Contacts of the helix formed by residues 138 - 160 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 1.3 74.2 - - - +
139D PRO* 1.4 66.0 - - - +
140D GLU* 3.4 15.1 + - - +
141D LYS* 3.5 16.0 + - - +
142D ARG* 2.7 34.8 + - - +
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Residues in contact with PRO 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D HIS* 5.4 1.6 - - - -
108D MET* 3.3 16.2 - - + +
138D SER* 1.4 89.6 - - - +
140D GLU* 1.3 59.5 + - - +
142D ARG* 3.5 22.9 - - + +
143D ALA* 3.3 19.1 + - - +
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D HIS* 5.3 6.8 - - + -
138D SER* 3.2 8.4 + - - +
139D PRO* 1.3 79.0 - - - +
141D LYS* 1.3 80.5 + - + +
143D ALA* 3.3 12.3 + - - +
144D ASP* 3.0 27.1 + - - +
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D LEU* 4.0 18.0 - - + +
138D SER* 3.3 15.6 + - - +
140D GLU* 1.3 94.2 + - - +
142D ARG* 1.3 64.7 + - - +
144D ASP* 3.4 23.1 + - + +
145D MET* 3.2 22.7 + - - +
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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
----------------------------------------------------------
108D MET* 3.6 16.9 - - + +
127D TRP* 3.6 39.8 - - + +
134D LEU* 3.1 35.1 + - + +
135D GLY* 4.1 12.5 + - - -
137D LEU* 2.7 40.1 + - + +
138D SER 2.7 21.6 + - - +
139D PRO* 3.5 36.8 - - - +
140D GLU 3.3 0.2 - - - -
141D LYS* 1.3 71.8 - - - +
143D ALA* 1.3 58.9 + - - +
145D MET 3.4 1.0 + - - -
146D LEU* 2.9 29.2 + - + +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ILE* 3.8 5.9 - - + +
105D HIS* 3.8 32.8 - - + +
108D MET* 3.5 22.2 - - + +
139D PRO 3.3 11.8 + - - +
140D GLU 3.5 10.1 - - - +
141D LYS 3.3 0.4 - - - -
142D ARG* 1.3 79.1 - - - +
144D ASP* 1.3 54.6 + - - +
146D LEU 3.4 0.3 + - - -
147D THR* 2.7 40.0 + - - -
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Residues in contact with ASP 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ASN* 5.7 3.1 + - - -
105D HIS* 5.3 3.6 + - - -
140D GLU* 3.0 21.2 - - - +
141D LYS* 3.4 34.5 + - + +
142D ARG 3.4 0.4 - - - -
143D ALA* 1.3 78.8 - - - +
145D MET* 1.3 61.0 + - - +
147D THR* 3.5 15.8 - - - -
148D LYS* 3.6 18.2 + - + +
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 4.2 11.0 - - + -
134D LEU* 3.6 24.5 - - + -
137D LEU* 4.1 10.3 - - + -
141D LYS 3.2 14.6 + - - +
143D ALA 3.3 0.2 - - - -
144D ASP* 1.3 75.8 - - - +
146D LEU* 1.3 59.4 + - - +
147D THR 3.2 1.8 - - - -
148D LYS* 3.2 17.6 + - - -
149D ILE* 3.0 34.7 + - + +
212D LEU* 3.8 44.0 - - + +
214D ILE 6.0 0.2 - - - +
215D LEU* 5.2 11.9 - - + -
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ILE* 4.1 9.9 - - + -
108D MET* 3.7 31.2 - - + -
123D ILE* 3.8 26.9 - - + +
126D ILE* 4.1 25.4 - - + -
127D TRP* 4.2 22.2 - - + +
134D LEU* 3.9 23.7 - - + +
142D ARG* 2.9 20.3 + - + +
143D ALA 3.9 3.4 - - - +
145D MET* 1.3 73.1 - - - +
147D THR* 1.3 60.9 + - - +
149D ILE* 4.4 4.5 - - + -
150D ASN* 2.9 32.5 + - + +
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Residues in contact with THR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLY* 5.0 2.0 - - - -
98D HIS 3.2 39.1 + - - +
99D THR* 4.9 3.9 - - + -
100D ASN 5.6 0.7 + - - -
101D CYS* 4.5 6.1 + - + +
104D ILE* 3.7 28.7 - - + +
105D HIS* 6.0 0.3 - - - -
143D ALA 2.7 23.8 + - - -
144D ASP* 3.5 10.1 - - - -
145D MET 3.2 0.2 - - - -
146D LEU* 1.3 79.1 - - - +
148D LYS* 1.3 61.8 + - + +
150D ASN* 3.5 4.2 + - - +
151D VAL* 3.4 21.8 + - - +
180D VAL* 4.9 8.1 - - + -
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Residues in contact with LYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ASP* 3.6 16.8 + - + +
145D MET* 3.2 22.9 + - + +
147D THR* 1.3 76.9 - - + +
149D ILE* 1.3 65.8 + - - +
150D ASN 3.2 0.2 - - - -
151D VAL* 3.2 13.2 + - - +
152D ALA* 3.3 11.3 + - - +
180D VAL* 4.2 16.8 - - + -
189D VAL* 5.2 5.9 - - - +
191D GLN* 2.8 46.9 + - - +
212D LEU* 3.8 26.8 - - + +
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ILE* 3.7 12.3 - - + -
130D HIS* 3.3 51.6 - - + +
133D LEU* 3.6 30.7 - - + -
134D LEU* 4.4 7.9 - - + -
145D MET* 3.0 26.4 + - + +
146D LEU* 4.0 6.7 - - + +
148D LYS* 1.3 75.0 - - - +
150D ASN* 1.3 59.4 - - - +
152D ALA* 3.2 7.8 + - - +
153D GLU* 2.9 27.5 + - + +
209D ILE* 4.7 5.8 - - + -
212D LEU* 3.9 20.2 - - + -
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Residues in contact with ASN 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ALA 3.0 27.1 + - - -
68D ASN* 3.5 16.8 + - - +
104D ILE* 4.0 13.9 - - + +
123D ILE* 3.0 23.4 - - + +
126D ILE* 3.6 7.5 - - + +
146D LEU* 2.9 22.0 + - + +
147D THR 3.5 7.9 + - - +
148D LYS 3.2 0.2 - - - -
149D ILE* 1.3 77.9 - - - +
151D VAL* 1.3 62.2 + - - +
153D GLU* 3.2 6.4 + - - +
154D GLN* 2.9 55.7 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASN* 4.0 8.5 - - - +
95D ILE* 3.9 11.4 - - + +
96D CYS 4.5 0.2 - - - -
97D GLY* 3.4 35.2 - - - +
147D THR 3.4 12.3 + - - +
148D LYS 3.2 9.2 + - - +
150D ASN* 1.3 76.1 - - - +
152D ALA* 1.3 63.0 + - - +
154D GLN* 3.3 3.7 + - - +
155D VAL* 3.0 29.0 + - + +
178D GLY* 3.3 40.4 - - - +
179D TRP 3.5 7.0 - - - +
180D VAL* 3.9 5.8 - - + -
191D GLN* 4.2 9.0 - - + -
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LYS 3.3 8.2 + - - +
149D ILE* 3.2 10.2 + - - +
151D VAL* 1.3 81.4 - - - +
153D GLU* 1.3 56.8 + - - +
155D VAL* 3.4 4.0 + - - +
156D TYR* 3.1 26.2 + - - +
191D GLN* 5.1 6.9 - - + +
193D VAL* 3.6 28.9 - - + +
205D TYR* 3.9 6.9 - - + -
208D ALA* 5.0 3.4 - - + -
209D ILE* 4.1 22.4 - - + -
212D LEU* 5.7 3.4 - - + -
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ILE* 3.7 38.3 - - + +
129D LYS* 3.0 27.1 + - - +
130D HIS* 2.6 24.8 + - - -
149D ILE* 2.9 22.4 + - + +
150D ASN 3.7 4.3 - - - +
152D ALA* 1.3 75.0 - - - +
154D GLN* 1.3 58.9 + - - +
156D TYR* 3.2 9.6 - - - +
157D ASN* 2.8 34.5 + - - +
205D TYR* 2.5 30.2 + - + -
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Residues in contact with GLN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASN 3.5 18.8 - - - +
69D GLN* 3.5 18.0 + - - +
70D VAL* 2.7 42.4 + - - +
95D ILE* 3.2 28.8 - - + +
126D ILE* 3.4 20.8 - - - +
150D ASN* 2.9 45.1 + - - +
151D VAL* 3.8 2.9 - - - +
153D GLU* 1.3 73.3 - - - +
155D VAL* 1.3 64.3 + - - +
156D TYR 3.1 0.7 - - - -
157D ASN* 3.2 10.2 + - - +
158D LEU* 3.0 20.1 + - - +
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 3.9 10.3 - - + -
151D VAL 3.0 22.2 + - - +
152D ALA 3.7 6.1 - - - +
154D GLN* 1.3 74.6 - - - +
156D TYR* 1.3 62.5 + - - +
158D LEU* 3.3 6.2 + - + +
159D GLY 3.1 18.0 + - - -
176D LEU* 3.9 27.6 - - + +
177D HIS 3.6 5.4 - - - +
178D GLY* 3.3 33.0 - - - +
193D VAL* 3.7 35.0 - - + +
194D MET 5.1 0.4 - - - +
195D ALA 5.3 0.4 - - - +
201D LEU* 3.8 8.2 - - + +
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Residues in contact with TYR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LYS* 4.7 7.6 - - - -
152D ALA 3.1 13.6 + - - +
153D GLU* 3.2 17.7 - - - +
154D GLN 3.1 0.4 - - - -
155D VAL* 1.3 74.6 - - - +
157D ASN* 1.3 63.6 + - - +
159D GLY 3.3 1.7 + - - -
160D ARG* 3.0 64.7 + - - +
193D VAL* 5.0 0.4 - - - +
198D ARG* 3.8 5.9 + - - -
201D LEU* 3.8 27.1 - - + +
202D GLU* 2.4 32.3 + - - -
205D TYR* 3.6 55.9 - + + -
231D SO4 4.8 1.9 + - - -
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Residues in contact with ASN 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU* 4.9 0.2 - - - +
125C ASP* 5.2 0.3 - - - +
70D VAL* 3.0 31.1 + - + +
71D ILE* 5.0 1.8 - - - +
72D HIS* 3.2 33.5 + - + +
126D ILE* 5.4 2.6 - - - +
153D GLU* 2.8 25.3 + - - +
154D GLN* 3.2 23.5 + - - +
155D VAL 3.5 0.2 - - - -
156D TYR* 1.3 74.5 - - - +
158D LEU* 1.3 61.4 + - - +
160D ARG* 3.4 18.8 + - - +
161D THR* 3.3 23.2 + - - +
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 4.6 3.6 - - + -
70D VAL* 4.0 16.2 - - + -
81D VAL* 3.9 30.1 - - + -
93D ILE* 3.5 34.3 - - + +
95D ILE* 4.3 20.0 - - + -
154D GLN 3.0 16.9 + - - +
155D VAL* 3.5 5.6 - - + +
156D TYR 3.1 0.2 - - - -
157D ASN* 1.3 78.0 - - - +
159D GLY* 1.3 56.0 + - - +
160D ARG 3.2 0.2 - - - -
161D THR* 2.7 30.5 + - + +
164D VAL* 3.2 23.3 - - + +
176D LEU* 4.1 20.6 - - + -
177D HIS 5.9 0.2 - - - +
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Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D VAL 3.1 10.3 + - - -
156D TYR 3.3 0.6 + - - -
158D LEU* 1.3 75.8 - - - +
160D ARG* 1.3 57.3 + - - +
161D THR 3.4 0.2 - - - -
164D VAL* 4.0 7.8 - - - +
165D LYS* 3.5 12.7 - - - +
168D TRP* 3.5 19.0 - - - -
176D LEU* 3.4 21.5 - - - +
198D ARG* 3.7 2.9 - - - -
201D LEU* 3.4 21.9 - - - +
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Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASN* 6.1 0.7 - - - +
121C LEU* 3.6 37.7 + - + +
124C ARG* 4.4 4.0 - - - +
125C ASP* 2.8 30.9 + - - +
128C PHE* 6.4 0.2 - - - +
72D HIS* 3.6 6.1 - - - -
129D LYS* 5.7 2.2 - - - +
156D TYR* 3.0 52.1 + - - +
157D ASN* 3.4 26.4 + - - +
158D LEU 3.2 0.2 - - - -
159D GLY* 1.3 78.5 - - - +
161D THR* 1.3 65.8 + - - +
162D SER 3.6 1.0 + - - -
165D LYS* 3.8 18.6 - - - -
198D ARG* 4.0 10.1 - - - +
201D LEU* 4.2 2.9 - - + -
231D SO4 2.9 43.2 + - - +
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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