Contacts of the helix formed by residues 119 - 142 (chain E) in PDB entry 5K58
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 ASP 119 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E GLU 4.5 2.9 - - - +
118E GLN* 1.3 75.5 - - - +
120E ARG* 1.3 57.2 + - - +
121E LEU 3.0 0.2 - - - -
122E GLN* 2.9 52.2 + - - +
123E GLY 3.6 1.0 + - - -
26F SER 4.5 7.3 - - - +
29F SER* 2.6 34.5 + - - -
30F GLN* 3.9 22.9 + - - +
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Residues in contact with ARG 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E THR* 3.9 17.7 - - - +
57E ARG* 3.0 43.4 - - - +
60E ASP* 3.6 7.5 + - - -
118E GLN* 3.0 32.1 + - + +
119E ASP* 1.3 79.0 - - - +
121E LEU* 1.3 76.5 + - + +
122E GLN 3.4 0.3 + - - -
123E GLY* 3.4 10.0 + - - -
124E ARG* 3.9 11.1 + - - +
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Residues in contact with LEU 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E THR* 4.2 19.3 - - + +
59E PHE* 4.3 16.6 - - + -
60E ASP* 3.3 31.9 - - - +
63E ILE* 3.6 14.2 - - + +
114E LEU* 3.7 22.4 - - + +
117E GLU* 3.5 18.6 - - + -
118E GLN* 3.0 35.6 + - + +
120E ARG* 1.3 89.4 - - + +
122E GLN* 1.3 64.6 + - - +
123E GLY 3.3 0.2 - - - -
124E ARG* 3.3 23.3 - - + +
125E ILE 3.7 1.7 + - - -
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Residues in contact with GLN 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E LEU* 3.7 19.6 - - + +
118E GLN 4.1 0.8 + - - -
119E ASP* 2.9 36.0 + - - +
121E LEU* 1.3 77.8 - - - +
123E GLY* 1.3 68.3 + - - +
125E ILE* 3.0 13.2 + - - +
126E ASN* 3.1 32.7 + - - +
29F SER* 4.3 12.1 + - - -
175F ARG* 4.4 4.9 + - - +
177F GLU* 2.9 36.2 + - - -
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Residues in contact with GLY 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ASP 3.6 1.2 + - - -
120E ARG 3.4 7.6 + - - -
121E LEU 3.3 0.8 - - - -
122E GLN* 1.3 85.6 - - - +
124E ARG* 1.3 51.5 - - - +
126E ASN* 3.4 8.4 + - - +
127E GLN* 2.7 55.3 + - - +
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Residues in contact with ARG 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ASP* 3.7 27.1 + - - +
63E ILE* 3.5 30.4 - - + +
64E GLU* 3.2 50.3 + - - +
67E GLU* 4.5 19.3 + - - +
120E ARG 3.9 11.1 + - - +
121E LEU* 3.3 17.5 - - - +
123E GLY* 1.3 74.0 - - - +
125E ILE* 1.3 58.0 + - - +
127E GLN* 3.4 11.0 + - - +
128E LEU* 2.8 28.8 + - - +
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Residues in contact with ILE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ILE* 4.0 18.6 - - + -
66E ILE* 5.7 3.1 - - + -
108E ILE* 3.4 29.4 - - + +
109E LEU* 3.4 37.5 - - + +
111E GLY* 6.0 0.4 - - - -
114E LEU* 3.8 19.7 - - + -
121E LEU 3.8 12.1 - - - +
122E GLN 3.0 6.7 + - - +
124E ARG* 1.3 72.4 - - - +
126E ASN* 1.3 58.9 + - - +
128E LEU* 3.0 13.9 + - + +
129E PHE* 2.7 50.3 + - + +
175F ARG* 4.8 1.8 - - - -
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Residues in contact with ASN 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E GLN* 3.1 30.2 + - - +
123E GLY* 3.6 8.1 - - - +
125E ILE* 1.3 74.8 - - - +
127E GLN* 1.3 53.3 + - + +
129E PHE* 2.7 7.1 + - - +
130E GLU* 2.7 43.5 + - + +
175F ARG* 3.1 69.4 + - - +
176F SER* 4.7 2.8 - - - +
177F GLU* 5.0 0.4 + - - -
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Residues in contact with GLN 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E GLU* 5.8 2.9 - - - +
123E GLY* 2.7 40.1 + - - +
124E ARG* 3.5 10.2 - - - +
126E ASN* 1.3 71.4 - - + +
128E LEU* 1.3 57.1 + - - +
130E GLU* 3.9 10.2 - - + +
131E ARG* 3.3 25.3 + - - +
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Residues in contact with LEU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ILE* 5.5 2.7 - - + +
66E ILE* 3.7 31.9 - - + +
67E GLU* 4.0 35.6 + - + +
70E LEU* 4.6 4.0 - - + -
71E ILE* 3.7 28.3 - - + -
109E LEU* 4.8 9.4 - - + -
124E ARG 2.8 13.9 + - - +
125E ILE* 3.2 15.5 - - + +
127E GLN* 1.3 74.9 - - - +
129E PHE* 1.3 52.9 + - + +
130E GLU 2.9 4.0 - - - -
131E ARG* 2.8 10.2 + - - +
132E ILE* 2.8 51.5 + - + +
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Residues in contact with PHE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E LEU* 6.0 2.0 - - + -
109E LEU* 3.6 36.1 - - + -
110E THR* 5.6 1.8 - - - -
125E ILE* 2.7 37.0 + - + -
126E ASN 2.7 7.8 + - - +
128E LEU* 1.3 72.6 - - + +
130E GLU* 1.3 57.0 + - - +
132E ILE* 3.9 16.4 - - + -
133E GLU* 3.2 27.4 + - - +
163E LEU* 3.4 28.2 - - + +
167E GLU* 3.3 38.6 - - + -
170E LEU* 4.9 13.2 - - + -
172F ARG* 4.9 0.3 + - - -
175F ARG* 3.3 36.1 - - - +
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ASN* 2.7 30.1 + - + +
127E GLN* 4.1 8.7 - - - +
129E PHE* 1.3 73.8 - - - +
131E ARG* 1.3 63.2 + - - +
132E ILE 3.4 0.2 - - - -
133E GLU* 4.1 10.0 - - - +
134E ALA* 3.4 19.4 + - - +
137E ARG* 3.8 9.4 + - - +
172F ARG* 4.2 2.8 + - - -
175F ARG* 3.8 17.7 + - - -
180F TYR* 3.5 34.7 + - - -
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Residues in contact with ARG 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E GLU* 3.2 43.9 + - - +
71E ILE* 4.1 30.1 - - + +
127E GLN 3.3 18.9 + - - +
128E LEU* 2.8 8.4 + - - +
130E GLU* 1.3 76.1 - - - +
132E ILE* 1.3 59.7 + - - +
134E ALA* 3.4 5.5 + - + +
135E GLN* 3.0 50.9 + - - +
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Residues in contact with ILE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LEU* 4.4 18.8 - - + -
71E ILE* 4.3 16.8 - - + -
74E ILE* 4.4 10.1 - - + -
91E ILE* 5.1 2.5 - - + -
95E LEU* 3.9 32.8 - - + -
128E LEU* 2.8 39.0 + - + +
129E PHE* 4.0 23.3 - - + +
131E ARG* 1.3 73.1 - - - +
133E GLU* 1.3 61.9 + - - +
134E ALA 3.0 4.5 - - - -
135E GLN* 3.2 10.3 + - - +
136E LEU* 3.1 28.7 + - + +
163E LEU* 4.1 11.2 - - + -
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Residues in contact with GLU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PHE 3.2 16.2 + - - +
130E GLU* 4.5 6.4 - - - +
131E ARG 3.5 0.2 - - - -
132E ILE* 1.3 78.8 - - - +
134E ALA* 1.3 57.5 + - - +
136E LEU* 3.5 8.4 - - - +
137E ARG* 2.6 58.6 + - - +
156E THR* 4.0 10.9 - - - +
159E ALA* 3.7 22.3 - - + +
160E SER* 4.0 17.0 + - - -
163E LEU* 4.1 10.1 - - + +
172F ARG* 2.4 35.2 + - - +
180F TYR* 3.5 14.2 + - - -
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Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU 3.4 17.6 + - - +
131E ARG* 3.4 9.2 + - + +
132E ILE 3.0 0.6 - - - -
133E GLU* 1.3 76.5 - - - +
135E GLN* 1.3 67.4 + - - +
136E LEU 3.1 1.1 - - - -
137E ARG* 3.3 23.7 + - - +
138E GLN* 3.1 26.0 + - - +
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Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ILE* 5.0 4.7 - - + +
74E ILE* 3.2 50.3 - - + +
75E ASN* 4.0 12.1 + - - +
91E ILE* 5.5 3.8 - - + -
131E ARG* 3.0 49.6 + - + +
132E ILE* 3.4 6.7 - - + +
134E ALA* 1.3 75.9 - - - +
136E LEU* 1.3 59.0 + - + +
138E GLN* 3.4 9.8 - - - +
139E VAL* 3.1 31.5 + - + +
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 3.7 20.9 - - + -
91E ILE* 3.6 42.0 - - + -
92E VAL* 5.7 0.2 - - + -
95E LEU* 5.8 1.3 - - + -
132E ILE* 3.1 20.0 + - + +
133E GLU* 3.5 10.8 - - - +
134E ALA 3.1 0.4 - - - -
135E GLN* 1.3 73.4 - - - +
137E ARG* 1.3 68.1 + - - +
138E GLN 3.1 1.9 + - - -
139E VAL* 3.3 11.6 + - - +
140E MET* 3.2 21.9 + - + +
159E ALA* 3.9 22.7 - - + +
162E ILE* 3.8 28.7 - - + -
163E LEU* 4.4 12.3 - - + -
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Residues in contact with ARG 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 3.8 11.1 + - - +
133E GLU* 2.6 53.7 + - - +
134E ALA* 3.3 39.4 + - - +
136E LEU* 1.3 73.9 - - - +
138E GLN* 1.3 55.6 + - - +
140E MET* 3.8 3.2 - - - +
141E ARG* 2.8 39.4 + - + +
155E GLU* 4.4 8.0 - - + +
156E THR* 3.6 37.7 - - - +
159E ALA* 4.1 12.1 - - + +
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Residues in contact with GLN 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E LEU* 6.4 2.5 - - + -
134E ALA 3.1 11.3 + - - +
135E GLN* 3.4 14.6 - - - +
137E ARG* 1.3 79.2 - - - +
139E VAL* 1.3 66.8 + - + +
140E MET 3.0 0.3 + - - -
141E ARG* 3.0 15.6 + - - +
142E GLU* 2.8 58.0 + - - +
145E MET* 5.7 0.3 - - - +
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Residues in contact with VAL 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ILE* 6.4 0.7 - - + -
78E LEU* 6.6 0.2 - - + -
84E THR* 3.5 34.7 - - - +
87E ARG* 3.6 40.7 + - + +
88E LEU* 3.7 16.6 - - + -
91E ILE* 3.6 25.4 - - + -
135E GLN* 3.1 17.7 + - + +
136E LEU* 3.3 6.5 + - - +
138E GLN* 1.3 77.1 - - + +
140E MET* 1.3 59.7 + - - +
142E GLU* 3.8 11.6 - - - +
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Residues in contact with MET 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E THR* 4.9 1.6 - - - +
88E LEU* 4.2 17.0 - - + -
136E LEU* 3.2 27.2 + - + +
137E ARG* 4.2 1.1 - - - +
138E GLN 3.1 0.4 - - - -
139E VAL* 1.3 76.6 - - - +
141E ARG* 1.3 67.0 + - - +
142E GLU 3.1 1.3 - - - -
143E LYS* 3.1 21.3 + - - +
144E ARG 4.9 0.2 + - - -
151E TYR* 3.2 42.0 - - + +
155E GLU* 4.0 26.3 - - + +
158E LEU* 4.1 13.7 - - + -
159E ALA* 4.0 9.4 - - - +
162E ILE* 3.7 32.3 - - + -
197E LEU* 4.0 10.3 - - - -
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Residues in contact with ARG 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ARG* 2.8 23.3 + - + +
138E GLN* 3.0 19.9 + - - +
140E MET* 1.3 77.7 - - - +
142E GLU* 1.3 58.0 + - + +
143E LYS 3.1 4.4 + - - -
144E ARG* 4.2 7.4 + - - +
145E MET* 4.8 5.3 + - + +
155E GLU* 3.5 31.6 + - + +
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Residues in contact with GLU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E LEU* 4.5 11.8 - - - +
84E THR* 5.0 0.2 - - - -
87E ARG* 2.7 32.3 + - - +
138E GLN* 2.8 40.7 + - - +
139E VAL 3.8 7.6 - - - +
140E MET 3.1 0.4 - - - -
141E ARG* 1.3 76.2 - - + +
143E LYS* 1.3 63.2 + - - +
144E ARG 3.5 0.7 - - - -
145E MET* 3.1 36.9 - - + +
146E ARG* 3.0 40.0 + - - +
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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