Contacts of the helix formed by residues 108 - 136 (chain D) in PDB entry 5AIX
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 108 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLU* 3.1 25.9 - - + +
107D LYS* 1.3 77.0 - - - +
109D GLN* 1.3 56.3 + - - +
110D ASP* 3.6 1.6 - - - -
111D VAL* 3.3 22.2 + - + +
112D LYS* 2.8 36.5 + - - +
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Residues in contact with GLN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LYS* 3.0 21.5 + - - +
108D LYS* 1.3 70.8 - - - +
110D ASP* 1.3 67.9 + - - +
112D LYS* 3.0 35.5 + - - +
113D GLU* 2.8 54.0 + - - +
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLN* 1.3 81.7 + - - +
111D VAL* 1.3 67.2 + - - +
113D GLU* 3.8 15.5 - - + +
114D GLN* 2.9 21.4 + - - +
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PRO* 4.9 0.9 - - - +
106D GLU* 4.4 12.8 - - - +
108D LYS* 3.3 30.6 + - + +
110D ASP* 1.3 85.1 - - - +
112D LYS* 1.3 59.4 + - - +
114D GLN* 3.2 11.2 - - + +
115D MET* 3.1 32.2 + - + +
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PRO* 3.8 21.2 - - - +
104D TRP 5.4 2.5 - - - +
106D GLU* 3.0 36.3 + - + +
107D LYS* 6.0 0.4 - - - +
108D LYS 2.8 18.4 + - - +
109D GLN* 3.0 32.1 - - - +
111D VAL* 1.3 71.8 - - - +
113D GLU* 1.3 74.7 + - - +
114D GLN 3.0 1.8 + - - -
115D MET 3.2 2.6 + - - -
116D PHE* 3.1 45.8 + - + -
163D PHE* 6.2 2.5 - - - -
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLN* 2.8 52.6 + - - +
110D ASP* 3.8 12.2 + - - +
112D LYS* 1.3 87.1 + - - +
114D GLN* 1.3 60.3 + - - +
116D PHE* 3.5 9.4 - - + +
117D ASN* 3.3 37.2 + - - +
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Residues in contact with GLN 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ASP 2.9 25.2 + - - +
111D VAL* 3.2 16.4 - - + +
112D LYS 3.0 1.4 - - - -
113D GLU* 1.3 79.1 - - - +
115D MET* 1.3 68.3 + - + +
117D ASN* 4.1 0.5 - - - +
118D GLU* 3.2 50.6 + - - +
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Residues in contact with MET 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C MET* 6.1 6.3 - - + -
103D PRO* 4.0 21.5 - - + -
111D VAL* 3.1 18.1 + - + +
114D GLN* 1.3 81.8 - - + +
116D PHE* 1.3 59.5 + - - +
118D GLU* 3.1 29.8 - - - +
119D LEU* 2.8 44.5 + - + +
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Residues in contact with PHE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PHE* 3.5 40.4 - + + -
103D PRO* 3.5 30.5 - - + +
104D TRP* 5.0 16.8 - + - -
112D LYS* 3.1 42.9 + - + -
113D GLU* 3.5 13.0 - - - +
114D GLN 3.3 0.2 - - - -
115D MET* 1.3 71.9 - - - +
117D ASN* 1.3 60.0 + - - +
118D GLU 2.9 2.9 - - - -
119D LEU* 2.7 24.6 + - - +
120D LEU* 2.8 25.9 + - + +
163D PHE* 3.4 47.3 - + + -
199D LEU* 6.5 0.2 - - + -
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Residues in contact with ASN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D GLU* 3.3 25.0 + - - +
114D GLN 4.1 1.3 - - - +
116D PHE* 1.3 78.2 - - - +
118D GLU* 1.3 56.8 + - - +
120D LEU* 3.4 22.7 - - + +
121D THR* 2.4 32.0 + - - +
122D TYR* 3.6 5.5 - - - -
163D PHE* 4.5 7.9 - - - +
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLN* 3.2 42.4 + - - +
115D MET* 3.1 34.1 - - - +
116D PHE 2.9 0.6 + - - -
117D ASN* 1.3 75.8 - - - +
119D LEU* 1.3 66.3 + - + +
122D TYR* 2.9 38.6 + - + +
123D ASN* 4.1 2.3 - - - +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.5 8.6 - - + -
101D CYS* 3.3 54.5 - - + +
102D PHE* 3.7 26.2 - - + -
103D PRO* 4.4 2.5 - - + -
115D MET* 2.8 30.9 + - + +
116D PHE 2.7 9.1 + - - +
118D GLU* 1.3 74.9 - - + +
120D LEU* 1.3 56.7 + - - +
123D ASN* 2.7 54.4 + - + +
124D ALA 3.1 7.1 + - - -
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 4.8 0.9 - - - -
102D PHE* 3.9 12.1 - - + -
116D PHE* 2.8 19.9 + - + +
117D ASN* 3.4 28.7 - - - +
119D LEU* 1.3 80.0 - - - +
121D THR* 1.3 61.1 + - - +
122D TYR 3.0 6.1 + - - -
124D ALA* 3.1 26.8 - - + +
125D PRO* 3.4 1.7 - - - +
160D LEU* 3.6 36.3 - - + +
163D PHE* 3.3 46.7 - - + +
164D LYS* 3.8 17.3 - - + +
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Residues in contact with THR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASN* 2.4 29.0 + - - +
118D GLU 3.6 2.2 + - - -
120D LEU* 1.3 75.1 - - - +
122D TYR* 1.3 85.9 + - + +
125D PRO* 3.5 15.4 - - - +
164D LYS* 3.3 28.4 + - + +
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASN 3.6 8.7 - - - -
118D GLU* 2.9 25.3 + - + +
120D LEU 3.1 0.2 - - - -
121D THR* 1.3 106.6 - - + +
123D ASN* 1.3 67.9 + - - +
125D PRO* 3.6 6.4 - - - +
126D HIS* 3.1 28.4 + - - -
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Residues in contact with ASN 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D PHE* 3.3 20.6 - - + -
118D GLU 4.1 3.1 - - - +
119D LEU* 2.7 47.6 + - - +
122D TYR* 1.3 77.2 - - - +
124D ALA* 1.3 62.8 + - - +
126D HIS* 3.2 10.9 + - - +
127D LEU* 3.1 17.8 + - - +
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Residues in contact with ALA 124 (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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98D PHE* 3.7 15.3 - - + -
119D LEU 3.1 5.1 + - - -
120D LEU* 3.1 22.7 - - + +
123D ASN* 1.3 72.9 - - - +
125D PRO* 1.3 68.5 - - + +
127D LEU* 2.8 4.0 + - - -
128D MET* 2.7 38.5 + - + +
160D LEU* 5.7 3.1 - - + -
164D LYS* 4.9 2.7 - - + -
167D LEU* 3.8 24.0 - - + -
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Residues in contact with PRO 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LEU 3.4 14.8 - - - +
121D THR* 3.5 17.3 - - - +
122D TYR* 3.6 9.0 - - - +
123D ASN 3.5 3.8 - - - -
124D ALA* 1.3 88.6 - - + +
126D HIS* 1.3 64.8 + - + +
128D MET* 3.9 6.0 - - + +
129D GLN* 2.9 31.5 + - - +
164D LYS* 4.9 9.9 - - - +
167D LEU* 5.3 0.6 - - + -
171D HIS* 4.5 3.9 + - - +
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Residues in contact with HIS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D TYR 3.1 27.0 + - - -
123D ASN* 3.2 6.8 + - - +
124D ALA 3.1 0.6 - - - -
125D PRO* 1.3 80.8 - - + +
127D LEU* 1.3 64.7 + - - +
129D GLN* 3.5 4.3 + - - +
130D ASP* 2.8 39.6 + - - +
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 4.9 4.3 - - + -
94D THR* 3.8 25.4 - - + +
95D LEU* 5.4 8.5 - - + -
98D PHE* 3.6 40.2 - - + -
123D ASN 3.1 11.7 + - - +
124D ALA* 2.8 9.4 + - - +
126D HIS* 1.3 74.9 - - - +
128D MET* 1.3 84.4 + - + +
130D ASP* 2.8 18.3 + - - +
131D LEU* 2.9 38.7 + - + +
160D LEU* 5.3 2.5 - - + -
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Residues in contact with MET 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ALA* 2.7 29.8 + - + +
125D PRO* 3.9 2.5 - - + +
127D LEU* 1.3 98.4 - - + +
129D GLN* 1.3 64.6 + - - +
131D LEU* 3.0 19.6 + - + +
132D ASP* 2.9 20.6 + - - +
153D TRP* 3.9 9.0 - - + -
160D LEU* 4.4 13.5 - - + -
167D LEU* 3.1 42.2 - - + +
168D LEU* 3.8 18.6 - - + -
171D HIS* 3.3 22.4 - - + +
174D LEU* 3.3 8.0 - - + +
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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
----------------------------------------------------------
125D PRO 2.9 19.7 + - - +
126D HIS* 3.8 6.7 - - - +
127D LEU 3.1 0.2 - - - -
128D MET* 1.3 78.9 - - - +
130D ASP* 1.3 62.8 + - - +
132D ASP* 3.3 7.1 - - - +
133D THR* 2.9 35.3 + - - +
171D HIS* 3.5 28.0 + - + -
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO 3.2 27.5 - - - +
48C PHE* 4.1 25.8 - - + +
126D HIS* 2.8 26.1 - - - +
127D LEU* 2.8 12.9 + - + +
129D GLN* 1.3 79.3 - - - +
131D LEU* 1.3 56.9 + - - +
133D THR* 3.8 6.1 - - - -
134D TYR* 2.7 35.5 + - - +
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 3.3 26.5 - - + -
91D ILE* 5.4 4.0 - - + -
94D THR* 4.7 3.4 - - + -
95D LEU* 4.5 13.2 - - + -
127D LEU* 2.9 40.1 + - + +
128D MET* 3.3 20.9 - - + +
130D ASP* 1.3 76.9 - - - +
132D ASP* 1.3 53.9 + - - +
134D TYR* 3.1 6.7 + - - +
135D LEU* 2.7 37.8 + - - +
141D LEU* 5.0 9.3 - - + +
153D TRP* 3.7 31.6 - - + -
174D LEU* 3.8 14.8 - - + -
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D MET 2.9 11.7 + - - +
129D GLN* 3.3 17.7 - - - +
131D LEU* 1.3 77.9 - - - +
133D THR* 1.3 58.7 + - - +
135D LEU* 3.3 3.5 + - - +
136D GLY 3.0 23.9 + - - -
170D ASN 4.5 0.3 - - - +
171D HIS* 3.0 44.2 + - - +
172D PRO* 4.6 1.7 - - - +
173D ARG* 2.6 46.7 + - - +
174D LEU* 3.8 15.6 + - + +
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Residues in contact with THR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 6.1 4.5 - - + +
129D GLN* 2.9 28.4 + - - +
130D ASP* 3.8 7.2 - - - -
132D ASP* 1.3 76.8 - - - +
134D TYR* 1.3 67.4 + - - +
136D GLY* 3.6 9.8 + - - +
173D ARG* 4.9 4.0 - - - +
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Residues in contact with TYR 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 5.0 11.7 - - + -
48C PHE* 3.7 28.9 - + + -
62C HIS* 5.2 4.9 + + - -
87D HIS* 3.9 34.7 + + - +
91D ILE* 3.6 31.8 - - + +
130D ASP 2.7 22.4 + - - +
131D LEU* 3.4 3.8 - - - +
133D THR* 1.3 76.4 - - - +
135D LEU* 1.3 66.0 + - - +
136D GLY* 4.2 0.7 - - - -
138D ARG* 3.5 18.7 + - - -
141D LEU* 3.4 36.3 + - + -
142D ILE* 4.5 1.4 - - - +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D LEU 2.7 21.0 + - - +
132D ASP* 3.3 4.7 + - - +
134D TYR* 1.3 75.2 - - - +
136D GLY* 1.3 61.0 + - - +
138D ARG* 2.8 53.0 + - - +
139D GLU 4.9 0.9 - - - +
140D TRP* 3.8 26.5 - - - +
141D LEU* 3.9 12.8 - - + -
173D ARG* 3.4 39.0 - - + +
174D LEU* 4.2 7.9 - - + -
177D LEU* 3.9 31.4 - - + -
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ASP 3.0 13.9 + - - -
133D THR* 4.0 8.3 - - - -
134D TYR 3.3 2.5 + - - -
135D LEU* 1.3 79.4 - - - +
137D GLY* 1.3 59.9 + - - -
138D ARG* 4.7 1.2 - - - +
173D ARG* 2.7 38.1 + - - -
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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