Clusters in each protein chain of the PDB file (1Z3E) are shown below.


Cluster table columns format
Column 1:CCR(ID)): Cluster ID within each protein chain (CCR(ID))
Coulmn 2:size: Number of conserved residues in the cluster
Column 3:Members: All conserved residues in the cluster. Format is residue ID (one letter code) and residue number as in PDB file
Column 4:Postive charge: Number of positively charged residues in the clutser (Lys and Arg).
Column 5:Negative charge: Number of negatively charged residues in the clutser (Asp and Glu).
Column 6:Dipole moment: Net dipole moment of the cluster about geometric center of the cluster, with charges assigned to CA position only.
Column 7:Average conservation: Mean of conservation scores of all residues in the cluster (scale 0 to 1).
Column 8:Average packing density: Mean of packing density of each residue in the cluster (packing density calculation includes non-conserved residue).
Column 9:Helical res. count: Number of residues in the cluster with helical secondary structure.
Column 10:Strand res. count: Number of residues in the cluster with strand secondary structure.
Column 11:Coil res. count: Number of residues in the cluster with coil secondary structure.
Column 12:Average ASA: Mean of relative ASA values (in % units) of all residues in the cluster.



Cluster results in 1Z3E chain: A
User selected parameters:
Packing density pdrange=7.0
Maximum number of aligned sequences to be included in multiple alignments and conservation scores
maxalign=50
#Clustering options
#cluster joining distance
mymaxdist=5.0
#residue conservation score cutoff
mymincons=0.7
#smallest cluster size to consider
myclsize=2
#rsa cutoff
rsaval=0
#########################################################################################################
################################ Clustering results: Chain A #####################################################
#########################################################################################################
Conserved clusters of residues (CCR) in the given structure are listed below.
ID size Members (residue:ID_in_PDB) Positive charge Negative charge Dipole moment Average conservation Average packing density Helical res. count Strand res. count Coil res. count Average ASA
CCR(1): 4 R:91 R:92 P:93 G:104 2 0 4.33 0.89 6.25 0 0 2 30.03

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Cluster results in 1Z3E chain: B
User selected parameters:
Packing density pdrange=7.0
Maximum number of aligned sequences to be included in multiple alignments and conservation scores
maxalign=50
#Clustering options
#cluster joining distance
mymaxdist=5.0
#residue conservation score cutoff
mymincons=0.7
#smallest cluster size to consider
myclsize=2
#rsa cutoff
rsaval=0
#########################################################################################################
################################ Clustering results: Chain B #####################################################
#########################################################################################################
Conserved clusters of residues (CCR) in the given structure are listed below.
ID size Members (residue:ID_in_PDB) Positive charge Negative charge Dipole moment Average conservation Average packing density Helical res. count Strand res. count Coil res. count Average ASA
CCR(1): 3 E:254 E:255 L:256 0 2 2.88 0.82 5.67 0 0 0 18.60
CCR(2): 5 L:258 S:259 V:260 R:261 S:262 1 0 3.56 0.89 8.40 3 0 1 10.52
CCR(3): 4 N:264 C:265 L:266 K:267 1 0 3.04 0.98 9.25 4 0 0 4.03
CCR(4): 2 E:276 L:277 0 1 1.91 0.87 7.50 2 0 0 24.25
CCR(5): 3 D:284 M:285 M:286 0 1 2.87 0.77 5.67 3 0 0 30.57
CCR(6): 3 N:290 L:291 G:292 0 0 0.00 0.92 4.67 0 0 2 47.00
CCR(7): 4 K:294 S:295 E:298 V:299 1 1 6.13 0.92 6.25 4 0 0 30.95

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Summary of clusters in interface (valid for multimeric proteins; interface distance cutoff=4.5 Angstrom for any atoms).

Chain A
Chains contacting CCR(1):: None
Chain B
Chains contacting CCR(1):: A
Chains contacting CCR(2):: A
Chains contacting CCR(3):: A
Chains contacting CCR(4):: A
Chains contacting CCR(5):: A
Chains contacting CCR(6):: A
Chains contacting CCR(7):: A