Contacts of the helix formed by residues 136 - 160 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A HIS 2.9 25.8 + - - +
264A HIS* 3.7 26.1 + - - +
134D SER* 3.0 10.0 + - - -
135D GLY* 1.3 76.0 - - - +
137D LEU* 1.3 58.8 + - - +
138D VAL* 2.8 23.5 + - - +
139D ALA* 2.9 11.0 + - + +
140D ASP* 2.9 24.2 + - - -
200D VAL* 4.2 14.5 - - - +
201D PRO* 4.4 4.9 - - - +
153E LEU* 3.7 28.4 - - + +
157E ARG* 4.7 0.4 - - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS 2.8 13.3 + - - +
265A GLN* 3.8 37.2 - - + +
45D GLN* 4.2 11.7 - - + +
49D SER* 4.1 12.8 - - - +
55D TYR* 4.1 21.3 - - + -
59D LEU* 4.1 24.9 - - + -
135D GLY* 5.5 2.0 - - - -
136D ASN* 1.3 70.4 - - - +
138D VAL* 1.3 61.4 + - - +
139D ALA 3.3 0.4 - - - -
140D ASP* 3.7 22.4 - - + +
141D MET* 2.8 38.3 + - + +
192D LEU* 3.6 13.5 - - + +
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS* 3.9 8.0 + - + +
136D ASN* 2.8 11.4 + - - +
137D LEU* 1.3 79.9 - - - +
139D ALA* 1.3 61.9 + - - +
141D MET* 4.2 1.8 - - - +
142D ARG* 3.3 29.3 + - - +
189D GLN* 4.7 3.1 - - + +
192D LEU* 3.9 17.3 - - + +
193D GLU* 3.9 29.2 - - + +
196D TYR* 3.9 35.2 - - + -
197D GLY 4.3 6.1 - - - +
200D VAL* 3.4 23.8 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER* 4.3 2.5 - - - +
136D ASN* 2.9 19.5 + - + +
138D VAL* 1.3 78.5 - - - +
140D ASP* 1.3 58.6 + - - +
142D ARG* 3.2 7.5 + - - +
143D PHE* 3.0 20.8 + - - +
200D VAL* 4.0 21.2 - - + +
146E VAL* 4.6 2.9 - - - +
149E SER* 4.3 14.1 - - - -
150E GLU* 3.4 29.2 - - - +
153E LEU* 4.7 1.8 - - + -
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Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLN* 3.8 26.8 - - - +
132D THR* 3.6 5.7 - - - +
133D SER* 3.4 7.3 + - - -
134D SER* 2.7 43.7 + - - -
135D GLY 3.9 3.5 + - - -
136D ASN 2.9 14.9 + - - +
137D LEU* 3.6 12.5 + - + +
138D VAL 3.4 0.2 - - - -
139D ALA* 1.3 73.0 - - - +
141D MET* 1.3 61.9 + - - +
143D PHE* 3.1 6.7 + - - +
144D ASN* 2.8 35.1 + - - +
150E GLU* 2.8 17.3 - - - +
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Residues in contact with MET 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D TYR* 4.0 25.6 - - + +
58D LEU* 4.5 7.0 - - + -
59D LEU* 3.9 31.0 - - + -
137D LEU* 2.8 30.1 + - + +
138D VAL 4.3 0.4 - - - +
140D ASP* 1.3 72.6 - - - +
142D ARG* 1.3 65.4 + - - +
144D ASN* 3.2 8.5 + - - +
145D VAL* 3.0 29.0 + - - +
185D PHE* 3.6 28.6 - - - +
188D ALA* 3.8 17.0 - - + -
189D GLN* 4.0 21.5 - - + -
192D LEU* 3.8 13.2 - - + -
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Residues in contact with ARG 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D VAL* 3.3 20.7 + - - +
139D ALA* 3.2 7.5 + - - +
141D MET* 1.3 78.2 - - - +
143D PHE* 1.3 62.1 + - - +
145D VAL* 3.3 4.4 + - - +
146D VAL* 3.0 25.3 + - - +
189D GLN* 3.5 26.5 + - - +
193D GLU* 2.7 33.9 + - - +
198D ILE* 2.7 29.7 + - - +
200D VAL* 3.5 13.3 - - - +
142E ARG* 5.5 0.4 - - - +
145E VAL* 3.8 21.3 - - + +
146E VAL* 3.4 14.8 - - + -
149E SER* 2.9 30.0 + - - -
182E GLN* 3.3 18.2 + - - +
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Residues in contact with PHE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TRP* 3.7 31.2 - + - -
37D THR* 4.6 0.7 - - + -
41D SER* 3.6 25.8 - - - -
42D PHE* 5.4 0.2 - + - -
45D GLN* 4.0 7.0 - - - -
130D TYR 3.8 21.3 - - - -
132D THR* 3.6 32.1 - - + -
139D ALA 3.0 13.3 + - - +
140D ASP* 3.1 11.6 + - - +
142D ARG* 1.3 76.6 - - - +
144D ASN* 1.3 69.7 + - - +
146D VAL* 3.1 5.2 + - + +
147D ARG* 2.8 35.9 + - + -
33E TRP* 3.9 17.9 - + - -
143E PHE* 6.3 0.2 - + - -
146E VAL* 3.4 17.6 - - + +
150E GLU* 4.4 3.8 - - - +
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Residues in contact with ASN 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.2 23.5 - - + -
45D GLN* 2.8 41.6 + - - -
59D LEU* 3.4 18.6 - - - +
140D ASP 2.8 18.6 + - - +
141D MET* 3.2 16.1 + - - +
143D PHE* 1.3 79.3 - - - +
145D VAL* 1.3 62.9 + - - +
147D ARG* 3.2 3.1 + - - +
148D GLU* 3.1 27.2 + - - +
185D PHE* 3.6 23.2 - - + -
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D MET 3.0 17.6 + - - +
142D ARG 3.6 6.7 - - - +
144D ASN* 1.3 77.8 - - - +
146D VAL* 1.3 54.3 + - - +
148D GLU* 3.3 6.3 + - - +
149D SER* 2.7 36.6 + - - +
182D GLN* 4.0 5.3 - - + +
185D PHE* 3.6 9.0 - - + -
186D MET* 3.6 44.4 - - + +
189D GLN* 3.7 16.4 - - - +
142E ARG* 3.8 34.1 - - + +
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Residues in contact with VAL 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TRP* 3.7 24.5 - - + -
142D ARG 3.0 17.9 + - - +
143D PHE* 3.1 9.4 + - + +
145D VAL* 1.3 74.5 - - - +
147D ARG* 1.3 67.2 + - - +
149D SER* 3.0 6.0 + - - -
150D GLU* 2.8 36.6 + - + +
139E ALA 4.8 1.1 - - - +
142E ARG* 3.3 19.7 - - + +
143E PHE* 3.3 43.7 - - + +
146E VAL* 3.6 5.8 - - + -
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Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TRP* 2.8 61.2 + - + +
34D GLY 3.0 11.7 + - - -
35D GLU* 3.0 23.0 + - - -
37D THR* 4.1 12.6 - - + -
38D GLY* 3.7 22.6 - - - +
42D PHE* 4.2 5.3 - - + -
66D GLU* 3.1 25.3 + - - -
143D PHE* 2.8 24.8 + - + +
144D ASN* 3.6 12.6 - - - +
146D VAL* 1.3 72.9 - - - +
148D GLU* 1.3 86.4 + - - +
150D GLU* 3.6 1.6 + - - +
151D ALA* 3.0 33.0 + - - +
178D GLU* 5.5 1.2 + - - +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.4 12.1 - - + -
66D GLU* 2.9 23.2 - - - +
144D ASN 3.1 17.5 + - - +
145D VAL 3.9 0.9 - - - +
147D ARG* 1.3 90.6 + - - +
149D SER* 1.3 57.8 + - - +
151D ALA* 3.9 3.3 - - - +
152D ARG* 3.0 23.2 + - - +
178D GLU* 3.4 29.7 - - - +
181D HIS* 3.3 32.5 + - + +
182D GLN* 3.2 32.3 + - + +
185D PHE* 4.0 9.0 - - + -
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D VAL 2.7 24.4 + - - -
146D VAL* 3.0 7.8 + - - -
148D GLU* 1.3 76.2 - - - +
150D GLU* 1.3 65.8 + - - +
152D ARG* 3.4 1.6 + - - +
153D LEU* 2.9 23.9 + - - +
182D GLN* 3.5 13.6 + - - +
139E ALA* 4.3 19.4 - - - +
142E ARG* 2.9 34.0 + - - -
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TRP* 3.5 41.9 - - + +
146D VAL* 2.8 26.9 + - + +
147D ARG 4.1 0.2 - - - +
149D SER* 1.3 73.8 - - - +
151D ALA* 1.3 63.9 + - - +
153D LEU* 3.4 8.7 + - - +
154D GLN* 3.0 30.5 + - - +
132E THR* 3.4 16.2 - - - +
134E SER* 3.2 24.3 + - - -
139E ALA* 3.4 22.4 - - + +
140E ASP* 2.8 23.0 - - - +
143E PHE* 4.5 2.6 - - - +
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TRP* 3.6 9.5 - - - +
34D GLY* 5.5 0.4 - - - -
35D GLU* 4.4 2.5 - - - +
147D ARG* 3.0 46.0 + - - +
148D GLU* 4.0 4.3 - - - +
150D GLU* 1.3 77.9 - - - +
152D ARG* 1.3 57.7 + - - +
154D GLN* 3.1 9.7 + - - +
155D VAL* 2.8 32.0 + - + +
178D GLU* 3.8 16.2 - - - +
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D GLU 3.0 20.3 + - - +
149D SER 4.0 1.1 - - - +
150D GLU 3.3 0.2 - - - -
151D ALA* 1.3 76.9 - - - +
153D LEU* 1.3 58.2 + - - +
155D VAL* 3.8 0.4 - - - -
156D SER* 2.8 41.0 + - - -
175D LEU* 3.0 47.2 + - + +
178D GLU* 3.1 25.3 + - + +
179D THR* 3.1 20.7 + - - +
182D GLN* 3.6 21.3 - - - +
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU 3.8 11.0 - - - +
262B HIS* 3.8 23.8 - - + +
149D SER 2.9 18.3 + - - +
150D GLU* 3.5 11.0 - - - +
151D ALA 3.2 0.2 - - - -
152D ARG* 1.3 77.0 - - - +
154D GLN* 1.3 60.0 + - + +
156D SER* 3.3 6.0 + - - -
157D ARG* 3.0 61.1 + - - +
134E SER* 3.4 35.0 - - - +
136E ASN* 3.7 18.8 - - + +
139E ALA* 4.8 4.3 - - + -
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Residues in contact with GLN 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.6 29.2 - - + +
111C VAL* 4.0 26.6 + - - +
27D GLU* 3.4 31.5 + - + +
28D SER* 5.1 5.0 + - - +
32D GLN* 5.5 0.8 + - - +
33D TRP* 4.2 37.0 + - - +
34D GLY* 5.3 0.3 - - - -
150D GLU* 3.0 21.1 + - - +
151D ALA* 3.1 8.9 + - - +
153D LEU* 1.3 78.9 - - + +
155D VAL* 1.3 58.6 + - + +
157D ARG* 3.1 5.5 + - - +
158D LEU* 2.8 37.3 + - + +
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D SER* 4.6 14.6 - - - +
35D GLU* 6.4 0.4 - - - -
151D ALA* 2.8 20.3 + - + +
152D ARG 3.9 2.0 - - - +
154D GLN* 1.3 75.7 - - + +
156D SER* 1.3 62.9 + - - +
158D LEU* 3.2 11.3 + - + +
159D TYR* 3.0 21.8 + - - +
171D LEU* 3.6 36.7 - - + +
174D LEU* 4.5 10.1 - - + -
175D LEU* 3.6 19.7 - - + +
178D GLU* 3.5 26.5 - - - +
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Residues in contact with SER 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B HIS* 4.0 31.6 + - - -
152D ARG* 2.8 32.3 + - - +
153D LEU* 3.4 8.1 - - - -
155D VAL* 1.3 78.4 - - - +
157D ARG* 1.3 61.4 + - - +
159D TYR* 3.3 20.4 + - - +
160D SER* 3.6 6.2 + - - -
175D LEU* 3.4 18.4 - - - +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG 4.0 14.4 - - - +
261B LEU* 2.8 28.8 + - + +
262B HIS* 4.5 1.8 + - + -
263B ASN* 2.8 25.5 + - - -
86C PHE* 5.7 1.0 - - + -
109C SER 3.8 8.9 + - - -
110C LEU* 3.0 35.9 + - + -
111C VAL 3.2 13.1 + - - -
113C GLY* 3.5 10.1 - - - +
153D LEU* 3.0 40.0 + - - +
154D GLN* 3.1 7.9 + - - +
156D SER* 1.3 76.8 - - - +
158D LEU* 1.3 63.1 + - - +
160D SER* 2.9 15.1 + - - -
161D MET* 3.2 25.3 + - + +
134E SER 2.7 30.7 + - - -
135E GLY* 4.2 2.0 - - - -
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.7 22.0 - - + -
21D MET* 3.6 22.7 - - + +
24D ARG* 3.8 32.1 - - + +
25D LEU* 3.8 16.8 - - + +
27D GLU* 5.9 0.2 - - + -
28D SER* 3.6 24.5 - - - +
154D GLN* 2.8 21.8 + - + +
155D VAL* 3.5 15.5 - - + +
157D ARG* 1.3 76.0 - - - +
159D TYR* 1.3 57.9 + - - +
161D MET* 2.9 28.5 + - - +
162D THR* 3.6 3.8 + - - +
171D LEU* 3.8 15.9 - - + -
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Residues in contact with TYR 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL 3.0 11.7 + - - +
156D SER* 3.3 15.3 - - - +
157D ARG 3.1 0.2 - - - -
158D LEU* 1.3 76.6 - - - +
160D SER* 1.3 64.3 + - - +
162D THR* 3.2 6.6 - - - +
165D GLU* 4.9 2.8 + - - -
168D ARG* 2.9 90.5 + - + +
171D LEU* 3.6 17.2 - - + +
172D LYS* 3.9 30.3 + - + +
175D LEU* 5.1 10.3 - - + -
----------------------------------------------------------
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG* 3.6 50.6 + - - +
262B HIS* 5.0 2.9 + - - -
86C PHE* 4.8 3.2 - - - -
87C GLY* 3.8 6.8 - - - -
88C PRO* 3.6 13.7 - - - +
89C GLU* 5.5 0.7 + - - +
156D SER 3.6 5.8 + - - -
157D ARG 2.9 11.5 + - - -
159D TYR* 1.3 82.9 - - - +
161D MET* 1.3 60.6 + - - +
162D THR 3.5 2.7 - - - -
168D ARG* 4.4 5.9 + - - +
----------------------------------------------------------
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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