Contacts of the helix formed by residues 134 - 164 (chain D) in PDB entry 1C03
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 ASN 134 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS 5.6 3.6 + - - +
56D LEU* 4.1 21.0 - - + +
91D LYS* 2.7 35.9 + - - -
132D ASP* 3.1 16.7 + - - +
133D GLU* 1.3 79.3 - - - +
135D SER* 1.3 54.3 + - - +
136D ILE 3.1 3.1 - - - -
137D TYR* 2.8 32.7 + - - +
138D LEU* 3.1 21.9 + - + +
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Residues in contact with SER 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ILE* 5.3 7.6 + - - +
131D LYS* 3.3 18.1 - - - +
132D ASP* 3.2 41.0 + - - +
133D GLU 3.4 0.2 - - - -
134D ASN* 1.3 77.7 - - - +
136D ILE* 1.3 56.6 + - - +
138D LEU* 3.6 11.7 + - - +
139D ILE* 3.1 38.4 + - - +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D HIS 5.6 1.1 - - - +
132D ASP 4.8 0.4 + - - -
133D GLU 4.4 7.6 + - - +
134D ASN 2.9 0.2 + - - -
135D SER* 1.3 80.0 - - - +
137D TYR* 1.3 87.7 + - + +
139D ILE* 3.5 18.2 + - + +
140D LEU* 3.1 48.4 + - + +
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D LEU* 4.5 13.2 - - + -
88D LEU* 3.4 32.8 - - + +
91D LYS* 3.7 41.5 - - + +
93D GLU 3.4 24.0 - - - -
94D HIS* 2.6 36.3 + + + -
133D GLU 4.3 7.9 - - - -
134D ASN 2.8 10.3 + - - +
136D ILE* 1.3 95.6 - - + +
138D LEU* 1.3 60.1 + - - +
140D LEU* 3.5 5.8 + - + +
141D ILE* 2.9 36.9 + - - +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 4.0 16.4 - - + +
54D LYS* 3.6 50.5 - - + +
56D LEU* 3.4 27.1 - - + -
59D LEU* 3.9 18.2 - - + -
126D ILE* 5.0 12.0 - - + +
132D ASP* 5.5 2.2 - - - +
134D ASN* 3.1 23.1 + - + +
135D SER* 3.9 10.8 - - - +
137D TYR* 1.3 76.6 - - - +
139D ILE* 1.3 58.9 + - - +
141D ILE* 4.0 3.1 - - - +
142D ALA* 3.1 27.7 + - - +
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ILE* 4.0 18.8 - - + +
126D ILE* 3.9 33.0 - - + +
135D SER* 3.1 23.2 + - - +
136D ILE* 3.7 21.1 - - + +
137D TYR 3.3 0.4 - - - -
138D LEU* 1.3 76.3 - - - +
140D LEU* 1.3 61.4 + - + +
142D ALA* 3.4 6.8 + - - +
143D LYS* 3.1 33.8 + - + +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LEU* 3.4 28.0 - - + +
94D HIS* 3.6 29.6 - - - +
95D PHE* 4.1 2.2 - - + -
96D PHE* 3.6 34.4 - - + +
136D ILE* 3.1 42.5 + - + +
137D TYR* 3.5 7.6 + - + +
139D ILE* 1.3 78.5 - - + +
141D ILE* 1.3 63.9 + - - +
142D ALA 3.3 0.2 - - - -
143D LYS* 3.6 17.1 + - + +
144D ALA* 3.1 15.9 + - - +
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D MET* 6.3 0.9 - - + -
50D LEU* 4.0 19.3 - - + -
56D LEU* 3.9 16.4 - - + -
59D LEU* 3.9 31.9 - - + -
85D ILE* 4.1 27.1 - - + +
88D LEU* 3.8 20.2 - - + -
89D GLY* 4.0 20.0 - - - +
137D TYR 2.9 21.9 + - - +
138D LEU* 4.0 4.9 - - - +
140D LEU* 1.3 75.4 - - - +
142D ALA* 1.3 58.6 + - - +
144D ALA* 2.8 21.7 + - - +
145D LEU* 2.8 14.2 + - + +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN* 6.3 0.4 - - - +
50D LEU* 4.0 25.8 - - + -
124D ILE* 3.8 25.6 - - + +
126D ILE* 6.2 1.3 - - + -
138D LEU 3.1 19.7 + - - +
139D ILE 3.6 6.3 - - - +
140D LEU 3.3 0.2 - - - -
141D ILE* 1.3 78.4 - - - +
143D LYS* 1.3 58.5 + - - +
145D LEU* 3.9 4.1 + - - +
146D ASN* 3.4 27.4 + - - -
149D ARG* 5.4 0.9 + - - -
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 2.7 35.9 + - + +
97D PRO 3.3 11.8 + - - -
98D ASN* 3.1 31.8 - - - +
99D LYS* 6.1 0.2 - - - -
124D ILE* 3.7 17.3 - - + -
139D ILE* 3.1 21.5 + - + +
140D LEU* 3.7 22.8 - - + +
141D ILE 3.1 0.2 - - - -
142D ALA* 1.3 76.5 - - - +
144D ALA* 1.3 63.0 + - - +
145D LEU 3.2 0.4 - - - -
146D ASN* 3.4 7.2 + - - +
147D GLN* 3.2 19.8 + - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D VAL* 3.2 9.8 - - + +
85D ILE* 3.6 22.9 - - + +
88D LEU* 4.5 4.3 - - + -
96D PHE* 3.7 32.3 - - + -
140D LEU 3.1 11.2 + - - +
141D ILE* 2.8 11.0 + - - +
143D LYS* 1.3 78.8 - - - +
145D LEU* 1.3 57.8 + - - +
147D GLN* 3.2 1.0 + - - +
148D SER* 2.9 30.5 + - - -
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 3.4 42.8 - - + +
46D MET* 3.9 29.6 - - + -
47D GLN* 3.8 10.1 - - - +
50D LEU* 3.7 25.4 - - + -
85D ILE* 4.3 6.5 - - + +
141D ILE* 2.8 15.1 + - + +
142D ALA* 4.0 7.4 - - - +
144D ALA* 1.3 75.2 - - - +
146D ASN* 1.3 58.5 + - - +
148D SER* 3.0 6.5 + - - -
149D ARG* 2.9 51.8 + - + +
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Residues in contact with ASN 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LYS* 4.3 8.0 + - - +
121D ASP* 3.3 34.2 + - - +
122D GLU 3.0 41.4 + - - +
124D ILE* 4.1 11.7 - - - +
142D ALA 3.4 17.1 + - - -
143D LYS* 3.4 9.6 + - - +
145D LEU* 1.3 77.3 - - - +
147D GLN* 1.3 59.2 - - - +
149D ARG* 3.1 24.6 + - - +
150D LEU* 3.4 18.4 + - - +
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Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D VAL* 4.1 17.7 - - + -
96D PHE* 3.9 11.1 - - + -
99D LYS* 3.3 43.8 - - - +
102D LEU* 3.6 33.7 - - + +
103D VAL* 4.6 2.6 - - - +
143D LYS 3.2 13.0 + - - +
144D ALA 3.5 9.0 - - - +
145D LEU 3.2 0.4 - - - -
146D ASN* 1.3 76.7 - - - +
148D SER* 1.3 60.8 + - - +
150D LEU* 3.3 10.5 + - - +
151D GLU* 2.7 57.4 + - - +
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 3.6 28.1 - - - -
78D ILE* 5.0 6.7 + - - +
81D VAL* 3.2 21.5 - - - +
82D CYS* 4.7 5.2 + - - -
85D ILE* 4.0 10.2 - - - +
144D ALA 2.9 16.3 + - - -
145D LEU* 3.0 12.8 + - - -
147D GLN* 1.3 75.3 - - - +
149D ARG* 1.3 59.1 + - - +
151D GLU* 3.4 6.1 + - - +
152D PHE* 2.9 28.8 + - - +
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Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 4.2 31.6 + - + +
44D ALA* 5.7 0.4 - - - +
47D GLN* 2.6 39.4 - - - +
120D ASP* 3.3 42.7 + - + +
122D GLU* 3.0 25.7 + - - +
142D ALA 5.4 0.6 + - - -
145D LEU* 2.9 36.0 + - - +
146D ASN* 3.1 26.2 + - - +
147D GLN 3.4 0.2 - - - -
148D SER* 1.3 77.0 - - - +
150D LEU* 1.3 60.0 + - - +
152D PHE* 3.5 9.9 + - - +
153D LYS* 3.2 22.0 + - - +
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LYS* 3.9 22.0 - - + -
103D VAL* 3.6 30.1 - - + -
112D ILE* 5.4 0.7 - - + -
115D ILE* 4.6 6.3 - - + -
117D ILE* 4.1 31.9 - - + +
119D GLU* 4.7 7.4 - - - +
120D ASP* 5.0 4.2 - - - +
146D ASN 3.4 12.0 + - - +
147D GLN* 3.3 16.2 + - - +
148D SER 3.2 0.6 - - - -
149D ARG* 1.3 75.9 - - - +
151D GLU* 1.3 70.1 + - - +
153D LYS* 3.4 5.4 + - + +
154D LEU* 3.1 44.9 + - + +
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.3 3.3 - - - +
8D ILE* 5.3 3.1 - - - +
77D ARG* 2.6 52.5 + - + +
78D ILE* 3.9 22.5 - - + +
81D VAL* 4.2 15.7 - - + -
103D VAL* 5.4 1.6 - - - +
147D GLN* 2.7 44.9 + - - +
148D SER* 3.4 5.1 + - - +
150D LEU* 1.3 77.5 - - - +
152D PHE* 1.3 65.1 + - - +
154D LEU* 3.4 14.5 + - - +
155D ALA* 3.0 24.3 + - - +
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Residues in contact with PHE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PHE* 3.8 23.6 - + - -
36D ILE* 3.5 38.8 - - + -
39D ALA* 3.5 22.2 - - + -
40D GLN* 3.7 26.0 - - + -
43D PHE* 3.8 21.1 - + + -
78D ILE* 3.7 12.3 - - + +
148D SER 2.9 18.4 + - - +
149D ARG* 3.5 8.1 - - - +
151D GLU* 1.3 74.9 - - - +
153D LYS* 1.3 62.7 + - + +
155D ALA* 3.0 15.9 + - + +
156D ARG* 3.0 39.2 + - + +
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Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 4.1 27.2 - - + +
119D GLU* 3.1 48.0 + - - +
120D ASP* 3.7 10.4 + - - +
149D ARG 3.2 10.7 + - - +
150D LEU* 3.7 9.9 - - + +
151D GLU 3.3 0.2 - - - -
152D PHE* 1.3 81.2 - - + +
154D LEU* 1.3 60.0 + - + +
156D ARG* 3.2 13.6 + - - +
157D ILE* 3.0 38.3 + - + +
168D HIS* 4.3 19.2 - - + -
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Residues in contact with LEU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 3.4 19.0 - - + +
103D VAL* 5.9 0.9 - - + -
106D LEU* 3.7 30.1 - - + -
111D ILE* 4.4 13.9 - - + +
112D ILE* 3.7 15.7 - - + -
115D ILE* 3.7 30.1 - - + -
150D LEU* 3.1 32.7 + - + +
151D GLU* 3.8 19.5 - - - +
152D PHE 3.3 0.2 - - - -
153D LYS* 1.3 75.0 - - + +
155D ALA* 1.3 61.8 + - - +
157D ILE* 4.0 7.9 - - + +
158D GLU* 3.1 29.8 + - - +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 3.8 16.1 - - + +
35D PHE* 5.7 0.2 - - + -
75D LEU* 4.2 21.8 - - + -
78D ILE* 4.0 18.4 - - + -
151D GLU 3.0 12.0 + - - +
152D PHE* 3.1 12.6 - - + +
154D LEU* 1.3 79.1 - - - +
156D ARG* 1.3 57.2 + - + +
158D GLU* 3.5 1.7 + - - +
159D LEU* 3.0 38.5 + - + +
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Residues in contact with ARG 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 3.5 34.3 - - + +
40D GLN* 3.2 22.6 + - - +
152D PHE* 3.0 39.2 + - + +
153D LYS* 3.4 10.2 - - - +
155D ALA* 1.3 74.1 - - + +
157D ILE* 1.3 65.1 + - - +
158D GLU 3.2 0.2 - - - -
159D LEU* 3.3 4.6 + - + -
160D SER* 3.0 26.7 + - - -
167D LEU* 3.0 38.0 + - - +
168D HIS* 3.3 32.5 - - + +
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ILE* 3.6 37.7 - - + +
115D ILE* 4.2 23.8 - - + -
153D LYS* 3.0 32.4 + - + +
154D LEU* 4.1 7.6 - - + +
156D ARG* 1.3 76.8 - - - +
158D GLU* 1.3 63.8 + - - +
160D SER* 3.2 19.9 + - - -
161D LYS* 3.7 7.6 + - + +
168D HIS* 3.5 28.7 - - + +
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 4.0 19.4 - - + +
9D ILE* 3.6 27.3 - - + +
11D TRP* 4.9 4.5 + - - -
111D ILE* 3.3 12.9 - - + +
154D LEU 3.1 20.9 + - - +
155D ALA 3.8 3.6 - - - +
157D ILE* 1.3 79.3 - - - +
159D LEU* 1.3 59.2 + - - +
160D SER 3.3 0.2 - - - -
161D LYS* 2.9 37.7 + - - +
162D TYR* 3.2 38.7 + - - -
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 3.6 25.8 - - + -
11D TRP* 5.3 0.4 - - + -
14D LEU* 4.1 15.3 - - + -
32D ILE* 4.0 39.9 - - + -
35D PHE* 6.3 0.4 - - + -
36D ILE* 6.2 0.7 - - + -
75D LEU* 4.1 24.0 - - + -
155D ALA* 3.0 28.5 + - + +
156D ARG* 4.0 3.4 - - + +
157D ILE 3.3 0.2 - - - -
158D GLU* 1.3 74.7 - - - +
160D SER* 1.3 64.0 + - - +
161D LYS 3.2 0.2 - - - -
162D TYR* 3.0 16.3 + - + +
163D TYR* 3.1 26.2 + - + -
167D LEU* 3.6 18.2 - - + -
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ARG 3.0 12.2 + - - -
157D ILE* 3.2 13.6 - - - -
159D LEU* 1.3 72.5 - - - +
161D LYS* 1.3 61.1 + - - +
162D TYR 3.0 6.6 + - - -
163D TYR* 4.4 1.3 - - - +
164D ASN* 3.2 21.7 + - - -
165D THR 3.2 16.7 + - - +
166D ASN* 3.7 11.8 + - - -
167D LEU* 2.9 31.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ASP* 5.0 10.1 + - - -
111D ILE* 3.7 19.2 - - - +
157D ILE* 4.1 5.8 - - + +
158D GLU* 2.9 44.7 + - - +
159D LEU 3.2 0.6 - - - -
160D SER* 1.3 77.2 - - - +
162D TYR* 1.3 78.6 + - + +
164D ASN* 4.5 9.0 - - - +
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Residues in contact with TYR 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 4.8 0.7 - - + -
11D TRP* 3.6 41.5 + + + -
158D GLU* 3.2 47.1 + - + -
159D LEU* 3.0 9.1 + - + +
160D SER 3.0 0.2 - - - -
161D LYS* 1.3 99.4 + - + +
163D TYR* 1.3 72.9 + - + +
164D ASN* 3.3 15.1 + - - -
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Residues in contact with TYR 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D TRP* 5.7 1.1 - + - -
14D LEU* 4.8 3.9 - - + +
18D ILE* 3.7 22.2 - - + +
21D ASP* 5.0 2.0 - - - -
28D SER* 2.8 34.2 + - - -
29D LYS* 3.6 39.7 + - + +
32D ILE* 3.5 24.7 - - + +
159D LEU* 3.1 38.2 + - + +
160D SER 4.8 0.4 - - - +
162D TYR* 1.3 87.7 - - + +
164D ASN* 1.3 69.8 + - - +
165D THR* 3.0 23.4 + - + +
167D LEU* 4.1 13.2 - - + -
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Residues in contact with ASN 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D SER 3.2 10.1 + - - -
161D LYS 4.5 8.2 - - - +
162D TYR 3.3 12.7 + - - -
163D TYR* 1.3 78.0 - - - +
165D THR* 1.3 58.6 + - - +
----------------------------------------------------------
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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