Clusters in each protein chain of the PDB file (1L9A) 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 1L9A 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): 3 Y:7 R:18 G:17 1 0 2.08 0.94 8.00 0 0 1 8.43
CCR(2): 2 A:25 I:26 0 0 0.00 0.78 9.00 0 0 1 4.10
CCR(3): 2 Y:53 P:54 0 0 0.00 0.80 6.00 0 0 1 40.20

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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):: B
Chains contacting CCR(2):: B
Chains contacting CCR(3):: B