Contacts of the helix formed by residues 118 - 150 (chain E) in PDB entry 1NF4
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 ASP 118 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LYS* 6.1 0.3 - - - -
12E VAL* 3.6 26.7 - - + +
66E ARG* 2.8 26.6 + - - -
70E LEU* 3.8 10.4 - - - +
113E CYS* 2.6 20.0 + - + +
114E LYS* 4.6 0.8 - - - +
116E GLN 4.4 2.2 - - - +
117E GLY* 1.3 72.0 - - - +
119E ILE* 1.3 57.7 + - - +
120E VAL* 3.4 4.0 + - - +
121E THR* 2.5 31.7 + - - +
122E ALA* 3.0 27.8 + - - +
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Residues in contact with ILE 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E LYS* 5.7 9.6 - - + -
117E GLY* 3.7 12.7 + - - +
118E ASP* 1.3 71.0 + - - +
120E VAL* 1.3 73.0 + - + +
122E ALA* 3.3 7.2 + - + +
123E ARG* 3.0 26.3 + - + +
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Residues in contact with VAL 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ARG* 3.4 37.0 - - - +
69E GLU* 4.9 2.7 - - - +
118E ASP* 3.4 1.8 + - - +
119E ILE* 1.3 81.4 - - + +
121E THR* 1.3 62.9 + - - +
123E ARG* 3.3 6.8 + - - +
124E LEU* 3.0 22.0 + - + +
127E ARG* 5.3 1.8 + - - +
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Residues in contact with THR 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 3.5 13.2 - - + +
16E LEU* 3.8 26.7 - - + -
66E ARG* 3.2 20.4 + - + +
70E LEU* 4.1 0.2 - - - +
113E CYS* 3.3 23.1 - - - -
118E ASP* 2.5 33.7 + - - -
120E VAL* 1.3 74.3 - - - +
122E ALA* 1.3 66.9 + - - +
124E LEU* 3.2 7.9 + - + +
125E PHE* 3.0 24.7 + - + -
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Residues in contact with ALA 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU* 3.3 22.9 - - + +
113E CYS* 3.8 17.7 - - + +
114E LYS* 4.2 21.8 - - + -
118E ASP 3.0 18.3 + - - +
119E ILE* 3.8 8.7 - - + +
120E VAL 3.3 0.4 - - - -
121E THR* 1.3 77.5 - - - +
123E ARG* 1.3 58.3 + - - +
125E PHE* 3.3 1.8 + - - +
126E GLU* 3.0 25.9 + - - +
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Residues in contact with ARG 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ARG* 4.2 24.1 - - - +
126D GLU* 5.6 1.1 - - - -
119E ILE* 3.0 21.4 + - + +
120E VAL* 3.6 6.3 - - - +
121E THR 3.1 0.2 - - - -
122E ALA* 1.3 76.6 - - - +
124E LEU* 1.3 64.2 + - - +
126E GLU* 3.2 44.7 + - - +
127E ARG* 3.0 80.4 + - - +
130E GLU* 4.7 6.7 + - - -
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Residues in contact with LEU 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 4.4 4.0 - - + -
62E ASN* 3.9 36.1 - - + +
63E PHE* 4.0 17.5 - - + -
66E ARG* 3.9 24.5 - - + -
120E VAL* 3.0 13.6 + - + +
121E THR* 3.4 9.6 - - - +
123E ARG* 1.3 77.7 - - - +
125E PHE* 1.3 62.7 + - - +
126E GLU 3.3 0.2 + - - -
127E ARG* 3.4 21.3 + - + +
128E ILE* 3.1 48.7 + - + +
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Residues in contact with PHE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 4.1 12.1 - - + -
16E LEU* 3.9 10.1 - - + -
19E ALA* 3.7 19.1 - - + -
63E PHE* 3.6 31.2 - + - -
106E TYR* 4.0 28.3 - + + +
109E PHE* 3.7 24.0 - + + -
110E LEU* 4.0 19.5 - - + -
113E CYS* 3.8 19.3 - - - -
121E THR* 3.0 38.8 + - + -
122E ALA 3.6 7.0 - - - +
124E LEU* 1.3 76.4 - - + +
126E GLU* 1.3 58.3 + - - +
128E ILE* 3.8 3.8 - - - +
129E ILE* 2.8 37.3 + - + +
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Residues in contact with GLU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 4.0 19.6 - - + +
123D ARG* 3.9 19.1 - - + +
126D GLU* 3.7 21.3 - - - +
110E LEU* 3.7 14.6 - - + +
114E LYS* 5.3 3.8 + - - -
122E ALA* 3.0 16.5 + - - +
123E ARG* 3.3 38.1 + - - +
124E LEU 3.2 0.2 - - - -
125E PHE* 1.3 79.4 - - - +
127E ARG* 1.3 62.0 + - - +
129E ILE* 3.4 6.4 + - - +
130E GLU* 3.2 26.5 + - + +
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Residues in contact with ARG 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E VAL* 5.3 1.6 + - - +
123E ARG* 3.0 65.9 + - - +
124E LEU* 3.5 38.9 - - + +
126E GLU* 1.3 75.9 - - - +
128E ILE* 1.3 64.2 + - + +
130E GLU* 3.2 21.3 + - - +
131E GLU* 3.3 19.6 + - - +
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Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E HIS* 3.7 35.2 - - + +
62E ASN* 4.7 3.6 - - + +
63E PHE* 3.4 30.1 - - + -
106E TYR* 3.7 20.4 - - + -
124E LEU* 3.1 41.9 + - + +
125E PHE* 4.0 3.1 - - - +
127E ARG* 1.3 75.1 - - + +
129E ILE* 1.3 60.5 + - - +
131E GLU* 3.0 11.0 + - - +
132E GLU* 2.8 50.6 + - - +
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Residues in contact with ILE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 4.1 28.0 - - + -
120D VAL* 3.9 19.5 - - + -
103E ILE* 4.3 21.1 - - + +
106E TYR* 3.5 46.7 - - + +
107E SER* 3.8 12.6 - - - +
110E LEU* 4.2 4.5 - - + -
125E PHE 2.8 30.3 + - - +
126E GLU 3.6 4.0 - - - +
127E ARG 3.3 0.2 - - - -
128E ILE* 1.3 75.1 - - - +
130E GLU* 1.3 61.2 + - - +
132E GLU* 3.4 9.1 + - - +
133E GLN* 3.1 21.1 + - - +
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 5.8 1.1 - - + -
120D VAL* 4.6 20.2 - - + +
123D ARG* 3.6 31.2 + - + +
127D ARG* 3.8 21.2 + - - -
123E ARG* 4.7 7.4 + - - -
126E GLU* 3.2 17.9 + - + +
127E ARG* 3.4 13.6 - - - +
128E ILE 3.2 0.6 - - - -
129E ILE* 1.3 76.3 - - + +
131E GLU* 1.3 63.5 + - + +
133E GLN* 3.3 9.0 + - - +
134E ALA* 3.2 19.2 + - - +
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Residues in contact with GLU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ARG* 2.5 26.7 + - - -
59E HIS* 2.5 39.5 + - + +
127E ARG* 3.3 15.8 + - - +
128E ILE* 3.0 11.2 + - - +
130E GLU* 1.3 76.5 - - + +
132E GLU* 1.3 65.1 + - - +
134E ALA* 3.1 6.4 + - - +
135E HIS* 3.1 27.5 + - + -
172F VAL* 3.5 27.1 - - + +
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Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU* 3.0 8.5 - - - +
59E HIS* 3.1 8.7 + - - -
99E GLU* 3.4 11.2 - - - +
102E THR* 4.0 13.1 - - + +
103E ILE* 3.9 19.1 - - + -
106E TYR* 3.5 14.4 - - + -
128E ILE* 2.8 24.7 + - + +
129E ILE* 3.7 8.3 - - - +
130E GLU 3.4 0.2 - - - -
131E GLU* 1.3 78.1 - - - +
133E GLN* 1.3 55.4 + - - +
135E HIS* 3.1 7.7 + - - +
136E LEU* 2.8 28.2 + - - +
200E FE2 2.1 28.1 - - - -
201E FE2 2.0 33.4 - - - -
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Residues in contact with GLN 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ARG* 3.3 28.8 + - - +
69D GLU* 4.4 13.5 + - - +
120D VAL* 4.0 26.9 - - + +
103E ILE* 4.1 13.6 - - + +
129E ILE 3.1 13.8 + - - +
130E GLU* 3.5 10.1 - - - +
131E GLU 3.1 0.6 - - - -
132E GLU* 1.3 72.8 - - - +
134E ALA* 1.3 65.6 + - - +
136E LEU* 3.9 23.6 - - - +
137E THR* 3.1 29.8 + - - +
140E GLU* 5.4 1.6 + - - -
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Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU 3.2 8.8 + - - +
131E GLU* 3.1 10.1 + - - +
133E GLN* 1.3 78.4 - - - +
135E HIS* 1.3 66.0 + - - +
137E THR* 3.5 6.2 + - - -
138E TYR* 3.1 21.8 + - - +
171F PHE* 4.0 9.7 - - + -
172F VAL* 4.0 19.1 - - + -
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Residues in contact with HIS 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E ILE* 3.9 24.9 - - + +
55E ASP* 2.7 45.1 + - + +
56E GLU* 3.4 12.0 + - - -
59E HIS* 4.1 6.5 - + - -
99E GLU* 3.4 15.3 - - + +
131E GLU 3.1 11.8 + - - -
132E GLU* 3.1 14.2 + - - +
134E ALA* 1.3 76.5 - - - +
136E LEU* 1.3 63.4 + - - +
138E TYR* 3.0 15.8 + - - +
139E TYR* 3.0 25.8 + - + -
201E FE2 2.3 27.3 - - - -
171F PHE* 4.0 9.4 - + - -
172F VAL* 3.8 5.0 - - + +
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ALA* 3.4 31.9 - - + +
99E GLU* 3.7 14.2 - - + +
100E ASP* 4.3 17.0 - - + +
103E ILE* 3.8 21.1 - - + -
132E GLU 2.8 19.6 + - - +
133E GLN* 3.7 20.9 - - - +
135E HIS* 1.3 72.5 - - - +
137E THR* 1.3 64.2 + - - +
139E TYR* 3.2 3.3 + - - +
140E GLU* 3.0 56.2 + - + +
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Residues in contact with THR 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU* 4.2 18.1 + - + +
133E GLN* 3.1 31.5 + - - +
134E ALA* 3.7 6.9 - - - -
136E LEU* 1.3 75.7 - - - +
138E TYR* 1.3 65.4 + - - +
140E GLU* 3.5 12.7 + - - +
141E ASN* 3.0 39.7 + - - +
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Residues in contact with TYR 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU* 3.7 25.1 + - - +
48E ASN* 3.3 39.3 + - + +
49E MET* 5.2 2.2 - - + -
52E ILE* 3.5 26.2 - - + -
92E TYR* 4.5 5.4 + + - -
134E ALA 3.1 9.5 + - - +
135E HIS* 3.0 8.7 + - - +
137E THR* 1.3 78.3 - - - +
139E TYR* 1.3 79.1 + + - +
141E ASN* 3.1 11.5 + - + +
142E ILE* 3.1 47.1 + - + +
171F PHE* 3.5 31.9 - + + -
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Residues in contact with TYR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 3.7 8.6 - - - -
49E MET* 3.3 39.2 - - + -
52E ILE* 3.3 31.6 - - + +
92E TYR* 3.7 30.9 - + - +
95E ASP* 3.6 28.3 - - + -
96E ALA* 3.8 17.0 - - + +
99E GLU* 3.7 32.3 - - + -
135E HIS* 3.0 22.1 + - + -
136E LEU 3.2 4.2 + - - +
138E TYR* 1.3 91.0 - + - +
140E GLU* 1.3 57.5 + - - +
142E ILE* 3.3 1.9 + - - +
143E GLY* 2.8 27.9 + - - -
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU 5.4 4.9 - - - +
96E ALA* 4.2 10.3 - - + +
133E GLN* 5.4 1.2 + - - -
136E LEU* 3.0 47.4 + - + +
137E THR* 3.8 13.3 + - - +
139E TYR* 1.3 77.2 - - - +
141E ASN* 1.3 60.9 + - - +
143E GLY* 3.8 0.8 - - - -
144E SER* 2.8 30.7 + - - -
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Residues in contact with ASN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP 5.0 2.0 + - - +
39C ASP 3.7 19.1 - - - +
41C ASP* 3.6 38.0 + - + +
137E THR* 3.0 37.6 + - - +
138E TYR* 3.1 10.8 + - + +
140E GLU* 1.3 80.4 - - - +
142E ILE* 1.3 65.0 + - + +
144E SER* 3.3 6.8 + - - -
145E HIS* 3.0 29.4 + - - -
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Residues in contact with ILE 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASP* 5.5 1.3 - - - +
159C GLY* 6.5 0.7 - - - -
45E LEU* 3.9 15.3 - - + -
92E TYR* 3.7 27.1 - - + -
138E TYR* 3.1 51.2 + - + +
139E TYR 3.9 1.1 - - - +
141E ASN* 1.3 78.0 - - + +
143E GLY* 1.3 59.4 + - - +
145E HIS* 2.9 10.3 + - + +
146E ILE* 2.8 48.9 + - + +
153E TYR* 3.3 26.7 - - + +
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Residues in contact with GLY 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E PRO* 5.9 1.3 - - - -
92E TYR* 3.8 18.5 - - - +
139E TYR 2.8 20.8 + - - -
140E GLU* 3.9 1.6 - - - -
142E ILE* 1.3 73.9 - - - +
144E SER* 1.3 57.0 + - - +
146E ILE* 3.9 7.0 - - - +
147E LYS* 2.9 30.6 + - - +
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Residues in contact with SER 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 5.0 8.8 + - - -
140E GLU 2.8 19.2 + - - -
141E ASN* 3.5 7.4 - - - -
142E ILE 3.1 0.2 - - - -
143E GLY* 1.3 77.2 - - - +
145E HIS* 1.3 63.2 + - - +
147E LYS* 3.3 3.7 + - - +
148E ASN* 2.8 37.6 + - - -
1403E SO4 3.1 34.4 + - - -
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Residues in contact with HIS 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET 3.4 17.9 + - - -
41C ASP* 2.6 47.7 + - + +
42C TYR* 4.5 7.9 + + - -
158C ALA* 3.6 22.7 - - + +
159C GLY* 3.6 6.7 + - - -
141E ASN* 3.0 22.1 + - - -
142E ILE* 2.9 10.2 + - + +
144E SER* 1.3 79.3 + - - +
146E ILE* 1.3 57.0 + - - +
148E ASN* 4.4 1.1 - - - +
149E LEU* 2.7 46.4 + - + +
150E GLY 3.5 0.5 + - - -
153E TYR* 4.0 36.7 - + + +
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Residues in contact with ILE 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU* 5.7 0.7 - - + -
88E VAL* 3.3 31.9 - - + +
89E PRO* 3.8 31.0 - - + -
92E TYR* 3.4 26.7 - - + -
142E ILE* 2.8 29.0 + - + +
143E GLY* 3.9 6.3 - - - +
145E HIS* 1.3 76.0 - - - +
147E LYS* 1.3 65.0 + - - +
150E GLY* 3.0 27.2 + - - +
153E TYR* 4.5 14.8 - - + -
154E LEU* 4.8 10.5 - - + -
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Residues in contact with LYS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E GLY 2.9 19.8 + - - +
144E SER* 3.6 2.7 - - - +
146E ILE* 1.3 82.1 - - - +
148E ASN* 1.3 71.5 + - - +
150E GLY 4.5 0.7 + - - -
1403E SO4 2.2 49.8 + - - +
85H GLY* 4.8 14.9 + - - +
87H ALA* 5.5 11.0 - - + +
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Residues in contact with ASN 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C TYR* 4.9 7.8 + - - +
151C ASP* 3.4 19.1 - - - +
144E SER* 2.8 32.8 + - - +
145E HIS* 5.0 0.4 - - - -
147E LYS* 1.3 84.6 + - - +
149E LEU* 1.3 69.3 + - + +
1403E SO4 2.1 34.6 + - - -
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Residues in contact with LEU 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASN* 5.9 0.9 + - - -
42C TYR* 4.0 20.6 - - - +
151C ASP* 3.7 39.2 - - + +
154C LEU* 4.1 5.6 - - + +
155C ALA* 3.5 29.4 - - + +
158C ALA* 3.8 20.9 - - + -
145E HIS* 2.7 27.5 + - + +
148E ASN* 1.3 84.1 - - + +
150E GLY* 1.3 64.4 + - - +
151E ASP 3.4 0.5 + - - -
152E THR* 3.3 18.1 + - - -
153E TYR* 3.8 17.7 - - + +
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Residues in contact with GLY 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASN* 6.2 1.8 - - - -
145E HIS 3.5 1.8 + - - -
146E ILE* 3.0 25.7 + - - -
147E LYS 4.5 0.6 + - - -
148E ASN 3.8 0.4 - - - -
149E LEU* 1.3 77.5 - - - +
151E ASP* 1.3 63.6 + - - -
153E TYR* 3.1 16.3 + - - +
154E LEU* 3.5 15.5 + - - +
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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