Contacts of the helix formed by residues 138 - 160 (chain E) in PDB entry 3E2A
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 SER 138 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E LEU* 1.3 76.3 - - - +
139E PRO* 1.4 74.0 - - - +
140E GLU* 2.7 38.5 + - - -
141E LYS* 3.0 23.5 + - - -
142E ARG* 3.4 9.3 + - - +
218E GLU 5.6 0.7 - - - -
219E ASN* 4.1 6.3 - - - +
220E ILE* 3.2 34.2 + - - +
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Residues in contact with PRO 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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108E MET* 5.9 1.0 - - - +
137E LEU 3.8 2.4 - - - +
138E SER* 1.4 91.3 - - - +
140E GLU* 1.3 65.1 + - - +
141E LYS 3.1 1.4 + - - -
142E ARG* 3.2 45.2 + - - +
143E ALA* 4.5 1.9 + - - +
220E ILE* 4.9 4.7 - - + -
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E SER* 2.7 31.6 + - - -
139E PRO* 1.3 79.9 - - - +
141E LYS* 1.3 74.0 + - + +
142E ARG 3.6 0.2 - - - -
143E ALA* 5.0 4.8 + - - +
144E ASP* 5.6 2.1 + - - +
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Residues in contact with LYS 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E LEU* 4.4 5.3 - - + +
138E SER* 3.0 14.6 + - - +
140E GLU* 1.3 95.3 + - + +
142E ARG* 1.3 61.8 + - - +
143E ALA 3.5 2.0 - - - -
144E ASP* 3.9 9.3 + - + +
145E MET* 3.3 22.4 + - - +
218E GLU* 3.3 30.4 + - - +
219E ASN* 3.4 37.7 - - + +
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Residues in contact with ARG 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E MET* 4.4 10.3 - - + -
127E TRP* 5.5 16.2 - - + +
134E LEU* 3.1 34.4 + - + +
135E GLY* 3.6 18.3 + - - -
137E LEU* 3.2 24.7 + - + -
138E SER 3.6 7.4 - - - +
139E PRO* 3.2 38.5 + - - +
141E LYS* 1.3 75.6 - - - +
143E ALA* 1.3 55.8 + - - +
145E MET* 3.4 6.1 + - - +
146E LEU* 2.7 37.2 + - - +
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Residues in contact with ALA 143 (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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104E ILE* 3.8 5.5 - - + +
105E HIS* 3.5 26.0 - - + +
108E MET* 3.2 34.5 - - + +
139E PRO 4.5 2.2 + - - +
140E GLU 5.0 4.6 + - - +
141E LYS 3.5 0.2 - - - -
142E ARG* 1.3 77.2 - - - +
144E ASP* 1.3 53.2 + - - +
146E LEU* 3.1 4.3 + - - +
147E THR* 2.7 40.3 + - - +
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Residues in contact with ASP 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E THR* 3.9 33.4 - - - +
100E ASN* 4.0 12.3 + - - +
105E HIS* 6.1 0.5 - - - -
140E GLU 5.6 2.1 + - - +
141E LYS* 3.9 11.7 + - + +
142E ARG 3.4 0.4 - - - -
143E ALA* 1.3 81.3 - - - +
145E MET* 1.3 62.2 + - - +
147E THR* 3.3 9.4 + - - -
148E LYS* 3.1 38.2 + - - +
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Residues in contact with MET 145 (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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133E LEU* 4.0 9.6 - - + -
134E LEU* 3.4 20.2 - - + -
137E LEU* 3.4 31.9 - - + -
141E LYS 3.3 11.8 + - - +
142E ARG 3.6 3.4 - - - +
143E ALA 3.3 0.4 - - - -
144E ASP* 1.3 77.2 - - - +
146E LEU* 1.3 62.6 + - - +
148E LYS* 3.0 14.8 + - + +
149E ILE* 2.9 32.3 + - + +
212E LEU* 3.6 48.5 - - + +
215E LEU* 4.3 8.1 - - + -
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Residues in contact with LEU 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E ILE* 4.1 8.1 - - + -
107E ALA* 5.5 0.2 - - + -
108E MET* 3.5 33.7 - - + -
123E ILE* 3.9 26.0 - - + -
126E ILE* 4.3 14.4 - - + -
127E TRP* 4.1 39.7 - - + +
134E LEU* 3.9 16.1 - - + +
142E ARG 2.7 21.8 + - - +
143E ALA 3.5 4.5 - - - +
145E MET* 1.3 72.4 - - - +
147E THR* 1.3 57.3 + - - +
149E ILE* 4.4 5.2 - - + -
150E ASN* 2.8 29.4 + - + +
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Residues in contact with THR 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ASN* 6.1 0.2 - - - +
97E GLY* 4.9 2.7 - - - -
98E HIS 3.3 39.0 + - - +
99E THR* 5.0 1.9 - - + -
101E CYS* 4.8 4.0 + - + +
104E ILE* 3.7 28.0 - - + +
143E ALA 2.7 29.5 + - - -
144E ASP* 3.3 16.0 + - - -
146E LEU* 1.3 72.0 - - - +
148E LYS* 1.3 62.2 + - - +
150E ASN* 3.4 6.2 + - + +
151E VAL* 3.2 23.6 + - - +
180E VAL* 4.7 10.1 - - + -
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Residues in contact with LYS 148 (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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144E ASP* 3.3 24.8 - - - +
145E MET* 3.0 17.2 + - - +
147E THR* 1.3 73.9 - - - +
149E ILE* 1.3 66.8 + - - +
151E VAL* 3.2 5.2 + - - +
152E ALA* 3.2 19.9 + - - +
180E VAL* 4.3 16.2 - - + -
191E GLN* 3.3 32.9 - - - +
212E LEU* 4.0 27.5 - - + +
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Residues in contact with ILE 149 (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 ILE* 3.7 12.1 - - + -
130E HIS* 3.4 55.0 - - + +
133E LEU* 4.2 14.4 - - + -
134E LEU* 4.1 12.6 - - + -
145E MET* 2.9 43.2 + - + +
146E LEU* 3.9 6.3 - - + +
148E LYS* 1.3 76.0 - - - +
150E ASN* 1.3 63.4 + - - +
152E ALA* 3.2 8.2 + - - +
153E GLU* 2.9 22.9 + - + +
209E ILE* 4.8 6.5 - - + -
212E LEU* 5.1 9.4 - - + -
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Residues in contact with ASN 150 (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 ALA 2.9 27.1 + - - -
68E ASN* 3.4 16.4 + - - +
104E ILE* 4.0 14.9 - - + +
123E ILE* 2.9 23.2 - - + +
126E ILE* 3.8 7.6 - - + +
146E LEU* 2.8 21.4 + - + +
147E THR* 3.5 8.0 + - - +
149E ILE* 1.3 77.2 - - - +
151E VAL* 1.3 62.4 + - - +
153E GLU* 3.2 5.4 + - - -
154E GLN* 2.7 56.3 + - - +
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Residues in contact with VAL 151 (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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68E ASN* 4.2 7.0 - - - +
95E ILE* 4.0 8.3 - - + +
96E CYS 4.7 0.2 - - - -
97E GLY* 3.6 19.3 - - - +
147E THR 3.2 13.9 + - - +
148E LYS 3.6 7.2 - - - +
149E ILE 3.2 0.2 - - - -
150E ASN* 1.3 77.1 - - - +
152E ALA* 1.3 64.5 + - - +
154E GLN* 3.0 7.5 + - - +
155E VAL* 3.0 22.5 + - - +
178E GLY* 3.3 42.0 - - - +
179E TRP 3.6 17.9 - - - +
180E VAL* 3.7 9.4 - - + -
191E GLN* 3.9 9.2 - - + -
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Residues in contact with ALA 152 (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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148E LYS 3.2 8.7 + - - +
149E ILE* 3.2 10.2 + - - +
151E VAL* 1.3 82.1 - - - +
153E GLU* 1.3 57.5 + - - +
155E VAL* 3.5 3.8 + - - +
156E TYR* 3.0 25.6 + - - +
191E GLN* 5.1 6.0 - - + +
193E VAL* 3.6 29.4 - - + +
205E TYR* 4.0 6.3 - - + -
208E ALA* 4.8 3.4 - - + -
209E ILE* 4.2 22.7 - - + -
212E LEU* 6.5 2.0 - - + -
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Residues in contact with GLU 153 (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 ILE* 3.8 36.9 - - + +
129E LYS* 2.8 27.2 + - - +
130E HIS* 2.5 30.1 + - - +
149E ILE* 2.9 19.9 + - + +
150E ASN 3.8 3.8 - - - +
152E ALA* 1.3 73.7 - - + +
154E GLN* 1.3 62.5 + - - +
156E TYR* 3.3 10.2 + - - +
157E ASN* 2.8 35.0 + - - +
160E ARG* 5.9 0.2 + - - -
205E TYR* 2.6 27.0 + - - -
209E ILE* 4.3 0.7 - - - +
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Residues in contact with GLN 154 (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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68E ASN 3.4 21.5 - - - +
69E GLN* 3.5 16.5 + - - +
70E VAL* 2.8 40.6 + - - +
95E ILE* 3.3 26.1 - - + +
126E ILE* 3.4 22.2 - - - +
150E ASN* 2.7 47.6 + - - +
151E VAL* 3.7 3.8 - - - +
153E GLU* 1.3 73.6 - - - +
155E VAL* 1.3 61.7 + - - +
157E ASN* 3.3 10.5 + - - +
158E LEU* 2.8 24.3 + - - +
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Residues in contact with VAL 155 (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 ILE* 3.7 12.3 - - + -
151E VAL 3.0 16.0 + - - +
152E ALA 3.7 6.7 - - - +
154E GLN* 1.3 74.1 - - - +
156E TYR* 1.3 59.8 + - - +
158E LEU* 3.1 4.5 + - + +
159E GLY* 2.8 27.9 + - - -
176E LEU* 3.9 26.1 - - + +
177E HIS 3.5 9.6 - - - +
178E GLY* 3.4 33.2 - - - +
193E VAL* 3.5 33.7 - - + +
194E MET 5.1 0.2 - - - +
195E ALA* 5.2 0.7 - - + -
201E LEU* 3.9 5.9 - - + +
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Residues in contact with TYR 156 (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 LYS* 4.7 5.4 - - - -
152E ALA 3.0 14.7 + - - +
153E GLU* 3.4 15.7 - - - +
155E VAL* 1.3 76.7 - - - +
157E ASN* 1.3 63.2 + - - +
159E GLY* 3.2 2.6 + - - -
160E ARG* 3.0 64.2 + - - +
193E VAL* 4.8 0.4 - - - +
198E ARG* 3.5 6.0 + - - -
201E LEU* 3.8 26.5 - - + -
202E GLU* 2.3 41.3 + - - -
205E TYR* 3.7 52.7 - + + -
231E SO4 4.5 1.0 + - - -
128F PHE* 5.5 8.7 - + - -
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Residues in contact with ASN 157 (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 VAL* 2.9 30.5 + - + +
71E ILE* 5.0 1.0 - - - +
72E HIS* 3.1 32.8 + - + +
126E ILE* 5.4 2.8 - - - +
153E GLU* 2.8 24.9 + - - +
154E GLN* 3.3 24.5 + - - +
156E TYR* 1.3 73.9 - - - +
158E LEU* 1.3 61.7 + - - +
160E ARG* 3.1 25.9 + - - +
161E THR* 3.3 16.2 + - - +
121F LEU* 5.1 0.3 - - - +
125F ASP* 5.2 0.3 - - - +
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Residues in contact with LEU 158 (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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40E ILE* 4.7 0.7 - - + -
70E VAL* 4.0 16.3 - - + +
81E VAL* 3.8 39.9 - - + -
93E ILE* 3.4 31.2 - - + +
95E ILE* 4.1 19.3 - - + -
154E GLN 2.8 20.4 + - - +
155E VAL* 3.1 6.0 + - - +
157E ASN* 1.3 72.5 - - - +
159E GLY* 1.3 58.4 + - - +
160E ARG 3.2 0.2 - - - -
161E THR* 2.8 34.4 + - + -
164E VAL* 3.2 11.5 - - + +
176E LEU* 3.8 28.3 - - + -
177E HIS 5.7 0.4 - - - +
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Residues in contact with GLY 159 (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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155E VAL 2.8 11.1 + - - -
156E TYR 3.2 0.2 + - - -
158E LEU* 1.3 75.3 - - - +
160E ARG* 1.3 57.2 + - - +
161E THR 3.4 0.4 - - - -
164E VAL* 4.2 3.2 - - - +
165E LYS* 3.8 11.4 - - - +
168E TRP* 3.6 17.9 - - - -
176E LEU* 3.4 20.5 - - - +
198E ARG* 4.4 2.3 + - - -
201E LEU* 3.4 28.4 - - - +
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Residues in contact with ARG 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E HIS* 3.7 5.3 - - - -
129E LYS* 5.8 1.6 - - - +
153E GLU* 5.9 0.4 + - - -
156E TYR* 3.0 51.5 + - + +
157E ASN* 3.1 27.5 + - - +
159E GLY* 1.3 76.7 - - - +
161E THR* 1.3 65.4 + - - +
162E SER 3.6 1.2 + - - -
165E LYS* 3.6 17.5 + - - +
198E ARG* 3.6 12.1 - - - +
201E LEU* 4.1 2.9 - - + -
231E SO4 2.8 42.3 + - - +
117F ASN* 6.0 1.6 - - - +
121F LEU* 3.6 38.8 + - + +
124F ARG* 4.5 1.4 - - - +
125F ASP* 2.9 28.9 + - - -
128F PHE* 4.4 10.4 - - - -
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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) + - + + + + + -
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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