Contacts of the helix formed by residues 127 - 157 (chain W) in PDB entry 3A68
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 GLY 127 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123W HIS* 2.7 25.1 + - - -
124W ALA 4.9 0.2 - - - -
125W ASP 3.4 1.8 - - - -
126W LYS* 1.3 78.4 - - - +
128W ASP* 1.3 67.6 + - - -
129W ALA 3.4 2.4 + - - -
130W LEU 3.5 1.0 + - - -
131W HIS* 3.1 19.4 + - - +
193W LYS* 3.9 17.8 - - - +
197W VAL* 6.5 0.2 - - - -
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Residues in contact with ASP 128 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P ARG* 3.2 41.1 + - - -
69W TYR* 4.1 13.6 + - + +
70W PHE* 3.6 16.4 - - + -
75W VAL* 3.5 14.9 - - - +
77W LEU* 3.8 1.7 - - - +
121W PHE 3.6 21.9 - - - +
122W ASP* 4.3 3.1 - - - -
123W HIS 3.9 5.8 + - - +
127W GLY* 1.3 71.9 - - - +
129W ALA* 1.3 78.8 + - - +
131W HIS* 3.4 1.3 + - - +
132W ALA* 2.9 26.9 + - - +
197W VAL* 4.9 0.3 - - - +
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Residues in contact with ALA 129 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70W PHE* 4.3 0.4 - - - -
77W LEU* 4.1 3.6 - - + -
80W LEU* 3.7 26.8 - - + +
127W GLY 3.4 0.6 - - - -
128W ASP* 1.3 84.2 + - - +
130W LEU* 1.3 64.0 + - - +
132W ALA* 3.3 1.9 + - - +
133W MET* 3.0 27.7 + - - +
188W LEU* 3.9 16.4 - - + -
197W VAL* 3.7 32.1 - - + -
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Residues in contact with LEU 130 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126W LYS* 3.6 36.1 + - + +
127W GLY 3.5 1.4 + - - -
128W ASP 3.4 0.4 - - - -
129W ALA* 1.3 79.2 - - - +
131W HIS* 1.3 64.8 + - - +
133W MET* 3.3 1.2 + - - -
134W GLU* 2.9 51.1 + - - +
185W VAL* 3.8 31.9 - - + +
188W LEU* 4.0 21.6 - - + +
189W ARG* 3.9 26.0 - - + +
197W VAL* 5.7 2.2 - - + +
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Residues in contact with HIS 131 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 5.5 4.1 - - + +
118W LEU* 6.1 2.0 - - - +
120W ASP 5.5 1.2 + - - -
121W PHE* 3.5 28.6 - - + -
122W ASP 4.0 3.6 + - - -
123W HIS* 3.5 39.2 + + + -
126W LYS* 4.1 14.3 - - + +
127W GLY 3.1 18.3 + - - +
128W ASP 3.7 2.7 - - - +
130W LEU* 1.3 79.0 - - - +
132W ALA* 1.3 57.0 + - - +
134W GLU* 3.3 4.0 + - - +
135W LEU* 2.9 65.9 + - + +
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Residues in contact with ALA 132 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66W MET* 3.1 34.6 - - + +
70W PHE* 3.4 25.4 - - + -
80W LEU* 4.8 0.4 - - + -
84W PHE* 4.1 6.1 - - + -
121W PHE* 4.7 4.7 - - + -
128W ASP 2.9 18.3 + - - +
129W ALA 3.7 3.4 - - - +
131W HIS* 1.3 79.7 - - - +
133W MET* 1.3 56.4 + - - +
135W LEU* 3.3 5.9 + - - +
136W ALA* 2.9 24.8 + - - +
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Residues in contact with MET 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80W LEU* 4.3 14.6 - - + -
83W PHE* 3.7 30.7 - - + -
84W PHE* 4.3 8.5 - - + -
129W ALA 3.0 14.2 + - - +
130W LEU 3.8 3.6 - - - +
132W ALA* 1.3 73.4 - - - +
134W GLU* 1.3 61.2 + - - +
136W ALA* 3.2 3.2 + - - +
137W LEU* 2.8 26.3 + - - +
181W ILE* 3.5 16.0 - - - +
184W TYR* 3.6 38.4 - - + -
185W VAL* 3.8 17.0 - - + +
188W LEU* 3.5 25.1 - - + -
200W PHE* 4.6 3.4 - - + -
204W LEU* 3.9 16.4 - - + -
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Residues in contact with GLU 134 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 4.2 13.9 - - + +
28I VAL* 4.1 15.5 - - + +
126W LYS* 2.9 37.6 + - - +
130W LEU* 2.9 39.2 + - + +
131W HIS* 3.7 4.7 - - - +
133W MET* 1.3 75.4 - - - +
135W LEU* 1.3 58.3 + - - +
137W LEU* 3.3 5.2 + - - +
138W SER* 3.0 32.1 + - - -
185W VAL* 4.1 15.5 - - + -
189W ARG* 2.8 35.8 + - - -
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Residues in contact with LEU 135 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I PHE* 4.8 14.4 - - + -
21I VAL* 5.4 7.1 - - + +
25I LEU* 3.4 33.7 - - + -
66W MET* 4.6 4.0 - - + -
118W LEU* 5.5 3.6 - - + -
121W PHE* 3.7 31.0 - - + -
131W HIS* 2.9 49.2 + - + +
132W ALA* 3.5 8.7 - - - +
134W GLU* 1.3 74.1 - - - +
136W ALA* 1.3 59.8 + - - +
138W SER* 3.1 6.4 + - - -
139W LEU* 2.9 39.3 + - + +
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Residues in contact with ALA 136 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63W TYR* 3.7 25.5 + - + +
66W MET* 4.7 1.3 - - + +
83W PHE* 5.3 0.4 - - + -
84W PHE* 4.1 13.0 - - + -
132W ALA 2.9 14.8 + - - +
133W MET* 3.5 12.1 - - - +
135W LEU* 1.3 75.8 - - - +
137W LEU* 1.3 63.8 + - - +
139W LEU* 3.2 11.0 + - - +
140W GLU* 2.9 27.5 + - - +
181W ILE* 4.2 15.3 - - + -
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Residues in contact with LEU 137 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I VAL* 4.7 20.6 - - + -
36I LEU* 3.9 27.1 - - + +
133W MET 2.8 17.8 + - - +
134W GLU* 3.5 6.7 - - - +
136W ALA* 1.3 77.2 - - - +
138W SER* 1.3 63.8 + - - +
140W GLU* 3.2 3.6 + - + -
141W LYS* 3.0 33.5 + - + +
178W ILE* 3.8 28.9 - - + +
181W ILE* 3.6 12.2 - - + +
182W SER* 3.4 26.9 - - - +
185W VAL* 4.4 14.6 - - + -
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Residues in contact with SER 138 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I VAL* 4.2 9.9 - - - -
24I GLU* 3.6 24.0 - - - +
25I LEU* 3.2 37.8 + - - +
28I VAL* 3.4 7.8 - - - +
134W GLU 3.0 15.2 + - - -
135W LEU* 3.1 8.3 + - - -
137W LEU* 1.3 77.1 - - - +
139W LEU* 1.3 57.0 + - - +
141W LYS* 3.4 2.8 + - - +
142W LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 139 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 6.2 0.2 - - + -
17I PRO* 4.2 19.5 - - + -
18I PHE* 5.7 5.6 - - + -
21I VAL* 3.4 28.7 - - + +
59W VAL* 5.0 18.2 - - + +
62W VAL* 3.7 31.9 - - + -
63W TYR* 4.2 17.9 - - + +
66W MET* 4.7 4.0 - - - -
135W LEU* 2.9 23.1 + - + +
136W ALA* 3.4 14.4 - - - +
138W SER* 1.3 76.4 - - - +
140W GLU* 1.3 57.6 + - - +
142W LEU* 3.3 6.3 + - + +
143W THR* 2.9 32.2 + - - -
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Residues in contact with GLU 140 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59W VAL* 4.0 7.0 - - - +
63W TYR* 2.6 39.4 + - - +
91W GLU* 3.7 14.5 - - - +
136W ALA 2.9 14.3 + - - +
137W LEU* 3.7 5.2 - - - +
139W LEU* 1.3 72.4 - - - +
141W LYS* 1.3 60.1 + - - +
143W THR* 3.4 5.2 + - - +
144W ASN* 2.9 18.4 + - - +
174W GLN* 2.7 50.3 + - - +
177W ALA* 4.0 13.4 - - + +
178W ILE* 4.0 14.1 - - + -
181W ILE* 3.5 20.2 - - + -
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Residues in contact with LYS 141 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLU* 3.7 27.2 + - + +
27I LEU* 5.5 6.3 + - - +
28I VAL* 5.6 5.1 - - + +
29I PRO* 5.0 8.3 - - - +
35I SER 5.4 0.4 + - - -
36I LEU 2.7 30.6 + - - -
37I ALA 3.6 14.6 - - - -
38I ARG 3.4 18.3 + - - -
39I GLN* 3.0 46.0 + - + +
137W LEU* 3.0 33.4 + - + +
138W SER* 3.8 4.9 - - - +
140W GLU* 1.3 74.0 - - - +
142W LEU* 1.3 66.5 + - - +
144W ASN 3.2 0.7 + - - -
145W GLU* 3.0 13.3 + - - +
178W ILE* 4.2 11.7 - - + -
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Residues in contact with LEU 142 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 3.5 32.5 - - + -
17I PRO* 4.1 2.2 - - + +
20I GLU* 4.0 27.6 - - + +
21I VAL* 3.5 26.2 - - + -
23I LYS* 6.3 0.4 - - + -
24I GLU* 3.9 11.3 - - + +
59W VAL* 6.6 0.2 - - + -
138W SER 2.9 18.4 + - - +
139W LEU* 3.5 8.1 - - + +
141W LYS* 1.3 76.3 - - - +
143W THR* 1.3 61.5 + - - +
145W GLU* 3.2 22.7 + - - +
146W LYS* 3.0 44.4 + - + +
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Residues in contact with THR 143 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 6.0 0.3 - - - -
52W GLN* 4.0 6.7 - - - +
55W VAL* 4.3 6.4 - - + +
56W GLU* 3.7 25.4 - - - +
59W VAL* 3.5 24.8 - - - +
91W GLU* 5.3 0.2 + - - -
139W LEU 2.9 19.1 + - - -
140W GLU* 3.6 8.8 + - - -
142W LEU* 1.3 76.7 - - - +
144W ASN* 1.3 58.1 + - - +
146W LYS* 3.2 8.6 + - - +
147W LEU* 2.8 30.3 + - + +
174W GLN* 4.0 18.8 - - - +
232W CA 4.2 8.1 - - - -
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Residues in contact with ASN 144 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I GLN* 3.0 31.0 + - - +
40I LYS* 5.6 0.6 - - - +
140W GLU 2.9 14.0 + - - +
141W LYS 3.2 8.9 + - - +
143W THR* 1.3 76.8 - - - +
145W GLU* 1.3 57.5 + - - +
147W LEU* 3.2 3.6 + - - +
148W LEU* 2.9 53.3 + - - +
171W LEU* 4.4 11.3 - - - +
174W GLN* 3.4 29.7 - - + +
175W VAL* 5.2 9.4 + - - +
178W ILE* 3.9 8.2 - - + +
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Residues in contact with GLU 145 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I LYS* 3.3 29.2 + - - +
24I GLU* 4.4 4.3 - - - +
39I GLN* 4.3 6.7 - - - +
40I LYS* 4.5 21.9 + - - +
141W LYS 3.0 12.6 + - - +
142W LEU* 3.4 25.2 - - - +
144W ASN* 1.3 76.2 - - - +
146W LYS* 1.3 63.6 + - - +
148W LEU* 3.3 7.0 + - - +
149W ASN* 2.9 50.9 + - - +
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Residues in contact with LYS 146 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ILE 5.3 3.2 + - - -
15I PHE* 3.5 21.3 - - + -
20I GLU* 3.0 29.2 + - - -
51W GLU* 5.4 7.7 + - + +
52W GLN* 3.4 22.8 - - - +
55W VAL* 4.2 23.0 - - + +
142W LEU* 3.0 24.9 + - + +
143W THR 3.2 7.2 + - - +
145W GLU* 1.3 84.1 + - - +
147W LEU* 1.3 57.1 + - - +
149W ASN* 3.2 18.2 + - + +
150W LEU* 2.9 24.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52W GLN* 3.5 29.4 - - + +
56W GLU* 4.0 5.8 - - - +
98W LEU* 5.5 0.2 - - + -
143W THR* 2.8 27.5 + - + +
144W ASN 3.6 3.8 - - - +
146W LYS* 1.3 72.4 - - - +
148W LEU* 1.3 58.1 + - - +
150W LEU* 3.2 8.9 + - + +
151W HIS* 2.9 27.5 + - - +
166W VAL* 3.9 12.4 - - + +
170W TYR* 3.8 41.3 - - + +
171W LEU* 3.8 14.4 - - + -
174W GLN* 3.9 35.7 - - + +
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Residues in contact with LEU 148 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LYS* 3.7 34.5 - - + -
160I VAL* 4.0 24.7 - - + +
161I GLN* 5.3 4.3 - - + +
144W ASN* 2.9 38.3 + - - +
145W GLU* 3.7 4.5 - - - +
147W LEU* 1.3 76.7 - - - +
149W ASN* 1.3 58.1 - - - +
151W HIS* 3.4 5.3 + - + +
152W SER* 2.9 31.8 + - - -
171W LEU* 3.9 28.9 - - + -
----------------------------------------------------------
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Residues in contact with ASN 149 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145W GLU* 2.9 38.1 + - - +
146W LYS* 3.3 23.2 - - + +
148W LEU* 1.3 75.9 - - - +
150W LEU* 1.3 64.3 + - - +
152W SER* 3.1 9.5 + - - -
153W VAL* 3.0 27.4 + - + +
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Residues in contact with LEU 150 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W ALA* 3.6 37.2 - - + +
49W VAL* 3.9 13.9 - - + +
52W GLN* 3.9 31.6 - - + +
98W LEU* 4.5 12.1 - - + -
146W LYS 2.9 12.9 + - - +
147W LEU* 3.2 11.4 + - + +
149W ASN* 1.3 74.6 - - - +
151W HIS* 1.3 63.8 + - - +
153W VAL* 3.2 6.7 + - - +
154W ALA* 3.0 21.2 + - - +
162W LEU* 4.5 10.8 - - + -
166W VAL* 3.6 29.6 - - + -
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Residues in contact with HIS 151 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I VAL* 3.5 32.8 - - + +
147W LEU 2.9 13.4 + - - +
148W LEU* 3.5 13.4 + - + +
150W LEU* 1.3 78.6 - - - +
152W SER* 1.3 59.3 + - - +
154W ALA* 3.3 6.5 + - - +
155W THR* 2.9 56.8 + - + +
163W ALA* 3.6 27.8 - - + +
166W VAL* 4.3 12.3 - - + +
167W GLU* 2.6 39.3 + - + +
171W LEU* 4.4 4.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 152 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148W LEU 2.9 15.7 + - - -
149W ASN* 3.1 12.4 + - - -
151W HIS* 1.3 78.6 + - - +
153W VAL* 1.3 60.2 + - - +
155W THR* 2.8 21.0 + - - -
156W LYS* 2.8 19.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W GLU* 3.8 36.8 - - + +
45W SER* 4.4 4.0 - - - -
48W ALA* 3.9 19.7 - - + -
149W ASN* 3.0 21.2 + - + +
150W LEU* 3.2 7.4 + - + +
152W SER* 1.3 75.9 - - - +
154W ALA* 1.3 64.1 + - - +
156W LYS* 3.7 4.6 - - - +
157W ASN* 2.9 45.6 + - - +
162W LEU* 6.0 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45W SER* 4.6 2.0 - - - -
150W LEU 3.0 11.6 + - - +
151W HIS* 3.6 8.7 - - - +
153W VAL* 1.3 78.4 - - - +
155W THR* 1.3 62.4 + - - +
157W ASN 3.3 2.1 + - - -
158W GLY 3.0 4.2 + - - -
159W ASP* 2.9 34.6 + - - +
162W LEU* 3.6 36.8 - - + +
163W ALA* 3.8 19.3 - - - +
166W VAL* 5.9 0.4 - - + -
----------------------------------------------------------
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Residues in contact with THR 155 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151W HIS* 2.9 48.1 + - + +
152W SER* 2.8 24.6 + - - -
154W ALA* 1.3 77.7 - - - +
156W LYS* 1.3 59.6 + - - +
158W GLY* 3.1 13.8 + - - +
159W ASP 5.0 0.7 - - - +
163W ALA* 4.2 10.5 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W GLU* 2.9 39.0 + - - +
152W SER 2.8 18.3 + - - +
153W VAL* 3.7 4.9 - - - +
155W THR* 1.3 77.4 + - - +
157W ASN* 1.3 70.9 + - - +
158W GLY 3.3 0.6 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42W VAL* 3.7 31.3 - - + +
44W GLU* 2.8 40.2 + - - +
45W SER* 4.1 8.8 + - - +
153W VAL* 2.9 33.3 + - - +
154W ALA 4.0 2.5 - - - +
156W LYS* 1.3 84.4 - - - +
158W GLY* 1.3 64.0 + - - +
159W ASP* 3.3 3.2 + - + +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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