138 CATALYZING INQUIRY
Calcium Model VOLUME
012345
ATOM-NAME-IS-ANY < > > >
ATOM-NAME-IS-C < < > > >
ATOM-NAME-IS-N < < >
ATOM-NAME-IS-O < > > > > >
AMIDE < < >
AMINE <
CARBONYL < > > > >
RING-SYSTEM <
PEPTIDE < > > >
VDW-VOLUME < < > >
CHARGE > > >
NEG-CHARGE > > >
CHARGE-WITH-HIS > > >
HYDROPHOBICITY < < < <
MOBILITY < > >
SOLVENT-ACCESSIBILITY < >
RESIDUE_NAME_IS_ASN > > > >
RESIDUE_NAME_IS_ASP > > > > >
RESIDUE_NAME_IS_GLU > > > > >
RESIDUE_NAME_IS_GLY > > >
RESIDUE_NAME_IS_ILE >
RESIDUE_NAME_IS_LEU >
RESIDUE_NAME_IS_LYS >
RESIDUE_NAME_IS_SER > >
RESIDUE_NAME_IS_VAL < <
RESIDUE_NAME_IS_HOH >
RESIDUE_CLASS1_IS_HYDROPHOBIC < <
RESIDUE_CLASS1_IS_CHARGED > > > > >
RESIDUE_CLASS1_IS_POLAR < > > >
RESIDUE_CLASS1_IS_UNKNOWN > >
RESIDUE_CLASS2_IS_NONPOLAR < <
RESIDUE_CLASS2_IS_POLAR < > >
RESIDUE_CLASS2_IS_BASIC <
RESIDUE_CLASS2_IS_ACIDIC > > > > >
RESIDUE_CLASS2_IS_UNKNOWN > >
SECONDARY_STRUCTURE1_IS_TURN >
SECONDARY_STRUCTURE1_IS_BEND > > > > >
SECONDARY_STRUCTURE1_IS_COIL > > > > >
SECONDARY_STRUCTURE1_IS_HET > >
SECONDARY_STRUCTURE2_IS_BETA < > >
SECONDARY_STRUCTURE2_IS_COIL > > > > >
SECONDARY_STRUCTURE2_IS_HET > >FIGURE 5.3 Statistical features of calcium binding sites determined by FEATURE. The volumes in this case corre-
spond to concentrate radial shells 1 Å in thickness around the calcium ion or a control nonsite location. The
column shows properties that are statistically significantly different (at p-value cutoff of 0.01) in at least one
volume between known examples of calcium binding sites and those of control nonsites. A “>” (greater than sign)
indicates that the calcium binding sites have significantly higher value for that property at that volume compared
to control nonsites. A “<” (less than sign) indicates the opposite. An empty box indicates the lack of statistically
significant difference. SOURCE: Courtesy of Liping Wei, Nexus Genomics, Inc., and Russ Altman, Stanford Uni-
versity, personal communication, December 4, 2003.