Contacts of the helix formed by residues 112 - 141 (chain K) in PDB entry 5M64
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 112 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K GLY 5.5 2.2 - - - -
107K THR* 4.2 1.5 - - - +
111K THR* 1.3 84.5 - - - +
113K ALA* 1.3 64.6 + - - +
114K VAL* 3.7 12.4 - - + +
115K ASP* 2.6 38.0 + - - +
116K ALA* 3.1 18.7 + - - +
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Residues in contact with ALA 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K GLY 4.4 15.9 + - - +
59K THR 5.0 1.8 - - - +
60K SER 4.9 0.2 - - - +
61K ALA* 3.6 31.0 - - + -
63K PHE* 4.7 2.7 - - + -
105K ILE* 3.7 17.3 - - + +
107K THR* 4.2 12.0 - - + +
111K THR 4.1 0.4 + - - -
112K THR* 1.3 71.6 - - - +
114K VAL* 1.3 68.1 + - + +
116K ALA* 3.2 4.8 + - - +
117K LEU* 3.0 23.4 + - - +
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Residues in contact with VAL 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ILE* 4.8 20.9 - - + -
49K LEU* 5.4 3.4 - - + -
63K PHE* 4.6 16.2 - - + -
112K THR* 3.7 15.7 - - + +
113K ALA* 1.3 77.6 - - + +
115K ASP* 1.3 67.0 + - - +
117K LEU* 3.7 6.3 + - - +
118K GLN* 2.9 27.4 + - - +
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Residues in contact with ASP 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K THR* 4.7 7.2 - - + -
112K THR* 2.6 34.5 + - - +
113K ALA 3.2 0.4 - - - -
114K VAL* 1.3 84.7 - - - +
116K ALA* 1.3 59.1 + - - +
118K GLN* 3.6 8.7 - - - +
119K LYS* 2.9 38.4 + - + +
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Residues in contact with ALA 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K ILE* 3.6 12.9 - - + +
83K ASN* 4.5 18.1 - - - +
85K ASP 5.7 0.2 - - - +
86K VAL* 5.0 10.3 - - + -
105K ILE* 4.9 7.0 - - + -
107K THR* 4.9 12.1 - - - +
111K THR* 4.6 10.0 - - + +
112K THR 3.1 14.4 + - - +
113K ALA* 3.2 11.0 + - - +
115K ASP* 1.3 77.5 - - - +
117K LEU* 1.3 57.1 + - - +
119K LYS* 3.5 3.5 + - - +
120K GLY 2.9 22.2 + - - -
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Residues in contact with LEU 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LEU 5.4 1.6 - - - +
47K ILE* 6.2 3.6 - - + -
63K PHE* 3.7 38.4 - - + -
76K LEU* 3.9 37.5 - - + -
80K ILE* 4.4 8.7 - - + -
103K ILE* 5.2 3.1 - - + -
105K ILE* 5.2 6.2 - - + +
113K ALA 3.0 9.8 + - - +
114K VAL* 4.1 4.0 - - - +
116K ALA* 1.3 73.8 - - - +
118K GLN* 1.3 62.5 + - - +
120K GLY 3.2 0.7 + - - +
121K LEU* 2.9 50.2 + - + +
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Residues in contact with GLN 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LYS* 4.2 27.7 + - - +
114K VAL 2.9 20.5 + - - +
115K ASP* 3.6 11.4 - - - +
116K ALA 3.3 0.4 - - - -
117K LEU* 1.3 79.8 - - - +
119K LYS* 1.3 60.9 + - + +
121K LEU* 3.2 8.6 + - - +
122K LYS* 2.9 62.6 + - + +
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Residues in contact with LYS 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K ASN* 4.8 9.9 - - - +
115K ASP* 2.9 26.8 + - + +
116K ALA* 3.9 5.6 - - - +
118K GLN* 1.3 75.6 - - + +
120K GLY* 1.3 58.0 + - - +
122K LYS* 3.3 15.5 + - + +
123K ASP* 2.9 40.1 + - - +
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Residues in contact with GLY 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76K LEU* 4.7 2.2 - - - -
79K VAL* 4.5 3.1 - - - +
80K ILE* 3.7 24.9 - - - -
83K ASN* 5.7 0.4 + - - -
116K ALA 2.9 11.7 + - - -
117K LEU 3.6 4.0 - - - -
118K GLN 3.1 0.4 - - - -
119K LYS* 1.3 76.6 - - - +
121K LEU* 1.3 58.3 + - - +
123K ASP* 2.9 25.9 + - - +
124K LEU* 3.0 22.3 + - - +
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Residues in contact with LEU 121 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ALA* 4.4 13.9 - - - +
328C LEU* 3.6 57.7 - - + +
329C LYS* 3.7 16.6 - - + +
72K LEU* 6.3 0.9 - - + -
76K LEU* 4.4 18.6 - - + -
117K LEU* 2.9 39.1 + - + +
118K GLN* 3.7 11.2 - - - +
120K GLY* 1.3 74.3 - - - +
122K LYS* 1.3 65.0 + - - +
124K LEU* 3.1 14.9 + - + +
125K MET* 3.0 22.7 + - - +
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Residues in contact with LYS 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LYS* 3.6 32.8 - - - +
118K GLN* 2.9 44.9 + - + +
119K LYS* 3.5 21.3 - - + +
120K GLY 3.2 0.2 - - - -
121K LEU* 1.3 79.6 - - - +
123K ASP* 1.3 58.5 + - - +
125K MET* 3.4 29.7 + - - +
126K ASP* 2.9 39.8 + - - +
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Residues in contact with ASP 123 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 4.9 11.2 - - + +
79K VAL* 3.6 28.1 - - + +
119K LYS* 2.9 28.4 + - - +
120K GLY* 2.9 12.7 + - - +
122K LYS* 1.3 75.6 - - - +
124K LEU* 1.3 59.4 + - - +
126K ASP* 4.0 9.4 - - - +
127K LEU* 2.8 32.1 + - - +
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Residues in contact with LEU 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 5.3 2.2 - - + -
321C LEU* 4.4 16.9 - - + +
325C ALA* 3.8 18.8 - - + -
72K LEU* 5.2 12.3 - - + -
75K ALA* 4.7 19.5 - - + -
76K LEU* 3.9 19.5 - - + +
79K VAL* 3.6 26.5 - - + -
120K GLY 3.0 27.9 + - - +
121K LEU* 3.1 15.2 + - + +
123K ASP* 1.3 73.4 - - - +
125K MET* 1.3 65.5 + - - +
127K LEU* 3.2 15.2 + - + +
128K CYS* 3.0 28.8 + - - +
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Residues in contact with MET 125 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C LYS* 3.7 25.1 - - + +
325C ALA* 4.5 5.7 - - + +
326C GLU* 4.1 32.1 - - + +
329C LYS* 4.7 5.8 - - + -
121K LEU 3.0 13.0 + - - +
122K LYS* 3.8 36.6 - - + +
123K ASP 3.4 0.2 - - - -
124K LEU* 1.3 75.7 - - - +
126K ASP* 1.3 62.8 + - - +
128K CYS* 3.2 11.6 - - - -
129K ASP* 3.0 29.6 + - + +
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Residues in contact with ASP 126 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.9 29.2 - - + +
122K LYS* 2.9 28.8 + - - +
123K ASP* 4.0 8.2 - - - +
125K MET* 1.3 78.5 - - - +
127K LEU* 1.3 66.8 + - - +
129K ASP* 3.2 8.7 + - - +
130K VAL* 3.1 25.9 + - - +
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Residues in contact with LEU 127 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TRP* 5.9 3.6 - - + +
33C VAL* 5.5 1.7 - - - +
36C PHE* 3.7 38.6 - - + -
59C ILE* 4.9 3.4 - - + -
63C ILE* 3.7 42.2 - - + -
67C PHE* 6.1 0.7 - - + -
78K TYR* 6.3 0.7 - - + -
79K VAL* 5.3 11.2 - - + -
123K ASP 2.8 19.8 + - - +
124K LEU* 3.2 13.0 + - + +
126K ASP* 1.3 76.1 - - - +
128K CYS* 1.3 62.6 + - - +
130K VAL* 3.2 7.7 - - - +
131K VAL* 3.1 33.6 + - + +
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Residues in contact with CYS 128 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 5.3 6.1 - - + -
318C VAL* 3.8 21.2 - - + +
321C LEU* 4.2 17.3 - - + -
322C LYS* 3.6 37.9 - - - -
325C ALA* 5.7 0.2 - - - -
124K LEU 3.0 26.1 + - - +
125K MET* 3.2 15.0 - - - -
127K LEU* 1.3 78.2 - - - +
129K ASP* 1.3 56.8 + - - +
131K VAL* 4.3 6.3 - - - -
132K GLU* 3.1 30.9 + - - +
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Residues in contact with ASP 129 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C LYS* 4.8 11.9 + - - +
125K MET* 3.0 22.1 + - + +
126K ASP* 3.4 10.9 - - - +
127K LEU 3.1 0.4 - - - -
128K CYS* 1.3 76.9 - - - +
130K VAL* 1.3 63.3 + - - +
132K GLU* 3.3 9.3 + - - +
133K SER* 2.7 42.2 + - - -
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Residues in contact with VAL 130 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 5.7 5.6 - - + +
36C PHE* 3.6 36.1 - - + -
37C LYS* 3.6 33.0 - - + -
40C PHE* 5.1 0.9 - - + -
126K ASP 3.1 13.5 + - - +
127K LEU* 3.2 20.4 - - - +
129K ASP* 1.3 75.7 + - - +
131K VAL* 1.3 59.9 + - - +
133K SER* 4.2 5.4 - - - -
134K LYS* 2.8 45.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL 131 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 4.1 21.3 - - + -
40C PHE* 4.2 28.5 - - + -
56C LEU* 5.1 6.3 - - + -
59C ILE* 4.9 4.0 - - + -
63C ILE* 5.6 0.2 - - + -
67C PHE* 3.8 31.9 - - + -
318C VAL* 5.2 8.7 - - + -
127K LEU* 3.1 26.6 + - + +
128K CYS* 4.2 5.6 - - - +
130K VAL* 1.3 74.8 - - - +
132K GLU* 1.3 61.4 + - - +
134K LYS* 4.6 0.3 - - - +
135K PHE* 3.2 26.3 + - + +
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Residues in contact with GLU 132 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C PHE* 5.4 4.0 - - + -
315C PHE* 3.7 12.7 - - + -
318C VAL* 4.4 15.9 - - + +
319C ARG* 2.6 52.1 + - - -
322C LYS* 4.5 13.5 + - - +
128K CYS* 3.1 21.4 + - - +
129K ASP* 3.7 6.9 - - - +
131K VAL* 1.3 75.8 - - - +
133K SER* 1.3 57.6 + - - +
135K PHE* 3.8 4.3 - - - +
136K THR* 2.5 45.6 + - - +
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Residues in contact with SER 133 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K ASP* 2.7 38.6 + - - -
130K VAL* 3.9 7.0 - - - -
132K GLU* 1.3 75.9 - - - +
134K LYS* 1.3 64.0 + - - +
136K THR* 3.1 8.3 + - - -
137K GLU* 3.0 22.5 + - - +
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Residues in contact with LYS 134 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LYS* 4.0 27.2 + - - +
40C PHE* 3.5 52.2 + - + +
41C GLU* 4.4 6.3 - - - +
42C VAL* 4.3 9.6 - - + +
130K VAL* 2.8 29.4 + - + +
133K SER* 1.3 73.5 - - - +
135K PHE* 1.3 58.8 + - - +
137K GLU* 3.2 15.6 + - + +
138K LYS* 3.0 46.3 + - + +
----------------------------------------------------------
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Residues in contact with PHE 135 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 4.3 11.7 - - + +
44C ILE* 5.1 2.0 - - + -
54C PHE* 3.4 47.8 - + - -
56C LEU* 6.0 1.1 - - + -
311C GLU* 5.6 3.1 - - - -
314C PHE* 3.4 61.7 - + + -
131K VAL* 3.2 22.1 + - + +
132K GLU* 4.0 2.0 - - - +
134K LYS* 1.3 78.3 - - - +
136K THR* 1.3 57.7 + - - +
138K LYS* 4.4 4.5 - - + +
139K ILE* 2.9 53.0 + - + +
----------------------------------------------------------
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Residues in contact with THR 136 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C PHE* 4.8 4.2 - - + -
315C PHE* 4.6 15.6 - - + -
132K GLU* 2.5 33.9 + - - +
133K SER* 3.1 8.9 + - - -
135K PHE* 1.3 77.1 - - - +
137K GLU* 1.3 56.7 + - - +
139K ILE* 3.2 11.6 - - + +
140K LYS* 3.0 32.5 + - + +
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Residues in contact with GLU 137 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133K SER 3.0 12.4 + - - +
134K LYS* 3.2 17.2 + - + +
136K THR* 1.3 76.7 - - - +
138K LYS* 1.3 66.0 + - + +
140K LYS* 3.5 5.3 + - - +
141K SER* 3.0 36.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 138 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 4.9 6.8 + - - +
42C VAL* 3.6 52.3 + - + +
43C ASN* 5.5 0.8 + - - -
44C ILE* 4.4 9.2 - - + +
134K LYS* 3.0 31.7 + - + +
135K PHE* 3.9 2.2 - - + +
137K GLU* 1.3 81.8 - - + +
139K ILE* 1.3 65.1 + - - +
140K LYS 3.1 1.6 - - - -
141K SER* 3.1 7.4 + - - +
142K MET* 3.1 26.0 + - - +
----------------------------------------------------------
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Residues in contact with ILE 139 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 3.7 16.7 - - + +
47C LEU* 3.8 18.4 - - + -
311C GLU* 5.3 11.9 - - + +
314C PHE* 5.1 7.0 - - + -
135K PHE* 2.9 42.6 + - + +
136K THR* 3.2 21.5 - - + +
138K LYS* 1.3 76.1 - - - +
140K LYS* 1.3 62.5 + - + +
142K MET* 3.3 44.8 - - + +
----------------------------------------------------------
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Residues in contact with LYS 140 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136K THR* 3.0 23.8 + - + +
137K GLU* 3.8 6.3 - - - +
139K ILE* 1.3 82.4 - - + +
141K SER* 1.3 59.4 + - - +
142K MET* 3.4 3.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 141 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K GLU* 3.0 24.9 + - - +
138K LYS* 3.1 11.2 + - - +
140K LYS* 1.3 80.7 - - - +
142K MET* 1.3 63.0 + - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il