Clusters in each protein chain of the PDB file (1A02) 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 1A02 chain: F
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 F #####################################################
#########################################################################################################
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): 19 R:143 R:144 E:145 R:146 N:147 K:148 A:150 A:151 A:152 K:153 S:154 R:155 N:156 R:157 R:158 R:159 E:160 L:161 T:162 9 2 17.75 0.86 5.05 19 0 0 55.72
CCR(2): 2 L:165 Q:166 0 0 0.00 0.84 8.00 2 0 0 13.25
CCR(3): 7 E:168 T:169 D:170 L:172 E:173 K:176 E:175 1 4 9.52 0.84 7.86 7 0 0 22.54
CCR(4): 4 L:179 Q:180 E:182 I:183 0 1 2.76 0.84 9.00 4 0 0 20.60
CCR(5): 4 K:188 E:189 K:190 E:191 2 2 3.73 0.83 4.50 4 0 0 59.83

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Cluster results in 1A02 chain: J
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 J #####################################################
#########################################################################################################
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): 17 R:267 K:268 R:271 N:272 R:273 A:275 A:276 S:279 R:280 K:281 R:282 K:283 L:284 E:285 R:286 I:287 K:278 10 1 28.63 0.88 4.65 16 0 1 59.80
CCR(2): 6 R:289 L:290 E:291 K:293 V:294 K:295 3 1 6.09 0.85 7.33 6 0 0 26.87
CCR(3): 2 L:297 K:298 1 0 1.90 0.83 8.00 2 0 0 32.30
CCR(4): 2 N:301 L:304 0 0 0.00 0.95 10.00 2 0 0 15.60
CCR(5): 2 L:311 R:312 1 0 1.89 0.88 7.00 2 0 0 27.80

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Cluster results in 1A02 chain: N
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 N #####################################################
#########################################################################################################
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 D:514 C:515 0 1 1.90 0.75 9.50 0 0 1 5.15
CCR(2): 2 G:517 I:518 0 0 0.00 0.74 8.50 0 2 0 0.00
CCR(3): 2 R:522 N:523 1 0 1.89 0.74 5.50 1 0 1 42.20
CCR(4): 2 F:546 R:547 1 0 1.90 0.73 7.50 0 2 0 2.15

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

Chain N
Chains contacting CCR(1):: None
Chains contacting CCR(2):: None
Chains contacting CCR(3):: B
Chains contacting CCR(4):: B
Chain F
Chains contacting CCR(1):: A B J
Chains contacting CCR(2):: A B J N
Chains contacting CCR(3):: A B J N
Chains contacting CCR(4):: A B J N
Chains contacting CCR(5):: A B J N
Chain J
Chains contacting CCR(1):: A B F N
Chains contacting CCR(2):: A B F N
Chains contacting CCR(3):: A B F N
Chains contacting CCR(4):: A B F N
Chains contacting CCR(5):: A B F N