Clusters in each protein chain of the PDB file (1AY7) 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 1AY7 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): 2 L:11 P:12 0 0 0.00 0.88 6.50 0 0 1 17.15
CCR(2): 8 L:21 I:22 D:25 G:26 P:27 F:28 P:29 Y:30 0 1 5.69 0.88 5.00 2 0 3 43.67
CCR(3): 21 D:33 G:34 Y:55 T:56 V:57 R:69 I:70 I:71 Y:81 T:82 F:89 E:54 R:68 Y:80 T:88 T:67 H:85 Y:86 G:66 D:84 R:65 3 3 14.99 0.94 7.62 0 9 6 10.92
CCR(4): 2 L:44 P:45 0 0 0.00 0.99 5.00 0 0 1 22.95
CCR(5): 4 G:50 Y:51 Y:52 G:73 0 0 0.00 0.93 6.50 0 0 2 16.97
CCR(6): 2 T:59 P:60 0 0 0.00 0.90 5.00 0 0 1 38.60

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Cluster results in 1AY7 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): 2 Y:29 Y:30 0 0 0.00 0.93 8.00 0 0 2 11.35
CCR(2): 5 L:34 D:35 A:36 L:37 W:38 0 1 2.72 0.89 8.40 5 0 0 3.46
CCR(3): 2 C:40 L:41 0 0 0.00 0.72 6.50 2 0 0 17.15

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