Contacts of the helix formed by residues 111 - 134 (chain D) in PDB entry 6N1G
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 LYS 111 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LYS 5.4 3.6 + - - -
33D MET* 3.6 30.4 - - - +
36D GLU* 5.7 1.0 - - - +
107D VAL* 5.2 0.9 - - + -
108D PRO* 3.0 37.0 + - + +
110D ARG* 1.3 82.3 - - + +
112D PHE* 1.3 58.0 + - - +
113D PRO 3.5 1.3 - - - -
114D VAL* 3.1 6.0 - - + +
115D TYR* 2.7 73.3 + - + +
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Residues in contact with PHE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ALA* 3.6 12.3 - - + -
98D THR* 3.4 24.9 - - + -
99D PHE* 3.3 59.2 - + + -
102D CYS* 3.9 17.7 - - + -
108D PRO 3.5 3.6 + - - +
109D TRP* 4.0 8.7 - - - +
111D LYS* 1.3 78.3 - - - +
113D PRO* 1.4 74.9 - - + +
115D TYR* 3.4 6.7 + - - +
116D VAL* 3.2 32.2 + - + +
262D LEU* 5.2 5.8 - - + -
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Residues in contact with PRO 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D TRP 3.4 13.9 - - - +
110D ARG* 4.0 9.0 - - - +
111D LYS 3.7 1.1 - - - -
112D PHE* 1.4 99.3 - - + +
114D VAL* 1.3 66.8 + - - +
116D VAL* 3.0 28.1 + - + +
117D LEU* 3.2 7.6 + - - +
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D MET* 3.4 34.5 - - + -
37D PHE* 2.7 55.1 - - + -
110D ARG 4.0 5.8 - - - +
111D LYS* 3.1 28.7 - - + +
113D PRO* 1.3 80.4 - - + +
115D TYR* 1.3 56.4 + - - +
117D LEU* 3.7 3.3 + - - +
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Residues in contact with TYR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D MET* 3.1 27.1 - - + -
36D GLU* 2.7 55.2 - - + +
37D PHE* 4.9 0.9 - - - -
40D GLU* 4.0 8.8 - - - +
89D SER 4.8 3.3 + - - -
92D HIS* 3.7 32.1 - + - -
98D THR* 4.0 12.6 - - + +
107D VAL* 5.1 5.2 - - + -
108D PRO* 5.0 0.7 - - - +
111D LYS* 2.7 61.5 + - + +
112D PHE* 3.6 6.7 - - - +
113D PRO 3.1 0.2 - - - -
114D VAL* 1.3 78.2 - - - +
116D VAL* 1.3 59.4 + - - +
118D GLY* 3.5 3.5 + - - -
119D GLN* 3.1 27.9 + - - +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ALA* 3.5 33.0 - - + -
98D THR* 5.9 1.3 - - - +
112D PHE* 3.2 25.4 + - + +
113D PRO* 3.0 24.7 + - + +
115D TYR* 1.3 76.3 - - - +
117D LEU* 1.3 58.9 + - + +
119D GLN* 3.4 10.8 + - + +
120D PHE* 3.1 29.7 + - + +
228D SER* 5.7 1.8 - - - -
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.5 19.2 - - + -
113D PRO 3.2 13.1 + - - +
114D VAL* 3.7 2.2 + - - +
115D TYR 3.3 0.2 - - - -
116D VAL* 1.3 79.6 - - + +
118D GLY* 1.3 56.8 + - - +
120D PHE* 4.1 13.9 - - + -
121D LEU* 3.3 31.0 + - + +
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Residues in contact with GLY 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.0 38.4 - - - -
40D GLU* 4.3 1.3 - - - -
41D PHE* 3.1 25.9 - - - -
115D TYR 3.5 3.8 + - - -
116D VAL 3.3 0.4 - - - -
117D LEU* 1.3 75.0 - - - +
119D GLN* 1.3 60.9 + - - +
120D PHE 3.5 0.2 - - - -
121D LEU* 4.7 1.1 - - - -
122D GLY* 3.0 20.5 + - - -
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLU* 2.5 29.6 + - + +
44D THR* 3.7 23.7 - - + +
93D MET 3.3 3.6 - - - +
94D ASN 3.2 24.7 - - - +
95D ALA* 3.3 27.0 + - - +
98D THR* 3.6 15.8 + - - -
115D TYR 3.1 17.7 + - - +
116D VAL* 3.4 15.0 + - - +
118D GLY* 1.3 75.4 - - - +
120D PHE* 1.3 60.8 + - - +
122D GLY 3.6 0.2 + - - -
123D SER* 3.1 21.8 + - - -
228D SER* 2.7 24.5 + - - +
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Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL* 3.1 18.4 + - + +
117D LEU* 4.4 13.9 - - + +
119D GLN* 1.3 73.2 - - - +
121D LEU* 1.3 67.5 + - + +
123D SER 3.1 1.6 + - - -
124D PHE* 2.9 26.6 + - + -
228D SER* 3.1 14.4 + - - +
231D LEU* 3.3 36.8 - - + -
232D PRO* 3.1 28.6 - - + +
235D ILE* 3.4 43.3 - - + -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.9 11.9 - - + -
41D PHE* 3.4 26.8 - - + -
117D LEU* 3.3 24.0 + - + +
120D PHE* 1.3 84.8 - - + +
122D GLY* 1.3 57.6 + - - +
124D PHE* 4.0 16.6 - - + +
125D LEU* 3.1 24.9 + - + +
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Residues in contact with GLY 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.4 38.3 - - - -
45D TYR* 2.9 33.1 - - - -
118D GLY 3.0 14.5 + - - -
119D GLN 4.0 1.8 - - - -
120D PHE 3.2 0.2 - - - -
121D LEU* 1.3 75.9 - - - +
123D SER* 1.3 56.9 + - - +
126D ALA* 3.2 6.7 + - - +
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Residues in contact with SER 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 2.9 32.8 + - - +
48D MET* 4.6 5.8 - - - -
119D GLN 3.1 6.0 + - - -
120D PHE 3.1 1.6 + - - -
122D GLY* 1.3 75.6 - - - +
124D PHE* 1.3 63.7 + - - +
125D LEU 3.3 0.9 - - - -
126D ALA* 3.4 9.0 - - - +
127D ALA* 3.0 23.7 + - - +
228D SER 3.0 25.4 + - - -
229D ARG* 4.5 1.7 - - - -
232D PRO* 3.6 9.2 - - - -
233D PRO* 4.1 12.0 - - - +
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D PHE* 2.9 16.7 + - + +
121D LEU* 4.0 20.6 - - + +
123D SER* 1.3 76.6 - - - +
125D LEU* 1.3 71.2 + - + +
127D ALA* 3.6 4.0 + - - +
128D ALA* 3.4 20.8 + - + +
232D PRO* 3.4 14.0 - - + +
235D ILE* 3.3 40.2 - - + -
236D PHE* 3.6 38.3 - + + +
239D ILE* 4.7 12.3 - - + -
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.3 30.7 - - + -
45D TYR* 2.5 38.2 + - + +
121D LEU* 3.1 18.0 + - + +
124D PHE* 1.3 84.7 - - + +
126D ALA* 1.3 59.1 + - - +
128D ALA* 3.3 12.0 + - + +
129D THR* 3.1 13.4 + - - +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D TYR* 3.0 32.7 - - + +
48D MET* 3.3 30.7 - - + -
49D VAL* 4.3 5.0 - - - +
122D GLY 3.2 17.9 + - - +
123D SER* 3.2 5.3 + - - +
125D LEU* 1.3 76.5 - - - +
127D ALA* 1.3 63.5 + - - +
128D ALA 3.2 0.5 + - - -
129D THR* 3.2 5.0 + - - -
130D ILE* 3.2 21.7 + - - +
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Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D MET* 4.5 1.0 - - - +
52D LEU* 3.7 18.2 - - + -
123D SER 3.0 14.5 + - - +
124D PHE 4.0 4.0 - - - +
125D LEU 3.4 0.2 - - - -
126D ALA* 1.3 76.7 - - - +
128D ALA* 1.3 57.0 + - - +
130D ILE* 3.0 12.0 - - - +
131D TYR* 2.9 31.0 + - - +
158D PHE* 3.8 13.1 - - + -
233D PRO* 4.1 15.7 - - + -
236D PHE* 3.7 14.8 - - + -
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D PHE* 3.4 12.9 + - + +
125D LEU* 3.3 20.2 + - + +
126D ALA 3.1 1.0 - - - -
127D ALA* 1.3 79.4 - - - +
129D THR* 1.3 54.5 + - - +
131D TYR* 3.4 1.9 + - - +
132D SER* 2.7 38.4 + - - +
236D PHE* 3.7 28.2 - - + -
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Residues in contact with THR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU* 4.9 7.4 - - + -
177B TRP* 3.8 37.4 - - + +
45D TYR* 1.9 35.0 + - - +
49D VAL* 5.8 1.6 - - + -
125D LEU* 3.1 4.2 + - - +
126D ALA 3.2 4.4 + - - -
128D ALA* 1.3 75.9 - - - +
130D ILE* 1.3 58.9 + - - +
132D SER* 3.8 5.4 - - - -
133D LEU* 3.0 46.2 + - + +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B SER 4.5 1.3 - - - +
217B LEU* 4.6 10.3 - - + -
49D VAL* 4.4 15.2 - - + +
52D LEU* 3.2 38.6 - - + +
53D GLY* 3.4 31.2 - - - +
56D ALA* 4.5 4.9 - - + -
126D ALA 3.2 11.4 + - - +
127D ALA 3.0 15.9 - - - +
129D THR* 1.3 75.5 - - - +
131D TYR* 1.3 59.2 + - - +
133D LEU* 4.5 2.5 - - + +
134D PHE* 3.1 62.1 + - + +
158D PHE* 4.5 3.1 - - + -
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Residues in contact with TYR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ALA 2.9 18.9 + - - +
128D ALA 4.9 0.9 - - - -
130D ILE* 1.3 76.0 - - - +
132D SER* 1.3 63.2 + - - +
133D LEU 3.3 0.2 - - - -
134D PHE* 3.9 2.5 - - - +
135D TYR* 3.0 62.6 + + - +
138D ILE* 3.4 45.0 - - + +
158D PHE* 4.1 17.9 - + + -
236D PHE* 3.5 28.9 - + + -
240D ALA* 4.3 20.0 + - + -
242D TRP* 4.4 10.8 - + - -
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Residues in contact with SER 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 3.7 19.1 + - - -
173B LEU* 5.4 14.0 - - - +
128D ALA* 2.7 24.6 + - - +
129D THR* 3.8 8.9 - - - -
130D ILE 3.4 0.2 - - - -
131D TYR* 1.3 81.5 - - - +
133D LEU* 1.3 64.7 + - - +
135D TYR* 3.8 7.3 - - - +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B MET* 4.0 9.7 - - - +
170B ARG* 3.7 13.8 + - - +
173B LEU* 2.8 37.2 - - + -
174B ASN* 3.8 30.4 - - + +
177B TRP* 4.1 13.9 - - + -
217B LEU* 3.8 25.1 - - + -
220B ASN* 3.5 13.9 - - - +
49D VAL* 5.8 1.3 - - + -
129D THR* 3.0 36.4 + - + +
130D ILE* 4.1 2.5 - - - +
132D SER* 1.3 78.1 - - - +
134D PHE* 1.3 69.6 + - + +
135D TYR 3.4 2.5 - - - -
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 5.9 0.2 - - - -
170B ARG* 4.1 0.7 - - - -
216B SER 3.5 19.3 - - - -
217B LEU* 4.6 2.5 - - + -
220B ASN* 3.1 32.8 - - - -
53D GLY 3.9 2.0 - - - -
56D ALA* 3.6 16.4 - - + -
57D HIS* 3.5 27.4 - + + -
60D LEU* 5.0 2.0 - - + -
61D ASN* 3.5 25.8 - - - -
130D ILE* 3.1 43.1 + - + +
131D TYR* 3.8 2.7 - - - +
133D LEU* 1.3 84.9 - - + +
135D TYR* 1.3 65.0 + - - +
136D THR 3.2 2.7 - - - -
137D ALA* 2.8 24.1 + - + +
138D ILE* 3.3 17.4 + - + +
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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) + - + + + + + -
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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