Contacts of the helix formed by residues 145 - 170 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.0 4.7 - - - +
142A ALA 4.5 13.0 - - - +
143A ARG* 3.3 7.0 + - - -
144A ARG* 1.3 77.8 - - - +
146A THR* 1.3 63.4 + - - +
147A LYS* 3.6 11.4 + - - +
148A MET* 3.3 28.7 + - - +
149A ALA* 3.2 19.9 + - - +
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.4 10.3 - - + +
69A TYR* 4.0 32.8 - - + +
145A THR* 1.3 72.5 - - - +
147A LYS* 1.3 63.1 + - - +
149A ALA* 3.3 9.4 + - - +
150A GLY* 2.9 24.6 + - - -
1202B OLC 3.8 21.7 + - - -
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A THR* 3.8 11.1 - - - +
146A THR* 1.3 83.5 + - - +
148A MET* 1.3 62.2 + - + +
150A GLY* 3.4 1.4 + - - -
151A LEU* 2.9 31.4 + - + +
425B PHE* 3.5 30.8 - - + +
426B CYS* 3.6 32.9 - - + -
428B SER* 4.5 7.2 + - - +
429B CYS* 3.9 8.8 - - - -
1202B OLC 5.2 0.2 - - - -
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Residues in contact with MET 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG 4.0 15.5 - - - +
144A ARG* 5.3 1.1 - - - -
145A THR* 3.3 24.9 + - + +
146A THR 3.3 0.2 - - - -
147A LYS* 1.3 82.9 - - + +
149A ALA* 1.3 60.2 + - - +
151A LEU* 3.3 27.0 + - + +
152A MET* 2.9 49.0 + - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.6 31.6 - - + -
69A TYR* 4.6 12.8 - - + -
70A PHE* 3.6 18.1 - - + -
145A THR 3.2 7.0 + - - +
146A THR* 3.4 12.1 - - - +
147A LYS 3.2 0.2 - - - -
148A MET* 1.3 78.6 - - - +
150A GLY* 1.3 56.4 + - - +
152A MET* 3.1 4.8 + - - +
153A ILE* 2.9 33.7 + - - +
1202B OLC 4.8 0.4 - - - +
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A THR 2.9 11.3 + - - -
149A ALA* 1.3 75.8 - - - +
151A LEU* 1.3 57.1 + - - +
153A ILE* 3.8 4.3 - - - +
154A ALA* 2.9 32.7 + - - +
425B PHE* 3.6 13.7 - - - -
1202B OLC 3.2 35.5 + - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS* 2.9 21.7 + - + +
148A MET* 3.4 33.2 - - + +
150A GLY* 1.3 77.8 - - - +
152A MET* 1.3 62.4 + - - +
154A ALA* 3.9 1.0 - - + +
155A ALA* 2.9 33.8 + - + +
425B PHE* 3.7 32.2 - - + -
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Residues in contact with MET 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.5 3.1 - - + -
125A ILE* 3.2 53.1 - - + +
148A MET* 2.9 34.7 + - + +
149A ALA* 3.1 8.3 + - - +
151A LEU* 1.3 79.6 - - - +
153A ILE* 1.3 59.2 + - - +
155A ALA* 3.3 11.5 + - + +
156A ALA 2.9 23.6 + - - -
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TYR* 3.7 30.5 - - + +
70A PHE* 3.7 22.9 - - + -
73A SER* 3.3 29.8 - - - +
122A ASN* 4.5 4.3 - - - +
125A ILE* 4.5 2.7 - - + -
149A ALA 2.9 24.1 + - - +
150A GLY* 3.8 7.6 - - - +
152A MET* 1.3 72.8 - - - +
154A ALA* 1.3 66.2 + - - +
156A ALA* 3.0 7.5 + - - +
157A TRP* 3.0 38.4 + - + +
1206A OLC 3.8 23.1 - - + -
1202B OLC 4.2 8.3 - - + +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLY 2.9 19.1 + - - +
151A LEU* 3.9 2.5 - - + +
153A ILE* 1.3 76.3 - - - +
155A ALA* 1.3 57.5 + - - +
157A TRP* 3.5 0.7 + - - +
158A VAL* 2.9 38.8 + - + +
421B LEU* 4.6 7.6 - - + -
425B PHE* 3.7 24.9 - - + -
1202B OLC 3.7 26.2 - - + +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MET* 4.9 0.4 - - + -
151A LEU* 2.9 23.1 + - + +
152A MET* 3.4 16.2 - - + +
154A ALA* 1.3 77.2 - - - +
156A ALA* 1.3 56.9 + - - +
158A VAL* 4.7 3.4 - - - -
159A LEU* 2.9 47.7 + - + +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA* 4.5 9.2 - - - +
121A MET* 3.8 32.2 - - + +
122A ASN* 4.7 3.4 - - - +
125A ILE* 3.9 16.8 - - + -
152A MET 2.9 13.8 + - - +
153A ILE* 3.0 10.5 + - - +
155A ALA* 1.3 75.9 - - - +
157A TRP* 1.3 57.6 + - + +
160A SER* 2.7 38.6 + - - -
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Residues in contact with TRP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A SER* 2.9 30.6 + - - -
77A ALA* 3.9 35.4 - - + -
80A ILE* 4.3 6.7 - - + -
114A VAL* 4.7 8.7 - - + +
115A VAL* 4.0 18.8 - - + -
118A ALA* 3.8 25.3 - - + +
122A ASN* 4.4 2.9 + - - -
153A ILE* 3.0 38.7 + - + +
154A ALA 4.0 0.4 - - - +
156A ALA* 1.3 80.3 - - + +
158A VAL* 1.3 57.2 + - - +
160A SER* 3.2 8.0 + - - -
161A PHE* 2.9 29.1 + - - +
1206A OLC 3.5 52.1 - - + +
1202B OLC 3.6 35.9 - - + +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA* 2.9 23.5 + - + +
155A ALA* 4.1 4.3 - - - +
157A TRP* 1.3 75.6 - - - +
159A LEU* 1.3 62.7 + - + +
161A PHE* 3.2 4.2 + - + +
162A VAL* 2.9 40.6 + - + +
421B LEU* 3.8 22.0 - - + -
1202B OLC 3.7 28.0 - - + -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MET* 3.8 23.6 - - + -
155A ALA* 2.9 32.9 + - + +
156A ALA 3.9 2.5 - - - +
158A VAL* 1.3 82.2 - - + +
160A SER* 1.3 58.3 + - - +
162A VAL* 3.9 9.8 - - + +
163A LEU* 2.9 48.3 + - + +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.5 23.6 - - - -
117A ASN* 2.9 32.1 + - - +
118A ALA* 3.2 16.6 + - - -
121A MET* 3.8 1.6 - - - -
156A ALA 2.7 22.8 + - - -
157A TRP 3.2 5.8 + - - -
159A LEU* 1.3 76.7 - - - +
161A PHE* 1.3 57.0 + - - +
163A LEU* 3.8 0.6 - - - -
164A TRP* 2.9 35.9 + - - +
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.9 15.7 - - + +
157A TRP 2.9 13.4 + - - +
158A VAL* 3.5 9.4 - - - +
160A SER* 1.3 76.7 - - - +
162A VAL* 1.3 67.9 + - + +
165A ALA* 2.9 59.0 + - + +
166A PRO* 3.3 2.5 - - + +
169A LEU* 5.8 2.7 - - + -
1206A OLC 4.2 30.5 - - + -
209B VAL* 4.3 22.7 - - + -
1202B OLC 4.9 15.3 - - + -
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A VAL* 2.9 33.8 + - + +
159A LEU* 3.9 12.3 - - + +
161A PHE* 1.3 84.5 - - + +
163A LEU* 1.3 64.0 + - + +
166A PRO* 3.1 26.4 - - + +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 5.0 4.5 - - - +
121A MET* 5.5 2.9 - - - -
159A LEU* 2.9 36.4 + - + +
160A SER* 3.9 3.6 - - - +
162A VAL* 1.3 85.4 - - + +
164A TRP* 1.3 63.9 + - + +
166A PRO* 4.3 1.3 - - - +
167A ALA* 4.2 4.3 + - - +
1208A OLC 3.1 81.4 - - + +
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Residues in contact with TRP 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 3.5 37.5 - + + -
114A VAL* 3.8 14.4 - - + +
117A ASN* 3.2 43.6 + - + +
160A SER 2.9 15.9 + - - +
163A LEU* 1.3 78.9 - - + +
165A ALA* 1.3 68.5 + - - +
166A PRO 3.3 2.0 - - - -
167A ALA* 3.1 6.9 + - + +
168A ILE* 3.1 43.1 + - + +
187A ILE* 4.2 4.7 - - + -
189A PHE* 5.1 5.6 - + - -
190A LEU* 4.1 17.9 - - + -
199A THR* 3.4 33.7 - - + -
203A ALA* 4.8 1.3 - - + -
1201A 0HK 3.5 24.0 - - + +
1208A OLC 3.7 26.3 - - + +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 5.0 6.3 - - + -
114A VAL* 4.1 7.5 - - + +
161A PHE* 2.9 58.2 + - + +
164A TRP* 1.3 73.7 - - - +
166A PRO* 1.3 58.2 - - + +
168A ILE* 4.8 3.1 - - - -
169A LEU* 2.9 48.3 + - + +
170A PHE* 5.3 0.4 - - - -
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Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 3.3 8.1 - - + +
162A VAL* 3.1 31.9 - - + +
163A LEU 4.3 0.4 - - - -
164A TRP 3.6 3.1 - - - +
165A ALA* 1.3 92.7 - - + +
167A ALA* 1.3 56.9 + - - +
170A PHE* 2.8 52.0 + - + +
171A TRP 3.5 2.1 + - - -
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU 4.2 12.5 + - - +
164A TRP* 3.1 12.2 + - + +
166A PRO* 1.3 79.7 - - - +
168A ILE* 1.3 60.1 + - + +
171A TRP* 3.2 27.5 - - - +
189A PHE* 3.3 44.5 + - + +
1208A OLC 4.5 10.1 - - + -
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASP* 4.2 13.1 - - - +
109A LEU* 3.6 50.5 - - + +
110A ALA* 3.8 15.3 - - - +
113A TYR* 3.7 15.0 - - + -
164A TRP* 3.1 26.5 + - + +
165A ALA 4.0 2.5 - - - +
167A ALA* 1.3 81.7 - - - +
169A LEU* 1.3 66.1 + - + +
171A TRP* 4.7 2.3 + - - +
172A GLN* 4.2 9.9 + - - +
187A ILE* 3.7 35.9 - - + +
188A GLN* 5.8 2.4 + - - +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASP* 3.6 42.4 - - + +
107A LEU* 4.7 0.7 - - - +
110A ALA* 4.2 13.7 - - + -
161A PHE* 5.8 2.7 - - + -
165A ALA* 2.9 30.3 + - + +
168A ILE* 1.3 83.0 - - + +
170A PHE* 1.3 68.9 - - + +
171A TRP 3.5 0.4 - - - -
172A GLN* 3.2 25.9 + - - +
209B VAL* 4.5 15.7 - - + +
212B THR* 5.5 7.2 - - + -
213B VAL* 3.9 22.9 - - + -
216B ILE* 3.3 18.9 - - + +
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ALA 5.3 0.2 - - - -
166A PRO* 2.8 35.0 + - + +
169A LEU* 1.3 80.2 - - + +
171A TRP* 1.3 60.5 + - - +
172A GLN 3.3 3.1 - - - -
173A PHE* 3.0 24.0 + + + +
174A VAL* 3.0 33.8 + - + +
212B THR* 3.5 31.9 - - + -
215B TYR* 6.1 4.0 - + - -
216B ILE* 3.7 21.3 - - + -
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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
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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