Contacts of the helix formed by residues 114 - 144 (chain M) in PDB entry 1BFR
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 TYR 114 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M ASP* 4.0 30.9 + - - -
112M HIS* 3.0 50.7 + + + -
113M ASP* 1.3 70.8 - - - +
115M VAL* 1.3 57.1 + - - +
117M ARG* 3.4 21.7 + - - +
118M ASP* 2.9 33.3 + - - +
102T ARG* 3.7 20.8 - - - +
105T ILE* 3.6 39.7 - - + -
106T GLY* 3.6 13.7 - - - -
109T ASP* 5.9 2.5 - - + +
117T ARG* 5.4 2.7 - - - -
121T ILE* 3.9 23.3 - - + -
124T LEU* 4.1 12.1 - - + -
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Residues in contact with VAL 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M ARG* 3.7 16.4 - - - +
113M ASP* 3.4 0.8 + - - -
114M TYR* 1.3 75.6 - - - +
116M SER* 1.3 61.6 + - - +
118M ASP* 3.4 4.9 + - - +
119M MET* 3.1 23.1 + - + +
102T ARG* 5.1 0.4 - - - +
121T ILE* 4.6 5.2 - - + +
124T LEU* 4.0 13.1 - - + +
125T ARG* 3.8 49.3 + - + +
128T GLU* 3.5 34.5 - - + +
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Residues in contact with SER 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M VAL* 4.0 11.8 - - - +
11M LEU* 4.3 6.5 - - - +
61M ARG* 3.0 25.6 + - - +
65M LEU* 3.8 7.6 - - - +
108M ALA* 4.6 0.2 - - - -
113M ASP* 2.8 39.2 + - - -
115M VAL* 1.3 73.6 - - - +
117M ARG* 1.3 61.8 + - - +
119M MET* 3.4 8.8 - - - +
120M MET* 3.1 35.7 + - - +
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Residues in contact with ARG 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K ASP* 4.9 2.2 + - - -
114K TYR* 5.4 2.6 - - - -
117K ARG* 3.2 28.9 - - - +
105M ILE* 3.6 26.8 - - + +
108M ALA* 4.0 7.5 - - + +
109M ASP* 3.2 39.6 + - - +
113M ASP 3.0 14.2 + - - +
114M TYR* 3.4 16.3 + - - +
115M VAL 3.3 0.2 - - - -
116M SER* 1.3 76.0 - - - +
118M ASP* 1.3 86.2 + - - +
120M MET* 3.1 14.4 + - - +
121M ILE* 3.0 25.5 + - + +
117T ARG* 3.0 33.4 - - - +
118T ASP* 5.1 0.2 + - - -
121T ILE* 3.3 14.9 - - - +
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Residues in contact with ASP 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K ARG* 5.1 0.2 + - - -
118K ASP* 5.8 2.9 - - - -
114M TYR 2.9 20.2 + - - +
115M VAL* 3.4 3.3 + - - +
117M ARG* 1.3 100.8 + - - +
119M MET* 1.3 63.1 + - - +
121M ILE* 3.1 11.4 + - - +
122M GLU* 3.1 29.8 + - - +
118T ASP* 5.6 3.5 - - - +
121T ILE* 3.3 25.4 - - + +
125T ARG* 3.6 23.9 + - - +
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Residues in contact with MET 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M LEU* 4.3 9.9 - - + -
57M ARG* 3.7 45.9 + - - +
58M TYR* 3.5 38.1 - - + -
61M ARG* 4.0 33.7 - - + -
115M VAL* 3.1 14.4 + - + +
116M SER* 3.4 8.7 - - - +
118M ASP* 1.3 73.4 - - - +
120M MET* 1.3 73.6 + - + +
122M GLU* 3.4 4.1 + - - +
123M ILE* 3.1 26.6 + - + +
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Residues in contact with MET 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M VAL* 5.3 2.2 - - + -
10M TYR* 5.7 1.8 - - + -
11M LEU* 3.9 15.3 - - + -
14M LEU* 3.6 26.9 - - - -
58M TYR* 4.4 6.5 - - + -
101M LEU* 3.9 12.3 - - + +
104M ALA* 3.7 25.8 - - + +
105M ILE* 3.6 15.3 - - + +
108M ALA* 3.6 29.8 - - + -
116M SER* 3.1 22.0 + - - +
117M ARG* 3.1 9.6 + - - +
119M MET* 1.3 88.6 - - + +
121M ILE* 1.3 55.3 + - - +
123M ILE* 3.2 6.6 + - - +
124M LEU* 2.8 29.5 + - - +
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Residues in contact with ILE 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K TYR* 3.9 25.4 - - + +
115K VAL* 4.8 3.6 - - + +
117K ARG* 3.2 29.6 - - - +
118K ASP* 3.3 26.9 - - - +
105M ILE* 3.7 34.1 - - + -
117M ARG* 3.0 28.9 + - - +
118M ASP* 3.1 11.2 + - - +
120M MET* 1.3 69.4 - - - +
122M GLU* 1.3 57.6 + - - +
124M LEU* 3.2 3.1 + - - +
125M ARG* 2.9 35.5 + - - +
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Residues in contact with GLU 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M ARG* 3.0 35.0 + - - +
118M ASP* 3.1 17.9 + - - +
119M MET* 3.4 7.6 - - - +
121M ILE* 1.3 73.0 - - - +
123M ILE* 1.3 64.7 + - - +
125M ARG* 3.3 27.3 + - - +
126M ASP* 3.2 25.8 + - - +
125T ARG* 4.7 12.8 + - - -
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Residues in contact with ILE 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M GLU* 4.0 7.0 - - - +
54M HIS* 3.6 46.4 - - + +
57M ARG* 4.1 19.1 - - + +
58M TYR* 3.6 45.8 - - + +
101M LEU* 4.7 4.9 - - + -
119M MET* 3.1 27.4 + - + +
120M MET* 3.7 6.1 - - - +
122M GLU* 1.3 74.1 - - - +
124M LEU* 1.3 62.3 + - - +
126M ASP* 3.1 5.5 + - - +
127M GLU* 3.0 24.4 + - + +
202M MN 4.1 1.8 - - - +
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Residues in contact with LEU 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K TYR* 4.0 21.3 - - + -
115K VAL* 4.1 11.2 - - + -
98M ALA* 4.1 23.8 - - + +
101M LEU* 3.9 27.1 - - + +
102M ARG* 3.8 31.4 - - + +
105M ILE* 3.8 23.3 - - + -
120M MET 2.8 20.8 + - - +
121M ILE* 3.2 5.6 + - - +
123M ILE* 1.3 70.5 - - - +
125M ARG* 1.3 59.2 + - - +
127M GLU* 3.2 3.6 + - + +
128M GLU* 2.9 32.4 + - + +
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Residues in contact with ARG 125 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K VAL* 3.7 30.4 + - + +
118K ASP* 3.4 37.8 + - - +
122K GLU* 4.8 10.4 + - - -
121M ILE* 2.9 22.4 + - - +
122M GLU* 3.5 31.7 - - - +
124M LEU* 1.3 76.8 - - - +
126M ASP* 1.3 65.1 + - - +
128M GLU* 3.4 3.0 + - - +
129M GLY* 3.2 17.3 + - - -
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Residues in contact with ASP 126 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ASP* 5.1 7.0 - - - +
54M HIS* 2.8 33.7 + - + -
57M ARG* 5.8 1.6 + - - -
122M GLU 3.2 13.7 + - - +
123M ILE* 3.1 8.2 + - - +
125M ARG* 1.3 78.6 - - - +
127M GLU* 1.3 62.3 + - - +
129M GLY* 3.2 3.9 + - - -
130M HIS* 3.1 32.8 + - - +
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Residues in contact with GLU 127 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M GLU* 5.3 0.2 - - - +
51M GLU* 2.9 7.3 - - - +
54M HIS* 3.1 13.7 - - - -
94M GLU* 2.8 22.0 - - - +
97M GLY* 5.8 2.5 - - - -
98M ALA* 5.2 6.3 - - + +
101M LEU* 4.1 20.2 - - + -
123M ILE* 3.0 14.7 + - + +
124M LEU* 3.6 10.1 - - + +
126M ASP* 1.3 71.4 - - - +
128M GLU* 1.3 66.1 + - - +
130M HIS* 3.0 3.1 + - - -
131M ILE* 2.9 32.5 + - + +
201M MN 2.2 29.2 + - - -
202M MN 2.5 30.6 + - - +
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Residues in contact with GLU 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K MET* 3.8 19.2 - - + +
61K ARG* 2.9 38.7 + - - +
64K PHE* 3.6 14.3 - - + -
115K VAL* 3.4 17.4 - - + +
102M ARG* 2.7 35.7 + - - +
124M LEU* 2.9 27.4 + - + +
125M ARG* 3.8 6.1 - - - +
127M GLU* 1.3 69.5 - - - +
129M GLY* 1.3 57.3 + - - +
131M ILE* 3.3 15.2 + - + +
132M ASP* 2.9 25.3 + - - +
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Residues in contact with GLY 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125M ARG 3.2 12.5 + - - -
126M ASP* 3.5 4.9 - - - -
127M GLU 3.2 0.8 - - - -
128M GLU* 1.3 73.9 - - - +
130M HIS* 1.3 65.5 + - - +
132M ASP* 3.3 8.5 + - - +
133M TRP* 3.2 19.8 + - - +
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Residues in contact with HIS 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M TYR* 3.5 14.6 + - - +
47M GLU* 3.5 34.1 - - + +
50M ASP* 2.8 34.5 + - + -
51M GLU* 3.4 13.2 + - - -
54M HIS* 4.9 0.9 - + - -
94M GLU* 3.2 12.6 - - - +
126M ASP* 3.1 17.8 + - - +
127M GLU* 3.0 6.2 + - - +
129M GLY* 1.3 75.5 - - - +
131M ILE* 1.3 63.5 + - - +
133M TRP* 3.2 3.0 + - - +
134M LEU* 3.0 28.5 + - - +
201M MN 2.1 32.6 + - - -
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Residues in contact with ILE 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K MET* 4.1 22.0 - - + -
64K PHE* 4.6 0.4 - - + -
91M LEU* 3.8 20.8 - - + +
94M GLU* 3.6 24.0 - - + +
95M LEU* 3.7 25.1 - - + -
98M ALA* 4.3 19.7 - - + -
127M GLU 2.9 21.8 + - - +
128M GLU* 3.5 17.7 - - + +
130M HIS* 1.3 75.6 - - - +
132M ASP* 1.3 62.7 + - - +
134M LEU* 3.3 2.5 + - - +
135M GLU* 3.0 44.9 + - - +
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Residues in contact with ASP 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K PHE* 3.5 36.3 - - + +
34L ASN* 4.2 11.7 - - - +
128M GLU 2.9 9.9 + - - +
129M GLY* 3.6 11.9 - - - +
130M HIS 3.3 0.2 - - - -
131M ILE* 1.3 75.7 - - - +
133M TRP* 1.3 61.5 + - - +
135M GLU* 3.8 6.2 - - - +
136M THR* 3.1 38.4 + - - -
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Residues in contact with TRP 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M ARG* 4.0 9.9 - - - +
40M LEU* 4.1 20.4 - - + -
43M VAL* 3.5 43.7 - - + +
44M GLU* 3.6 28.7 - - + -
47M GLU* 3.8 18.2 - - - +
87M LEU* 4.8 5.8 - - + -
129M GLY 3.2 10.0 + - - +
130M HIS 3.2 5.4 + - - +
132M ASP* 1.3 77.8 - - - +
134M LEU* 1.3 91.7 + - + +
136M THR* 3.7 4.9 - - - -
137M GLU* 3.0 60.3 + - + +
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Residues in contact with LEU 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M TYR* 3.8 22.0 - - - +
44M GLU* 4.1 6.1 - - - +
47M GLU* 4.6 1.6 - - - +
87M LEU* 3.8 31.0 - - + +
90M ASP* 3.9 13.5 - - + -
91M LEU* 3.8 33.2 - - + +
94M GLU* 4.1 6.3 - - + -
130M HIS 3.0 21.7 + - - +
131M ILE* 3.9 3.8 - - - +
133M TRP* 1.3 101.5 - - + +
135M GLU* 1.3 62.7 + - - +
137M GLU* 3.3 3.8 + - - +
138M LEU* 3.0 29.9 + - + +
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Residues in contact with GLU 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K MET* 2.8 43.7 + - - +
64K PHE* 3.9 13.2 - - - -
66K GLU* 4.3 3.9 - - - +
91M LEU* 4.1 24.6 - - + +
95M LEU* 5.5 1.9 - - - +
131M ILE* 3.0 30.9 + - - +
132M ASP* 3.8 5.2 - - - +
134M LEU* 1.3 76.1 - - - +
136M THR* 1.3 64.0 + - - +
138M LEU* 3.3 3.1 + - - +
139M ASP* 3.0 31.6 + - - +
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Residues in contact with THR 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L LYS 5.4 0.2 - - - +
34L ASN* 3.5 13.0 + - - +
35L TRP* 3.7 8.1 - - - +
36L GLY* 3.6 36.3 - - - +
132M ASP* 3.1 25.5 + - - -
133M TRP* 3.7 5.2 - - - -
135M GLU* 1.3 75.5 - - - +
137M GLU* 1.3 66.2 + - - +
139M ASP* 3.2 8.1 + - - +
140M LEU* 2.9 28.2 + - + +
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Residues in contact with GLU 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M ARG* 3.1 38.7 + - - -
87M LEU* 4.2 10.5 - - + -
133M TRP* 3.0 47.1 + - + +
134M LEU* 3.7 6.5 - - - +
136M THR* 1.3 76.0 - - - +
138M LEU* 1.3 63.7 + - - +
140M LEU* 3.1 17.7 + - - +
141M ILE* 2.9 29.1 + - - +
149M TYR* 2.6 36.8 + - - +
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Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M GLU* 3.9 20.9 - - + +
87M LEU* 3.8 27.6 - - + +
88M ARG* 3.9 49.4 - - + +
91M LEU* 3.7 30.3 - - + -
134M LEU 3.0 19.0 + - - +
135M GLU* 3.8 4.0 - - - +
137M GLU* 1.3 75.5 - - - +
139M ASP* 1.3 64.1 + - - +
141M ILE* 3.6 8.7 + - + +
142M GLN* 2.8 30.5 + - - -
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Residues in contact with ASP 139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L TRP* 5.7 3.1 - - + +
135M GLU* 3.0 21.0 + - - +
136M THR* 3.6 9.9 - - + +
138M LEU* 1.3 74.5 - - - +
140M LEU* 1.3 62.1 + - + +
142M GLN* 3.1 10.8 + - - +
143M LYS* 2.9 53.4 + - - +
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Residues in contact with LEU 140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L TRP 3.2 21.1 - - - +
36L GLY* 4.3 7.9 - - - +
37L LEU* 4.0 17.7 - - + -
150L LEU* 6.0 0.9 - - + -
154L ILE* 4.5 12.1 - - + -
136M THR* 2.9 38.4 + - + +
137M GLU* 3.5 18.8 - - - +
139M ASP* 1.3 72.1 - - + +
141M ILE* 1.3 63.5 + - - +
143M LYS* 3.2 14.7 + - + +
144M MET* 2.9 54.1 + - + +
149M TYR* 4.5 9.0 - - + -
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Residues in contact with ILE 141 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M VAL* 4.6 3.6 - - + -
84M GLU* 4.2 29.6 - - + +
87M LEU* 4.1 18.6 - - + -
137M GLU 2.9 20.2 + - - +
138M LEU* 3.6 19.5 - - + +
139M ASP 3.3 0.2 - - - -
140M LEU* 1.3 73.3 - - - +
142M GLN* 1.3 65.2 + - - +
145M GLY* 3.0 23.6 + - - -
146M LEU* 3.8 30.0 + - + +
149M TYR* 3.7 40.3 - - + -
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Residues in contact with GLN 142 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147L GLN* 4.9 2.4 + - - -
84M GLU* 3.2 30.7 + - - +
88M ARG* 3.4 15.3 + - - +
138M LEU* 2.8 26.2 + - - +
139M ASP* 3.1 11.8 + - - +
141M ILE* 1.3 82.8 - - - +
143M LYS* 1.3 65.0 + - + +
144M MET 3.6 0.2 + - - -
145M GLY* 3.7 5.2 + - - -
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Residues in contact with LYS 143 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L TRP* 3.5 48.0 + - + +
37L LEU* 6.0 2.9 - - + -
146L LEU* 6.0 1.2 - - - +
147L GLN* 3.8 15.6 + - - +
150L LEU* 3.8 29.4 - - + +
139M ASP* 2.9 45.2 + - - +
140M LEU* 3.9 12.8 - - + +
142M GLN* 1.3 75.0 - - + +
144M MET* 1.3 59.7 + - - +
----------------------------------------------------------
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Residues in contact with MET 144 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147L GLN* 3.5 40.0 + - - +
150L LEU* 4.2 7.9 - - + -
151L GLN* 3.9 32.8 - - - +
154L ILE* 3.9 27.4 - - + -
140M LEU* 2.9 51.3 + - + +
143M LYS* 1.3 73.2 - - - +
145M GLY* 1.3 69.1 + - - +
148M ASN* 3.3 15.7 + - + +
149M TYR* 3.8 27.8 - - - +
----------------------------------------------------------
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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