Contacts of the helix formed by residues 126 - 150 (chain D) in PDB entry 3J41
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 SER 126 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLY 4.0 1.4 + - - -
125D VAL* 1.3 77.8 - - - +
127D VAL* 1.3 58.7 + - - +
128D GLY* 3.2 6.2 + - - -
129D GLN* 3.0 40.5 + - - +
130D ALA* 2.9 25.5 + - - +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 5.1 2.7 - - - -
125D VAL 3.8 0.8 + - - -
126D SER* 1.3 73.5 - - - +
128D GLY* 1.3 56.7 + - - +
130D ALA* 3.7 7.5 - - - +
131D THR* 2.6 40.5 + - - +
200D ASN* 4.5 16.8 - - - +
202D TRP* 4.4 14.4 - - + +
203D VAL* 3.6 22.2 - - + +
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Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D SER* 3.1 6.7 + - - -
127D VAL* 1.3 81.3 - - - +
129D GLN* 1.3 63.3 + - - +
131D THR* 3.3 7.5 + - - -
132D ILE* 3.2 29.5 + - - +
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Residues in contact with GLN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER 2.6 31.3 + - - +
107A VAL* 2.8 48.1 - - + +
108A THR 4.1 6.1 + - - +
109A PRO* 5.2 2.5 - - - +
113A ARG* 5.0 4.4 - - - +
124D GLY 3.9 5.5 - - - +
125D VAL* 3.9 10.3 - - + -
126D SER* 3.0 38.9 + - - +
128D GLY* 1.3 76.1 - - - +
130D ALA* 1.3 57.3 + - - +
132D ILE* 3.1 8.7 + - + +
133D VAL* 2.9 17.5 + - - +
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 3.0 39.7 - - + -
125D VAL* 3.6 8.2 - - + +
126D SER 2.9 18.0 + - - +
127D VAL 3.7 5.6 - - - +
129D GLN* 1.3 78.8 - - - +
131D THR* 1.3 55.7 + - - +
133D VAL* 3.6 4.8 - - - +
134D GLU* 3.0 32.7 + - - +
179D THR* 3.5 9.0 - - + +
203D VAL* 3.9 5.2 - - + -
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Residues in contact with THR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D VAL* 2.6 25.0 + - - +
128D GLY* 3.6 7.8 - - - -
129D GLN 3.2 0.2 - - - -
130D ALA* 1.3 74.1 - - - +
132D ILE* 1.3 61.1 + - + +
134D GLU* 4.4 1.6 - - - -
135D ILE* 2.9 41.2 + - + +
202D TRP* 4.4 5.8 + - - +
203D VAL* 3.6 22.7 - - - +
206D VAL* 3.6 31.9 - - + -
207D GLY* 3.7 8.7 - - - +
210D ILE* 5.3 0.7 - - + -
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Residues in contact with ILE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 6.0 0.7 - - + -
103A VAL* 4.6 4.9 - - + -
106A SER* 5.5 2.0 - - - +
107A VAL* 3.6 26.9 - - + -
128D GLY 3.2 17.6 + - - +
129D GLN* 3.1 9.8 + - + +
131D THR* 1.3 75.1 - - - +
133D VAL* 1.3 67.1 + - - +
135D ILE* 3.2 13.7 + - + +
136D PHE* 3.0 45.1 + - + -
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 5.1 3.6 - - + -
107A VAL* 3.1 32.3 - - + -
125D VAL* 5.6 0.2 - - + -
129D GLN 2.9 9.4 + - - +
130D ALA* 3.6 9.9 - - - +
131D THR 3.3 0.2 - - - -
132D ILE* 1.3 77.8 - - - +
134D GLU* 1.3 64.2 + - - +
136D PHE* 3.1 6.7 + - - +
137D LEU* 2.9 41.3 + - + +
174D PHE* 3.6 30.5 - - + -
175D GLY* 4.6 0.9 - - - -
178D TYR* 4.1 32.8 - - + -
179D THR* 4.5 4.9 - - + +
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Residues in contact with GLU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ALA 3.0 20.9 + - - +
131D THR 3.8 0.4 - - - +
133D VAL* 1.3 76.6 - - - +
135D ILE* 1.3 56.7 + - - +
137D LEU* 3.6 8.2 - - - +
138D THR* 2.8 35.3 + - - -
179D THR* 2.6 27.0 + - - +
181D ALA* 3.4 2.4 - - - -
182D GLY* 2.7 23.5 + - - -
183D MET* 2.7 29.3 + - - -
203D VAL* 3.9 18.6 - - + +
204D TYR* 3.8 8.9 - - + -
207D GLY* 3.8 20.8 - - - -
208D PRO* 3.6 7.4 - - + +
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Residues in contact with ILE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D THR* 2.9 37.1 + - + +
132D ILE* 3.3 17.3 - - + +
133D VAL 3.1 0.4 - - - -
134D GLU* 1.3 76.0 - - - +
136D PHE* 1.3 70.5 + - + +
138D THR 3.4 0.2 + - - -
139D LEU* 2.8 35.2 + - + +
207D GLY* 3.4 22.7 - - - +
210D ILE* 3.7 25.6 - - + -
211D GLY* 3.3 15.6 - - - +
214D LEU* 3.9 19.3 - - + -
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Residues in contact with PHE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.6 28.3 - - + -
22A PHE* 4.0 22.5 - + - -
25A PHE* 3.9 37.0 - + + -
26A PHE* 3.4 6.2 - - + -
103A VAL* 3.5 27.6 - - + -
132D ILE* 3.0 41.2 + - + +
133D VAL 3.7 5.4 - - - +
135D ILE* 1.3 85.2 - - + +
137D LEU* 1.3 63.4 + - - +
139D LEU* 3.6 11.9 - - + +
140D GLN* 3.1 26.7 + - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.6 13.7 - - + -
133D VAL* 2.9 33.2 + - + +
134D GLU* 3.6 30.1 - - - +
136D PHE* 1.3 76.1 - - - +
138D THR* 1.3 62.9 + - - +
140D GLN* 3.0 26.7 - - - +
141D PHE* 3.2 6.8 + - - +
171D GLY* 3.5 21.1 - - - +
174D PHE* 3.3 37.2 - - + -
175D GLY* 4.1 2.9 - - - -
179D THR* 4.3 0.2 - - - +
181D ALA* 4.1 9.4 - - - -
183D MET* 3.5 24.7 - - + +
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Residues in contact with THR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN* 5.6 0.4 - - - +
70D ALA* 4.3 5.8 - - + -
71D VAL* 5.9 0.2 - - + -
134D GLU 2.8 18.1 + - - -
135D ILE 4.0 2.0 - - - -
137D LEU* 1.3 74.6 - - - +
139D LEU* 1.3 56.3 + - - +
141D PHE* 3.9 9.6 - - + -
142D VAL* 2.7 45.1 + - + +
183D MET* 3.6 20.3 - - - +
208D PRO* 3.0 47.5 - - + +
211D GLY* 4.2 0.9 - - - -
212D ALA* 3.7 8.1 - - + +
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Residues in contact with LEU 139 (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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22A PHE* 3.7 29.4 - - + -
135D ILE* 2.8 21.8 + - + +
136D PHE* 3.6 14.8 - - + +
137D LEU 3.3 0.2 - - - -
138D THR* 1.3 74.4 - - - +
140D GLN* 1.3 62.6 + - - +
142D VAL* 4.0 0.9 - - - +
143D LEU* 2.9 32.7 + - + +
211D GLY* 3.5 12.1 + - - +
214D LEU* 3.8 23.3 - - + +
215D GLY* 3.2 31.9 - - - +
218D LEU* 4.2 16.8 - - + -
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Residues in contact with GLN 140 (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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22A PHE* 4.9 13.0 - - + -
26A PHE* 3.3 26.0 - - + -
54A THR* 3.5 20.0 - - + +
55A LEU* 5.5 4.0 - - + -
58A ALA* 5.7 0.3 - - - +
136D PHE 3.1 13.9 + - - +
137D LEU 3.0 17.8 - - - +
139D LEU* 1.3 77.2 - - - +
141D PHE* 1.3 67.6 + - - +
143D LEU* 3.6 10.3 - - - +
144D CYS* 3.0 21.5 + - - +
167D SER* 2.6 44.0 + - - +
170D LEU* 4.0 12.2 - - + +
171D GLY* 3.8 8.7 + - - -
183D MET* 3.7 7.3 - - - +
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Residues in contact with PHE 141 (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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23D TYR* 5.7 0.9 - - - -
52D LEU* 3.3 27.4 - - + -
68D ASN* 3.9 11.7 - - + -
71D VAL* 3.8 26.0 - - + -
137D LEU 3.2 15.0 - - - +
138D THR* 3.4 11.0 - - + +
139D LEU 3.1 0.4 - - - -
140D GLN* 1.3 83.0 - - - +
142D VAL* 1.3 62.0 + - - +
144D CYS* 3.1 6.6 + - - +
145D ILE* 3.0 36.5 + - + +
164D VAL* 3.5 28.5 - - + -
167D SER* 3.3 20.9 - - - -
168D LEU* 3.9 19.5 - - + -
183D MET* 3.7 22.4 - - + -
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 4.6 16.2 - - + -
74D ALA* 3.8 12.3 - - + -
138D THR* 2.7 28.7 + - + +
139D LEU 4.1 1.8 - - - +
141D PHE* 1.3 70.9 - - + +
143D LEU* 1.3 61.2 + - - +
145D ILE* 3.0 10.5 + - + +
146D PHE* 2.8 49.3 + - + -
212D ALA* 3.5 45.3 - - + +
215D GLY* 4.1 2.0 - - - -
216D SER 3.9 10.5 - - - +
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 5.9 1.1 - - + -
22A PHE* 3.9 30.7 - - + -
55A LEU* 5.4 2.7 - - + -
58A ALA* 3.7 29.4 - - + +
59A VAL* 5.0 10.1 - - + -
139D LEU* 2.9 21.0 + - + +
140D GLN* 3.6 6.3 - - - +
142D VAL* 1.3 79.1 - - - +
144D CYS* 1.3 56.7 + - - +
146D PHE* 4.0 3.9 - - - +
147D ALA* 3.0 24.4 + - - +
215D GLY* 4.6 6.9 - - - +
218D LEU* 4.2 15.3 - - + -
219D TYR* 3.7 32.8 - - + +
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Residues in contact with CYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.0 24.9 - - + -
57A GLN* 4.4 2.5 - - - -
58A ALA* 4.6 7.9 - - - +
140D GLN 3.0 14.3 + - - +
141D PHE 3.4 9.2 - - - +
143D LEU* 1.3 74.3 - - - +
145D ILE* 1.3 57.1 + - + +
147D ALA* 4.6 1.3 - - - -
148D THR* 2.6 56.2 + - - +
163D ALA* 3.9 29.2 - - - -
164D VAL* 4.3 3.1 - - - -
167D SER* 3.8 13.5 - - - +
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 3.7 33.9 - - + -
75D PHE* 3.5 32.3 - - + -
141D PHE* 3.0 33.6 + - + +
142D VAL* 3.0 12.0 + - + +
144D CYS* 1.3 76.0 - - - +
146D PHE* 1.3 62.2 + - + +
148D THR* 3.2 6.0 + - - -
149D TYR* 2.8 51.6 + - + +
164D VAL* 3.9 24.0 - - + -
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Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 6.1 0.2 - - + -
74D ALA* 3.3 32.8 - - + -
75D PHE* 3.7 36.3 - + - -
78D GLY* 4.6 3.8 - - - -
80D GLN* 4.2 14.4 - - - -
142D VAL* 2.8 39.8 + - + +
143D LEU* 4.0 3.4 - - - +
145D ILE* 1.3 74.3 - - + +
147D ALA* 1.3 62.6 + - - +
149D TYR* 3.9 2.7 - - - +
150D ASP* 2.9 26.0 + - - +
216D SER* 3.3 27.4 - - - -
219D TYR* 3.8 27.2 - + + -
220D ASP* 3.5 22.0 - - - -
222D LEU* 6.4 0.7 - - + -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 3.6 7.0 - - - +
58A ALA* 3.4 37.0 - - - +
61A HIS* 4.0 0.2 - - - +
143D LEU 3.0 18.6 + - - +
144D CYS 4.1 2.2 - - - +
146D PHE* 1.3 76.4 - - - +
148D THR* 1.3 58.1 + - - +
150D ASP* 3.3 17.7 - - - +
153D ARG* 3.0 21.5 + - - +
219D TYR* 3.5 18.5 - - + -
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Residues in contact with THR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 3.8 35.9 - - + +
156C ARG* 3.8 12.0 + - - -
144D CYS* 2.6 30.3 + - - +
145D ILE 3.2 6.4 + - - -
147D ALA* 1.3 73.5 - - - +
149D TYR* 1.3 71.6 + - - +
150D ASP 3.3 1.3 - - - +
157D LEU* 3.9 12.3 - - + +
160D VAL* 3.6 31.3 - - - +
163D ALA* 4.1 11.4 - - + -
164D VAL* 3.6 11.3 - - - +
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Residues in contact with TYR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ARG* 4.7 6.2 + - - +
56D VAL* 4.0 17.9 - - + +
60D GLY* 6.1 0.2 - - - -
64D GLY* 2.7 37.5 + - - -
65D ALA 3.5 9.5 + - - -
66D HIS* 5.0 0.4 - + - -
75D PHE* 3.5 33.9 - + + -
80D GLN* 6.0 2.5 - - - +
145D ILE* 2.8 33.5 + - + +
146D PHE* 4.0 3.6 - - - +
148D THR* 1.3 81.5 - - - +
150D ASP* 1.3 65.4 + - - +
151D GLU* 3.0 9.5 + - - +
160D VAL* 4.2 16.6 - - + -
164D VAL* 4.1 19.4 - - + +
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Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A HIS* 4.6 2.1 - - - -
156C ARG* 3.3 12.5 + - - -
146D PHE 2.9 18.7 + - - +
147D ALA 3.3 11.7 - - - +
148D THR 3.3 0.5 - - - +
149D TYR* 1.3 74.0 - - - +
151D GLU* 1.3 69.1 + - - +
152D ARG* 3.0 55.1 + - - +
153D ARG* 3.4 17.6 + - + +
219D TYR* 2.4 25.2 + - - +
222D LEU* 4.0 8.3 - - + +
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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