Contacts of the helix formed by residues 115 - 147 (chain A) in PDB entry 1S3Q
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 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER 6.1 0.2 - - - -
4A ILE* 3.3 22.1 - - - +
5A SER 5.9 0.2 - - - -
8A MSE 3.5 8.4 - - - +
66A ARG* 3.0 25.6 + - - -
110A ALA* 3.0 21.1 + - - +
113A GLU* 3.1 14.4 - - + +
114A LYS* 1.3 72.9 - - - +
116A PHE* 1.3 63.1 + - - +
117A ALA 3.6 2.4 + - - -
118A THR* 2.6 29.0 + - - -
119A TYR* 3.0 22.7 + - - +
104D HIS* 5.8 0.9 - - - -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA 5.7 0.4 - - - -
111A MSE 5.5 4.5 - - - -
114A LYS* 3.0 35.3 + - + -
115A ASP* 1.3 72.8 - - - +
117A ALA* 1.3 59.8 + - - +
119A TYR* 3.5 13.9 - + + +
120A ASN* 2.8 32.9 + - - +
104D HIS* 3.5 61.4 - + + +
107D VAL* 3.8 19.3 - - + -
108D GLU* 3.9 15.7 - - + -
111D MSE 3.6 35.0 - - + -
119D TYR* 5.7 2.2 - - - -
123D GLN* 5.0 2.8 - - - +
126D VAL* 3.6 13.1 - - + +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 3.8 3.9 - - - -
66A ARG* 3.4 27.4 - - - +
115A ASP* 3.2 1.7 + - - +
116A PHE* 1.3 79.3 - - - +
118A THR* 1.3 63.0 + - - +
120A ASN* 3.4 2.9 + - - +
121A PHE* 3.0 22.7 + - - +
104D HIS* 4.6 9.1 - - + +
126D VAL* 3.7 15.0 - - + +
127D ALA* 6.1 0.2 - - - +
130D VAL* 3.5 30.1 - - + +
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.0 4.5 - - - +
8A MSE 4.0 24.9 - - + -
12A LEU* 4.2 8.6 - - + +
62A PHE* 3.6 21.5 - - + -
66A ARG* 2.8 15.2 + - - -
110A ALA* 4.2 2.5 - - + -
115A ASP* 2.6 30.7 + - - -
117A ALA* 1.3 73.7 - - - +
119A TYR* 1.3 67.9 + - - +
121A PHE* 3.0 2.4 + - - +
122A LEU* 2.9 48.2 + - + +
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Residues in contact with TYR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.6 31.6 - - + -
110A ALA* 3.7 13.8 - - + +
111A MSE 3.6 34.3 - - + -
115A ASP 3.0 17.5 + - - +
116A PHE* 3.5 15.9 - + + +
118A THR* 1.3 79.1 - - - +
120A ASN* 1.3 67.2 + - - +
122A LEU* 3.3 10.6 + - - +
123A GLN* 3.1 41.9 + - + -
119D TYR* 3.4 26.0 + + - -
123D GLN* 4.5 7.9 - - - -
116E PHE* 5.7 3.0 - + - -
119E TYR* 3.4 33.1 + + - -
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE 2.8 17.8 + - - +
117A ALA 3.8 4.1 - - - +
119A TYR* 1.3 81.3 - - - +
121A PHE* 1.3 65.8 + - - +
123A GLN* 3.1 30.5 + - - +
124A TRP 4.3 0.9 + - - -
123D GLN* 3.8 44.1 + - - +
126D VAL* 4.2 7.6 - - + -
127D ALA* 3.5 23.9 - - - +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.3 1.3 - - + -
58A LYS* 3.8 38.1 + - + -
59A MSE 3.9 20.4 - - + -
62A PHE* 3.4 64.6 - + + -
117A ALA 3.0 16.5 + - - +
118A THR* 3.0 4.8 + - + +
120A ASN* 1.3 80.9 + - - +
122A LEU* 1.3 72.1 - - + +
123A GLN 3.3 0.9 + - - -
124A TRP* 3.4 18.4 + - - +
125A TYR* 3.6 29.3 - + - -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.3 5.2 - - + -
59A MSE 4.0 26.2 - - + -
103A ILE* 4.5 3.8 - - + +
106A LEU* 3.7 50.3 - - + +
107A VAL* 3.9 16.6 - - + +
110A ALA* 4.5 1.8 - - + -
118A THR* 2.9 36.7 + - + +
119A TYR* 3.7 5.4 - - - +
120A ASN 3.2 0.4 - - - -
121A PHE* 1.3 84.4 - - + +
123A GLN* 1.3 60.1 + - - +
124A TRP 3.1 0.4 - - - -
125A TYR* 2.9 30.6 + - + +
126A VAL* 3.0 13.4 + - - +
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Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 4.2 15.0 - - - +
119A TYR* 3.1 55.3 + - + +
120A ASN* 3.1 25.5 + - - +
122A LEU* 1.3 76.0 - - - +
124A TRP* 1.3 62.4 + - - +
126A VAL* 3.2 11.9 + - - +
127A ALA* 3.0 23.9 + - - +
116E PHE* 4.9 2.8 - - - +
119E TYR* 4.5 7.9 - - - -
120E ASN* 3.8 37.0 + - - +
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Residues in contact with TRP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A MSE 4.0 24.2 - - + -
55A HIS* 3.7 30.5 - + - -
58A LYS* 3.6 32.2 - - + +
120A ASN 4.3 0.8 + - - -
121A PHE 3.4 13.9 + - - +
122A LEU 3.1 0.8 - - - -
123A GLN* 1.3 76.5 - - - +
125A TYR* 1.3 85.7 + + + +
127A ALA* 3.4 6.3 + - + +
128A GLU* 2.9 52.9 + - + +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 4.3 15.7 - - + -
55A HIS* 2.7 40.1 + + + -
58A LYS* 3.4 13.7 - - + +
59A MSE 3.3 37.8 + - + +
103A ILE* 3.9 25.6 - - + -
121A PHE* 3.6 33.9 - + - -
122A LEU* 2.9 17.7 + - + +
124A TRP* 1.3 101.6 - + - +
126A VAL* 1.3 67.1 + - - +
128A GLU* 3.7 3.0 - - + +
129A GLN* 2.9 32.4 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 4.1 10.1 - - + +
104A HIS* 4.4 10.3 + - + +
107A VAL* 3.9 24.7 - - + -
122A LEU 3.0 13.9 + - - +
123A GLN* 3.4 19.5 - - - +
125A TYR* 1.3 79.3 - - - +
127A ALA* 1.3 62.2 + - - +
129A GLN* 3.6 9.1 + - - +
130A VAL* 3.6 13.3 + - - +
116E PHE* 3.6 43.1 - - + +
117E ALA* 3.6 9.2 - - - +
120E ASN* 4.1 9.9 - - + -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLN 3.0 11.2 + - - +
124A TRP* 3.7 9.9 - - + +
126A VAL* 1.3 74.4 - - - +
128A GLU* 1.3 66.4 - - - +
130A VAL* 3.2 23.8 + - - +
131A GLU* 3.6 9.5 + - - +
117E ALA* 6.1 0.2 - - - +
120E ASN* 3.6 21.3 + - - +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.6 27.7 - - - +
54A MSE 5.8 0.7 - - - +
55A HIS* 3.4 27.0 + - + +
124A TRP* 2.9 44.1 + - + +
125A TYR* 3.7 6.5 - - + +
127A ALA* 1.3 78.5 - - - +
129A GLN* 1.3 61.6 + - - +
131A GLU* 3.1 26.1 + - - +
132A GLU* 2.7 41.9 + - + +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 2.8 40.9 + - - +
99A VAL* 3.8 17.8 - - - +
100A THR* 3.1 38.0 + - + +
103A ILE* 3.7 20.5 - - + +
104A HIS* 5.7 0.2 - - - +
125A TYR* 2.9 23.1 + - - +
126A VAL* 3.9 5.8 - - - +
127A ALA 3.3 0.4 - - - -
128A GLU* 1.3 76.7 - - - +
130A VAL* 1.3 67.6 + - - +
132A GLU* 3.8 13.0 - - - +
133A GLU* 2.9 30.3 + - - +
901A ZN 4.2 6.2 - - - -
902A ZN 4.0 3.8 - - - -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL 3.6 10.7 + - - +
127A ALA* 3.2 13.4 + - - +
128A GLU 3.2 0.4 - - - -
129A GLN* 1.3 80.9 - - - +
131A GLU* 1.3 61.1 + - + +
133A GLU* 4.1 5.0 - - - +
134A ALA* 3.2 22.9 + - - +
62E PHE* 4.5 12.1 - - + -
65E GLU* 3.5 30.9 - - + +
66E ARG* 4.2 20.6 - - + +
117E ALA* 3.6 33.0 - - + +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA 3.6 9.9 + - - +
128A GLU* 3.1 28.4 + - - +
130A VAL* 1.3 79.5 - - + +
132A GLU* 1.3 66.9 + - - +
134A ALA* 3.4 1.8 + - - +
135A SER* 2.9 33.4 + - - +
65E GLU* 3.9 19.7 - - - +
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLN* 2.8 21.3 + - - +
51A GLU* 2.6 26.8 - - - +
55A HIS* 4.1 0.9 - - - -
96A GLU* 3.2 23.5 - - + +
128A GLU* 2.7 31.7 + - + +
129A GLN* 3.8 17.3 - - - +
130A VAL 3.5 0.2 - - - -
131A GLU* 1.3 75.9 - - - +
133A GLU* 1.3 61.0 + - - +
135A SER* 4.0 3.7 - - - -
136A ALA* 3.2 24.4 + - - +
163A ARG* 5.4 0.5 + - - -
902A ZN 2.3 35.6 - - - -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.6 21.7 + - + -
96A GLU* 4.5 5.8 - - + -
97A VAL* 4.1 34.7 - - + +
100A THR* 2.7 40.8 + - - +
129A GLN* 2.9 23.4 + - - +
130A VAL* 4.1 4.5 - - - +
132A GLU* 1.3 72.7 - - - +
134A ALA* 1.3 57.9 + - - +
136A ALA* 4.7 0.9 - - - -
137A LEU* 2.9 32.0 + - - +
3E SER* 5.5 6.8 - - - -
66E ARG* 5.7 3.1 + - - -
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL 3.2 17.9 + - - +
131A GLU 3.9 2.5 - - - +
133A GLU* 1.3 77.7 - - - +
135A SER* 1.3 63.2 + - - +
137A LEU* 4.4 5.6 - - - +
138A ASP* 2.9 41.9 + - - +
65E GLU* 3.6 42.3 + - - +
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 4.6 15.7 - - - -
131A GLU* 2.9 22.3 + - - +
132A GLU* 4.0 3.8 - - - -
134A ALA* 1.3 78.0 - - - +
136A ALA* 1.3 64.0 + - - +
138A ASP* 3.5 7.0 + - - +
139A ILE* 3.4 30.4 + - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 5.1 2.8 - - + -
89A PHE* 4.1 11.9 - - + -
92A VAL* 3.8 29.6 - - + +
93A TYR* 3.9 20.0 - - + +
96A GLU* 5.3 1.1 - - + -
132A GLU 3.2 16.2 + - - +
133A GLU* 3.8 3.4 - - - +
135A SER* 1.3 80.7 - - - +
137A LEU* 1.3 58.1 + - - +
139A ILE* 3.3 4.3 + - - +
140A VAL* 3.0 31.4 + - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.9 36.3 - - + +
133A GLU 2.9 20.7 + - - +
134A ALA* 4.0 5.8 - - - +
136A ALA* 1.3 73.7 - - - +
138A ASP* 1.3 62.6 + - - +
140A VAL* 3.3 16.1 + - + -
141A GLU* 2.9 54.8 + - + +
144A ARG* 5.2 5.4 - - - +
67E GLY* 5.2 14.1 - - - -
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ALA* 2.9 30.6 + - - +
135A SER* 3.8 7.9 - - - +
136A ALA 3.2 0.4 - - - -
137A LEU* 1.3 80.0 - - - +
139A ILE* 1.3 59.2 + - + +
141A GLU* 3.4 14.6 + - - +
142A LYS* 3.0 33.4 + - + +
65E GLU* 5.6 1.0 - - - +
39F LYS* 5.0 14.1 - - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.5 6.3 - - + -
44A TRP* 3.6 32.1 - - + +
89A PHE* 3.5 51.8 - - + -
135A SER* 3.4 14.1 + - - +
136A ALA 3.3 2.5 + - - +
137A LEU 3.3 0.2 - - - -
138A ASP* 1.3 75.9 - - + +
140A VAL* 1.3 65.1 + - - +
142A LYS* 3.2 6.8 + - + +
143A LEU* 2.9 33.5 + - + +
156A LEU* 4.5 9.9 - - + -
160A LEU* 4.2 16.4 - - + -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.8 11.8 - - + +
89A PHE* 3.2 37.5 - - + +
90A GLU* 3.7 8.7 - - + +
93A TYR* 4.3 11.0 - - + -
136A ALA 3.0 16.6 + - - +
137A LEU* 3.3 17.2 + - + +
139A ILE* 1.3 75.9 - - - +
141A GLU* 1.3 58.6 + - - +
143A LEU* 3.1 3.1 + - - +
144A ARG* 2.9 65.8 + - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 2.9 49.9 + - + +
138A ASP* 3.7 12.8 - - - +
139A ILE 3.3 0.2 - - - -
140A VAL* 1.3 74.9 - - + +
142A LYS* 1.3 57.8 + - + +
144A ARG* 3.2 15.6 + - - +
145A LEU* 3.0 29.0 + - - +
34F ASP 5.3 2.3 - - - +
35F SER 4.7 10.8 - - - +
36F ILE 5.3 1.1 - - - -
37F GLY* 4.7 17.5 + - - -
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 3.0 21.0 + - + +
139A ILE* 3.2 7.6 + - + +
141A GLU* 1.3 76.1 - - + +
143A LEU* 1.3 57.3 + - - +
145A LEU* 3.3 12.3 + - + +
146A ILE* 2.9 37.2 + - + +
156A LEU* 4.3 25.2 - - + +
37F GLY* 3.1 33.0 + - - -
38F LEU* 4.9 4.7 - - - +
39F LYS* 5.5 4.4 - - - +
154F LEU* 4.1 32.9 - - + +
157F ASP* 4.6 10.5 + - - -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.1 9.0 - - + -
85A PRO* 3.9 15.3 - - + +
86A LEU* 3.8 42.1 - - + +
89A PHE* 4.0 7.0 - - + -
139A ILE* 2.9 36.6 + - + +
140A VAL* 3.5 4.7 - - - +
142A LYS* 1.3 73.9 - - - +
144A ARG* 1.3 60.6 + - - +
146A ILE* 3.6 10.7 - - + +
147A GLY* 2.9 26.3 + - - +
153A LEU* 3.8 24.9 - - + -
156A LEU* 3.7 22.4 - - + -
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.8 17.2 - - + +
90A GLU* 2.8 33.3 + - - +
137A LEU* 5.2 6.9 - - - +
140A VAL* 2.9 38.0 + - - +
141A GLU* 3.6 14.8 - - - +
143A LEU* 1.3 76.7 - - - +
145A LEU* 1.3 61.4 + - - +
147A GLY* 3.3 13.1 + - - -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU 3.0 16.8 + - - +
142A LYS* 3.3 16.8 + - + +
144A ARG* 1.3 76.7 - - - +
146A ILE* 1.3 58.7 - - + +
36F ILE 3.9 21.5 - - - +
37F GLY* 5.5 0.7 - - - -
38F LEU* 4.7 16.4 - - + -
150F LYS* 2.7 51.0 + - + +
153F LEU* 4.9 12.8 - - + -
154F LEU* 4.4 19.3 - - + -
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 2.9 21.6 + - + +
143A LEU* 3.6 13.2 - - + +
145A LEU* 1.3 82.9 - - + +
147A GLY* 1.3 74.4 + - - +
148A GLU 3.1 1.2 + - - -
149A ASP* 3.1 28.5 + - - +
152A ALA* 3.7 34.1 - - + +
153A LEU* 4.2 12.6 - - + +
156A LEU* 3.9 26.2 - - + -
150F LYS* 2.9 22.0 + - - -
154F LEU* 3.9 19.5 - - + -
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU 2.9 16.4 + - - +
144A ARG* 3.3 10.6 + - - -
146A ILE* 1.3 84.5 - - - +
148A GLU* 1.3 71.2 + - - +
150F LYS* 4.3 4.3 - - - -
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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