Clusters in each protein chain of the PDB file (1MNM) 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 1MNM 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): 5 K:20 I:21 E:22 I:23 K:24 2 1 2.80 0.77 3.20 0 0 3 53.92
CCR(2): 10 R:32 H:33 V:34 T:35 F:36 S:37 K:38 R:39 K:40 G:42 4 0 4.91 0.87 5.80 10 0 0 36.02
CCR(3): 3 K:45 K:46 A:47 2 0 2.83 0.94 7.33 3 0 0 30.93
CCR(4): 7 E:49 L:50 S:51 V:52 L:53 G:55 T:56 0 1 5.18 0.82 8.29 5 0 1 17.24

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Cluster results in 1MNM 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): 5 K:20 I:21 E:22 I:23 K:24 2 1 0.74 0.79 3.60 0 0 4 43.82
CCR(2): 3 I:26 E:27 N:28 0 1 1.64 0.80 5.00 0 0 2 55.60
CCR(3): 10 R:32 H:33 V:34 T:35 F:36 S:37 K:38 R:39 K:40 G:42 4 0 4.75 0.87 6.20 10 0 0 33.87
CCR(4): 3 K:45 K:46 A:47 2 0 2.83 0.95 7.33 3 0 0 30.60
CCR(5): 8 E:49 L:50 S:51 V:52 L:53 T:54 G:55 T:56 0 1 5.45 0.81 8.75 6 0 1 12.45

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Cluster results in 1MNM chain: C
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 C #####################################################
#########################################################################################################
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 P:155 Y:156 L:157 0 0 0.00 0.81 4.33 0 0 3 34.07
CCR(2): 3 R:184 R:185 K:186 3 0 0.00 0.78 4.33 3 0 0 55.17

--------------------------------------------------------------------------------------------------------------------------------
Cluster results in 1MNM chain: D
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 D #####################################################
#########################################################################################################
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 P:155 Y:156 L:157 0 0 0.00 0.81 4.67 0 0 3 32.50
CCR(2): 3 R:184 R:185 K:186 3 0 0.00 0.78 5.00 3 0 0 50.90

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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 E F
Chains contacting CCR(2):: B E F
Chains contacting CCR(3):: B E F
Chains contacting CCR(4):: B E F
Chain B
Chains contacting CCR(1):: A E F
Chains contacting CCR(2):: A E F
Chains contacting CCR(3):: A E F
Chains contacting CCR(4):: A E F
Chains contacting CCR(5):: A C E F
Chain C
Chains contacting CCR(1):: F
Chains contacting CCR(2):: E F
Chain D
Chains contacting CCR(1):: None
Chains contacting CCR(2):: A E F