Contacts of the helix formed by residues 129 - 165 (chain A) in PDB entry 4IE6
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 GLU 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 3.6 18.2 - - + +
128A THR* 1.3 86.5 + - - +
130A ALA* 1.3 70.2 + - - +
131A GLU 3.5 0.2 - - - -
132A ILE* 3.2 38.3 + - + +
133A ALA* 4.3 0.5 - - - +
391A LYS 5.3 2.6 + - - +
392A CYS 4.3 1.2 + - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 5.1 0.2 + - - -
128A THR 3.6 1.9 + - - -
129A GLU* 1.3 76.5 - - - +
131A GLU* 1.3 73.8 + - + +
132A ILE 3.3 0.2 + - - -
133A ALA* 3.6 10.0 + - - +
134A ALA* 3.9 6.9 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 3.4 23.5 - - + +
75A HIS* 2.6 41.5 + - - -
130A ALA* 1.3 82.7 + - + +
132A ILE* 1.3 64.9 + - - +
134A ALA* 2.9 12.7 + - + +
135A ALA* 2.8 22.0 + - - +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 4.5 2.2 - - + +
72A LEU* 4.4 18.6 - - + -
75A HIS* 3.9 18.6 - - + +
77A CYS* 3.6 28.3 - - - -
116A VAL* 5.2 2.0 - - + -
128A THR* 4.0 5.2 - - + +
129A GLU* 3.3 35.2 - - + +
130A ALA 3.2 1.2 - - - -
131A GLU* 1.3 77.4 + - - +
133A ALA* 1.3 64.2 + - - +
135A ALA* 3.1 5.1 + - - +
136A CYS* 3.0 31.0 + - - -
391A LYS 3.9 15.0 - - - +
392A CYS* 3.7 24.2 - - + +
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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
----------------------------------------------------------
119A PRO* 4.9 3.8 - - - +
128A THR* 3.2 23.5 + - + +
129A GLU 3.5 1.0 + - - +
130A ALA 4.0 7.9 - - - +
131A GLU 3.3 0.4 - - - -
132A ILE* 1.3 80.3 - - - +
134A ALA* 1.3 57.5 + - - +
136A CYS* 3.4 9.1 + - - +
137A GLU* 3.0 27.8 + - - +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA 3.9 3.3 + - - +
131A GLU* 2.9 19.7 + - + +
133A ALA* 1.3 76.9 - - - +
135A ALA* 1.3 58.4 + - - +
137A GLU* 3.5 19.4 - - - +
138A THR* 2.9 29.6 + - - -
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 3.8 25.6 - - + +
71A THR* 4.6 5.2 - - + -
72A LEU* 3.7 32.3 - - + -
131A GLU 2.8 11.0 + - - +
132A ILE* 3.1 8.7 + - - +
134A ALA* 1.3 73.4 - - - +
136A CYS* 1.3 66.8 + - - +
137A GLU 3.2 0.2 - - - -
138A THR* 3.2 2.1 + - - -
139A PHE* 3.0 31.1 + - - -
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Residues in contact with CYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.0 3.8 - - - -
99A ILE* 4.2 26.2 - - + -
116A VAL* 3.5 32.3 - - - -
117A PRO 3.9 16.6 - - - +
118A TRP* 3.5 15.0 - - + +
119A PRO* 4.1 3.6 - - + -
132A ILE* 3.0 23.6 + - - -
133A ALA* 3.6 11.4 - - - +
135A ALA* 1.3 78.0 - - - +
137A GLU* 1.3 59.8 + - - +
139A PHE* 3.4 2.3 + - - +
140A LEU 3.0 18.4 + - - -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 5.2 4.2 - - - +
119A PRO* 3.8 27.1 - - + +
133A ALA 3.0 16.5 + - - +
134A ALA* 3.5 17.6 - - - +
136A CYS* 1.3 75.4 - - - +
138A THR* 1.3 63.3 + - - +
140A LEU* 3.2 7.9 - - + +
141A LYS* 3.0 19.9 + - - +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.6 0.2 - - + -
64A GLU* 2.8 64.0 + - + +
65A VAL* 3.7 18.3 - - + +
68A ALA* 3.8 10.9 - - + +
134A ALA 2.9 16.5 + - - -
135A ALA 3.2 8.9 + - - -
137A GLU* 1.3 78.7 - - - +
139A PHE* 1.3 59.0 + - + +
141A LYS* 2.8 21.5 + - + +
142A LEU* 2.9 12.3 + - - +
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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
----------------------------------------------------------
65A VAL* 4.0 22.0 - - + -
68A ALA* 3.6 18.8 - - + -
69A PHE* 3.3 48.0 - + - -
72A LEU* 3.7 20.0 - - + -
99A ILE* 4.0 16.8 - - + -
118A TRP* 3.5 9.0 - - + -
135A ALA 3.0 28.4 + - - +
136A CYS 3.4 3.3 + - - +
138A THR* 1.3 71.7 - - + +
140A LEU* 1.3 60.1 + - - +
142A LEU* 3.9 11.7 - - + -
143A ASN* 2.9 26.2 + - - +
202A THR* 4.4 13.7 - - + -
204A LEU* 3.7 5.8 - - + -
319A SER* 3.6 20.9 - - - -
321A HIS* 3.7 4.4 - - - -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 3.4 42.9 - - + +
119A PRO* 3.7 40.4 - - + +
120A VAL* 4.0 4.9 - - + +
136A CYS 3.0 12.9 + - - +
137A GLU* 3.2 13.2 - - + +
138A THR 3.1 0.2 - - - -
139A PHE* 1.3 78.0 - - - +
141A LYS* 1.3 57.0 + - - +
143A ASN* 2.9 27.0 + - + +
144A ASP* 3.0 25.9 + - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.9 12.8 - - + -
64A GLU* 4.9 8.5 - - - +
137A GLU 3.0 11.3 + - - +
138A THR* 2.8 17.0 + - - +
140A LEU* 1.3 73.4 - - - +
142A LEU* 1.3 64.0 + - - +
143A ASN 3.2 0.3 + - - -
144A ASP* 3.2 12.5 + - - +
145A TYR* 3.1 21.5 + - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 5.6 1.1 - - + -
61A LEU* 4.0 27.1 - - + +
65A VAL* 4.1 26.5 - - + -
138A THR 2.9 10.5 + - - +
139A PHE* 3.8 13.9 - - + +
141A LYS* 1.3 75.0 - - - +
143A ASN* 1.3 56.3 + - - +
145A TYR* 3.2 6.8 + - + +
146A LEU* 3.0 47.8 + - + +
245A TYR* 3.7 40.8 - - + -
294A CYS* 5.7 0.2 - - - -
319A SER* 4.1 9.2 - - - +
321A HIS* 3.6 21.1 - - + +
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Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TRP* 3.3 25.0 - - + -
139A PHE 2.9 16.5 + - - +
140A LEU* 2.9 20.6 + - + +
142A LEU* 1.3 73.1 - - - +
144A ASP* 1.3 66.5 + - - +
146A LEU* 3.4 2.1 + - - +
147A GLN* 3.0 34.0 + - - +
199A TYR* 3.0 42.6 + - - +
201A VAL 4.4 0.3 - - - +
321A HIS* 2.6 31.1 + - - -
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 3.0 30.2 + - - +
141A LYS* 3.4 11.1 - - - +
143A ASN* 1.3 76.2 + - - +
145A TYR* 1.3 62.6 + - - +
147A GLN* 3.4 11.3 - - - +
148A ILE* 3.1 32.5 + - + +
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 2.9 27.5 + - - -
57A VAL* 4.0 23.8 - - + +
58A SER* 5.1 2.6 + - - -
61A LEU* 4.1 24.7 - - + -
141A LYS 3.1 9.8 + - - +
142A LEU* 3.5 10.5 - - + +
143A ASN 3.1 0.2 - - - -
144A ASP* 1.3 80.3 - - - +
146A LEU* 1.3 77.2 + - + +
148A ILE* 3.2 17.5 + - + +
149A GLU* 3.0 54.3 + - + +
294A CYS* 5.9 0.2 - - - -
296A PHE* 6.3 0.2 - + - -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.0 31.6 + - + +
143A ASN* 4.0 2.7 - - - +
145A TYR* 1.3 90.0 - - + +
147A GLN* 1.3 57.1 + - - +
149A GLU* 3.3 4.8 + - - +
150A THR* 2.8 35.2 + - - -
199A TYR* 4.2 5.4 - - + -
243A ALA* 3.9 22.9 - - + +
245A TYR 4.8 5.6 - - - +
294A CYS* 4.1 22.2 - - + -
296A PHE* 3.9 21.8 - - + -
321A HIS* 3.3 40.8 - - + +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 3.0 31.0 + - - +
144A ASP* 3.4 10.5 - - - +
145A TYR 3.1 0.2 - - - -
146A LEU* 1.3 75.0 - - - +
148A ILE* 1.3 66.2 + - + +
150A THR* 3.1 2.5 + - - -
151A ILE* 3.1 45.0 + - + +
194A LYS 4.7 2.6 + - - -
197A ALA 3.2 26.1 + - - +
198A ALA* 4.0 15.0 - - - +
199A TYR* 4.1 14.7 + - + +
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 3.1 22.6 + - + +
145A TYR* 3.4 14.1 - - + +
147A GLN* 1.3 79.5 - - + +
149A GLU* 1.3 67.9 + - + +
151A ILE* 3.5 8.2 + - - +
152A GLN* 3.0 24.4 + - + +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.0 35.8 + - + +
56A SER* 5.0 2.4 - - - +
145A TYR* 3.0 57.1 + - + +
146A LEU* 3.3 8.0 + - - +
148A ILE* 1.3 80.2 - - + +
150A THR* 1.3 57.9 + - - +
152A GLN* 3.3 20.9 + - - +
153A ALA* 2.9 28.6 + - - +
296A PHE* 4.0 20.6 - - + -
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU 2.8 24.0 + - - -
147A GLN 3.1 3.8 + - - -
149A GLU* 1.3 74.1 - - - +
151A ILE* 1.3 58.8 + - - +
153A ALA* 3.1 6.0 + - - +
154A LEU* 2.9 35.7 + - + +
197A ALA* 3.7 17.5 - - + -
199A TYR* 2.7 30.9 + - - +
241A ALA* 3.6 21.5 - - + -
296A PHE* 3.4 18.1 - - + -
298A LEU* 4.3 6.1 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLN* 3.1 34.9 + - + +
148A ILE* 3.7 7.0 - - - +
150A THR* 1.3 74.4 - - - +
152A GLN* 1.3 65.1 + - - +
154A LEU* 3.9 1.1 - - - +
155A GLU* 3.0 42.8 + - - +
193A ILE* 3.9 23.2 - - + +
194A LYS* 4.4 23.6 - - + -
197A ALA* 3.6 17.9 - - + -
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Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 4.4 9.5 - - - +
148A ILE* 3.0 17.5 + - + +
149A GLU* 3.5 29.7 + - - +
151A ILE* 1.3 76.6 - - - +
153A ALA* 1.3 58.1 + - - +
155A GLU* 3.3 15.9 - - - +
156A GLU* 3.1 53.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.6 30.5 - - + +
52A ARG* 4.0 12.3 - - - +
149A GLU 2.9 15.9 + - - +
150A THR* 3.1 6.9 + - - +
152A GLN* 1.3 76.3 - - - +
154A LEU* 1.3 60.0 + - - +
156A GLU* 3.4 12.8 + - - +
157A LEU* 2.9 27.7 + - - +
296A PHE* 5.9 2.9 - - + -
298A LEU* 4.0 10.9 - - + +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 2.9 36.3 + - + +
151A ILE 4.0 3.1 - - - +
153A ALA* 1.3 74.3 - - - +
155A GLU* 1.3 66.4 + - - +
157A LEU* 3.5 13.7 - - + +
158A ALA* 3.1 24.8 + - - +
193A ILE* 3.9 45.0 - - + +
196A ARG* 4.6 16.4 - - + -
197A ALA* 4.7 1.1 - - + -
239A ARG 6.0 0.2 - - - +
241A ALA* 4.9 3.4 - - + -
298A LEU* 3.9 31.4 - - + -
299A ASP* 4.3 13.2 - - + +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.0 38.7 + - + +
152A GLN* 3.3 15.9 - - - +
154A LEU* 1.3 79.8 - - - +
156A GLU* 1.3 63.8 + - + +
158A ALA* 3.2 3.7 + - - +
159A ALA* 3.1 20.8 + - - +
193A ILE* 4.2 18.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.6 1.9 - - - +
52A ARG* 3.9 16.8 + - - -
152A GLN* 3.1 39.3 + - + +
153A ALA* 3.7 9.9 - - - +
154A LEU 3.4 0.2 - - - -
155A GLU* 1.3 75.6 - - + +
157A LEU* 1.3 62.4 + - - +
159A ALA* 3.2 9.8 + - - +
160A LYS* 3.1 21.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 4.5 13.2 - - + +
48A LYS* 4.1 34.1 - - + -
50A ILE* 6.1 1.3 - - + -
153A ALA 2.9 18.6 + - - +
154A LEU* 3.5 17.7 - - + +
155A GLU 3.2 0.2 - - - -
156A GLU* 1.3 74.7 - - - +
158A ALA* 1.3 59.1 + - - +
160A LYS* 3.4 11.3 + - + +
161A GLU* 3.0 41.2 + - + +
298A LEU* 4.2 17.5 - - + -
299A ASP* 4.5 11.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU 3.1 16.1 + - - +
155A GLU* 3.2 5.6 + - - +
157A LEU* 1.3 75.5 - - - +
159A ALA* 1.3 60.2 + - - +
161A GLU* 3.0 13.8 + - + +
162A LYS* 2.9 30.3 + - - +
193A ILE* 5.2 8.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU 3.1 12.9 + - - +
156A GLU* 3.2 13.7 + - - +
158A ALA* 1.3 76.0 - - - +
160A LYS* 1.3 64.0 + - - +
162A LYS* 3.3 4.5 + - - +
163A ALA* 3.0 24.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLU 3.1 11.2 + - - +
157A LEU* 3.5 14.1 - - + +
158A ALA 3.3 0.2 - - - -
159A ALA* 1.3 74.7 - - - +
161A GLU* 1.3 65.2 + - - +
163A ALA* 3.1 6.2 + - - +
164A ASN* 3.0 40.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 161 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 4.3 16.8 + - - -
157A LEU* 3.0 33.0 + - + +
158A ALA* 3.0 15.6 + - - +
160A LYS* 1.3 75.6 - - + +
162A LYS* 1.3 57.8 + - - +
164A ASN* 4.6 1.2 - - - +
165A GLU* 3.2 38.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 162 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ALA 2.9 16.0 + - - +
159A ALA* 4.1 5.2 - - - +
161A GLU* 1.3 71.7 - - - +
163A ALA* 1.3 67.9 + - - +
165A GLU 3.3 18.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 163 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ALA 3.0 17.6 + - - +
160A LYS* 3.1 8.0 + - - +
162A LYS* 1.3 80.8 - - - +
164A ASN* 1.3 69.4 + - - +
165A GLU 4.8 0.3 - - - +
----------------------------------------------------------
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Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LYS* 3.0 33.6 + - - +
161A GLU* 4.6 1.3 - - - +
163A ALA* 1.3 81.1 - - - +
165A GLU* 1.3 73.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 165 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 3.2 28.1 + - - +
162A LYS* 3.3 16.4 - - - +
163A ALA 4.8 0.2 - - - +
164A ASN* 1.3 89.0 - - + +
----------------------------------------------------------
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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