Contacts of the helix formed by residues 94 - 132 (chain G) in PDB entry 3MIW
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 MET 94 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ILE* 1.3 57.1 + - - +
96G GLU 3.4 2.0 - - - -
97G GLN* 2.7 22.6 + - + -
98G GLN* 2.3 59.8 + - + +
96I GLU* 2.8 28.0 + - - +
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Residues in contact with ILE 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ILE* 4.2 16.6 - - + -
94G MET* 1.3 79.2 - - - +
96G GLU* 1.3 59.6 + - - +
98G GLN* 3.1 2.9 + - - +
99G MET* 2.8 26.0 + - - +
95I ILE* 4.9 7.9 - - + -
96I GLU* 3.1 21.4 + - + +
99I MET* 3.5 22.3 - - + +
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Residues in contact with GLU 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ILE* 4.5 19.0 - - + +
94G MET 3.4 0.4 - - - -
95G ILE* 1.3 77.3 - - - +
97G GLN* 1.3 56.3 - - - +
99G MET* 3.0 27.5 - - - +
100G ASP* 3.7 9.9 - - - +
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Residues in contact with GLN 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G MET* 2.7 27.7 + - + +
96G GLU* 1.3 72.7 - - - +
98G GLN* 1.3 58.2 + - - +
99G MET 2.9 5.5 + - - -
100G ASP* 3.7 6.7 + - - +
101G ARG* 3.6 19.2 + - - +
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Residues in contact with GLN 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G MET* 2.3 47.8 + - + +
95G ILE 3.6 4.3 - - - +
97G GLN* 1.3 68.8 - - - +
99G MET* 1.3 61.1 + - - +
100G ASP 3.5 0.2 - - - -
101G ARG* 4.0 9.2 - - - +
102G ILE* 3.1 32.4 + - - +
96I GLU* 2.7 41.0 + - - +
99I MET* 3.0 37.4 - - + +
100I ASP* 2.6 31.2 - - - +
103I VAL* 4.8 5.6 - - + +
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Residues in contact with MET 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ILE* 3.3 31.9 - - + +
98E GLN* 3.7 27.8 - - + -
99E MET* 3.9 20.9 - - - +
102E ILE* 4.0 16.4 - - + -
95G ILE 2.8 23.4 + - - +
96G GLU* 3.0 24.9 - - - +
98G GLN* 1.3 80.2 - - - +
100G ASP* 1.3 57.7 + - - +
102G ILE* 3.3 19.1 - - + +
103G VAL* 3.0 30.8 + - - +
99I MET* 4.4 11.2 - - - +
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Residues in contact with ASP 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E GLN* 4.9 5.9 - - - +
96G GLU 3.7 12.1 + - - +
97G GLN* 3.7 7.9 + - - +
99G MET* 1.3 77.2 - - - +
101G ARG* 1.3 59.3 + - - +
102G ILE 3.0 2.2 - - - -
103G VAL* 3.8 9.1 - - + +
104G LYS* 2.7 36.4 + - - +
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Residues in contact with ARG 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G GLN 3.6 15.5 + - - +
98G GLN* 4.1 8.1 - - - +
99G MET 3.4 0.4 - - - -
100G ASP* 1.3 75.8 - - - +
102G ILE* 1.3 59.6 + - - +
104G LYS* 3.1 25.6 - - + +
105G GLU* 3.4 20.7 + - - +
103I VAL* 4.9 20.9 - - + -
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Residues in contact with ILE 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ILE* 3.8 22.9 - - + -
98G GLN 3.1 18.9 + - - +
99G MET* 3.3 18.2 - - + +
101G ARG* 1.3 75.7 - - - +
103G VAL* 1.3 65.3 + - - +
104G LYS 3.1 2.1 + - - -
105G GLU* 3.3 17.4 + - - +
106G MET* 3.4 15.8 + - + +
99I MET* 4.0 27.1 - - + -
102I ILE* 3.9 26.7 - - + -
103I VAL* 3.9 17.9 - - + -
106I MET* 4.1 14.4 - - - +
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Residues in contact with VAL 103 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E GLN* 4.5 6.5 - - + +
101E ARG* 4.2 21.8 - - + -
102E ILE* 3.6 25.1 - - + -
105E GLU* 4.4 9.9 - - + -
99G MET 3.0 18.9 + - - +
100G ASP* 3.1 10.3 + - + +
102G ILE* 1.3 72.4 - - - +
104G LYS* 1.3 65.3 + - - +
106G MET* 3.2 22.4 + - - +
107G ARG* 3.1 44.3 - - - +
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Residues in contact with LYS 104 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G ASP 2.7 13.8 + - - +
101G ARG* 3.1 21.1 - - - +
103G VAL* 1.3 77.6 - - - +
105G GLU* 1.3 61.4 + - - +
107G ARG* 2.8 36.2 + - - +
108G ARG* 3.1 17.5 + - + +
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Residues in contact with GLU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G ARG* 3.4 21.6 - - + +
102G ILE* 3.3 8.6 + - - +
104G LYS* 1.3 80.9 - - - +
106G MET* 1.3 57.5 + - - +
107G ARG 3.2 0.2 - - - -
108G ARG* 4.4 10.5 - - - +
109G GLN* 2.9 33.1 + - - +
103I VAL* 5.2 13.5 - - + +
106I MET* 4.1 30.7 - - + +
107I ARG* 4.6 12.2 - - - +
110I LEU* 3.9 22.0 - - + +
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Residues in contact with MET 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLN* 5.7 2.7 - - - +
102E ILE* 3.7 38.8 - - + +
105E GLU* 4.0 24.6 - - + +
106E MET* 3.2 33.9 - - + -
109E GLN* 3.6 18.0 + - + +
102G ILE* 3.4 17.7 - - + +
103G VAL* 3.3 12.6 - - - +
104G LYS 3.0 1.4 + - - -
105G GLU* 1.3 76.7 - - - +
107G ARG* 1.3 60.0 + - - +
109G GLN* 4.4 3.6 - - - -
110G LEU* 3.1 23.6 + - - +
106I MET* 4.3 21.5 - - + -
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Residues in contact with ARG 107 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ARG* 5.2 5.3 - - - +
105E GLU* 3.5 24.5 + - - +
103G VAL* 3.1 42.4 - - - +
104G LYS* 2.8 12.6 + - - +
106G MET* 1.3 77.4 - - - +
108G ARG* 1.3 60.8 + - + +
109G GLN 3.2 1.6 - - - -
110G LEU* 3.3 12.7 + - + +
111G GLU* 3.1 33.0 + - - +
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Residues in contact with ARG 108 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G LYS* 3.1 20.4 + - + +
105G GLU* 4.4 12.6 - - - +
107G ARG* 1.3 76.9 - - + +
109G GLN* 1.3 61.3 + - - +
110G LEU 3.2 0.4 - - - -
111G GLU* 3.6 29.7 + - - +
112G MET* 3.5 23.4 + - - +
110I LEU* 3.9 14.1 - - + +
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Residues in contact with GLN 109 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLN* 4.6 2.8 + - - -
109C GLN* 4.8 1.4 - - - +
109E GLN* 3.7 26.9 + - - +
105G GLU 2.9 20.1 + - - +
106G MET* 4.4 1.3 - - - -
108G ARG* 1.3 75.1 - - - +
110G LEU* 1.3 60.3 + - - +
111G GLU 3.0 5.1 + - - -
112G MET* 3.5 1.5 + - - +
113G ILE* 3.4 26.6 + - + +
106I MET* 3.0 43.3 - - - +
109I GLN* 3.5 35.0 + - - +
110I LEU* 3.9 24.7 - - + +
113I ILE* 4.5 15.1 - - + +
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Residues in contact with LEU 110 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E GLU* 3.8 20.0 - - - +
108E ARG* 3.4 50.7 - - + +
109E GLN* 3.7 17.3 - - + +
112E MET* 4.2 13.7 - - + +
42G EDO 4.4 0.7 - - - -
106G MET 3.1 15.8 + - - +
107G ARG* 3.3 13.5 - - + +
108G ARG 3.2 0.2 - - - -
109G GLN* 1.3 80.4 - - - +
111G GLU* 1.3 56.4 + - - +
113G ILE* 4.9 2.0 - - + +
114G ASP* 3.1 26.2 + - - +
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Residues in contact with GLU 111 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G EDO 3.1 44.9 + - - +
107G ARG* 3.1 19.2 - - - +
108G ARG* 3.6 39.3 + - - +
109G GLN 3.0 0.4 - - - -
110G LEU* 1.3 79.2 - - - +
112G MET* 1.3 60.9 + - + +
113G ILE 3.3 0.2 - - - -
115G LYS* 2.8 29.5 + - - +
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Residues in contact with MET 112 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ARG 3.5 7.4 - - - +
109G GLN 3.5 6.5 + - - +
111G GLU* 1.3 79.4 - - - +
113G ILE* 1.3 58.3 + - - +
115G LYS* 3.7 27.8 + - - +
116G LEU* 2.9 31.1 + - - +
110I LEU* 3.2 29.6 - - + +
113I ILE* 3.5 23.3 - - + +
114I ASP* 2.5 51.1 - - + +
117I THR* 3.7 2.5 + - - -
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Residues in contact with ILE 113 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E GLN* 3.9 20.2 - - - +
112E MET* 3.4 30.7 - - + -
113E ILE* 3.7 36.8 - - + +
116E LEU* 4.9 13.0 - - + -
109G GLN* 3.4 12.9 + - - +
110G LEU* 4.6 1.3 - - - +
111G GLU 3.3 0.2 - - - -
112G MET* 1.3 77.0 - - - +
114G ASP* 1.3 60.8 + - - +
116G LEU* 3.4 9.5 + - + +
117G THR* 2.7 37.5 + - - +
113I ILE* 3.2 27.4 - - + -
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Residues in contact with ASP 114 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E MET* 3.6 24.6 - - + +
42G EDO 2.9 30.0 + - - -
110G LEU 3.1 21.3 + - - +
111G GLU 3.3 5.3 + - - +
113G ILE* 1.3 80.3 - - - +
115G LYS* 1.3 61.0 + - - +
117G THR* 3.1 18.7 - - - +
118G THR* 3.3 7.1 + - - -
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Residues in contact with LYS 115 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G EDO 4.4 8.3 - - - +
111G GLU 2.8 17.8 + - - +
112G MET* 3.7 21.2 + - - +
114G ASP* 1.3 70.4 + - - +
116G LEU* 1.3 55.5 + - - +
117G THR 2.7 6.8 + - - -
118G THR* 2.6 32.3 + - - +
119G ARG* 3.1 32.7 + - - +
114I ASP* 5.6 0.2 - - - -
117I THR* 2.8 44.8 + - + +
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Residues in contact with LEU 116 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 3.9 27.6 - - + -
112G MET 2.9 16.3 + - - +
113G ILE* 3.6 12.6 - - + +
115G LYS* 1.3 76.0 - - - +
117G THR* 1.3 56.5 + - - +
119G ARG* 3.7 8.5 - - - +
120G GLU* 3.3 23.1 + - + +
113I ILE* 4.8 9.6 - - + -
116I LEU* 3.8 26.0 - - + +
117I THR* 2.9 35.2 - - - +
120I GLU* 3.2 35.6 - - + +
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Residues in contact with THR 117 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E MET* 4.6 6.6 - - + +
115E LYS* 5.3 6.7 - - + -
116E LEU* 3.8 35.2 - - + +
119E ARG* 5.1 5.1 - - + +
113G ILE* 2.7 20.2 + - - +
114G ASP* 3.1 17.7 - - - +
115G LYS 2.7 1.0 + - - -
116G LEU* 1.3 75.1 - - - +
118G THR* 1.3 60.6 + - - +
119G ARG 3.0 4.9 - - - -
120G GLU* 3.0 17.8 + - + +
121G ILE* 3.0 14.8 + - + +
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Residues in contact with THR 118 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G ASP 3.3 7.1 + - - -
115G LYS* 2.6 20.6 + - - -
117G THR* 1.3 75.5 - - - +
119G ARG* 1.3 62.7 + - - -
121G ILE* 3.7 8.3 + - - +
122G GLU* 2.9 27.4 + - - +
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Residues in contact with ARG 119 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G LYS* 3.5 35.9 - - + +
116G LEU* 3.7 11.2 - - - +
117G THR 3.0 0.2 - - - -
118G THR* 1.3 79.8 - - - +
120G GLU* 1.3 63.2 + - - +
121G ILE 3.1 2.0 - - - -
122G GLU* 3.0 44.4 + - - +
123G GLN* 3.1 16.5 + - - +
117I THR* 5.3 0.9 - - + -
120I GLU* 4.4 13.9 - - + +
121I ILE* 2.8 46.4 - - + +
124I ILE* 4.2 2.4 - - + +
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Residues in contact with GLU 120 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 3.2 26.0 - - + -
119E ARG* 3.8 15.8 - - + +
120E GLU* 2.5 30.3 + - - +
123E GLN* 2.7 26.3 + - - +
116G LEU* 3.3 12.1 + - + +
117G THR 3.0 9.7 + - - +
119G ARG* 1.3 78.9 - - - +
121G ILE* 1.3 57.6 + - - +
123G GLN* 3.3 13.7 + - - +
124G ILE* 3.2 28.3 + - - +
120I GLU* 2.7 34.4 - - + +
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Residues in contact with ILE 121 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ARG* 5.1 1.3 - - + +
117G THR* 3.0 14.9 + - + +
118G THR* 3.9 9.4 - - - +
119G ARG 3.1 0.2 - - - -
120G GLU* 1.3 74.5 - - - +
122G GLU* 1.3 66.2 + - - +
123G GLN 3.1 0.4 - - - -
124G ILE* 3.0 30.6 - - + +
125G GLU* 3.1 16.5 + - - +
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Residues in contact with GLU 122 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G THR* 2.9 22.9 - - - +
119G ARG* 3.0 48.3 + - - +
121G ILE* 1.3 77.6 - - + +
123G GLN* 1.3 61.4 + - - +
125G GLU* 3.6 1.9 + - - +
126G LEU* 3.1 31.4 + - + +
124I ILE* 3.0 26.5 - - + +
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Residues in contact with GLN 123 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLN* 5.5 0.7 - - - +
127B LEU* 5.1 0.6 - - - +
123E GLN* 2.6 36.9 + - - +
119G ARG 3.1 11.7 + - - +
120G GLU* 3.3 13.6 - - - +
122G GLU* 1.3 77.2 - - - +
124G ILE* 1.3 55.5 + - - +
126G LEU* 2.9 4.3 + - - +
127G LEU* 2.9 34.3 + - + +
120I GLU* 3.1 19.9 + - - +
123I GLN* 2.7 45.1 + - - +
124I ILE* 3.0 25.7 - - + +
127I LEU* 4.0 15.0 - - + +
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Residues in contact with ILE 124 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ARG* 3.5 24.7 - - + +
122E GLU* 3.8 14.1 - - + +
123E GLN* 3.0 42.2 - - + +
126E LEU* 5.3 1.6 - - - +
120G GLU 3.2 7.6 - - - +
121G ILE* 3.0 36.6 - - + +
123G GLN* 1.3 77.7 - - - +
125G GLU* 1.3 62.7 + - - +
127G LEU* 3.2 7.6 + - - +
128G LYS* 2.9 27.5 + - - +
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Residues in contact with GLU 125 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G ILE* 3.1 19.0 + - - +
122G GLU* 3.9 2.7 - - - +
124G ILE* 1.3 83.1 - - - +
126G LEU* 1.3 61.0 + - - +
127G LEU 3.1 0.9 - - - -
128G LYS* 4.3 11.8 - - + +
129G ARG* 3.0 25.3 + - + +
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Residues in contact with LEU 126 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G GLU* 3.1 17.7 + - + +
123G GLN* 2.9 7.7 + - - +
125G GLU* 1.3 80.9 - - - +
127G LEU* 1.3 59.7 - - - +
129G ARG* 3.8 6.9 - - + +
130G ILE* 3.1 28.9 - - - +
124I ILE* 3.2 41.5 - - + +
127I LEU* 3.9 22.4 - - + +
128I LYS* 4.3 13.0 - - + +
131I HIS* 4.7 18.9 - - + -
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Residues in contact with LEU 127 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E GLN* 4.1 32.8 - - + +
126E LEU* 4.1 12.3 - - + -
127E LEU* 4.0 35.9 - - + -
130E ILE* 3.8 8.2 - - + +
123G GLN* 2.9 21.0 + - - +
124G ILE 3.2 5.6 + - - +
125G GLU 3.1 0.2 - - - -
126G LEU* 1.3 83.4 - - + +
128G LYS* 1.3 53.6 + - - +
129G ARG 3.0 1.1 - - - -
130G ILE* 2.9 16.1 + - + +
131G HIS* 2.7 32.7 + - - +
127I LEU* 4.3 26.9 - - + -
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Residues in contact with LYS 128 (chain G).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E LEU* 4.8 5.7 - - + +
124G ILE 2.9 15.1 + - - +
125G GLU* 4.6 12.8 - - + +
127G LEU* 1.3 70.8 - - - +
129G ARG* 1.3 56.4 + - - +
130G ILE 2.8 10.8 + - - -
131G HIS* 3.4 15.6 + - - +
132G ASP* 3.5 27.6 + - - +
133G ASN 4.6 0.2 + - - -
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Residues in contact with ARG 129 (chain G).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G GLU* 3.0 21.7 + - + +
126G LEU* 3.8 10.3 - - + +
127G LEU 3.0 0.4 - - - -
128G LYS* 1.3 76.0 - - - +
130G ILE* 1.3 59.1 + - - +
133G ASN* 2.8 25.6 + - - +
131I HIS* 3.7 22.0 + - + +
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Residues in contact with ILE 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ILE* 3.6 28.1 - - + +
126G LEU 3.1 22.0 - - - +
127G LEU* 3.1 20.6 - - + +
128G LYS 2.8 3.0 + - - -
129G ARG* 1.3 82.9 - - - +
131G HIS* 1.3 63.8 + - - +
132G ASP 3.6 0.4 - - - -
133G ASN* 3.1 26.9 - - - +
134G LEU* 5.2 0.3 - - - +
127I LEU* 4.6 12.6 - - + +
130I ILE* 4.0 26.7 - - + -
131I HIS* 4.8 11.2 - - + -
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Residues in contact with HIS 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E LEU* 4.4 7.2 - - + +
129E ARG* 3.3 37.1 + - + +
130E ILE* 3.6 20.2 - - + -
133E ASN* 3.4 27.5 + - - +
9G EDO 4.4 18.4 - - - -
127G LEU 2.7 16.0 + - - +
128G LYS* 3.4 7.6 + - - +
130G ILE* 1.3 71.9 - - - +
132G ASP* 1.3 90.6 + - - +
133G ASN 2.7 15.5 + - - -
134G LEU* 3.2 19.4 + - - +
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Residues in contact with ASP 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G LYS* 3.5 19.7 + - - +
131G HIS* 1.3 104.7 + - - +
133G ASN* 1.3 52.9 + - - +
134G LEU* 2.6 21.3 + - - -
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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