Contacts of the helix formed by residues 136 - 160 (chain E) in PDB entry 1O9I
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 ASN 136 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B HIS* 2.8 26.4 + - - +
264B HIS* 3.7 26.2 + - - +
153D LEU* 3.7 29.5 - - + +
157D ARG* 4.7 0.4 - - - +
134E SER* 3.0 4.6 + - - -
135E GLY* 1.3 76.8 - - - +
137E LEU* 1.3 59.4 + - - +
138E VAL* 2.9 23.5 + - - +
139E ALA* 2.9 15.3 + - + +
140E ASP* 2.9 29.5 + - - -
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Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS 2.8 13.2 + - - +
265B GLN* 3.8 38.6 - - + +
45E GLN* 4.3 11.0 - - + +
49E SER* 4.1 12.6 - - - +
55E TYR* 4.2 22.7 - - + -
59E LEU* 4.1 25.1 - - + -
135E GLY* 4.0 2.2 + - - +
136E ASN* 1.3 72.7 - - - +
138E VAL* 1.3 61.7 + - - +
139E ALA 3.3 0.4 - - - -
140E ASP* 3.6 22.2 - - + +
141E MET* 2.8 41.9 + - + +
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS* 3.8 21.9 + - + +
136E ASN* 2.9 11.7 + - - +
137E LEU* 1.3 79.7 - - - +
139E ALA* 1.3 62.5 + - - +
141E MET* 4.2 2.1 - - - +
142E ARG* 3.3 49.3 + - - +
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Residues in contact with ALA 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D VAL* 4.6 2.6 - - - +
149D SER* 4.3 27.4 - - - +
150D GLU* 3.4 28.4 - - + +
153D LEU* 4.8 3.6 - - + -
134E SER* 4.4 1.8 - - - +
136E ASN* 2.9 21.9 + - + +
138E VAL* 1.3 77.8 - - - +
140E ASP* 1.3 59.0 + - - +
142E ARG* 3.2 8.0 + - - +
143E PHE* 3.0 22.2 + - - +
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Residues in contact with ASP 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D GLU* 2.8 17.2 - - - +
45E GLN* 3.7 28.2 - - - +
132E THR* 3.7 5.0 - - - +
133E SER* 3.4 7.4 + - - -
134E SER* 2.7 42.0 + - - -
135E GLY 3.9 3.8 + - - -
136E ASN 2.9 18.2 + - - +
137E LEU* 3.6 11.2 + - + +
139E ALA* 1.3 74.3 - - - +
141E MET* 1.3 60.3 - - - +
143E PHE* 3.2 6.8 + - - +
144E ASN* 2.8 36.0 + - - +
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Residues in contact with MET 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E TYR* 4.0 28.3 - - + -
58E LEU* 4.4 13.7 - - + -
59E LEU* 3.9 31.4 - - + -
137E LEU* 2.8 31.9 + - + +
138E VAL* 4.2 2.7 - - - +
140E ASP* 1.3 73.1 - - - +
142E ARG* 1.3 66.5 + - - +
144E ASN* 3.2 9.0 + - - +
145E VAL* 3.0 28.8 + - - +
185E PHE* 3.6 43.1 - - - +
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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
----------------------------------------------------------
142D ARG* 5.5 0.4 - - - +
145D VAL* 3.8 12.8 - - + +
146D VAL* 3.3 14.6 - - + -
149D SER* 2.9 38.6 + - - -
182D GLN* 3.2 18.0 + - - -
186D MET* 3.4 28.3 - - - +
138E VAL* 3.3 35.7 + - + +
139E ALA 3.2 7.5 + - - +
141E MET* 1.3 77.7 - - - +
143E PHE* 1.3 63.9 + - - +
145E VAL* 3.2 10.0 + - - +
146E VAL* 3.0 24.3 + - - +
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Residues in contact with PHE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TRP* 3.9 18.8 - + - -
146D VAL* 3.3 19.4 - - + +
150D GLU* 4.5 4.5 - - - +
33E TRP* 3.7 33.0 - + - -
37E THR* 4.7 0.7 - - + -
41E SER* 3.6 25.8 - - - -
45E GLN* 4.0 3.8 - - - -
130E TYR 3.8 21.3 - - - -
132E THR* 3.7 32.5 - - + -
139E ALA 3.0 13.5 + - - +
140E ASP* 3.3 11.0 - - - +
142E ARG* 1.3 76.2 - - - +
144E ASN* 1.3 71.9 + - - +
146E VAL* 3.0 5.2 + - + +
147E ARG* 2.8 36.2 + - + +
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Residues in contact with ASN 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.2 26.8 - - + -
45E GLN* 2.8 41.8 + - - -
59E LEU* 3.4 17.8 - - - +
140E ASP 2.8 20.2 + - - +
141E MET* 3.2 17.6 + - - +
143E PHE* 1.3 76.0 - - - +
145E VAL* 1.3 66.6 + - - +
147E ARG* 3.2 2.5 + - - +
148E GLU* 3.0 28.8 + - - +
185E PHE* 3.7 18.7 - - + -
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Residues in contact with VAL 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ARG* 3.8 35.7 - - + +
189D GLN* 6.1 0.7 - - - +
141E MET 3.0 20.2 + - - +
142E ARG* 3.2 9.8 + - - +
144E ASN* 1.3 78.3 - - - +
146E VAL* 1.3 53.0 + - - +
148E GLU* 3.3 6.5 + - - +
149E SER* 2.7 36.1 + - - +
182E GLN* 4.0 16.1 - - + +
185E PHE* 3.6 31.6 - - + +
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Residues in contact with VAL 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ALA 4.7 1.3 - - - +
142D ARG* 3.4 43.3 - - + +
143D PHE* 3.4 17.5 - - + +
146D VAL* 3.6 8.3 - - + -
33E TRP* 3.7 26.5 - - + -
142E ARG 3.0 17.8 + - - +
143E PHE* 3.0 9.8 + - + +
145E VAL* 1.3 74.6 - - - +
147E ARG* 1.3 66.1 + - - +
149E SER* 4.1 5.4 - - - -
150E GLU* 2.9 36.1 + - + +
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Residues in contact with ARG 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TRP* 2.8 63.5 + - + -
34E GLY 3.0 16.9 + - - -
35E GLU* 3.1 17.8 + - - -
37E THR* 4.1 12.8 - - + +
38E GLY* 3.6 18.1 - - - +
42E PHE* 4.2 5.7 - - + -
66E GLU* 3.2 24.9 + - - -
143E PHE* 2.8 24.6 + - + +
144E ASN* 3.2 12.1 + - - +
146E VAL* 1.3 72.0 - - - +
148E GLU* 1.3 85.9 + - - +
150E GLU* 3.9 1.2 - - - +
151E ALA* 3.0 35.2 + - - +
178E GLU* 5.6 0.8 + - - +
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.3 15.2 - - + -
66E GLU* 2.8 24.4 - - - +
144E ASN 3.0 17.4 + - - +
145E VAL 3.9 0.7 - - - +
147E ARG* 1.3 90.7 + - - +
149E SER* 1.3 58.6 + - - +
151E ALA* 3.9 3.7 - - - +
152E ARG* 3.0 23.6 + - - +
178E GLU* 3.4 28.3 - - - +
181E HIS* 3.3 35.7 + - + +
182E GLN* 3.2 31.2 + - + +
185E PHE* 5.4 1.6 - - + -
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Residues in contact with SER 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ALA* 4.3 12.1 - - - -
142D ARG* 2.9 28.6 + - - -
200D VAL* 3.5 23.7 - - - +
145E VAL 2.7 22.3 + - - -
146E VAL* 3.1 8.0 + - - -
148E GLU* 1.3 76.6 - - - +
150E GLU* 1.3 60.4 + - - +
152E ARG* 3.4 0.7 + - - -
153E LEU* 3.0 29.3 + - - +
182E GLN* 3.5 11.5 - - - +
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Residues in contact with GLU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D THR* 3.4 15.2 - - - +
134D SER* 3.2 24.8 + - - -
139D ALA* 3.4 21.8 - - + +
140D ASP* 2.8 22.5 - - - +
143D PHE* 4.4 2.6 - - - +
33E TRP* 3.5 41.7 + - + +
146E VAL* 2.9 23.3 + - + +
149E SER* 1.3 76.5 - - - +
151E ALA* 1.3 63.3 + - - +
153E LEU* 3.4 7.4 + - - +
154E GLN* 3.0 32.0 + - - +
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Residues in contact with ALA 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E TRP* 3.6 9.5 - - - +
34E GLY* 5.5 0.2 - - - -
35E GLU* 4.4 2.2 - - - +
147E ARG* 3.0 44.2 + - - +
148E GLU* 4.0 4.0 - - - +
150E GLU* 1.3 77.4 - - - +
152E ARG* 1.3 57.0 + - - +
154E GLN* 3.1 9.5 + - - +
155E VAL* 2.9 32.2 + - + +
178E GLU* 3.9 16.6 - - - +
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Residues in contact with ARG 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ILE* 3.4 12.2 - - - +
200D VAL 3.1 19.9 + - - +
201D PRO* 2.9 34.0 + - - +
204D MET* 3.7 26.9 + - - +
205D LYS* 4.5 1.6 - - - +
208D GLU* 2.8 26.5 + - - -
148E GLU 3.0 20.0 + - - +
149E SER 4.0 0.2 - - - +
150E GLU 3.3 0.2 - - - -
151E ALA* 1.3 76.1 - - - +
153E LEU* 1.3 57.6 + - - +
155E VAL 3.8 0.2 - - - -
156E SER* 2.8 33.3 + - - -
175E LEU* 3.0 33.8 + - + +
178E GLU* 3.1 25.5 + - + +
179E THR* 3.1 10.9 + - - +
182E GLN* 3.6 10.3 - - - +
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Residues in contact with LEU 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU 3.8 10.3 - - - +
262A HIS* 3.9 22.0 - - + +
134D SER* 3.4 35.2 - - - +
136D ASN* 3.7 19.5 - - + +
139D ALA* 4.7 2.9 - - + -
200D VAL* 4.3 5.2 - - + -
201D PRO* 3.8 12.0 - - + +
149E SER 3.0 17.0 + - - +
150E GLU* 3.5 11.0 - - - +
151E ALA 3.2 0.2 - - - -
152E ARG* 1.3 76.8 - - - +
154E GLN* 1.3 63.8 + - + +
156E SER* 3.3 3.5 + - - -
157E ARG* 3.0 55.9 + - - +
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Residues in contact with GLN 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLU* 3.5 40.7 + - + +
28E SER* 5.1 5.2 + - - +
32E GLN* 5.5 1.2 + - - +
33E TRP* 4.2 36.1 - - - +
34E GLY* 5.3 0.3 - - - -
150E GLU* 3.0 20.0 + - - +
151E ALA* 3.6 8.6 - - - +
153E LEU* 1.3 80.6 - - + +
155E VAL* 1.3 57.3 + - + +
157E ARG* 3.1 17.8 + - - +
158E LEU* 2.8 38.9 + - + +
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Residues in contact with VAL 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E SER* 4.7 13.9 - - - +
35E GLU* 6.0 0.4 - - - +
151E ALA* 2.9 20.3 + - + +
152E ARG 3.8 1.8 - - - +
154E GLN* 1.3 75.5 - - + +
156E SER* 1.3 62.6 + - - +
158E LEU* 3.2 11.9 + - + +
159E TYR* 3.0 21.8 + - - +
171E LEU* 3.7 35.9 - - + +
174E LEU* 4.4 9.4 - - + -
175E LEU* 3.5 21.1 - - + +
178E GLU* 3.5 27.1 - - - +
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Residues in contact with SER 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A HIS* 4.0 16.9 + - - -
201D PRO* 3.3 28.1 - - - +
204D MET* 3.3 30.7 - - - +
152E ARG 2.8 23.3 + - - -
153E LEU 3.5 4.9 - - - -
155E VAL* 1.3 77.4 - - - +
157E ARG* 1.3 62.1 + - - +
159E TYR* 3.2 16.3 + - - +
160E SER* 3.6 5.7 + - - -
175E LEU* 3.5 9.0 - - - +
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Residues in contact with ARG 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG 4.2 15.0 - - - +
261A LEU* 2.8 37.7 + - + +
262A HIS* 4.5 1.7 + - + -
263A ASN* 2.8 24.9 + - - -
134D SER* 2.8 32.9 + - - +
135D GLY* 4.3 2.2 - - - -
153E LEU* 3.0 44.2 + - - +
154E GLN* 3.1 16.9 + - - +
156E SER* 1.3 76.6 - - - +
158E LEU* 1.3 63.8 + - - +
160E SER* 2.9 15.1 + - - -
161E MET* 3.2 31.7 - - + +
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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
----------------------------------------------------------
21E MET* 3.6 24.1 - - + +
24E ARG* 3.7 37.0 - - + +
25E LEU* 3.8 17.0 - - + +
27E GLU* 5.9 2.2 - - + -
28E SER* 3.6 23.8 - - - +
154E GLN* 2.8 24.0 + - + +
155E VAL* 3.2 15.9 + - + +
157E ARG* 1.3 74.9 - - - +
159E TYR* 1.3 57.5 + - - +
161E MET* 2.9 34.2 + - - +
162E THR* 3.6 5.7 + - - +
171E LEU* 3.8 11.4 - - + -
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Residues in contact with TYR 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D MET* 4.4 12.1 - - + -
207D ILE* 3.5 45.3 - - + +
155E VAL 3.0 11.7 + - - +
156E SER 3.3 11.9 - - - +
157E ARG 3.1 0.6 - - - -
158E LEU* 1.3 77.5 - - - +
160E SER* 1.3 63.6 + - - +
161E MET 3.2 0.2 - - - -
162E THR* 3.1 7.4 - - - +
165E GLU* 5.4 0.9 + - - -
168E ARG* 2.9 86.7 + - + +
171E LEU* 3.7 17.7 - - + +
172E LYS* 3.6 25.8 + - + -
175E LEU* 5.0 2.5 - - + -
----------------------------------------------------------
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Residues in contact with SER 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG* 3.7 58.3 + - - +
262A HIS* 5.0 2.9 + - - -
156E SER 3.6 4.9 + - - -
157E ARG 2.9 11.0 + - - -
159E TYR* 1.3 81.5 - - - +
161E MET* 1.3 61.9 + - - +
162E THR 3.5 3.1 - - - -
168E ARG* 4.4 5.7 + - - +
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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