Clusters in each protein chain of the PDB file (1AVX) 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 1AVX 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 V:17 G:18 G:19 0 0 0.00 0.86 7.67 0 0 1 31.13
CCR(2): 2 P:28 V:118 0 0 0.00 0.83 8.00 0 0 0 11.25
CCR(3): 18 C:42 G:43 G:44 G:196 G:197 P:198 A:55 A:56 H:57 C:58 D:102 I:103 S:195 D:194 G:140 W:141 G:142 G:193 0 2 7.34 0.91 10.00 0 5 6 0.92
CCR(4): 7 L:46 V:52 I:106 K:107 L:108 W:51 L:105 1 0 3.70 0.85 8.71 0 7 0 2.46
CCR(5): 2 L:67 G:69 0 0 0.00 0.86 7.50 0 1 0 4.90
CCR(6): 2 H:71 N:72 0 0 0.00 0.74 7.00 0 0 0 14.10
CCR(7): 2 L:123 P:124 0 0 0.00 0.83 7.50 0 0 2 10.65
CCR(8): 4 C:136 C:201 V:200 L:209 0 0 0.00 0.73 9.25 0 4 0 3.47
CCR(9): 8 C:182 V:227 Y:228 W:215 G:216 G:226 S:214 P:225 0 0 0.00 0.84 9.00 0 6 2 1.08
CCR(10): 2 G:187 G:188 0 0 0.00 0.82 6.50 0 0 1 35.50
CCR(11): 2 W:237 I:238 0 0 0.00 0.84 6.00 2 0 0 9.35

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Cluster results in 1AVX 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 Y:517 Y:518 G:555 0 0 0.00 0.83 8.33 0 3 0 12.73
CCR(2): 2 G:528 G:553 0 0 0.00 0.86 8.00 0 0 2 7.60
CCR(3): 2 C:539 P:540 0 0 0.00 0.91 6.00 0 0 1 12.55
CCR(4): 3 Y:631 K:632 L:633 1 0 1.02 0.84 7.67 0 3 0 7.93

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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
Chains contacting CCR(7):: B
Chains contacting CCR(8):: B
Chains contacting CCR(9):: B
Chains contacting CCR(10):: B
Chains contacting CCR(11):: B
Chain B
Chains contacting CCR(1):: None
Chains contacting CCR(2):: None
Chains contacting CCR(3):: None
Chains contacting CCR(4):: None