
153A GLN* 1.3 70.1 - - + +
155A VAL* 1.3 66.8 + - + +
157A GLN* 3.3 20.6 + - - +
158A VAL* 2.9 32.2 + - + +
165A LEU* 3.9 25.5 - - + +
51B GLN* 4.9 4.5 - - - +
100B ILE 4.5 7.2 - - - +
101B GLN* 4.4 26.7 - - - +
102B THR 4.6 11.4 - - - +
103B VAL* 4.7 11.0 - - + -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 2.8 44.1 + - + +
152A LYS* 3.7 9.9 - - - +
153A GLN 3.2 0.2 - - - -
154A LEU* 1.3 77.7 - - + +
156A SER* 1.3 60.3 + - - +
158A VAL* 3.5 6.7 + - - +
159A LEU* 3.1 46.4 + - + +
----------------------------------------------------------
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LYS* 3.1 23.1 + - - -
153A GLN* 3.4 8.3 - - - -
155A VAL* 1.3 76.0 - - - +
157A GLN* 1.3 61.9 + - - +
159A LEU* 3.1 9.1 + - - +
160A ASN* 2.8 44.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 2.9 49.5 + - + +
154A LEU* 3.6 14.7 - - - +
156A SER* 1.3 78.0 - - - +
158A VAL* 1.3 63.9 + - - +
160A ASN* 3.5 9.1 + - - +
161A GLY 3.5 0.7 + - - -
162A ASP* 2.9 34.0 + - + +
165A LEU* 3.4 26.7 - - + +
51B GLN* 5.4 3.7 + - - +
----------------------------------------------------------
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 2.9 24.7 + - + +
155A VAL* 3.6 7.2 - - - +
156A SER 3.2 0.2 - - - -
157A GLN* 1.3 75.2 - - - +
159A LEU* 1.3 60.8 + - + +
161A GLY* 2.7 27.0 + - - -
162A ASP* 3.2 11.5 + - - +
165A LEU* 3.9 29.8 - - + +
166A LYS* 4.0 36.1 + - + -
169A VAL* 4.5 13.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.1 30.3 + - + +
156A SER* 3.1 10.2 + - - +
158A VAL* 1.3 86.7 - - + +
160A ASN* 1.3 61.0 + - - +
161A GLY* 2.8 6.2 + - - -
166A LYS* 5.8 0.3 + - - -
----------------------------------------------------------
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Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A SER* 2.8 42.1 + - - +
157A GLN* 3.5 5.6 + - - +
158A VAL 3.2 0.4 + - - -
159A LEU* 1.3 74.4 - - - +
161A GLY* 1.3 57.9 + - - +
162A ASP 3.8 0.9 - - - -
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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