Contacts of the helix formed by residues 145 - 170 (chain B) in PDB entry 5DSG
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 THR 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL* 4.2 3.9 - - - +
142B ALA 4.7 7.4 - - - +
143B ARG* 3.4 13.2 + - - +
144B ARG* 1.3 79.3 - - - +
146B THR* 1.3 64.3 + - - +
147B LYS* 3.8 10.0 + - - +
148B MET* 3.6 21.5 + - - +
149B ALA* 3.4 18.0 + - - +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL* 4.3 11.7 - - + +
69B TYR* 4.2 36.5 - - + +
145B THR* 1.3 74.7 - - - +
147B LYS* 1.3 62.3 + - - +
149B ALA* 3.3 8.7 + - - +
150B GLY* 2.9 26.5 + - - -
1203B OLA 4.8 2.3 - - - +
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B THR* 3.3 10.4 - - - +
146B THR* 1.3 82.4 + - - +
148B MET* 1.3 57.2 + - - +
150B GLY* 3.4 1.8 + - - -
151B LEU* 2.9 31.8 + - + +
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ARG 5.1 5.4 - - - +
144B ARG* 5.8 0.9 - - - -
145B THR* 3.6 21.6 + - - +
146B THR 3.4 0.2 - - - -
147B LYS* 1.3 77.2 - - - +
149B ALA* 1.3 60.2 + - - +
151B LEU* 3.3 12.3 + - + +
152B MET* 2.9 48.1 + - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL* 3.8 18.4 - - + -
69B TYR* 4.9 10.8 - - + -
70B PHE* 3.7 26.4 - - + -
145B THR 3.4 11.3 + - - +
146B THR* 3.3 13.2 + - - +
147B LYS 3.2 0.2 - - - -
148B MET* 1.3 78.4 - - - +
150B GLY* 1.3 57.2 + - - +
152B MET* 3.1 6.2 + - - +
153B ILE* 2.9 34.3 + - - +
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Residues in contact with GLY 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B THR 2.9 14.3 + - - -
147B LYS* 3.8 1.6 - - - -
149B ALA* 1.3 75.6 - - - +
151B LEU* 1.3 56.3 + - - +
153B ILE* 3.8 2.9 - - - +
154B ALA* 2.9 32.3 + - - +
1203B OLA 3.3 34.9 + - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LYS* 2.9 19.8 + - + +
148B MET* 3.4 15.3 - - + +
149B ALA 3.2 0.2 - - - -
150B GLY* 1.3 77.0 - - - +
152B MET* 1.3 59.1 + - + +
154B ALA* 3.6 5.5 + - + +
155B ALA* 2.9 34.1 + - + +
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Residues in contact with MET 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 4.3 11.7 - - - -
125B ILE* 3.2 46.7 - - + +
129B ASP* 5.6 2.0 - - - +
132B PHE* 6.4 2.5 - - + -
140B TYR* 4.8 15.7 - - + +
148B MET* 2.9 29.9 + - + +
149B ALA* 3.1 6.9 + - - +
151B LEU* 1.3 77.1 - - + +
153B ILE* 1.3 59.5 + - - +
155B ALA* 3.3 7.5 + - - +
156B ALA 2.9 23.6 + - - -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B TYR* 3.8 29.4 - - + +
70B PHE* 4.0 21.1 - - + -
73B SER* 3.3 30.7 - - - +
122B ASN* 4.9 2.9 - - - +
125B ILE* 4.4 6.5 - - + -
149B ALA 2.9 24.2 + - - +
150B GLY* 3.8 4.3 - - - +
151B LEU 3.4 0.2 - - - -
152B MET* 1.3 72.8 - - - +
154B ALA* 1.3 66.2 + - - +
156B ALA* 3.0 4.4 + - - +
157B TRP* 3.0 38.9 + - + +
1203B OLA 4.1 22.7 - - + +
1204B OLA 3.9 13.7 - - + +
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLY 2.9 18.2 + - - +
151B LEU* 3.9 7.4 - - + +
153B ILE* 1.3 76.3 - - - +
155B ALA* 1.3 56.9 + - - +
158B VAL* 2.9 40.7 + - + +
1203B OLA 3.7 29.8 - - + +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B MET* 4.7 3.1 - - + -
151B LEU* 2.9 24.8 + - + +
152B MET* 3.4 9.2 - - - +
154B ALA* 1.3 77.7 - - - +
156B ALA* 1.3 56.2 + - - +
158B VAL* 4.2 3.5 - - - +
159B LEU* 2.9 36.2 + - + +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ALA* 4.6 9.2 - - - +
121B MET* 3.7 32.5 - - + +
122B ASN* 4.6 3.1 - - - +
125B ILE* 3.8 17.9 - - + -
152B MET 2.9 13.3 + - - +
153B ILE* 3.0 9.6 + - - +
155B ALA* 1.3 76.4 - - - +
157B TRP* 1.3 57.7 + - + +
160B SER* 2.7 39.2 + - - -
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Residues in contact with TRP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER* 2.9 36.7 + - - -
76B CYS 4.7 0.2 - - - -
77B ALA* 3.9 30.7 - - + -
80B ILE* 4.2 9.9 - - + -
114B VAL* 4.6 5.5 - - + +
115B VAL* 4.1 21.8 - - + -
118B ALA* 3.9 22.1 + - + +
122B ASN* 4.4 2.0 + - - -
153B ILE* 3.0 39.2 + - + +
154B ALA 4.1 0.2 - - - +
156B ALA* 1.3 81.1 - - + +
158B VAL* 1.3 59.3 + - - +
160B SER* 3.2 6.6 + - - -
161B PHE* 2.9 29.1 + - - +
1203B OLA 3.6 32.2 - - + +
1204B OLA 3.7 56.1 - - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ALA* 2.9 25.1 + - + +
155B ALA* 4.2 2.7 - - - +
157B TRP* 1.3 75.2 - - - +
159B LEU* 1.3 61.1 + - + +
161B PHE* 3.2 6.5 + - - +
162B VAL* 2.9 42.3 + - + +
1203B OLA 3.9 24.7 - - + -
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B MET* 3.7 26.0 - - + -
155B ALA* 2.9 20.8 + - + +
156B ALA 4.0 1.8 - - - +
158B VAL* 1.3 79.6 - - + +
160B SER* 1.3 58.5 + - - +
162B VAL* 3.8 10.1 - - + +
163B LEU* 2.9 55.7 + - + +
1206B OLC 6.3 0.2 - - + -
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 3.4 26.5 - - - -
117B ASN* 2.8 31.1 + - - +
118B ALA* 3.2 16.2 + - - -
121B MET* 3.7 1.8 - - - -
156B ALA 2.7 22.5 + - - -
157B TRP 3.2 5.6 + - - -
159B LEU* 1.3 76.7 - - - +
161B PHE* 1.3 57.4 + - - +
163B LEU* 3.8 1.1 - - - -
164B TRP* 2.9 35.9 + - - +
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 3.8 10.9 - - + +
157B TRP 2.9 13.4 + - - +
158B VAL* 3.2 8.0 + - - +
160B SER* 1.3 77.2 - - - +
162B VAL* 1.3 68.1 + - + +
165B ALA* 2.9 58.5 + - + +
166B PRO* 3.2 3.9 - - + +
169B LEU* 6.0 3.4 - - + -
1203B OLA 3.8 44.9 - - + -
1204B OLA 3.9 33.7 - - + -
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 2.9 34.0 + - + +
159B LEU* 3.9 12.6 - - + +
161B PHE* 1.3 84.2 - - + +
163B LEU* 1.3 64.2 + - + +
166B PRO* 3.2 26.9 - - + +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASN* 5.1 1.1 - - - +
121B MET* 5.6 0.4 - - - -
159B LEU* 2.9 44.0 + - + +
160B SER* 3.9 2.9 - - - +
162B VAL* 1.3 85.0 - - + +
164B TRP* 1.3 62.4 + - + +
166B PRO* 4.4 0.7 - - - +
167B ALA* 4.2 4.7 - - - +
1206B OLC 3.6 77.9 - - + +
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Residues in contact with TRP 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TYR* 3.5 31.2 - + + -
114B VAL* 3.7 14.6 - - + +
117B ASN* 3.2 45.3 + - + +
160B SER 2.9 14.8 + - - +
163B LEU* 1.3 78.8 - - + +
165B ALA* 1.3 67.0 + - - +
166B PRO* 3.4 2.2 - - - -
167B ALA* 3.2 6.1 + - + +
168B ILE* 3.1 50.1 + - + +
187B ILE* 4.4 4.7 - - + -
189B PHE* 4.8 4.0 - + - -
190B LEU* 4.2 17.0 - - + -
199B THR* 3.4 34.5 - - + -
203B ALA* 4.7 1.1 - - + -
1201B 0HK 3.4 25.6 - - + +
1206B OLC 3.7 29.9 - - + +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA* 4.8 7.6 - - + -
114B VAL* 3.9 8.6 - - + +
161B PHE* 2.9 54.3 + - + +
164B TRP* 1.3 74.6 - - - +
166B PRO* 1.3 59.2 - - + +
168B ILE* 3.8 3.8 - - - -
169B LEU* 2.9 47.6 + - + +
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Residues in contact with PRO 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 3.2 9.4 - - + +
162B VAL* 3.2 32.1 - - + +
163B LEU 4.4 0.7 - - - +
164B TRP 3.6 1.8 - - - -
165B ALA* 1.3 92.9 - - + +
167B ALA* 1.3 57.0 + - - +
170B PHE* 2.8 53.4 + - + +
171B TRP 3.7 1.2 + - - -
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU 4.2 5.4 + - - +
164B TRP* 3.2 9.9 + - + +
166B PRO* 1.3 79.2 - - - +
168B ILE* 1.3 59.5 + - + +
171B TRP* 3.2 29.4 - - - +
189B PHE* 3.4 31.5 - - + +
1206B OLC 4.1 26.7 - - + -
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ASP* 4.3 13.8 - - - +
109B LEU* 3.7 46.7 - - + +
110B ALA* 3.8 14.4 - - - +
113B TYR* 3.8 6.1 - - + -
164B TRP* 3.1 39.5 + - + +
165B ALA* 3.9 4.0 - - - +
167B ALA* 1.3 80.8 - - - +
169B LEU* 1.3 64.2 + - + +
171B TRP* 4.8 2.3 + - - +
172B GLN* 4.3 7.8 + - - +
187B ILE* 3.8 37.5 - - + +
188B GLN 5.8 1.2 + - - -
189B PHE* 5.8 0.2 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ASP* 3.6 41.7 - - + +
107B LEU* 4.7 9.4 - - + +
110B ALA* 4.2 12.8 - - + -
161B PHE* 6.0 2.7 - - + -
165B ALA* 2.9 30.7 + - + +
168B ILE* 1.3 81.4 - - + +
170B PHE* 1.3 73.2 + - + +
171B TRP 3.5 0.4 - - - -
172B GLN* 2.9 30.3 + - - +
173B PHE* 5.2 0.9 - - - +
1204B OLA 6.4 1.1 - - + -
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Residues in contact with PHE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B PRO* 2.8 36.7 + - + +
169B LEU* 1.3 85.1 - - + +
171B TRP* 1.3 65.5 + - - +
172B GLN 3.2 2.5 - - - -
173B PHE* 3.0 33.8 + + + +
174B VAL* 3.0 28.9 + - + +
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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) + - + + + + + -
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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