Contacts of the helix formed by residues 149 - 173 (chain B) in PDB entry 3CJD
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 ASP 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLU 3.8 1.6 + - - -
148B SER* 1.3 75.6 - - - +
150B ASP* 1.3 59.5 + - - +
151B ALA* 3.3 10.8 + - - +
152B GLU* 2.9 58.7 + - - +
153B LEU* 2.9 28.0 + - - +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASP* 1.3 75.3 - - - +
151B ALA* 1.3 56.7 + - - +
153B LEU* 3.4 15.7 + - - +
154B ASP* 3.0 29.3 + - - +
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Residues in contact with ALA 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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149B ASP* 3.3 11.5 + - - +
150B ASP* 1.3 74.3 - - - +
152B GLU* 1.3 66.0 + - + +
154B ASP* 3.4 7.6 + - - +
155B LEU* 3.1 30.5 + - + +
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A MSE 5.3 1.2 - - - +
147B GLU 4.1 3.1 - - - +
148B SER* 3.4 20.4 + - - +
149B ASP* 2.9 46.1 + - - +
151B ALA* 1.3 75.0 - - + +
153B LEU* 1.3 57.6 + - - +
155B LEU* 3.3 12.0 + - + +
156B MSE 3.0 29.3 + - - +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 4.1 17.9 - - + +
141B LEU* 3.7 39.4 - - + +
142B ALA* 3.8 22.9 - - + +
145B PHE* 4.1 8.7 - - + +
148B SER* 3.8 30.7 - - - +
149B ASP 2.9 19.4 + - - +
150B ASP* 3.7 15.0 - - - +
151B ALA 3.3 0.2 - - - -
152B GLU* 1.3 76.9 - - - +
154B ASP* 1.3 49.1 + - - +
156B MSE 3.4 5.9 + - + +
157B THR* 2.8 40.8 + - - -
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Residues in contact with ASP 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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134B PHE* 5.1 6.6 - - - +
138B THR* 5.2 4.0 + - - +
150B ASP 3.0 17.8 + - - +
151B ALA* 3.7 7.6 - - - +
153B LEU* 1.3 71.6 - - - +
155B LEU* 1.3 63.8 + - - +
157B THR* 3.3 8.0 + - - +
158B ARG* 2.9 68.7 + - - +
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Residues in contact with LEU 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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179A VAL* 4.3 4.2 - - + +
180A PRO* 3.7 32.5 - - + -
183A GLN* 3.8 37.0 - - + +
186A THR* 6.0 0.2 - - + -
187A MSE 3.6 25.8 - - - -
151B ALA* 3.1 21.6 + - + +
152B GLU* 3.7 10.8 - - + +
154B ASP* 1.3 80.1 - - + +
156B MSE 1.3 52.7 + - - +
158B ARG* 3.4 7.7 + - - +
159B THR* 2.7 36.7 + - - -
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Residues in contact with MSE 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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187A MSE 4.0 21.0 - - + +
190A LEU* 4.2 17.5 - - + +
191A LEU* 5.5 2.0 - - - -
194A GLN* 3.7 27.8 - - - +
141B LEU* 3.8 15.2 - - + +
145B PHE* 4.1 26.0 - - + -
152B GLU 3.0 16.9 + - - +
153B LEU* 3.8 7.2 - - + +
154B ASP 3.4 0.2 - - - -
155B LEU* 1.3 71.9 - - - +
157B THR* 1.3 65.3 + - - +
159B THR* 4.1 10.5 - - - -
160B LEU* 3.1 48.5 + - + +
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Residues in contact with THR 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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134B PHE* 3.6 35.0 - - + +
137B ILE* 3.7 17.7 - - + +
138B THR* 2.7 30.8 + - - +
141B LEU* 3.4 17.9 - - - +
153B LEU 2.8 25.8 + - - -
154B ASP* 3.3 9.8 + - - +
156B MSE 1.3 73.4 - - - +
158B ARG* 1.3 57.6 + - - +
160B LEU* 4.0 0.9 - - - +
161B PHE* 3.0 30.5 + - - +
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Residues in contact with ARG 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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175A ARG 5.0 0.2 + - - -
176A ILE* 2.9 29.7 + - - +
177A SER* 3.8 12.4 - - - +
178A GLY 3.1 21.5 + - - -
179A VAL* 3.9 14.8 - - + -
180A PRO* 4.3 16.9 - - - +
130B MSE 5.0 3.6 - - - +
134B PHE* 3.7 25.0 - - + -
154B ASP* 2.9 48.2 + - - +
155B LEU* 3.6 7.6 - - - +
157B THR* 1.3 75.3 - - - +
159B THR* 1.3 53.1 + - - +
161B PHE* 3.9 1.3 - - - +
162B SER* 2.7 38.7 + - - -
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Residues in contact with THR 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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167A ILE* 3.7 22.2 - - + +
179A VAL* 3.6 7.3 - - - +
187A MSE 3.1 52.1 - - + +
191A LEU* 4.0 14.8 - - + -
155B LEU 2.7 21.4 + - - -
156B MSE 3.7 13.2 - - - -
158B ARG* 1.3 75.9 - - - +
160B LEU* 1.3 54.3 + - + +
162B SER 3.6 0.2 + - - -
163B SER* 2.7 35.5 + - - +
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Residues in contact with LEU 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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191A LEU* 3.9 25.4 - - + -
194A GLN* 6.1 0.7 - - - +
201A STE 3.7 19.3 - - + -
90B LEU* 4.8 1.3 - - + -
137B ILE* 5.5 0.2 - - + -
141B LEU* 3.5 34.3 - - + -
156B MSE 3.1 29.0 + - + +
157B THR 4.3 0.9 - - - +
159B THR* 1.3 74.1 - - + +
161B PHE* 1.3 66.9 + - - +
163B SER* 3.6 5.5 - - - +
164B VAL* 3.0 28.9 + - - +
191B LEU* 5.6 1.8 - - + -
192B LEU* 4.5 11.4 - - + +
195B VAL* 3.8 36.8 - - + -
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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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170A LEU* 3.9 17.0 - - + -
177A SER* 3.8 25.1 - - - -
201A STE 3.3 63.7 - - + +
97B TYR* 3.5 40.6 - + - -
112B PHE* 4.0 4.7 - + - -
134B PHE* 3.9 21.3 - + + -
137B ILE* 4.1 9.6 - - + -
157B THR 3.0 18.8 + - - +
158B ARG 3.9 2.7 - - - +
160B LEU* 1.3 75.0 - - - +
162B SER* 1.3 60.0 - - - +
164B VAL* 3.2 3.6 + - + -
165B HIS* 2.9 29.3 + - + +
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Residues in contact with SER 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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166A GLY* 3.3 18.6 - - - -
167A ILE* 3.7 27.1 + - - -
170A LEU* 3.7 27.3 - - - +
177A SER 4.1 1.4 + - - -
178A GLY* 4.1 10.0 - - - -
179A VAL* 4.3 2.6 + - - +
158B ARG 2.7 24.0 + - - -
159B THR* 3.7 4.0 - - - -
161B PHE* 1.3 77.1 - - - +
163B SER* 1.3 55.6 + - - +
165B HIS* 3.7 1.4 - - - +
166B GLY 3.0 22.7 + - - -
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Residues in contact with SER 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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163A SER* 3.5 31.6 - - - -
167A ILE* 3.5 4.3 - - - +
191A LEU* 3.5 26.2 - - - +
159B THR 2.7 22.5 + - - -
160B LEU* 3.6 9.4 - - - -
161B PHE 3.2 0.4 - - - -
162B SER* 1.3 73.1 - - - +
164B VAL* 1.3 66.9 + - - +
166B GLY 3.3 0.9 + - - -
167B ILE* 3.1 27.0 + - - +
191B LEU* 3.9 11.7 - - - -
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Residues in contact with VAL 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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201A STE 4.0 15.7 - - + -
94B SER* 3.6 38.4 - - - +
97B TYR* 4.2 20.0 - - + -
160B LEU 3.0 21.5 + - - +
161B PHE* 3.7 3.8 - - + +
163B SER* 1.3 75.1 - - - +
165B HIS* 1.3 58.8 + - - +
167B ILE* 3.2 8.9 + - - +
168B VAL* 3.0 28.4 + - + +
188B ILE* 4.3 18.2 - - + -
191B LEU* 4.7 6.3 - - + -
192B LEU* 4.2 13.7 - - + -
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Residues in contact with HIS 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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166A GLY* 5.3 1.8 - - - -
169A LEU* 5.1 2.6 - - + +
170A LEU* 3.8 28.4 - - + +
97B TYR* 2.7 31.1 + - - +
108B TRP* 3.7 17.2 - + - -
109B ARG* 4.9 1.9 + - - -
112B PHE* 3.3 42.6 - + - -
161B PHE* 2.9 25.8 + - + +
162B SER 3.7 5.4 - - - +
164B VAL* 1.3 75.7 - - - +
166B GLY* 1.3 52.8 + - - +
168B VAL* 3.7 0.6 - - - +
169B LEU* 2.8 62.8 + - + +
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Residues in contact with GLY 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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162A SER* 3.3 23.2 - - - -
165A HIS* 5.3 1.3 - - - -
166A GLY* 3.8 13.7 - - - -
162B SER 3.0 11.1 + - - -
163B SER 3.3 1.1 + - - -
164B VAL 3.2 0.4 - - - -
165B HIS* 1.3 74.2 - - - +
167B ILE* 1.3 64.2 - - - +
169B LEU* 4.4 6.3 - - - -
170B LEU* 3.0 33.5 + - - +
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Residues in contact with ILE 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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159A THR* 3.8 33.4 - - + +
162A SER* 3.6 11.9 + - - -
163A SER* 3.8 3.1 - - - +
163B SER 3.1 11.6 + - - +
164B VAL* 3.4 10.5 - - - +
166B GLY* 1.3 75.3 - - - +
168B VAL* 1.3 58.8 + - - +
170B LEU* 4.6 0.5 - - - +
171B GLY 3.0 22.7 + - - -
179B VAL* 4.5 11.8 - - + +
184B LEU* 3.3 28.0 - - + +
187B MSE 4.4 7.2 - - + +
188B ILE* 4.0 24.2 - - + +
191B LEU* 3.5 32.3 - - + -
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Residues in contact with VAL 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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97B TYR* 4.3 16.6 - - + -
98B LEU* 3.9 28.3 - - + -
101B ALA* 3.7 16.8 - - + -
108B TRP* 4.0 8.3 - - + -
164B VAL* 3.0 20.5 + - + +
165B HIS 3.9 3.6 - - - +
167B ILE* 1.3 72.7 - - + +
169B LEU* 1.3 56.1 + - - +
172B LEU* 2.8 65.2 + - + +
184B LEU* 4.7 4.5 - - + -
188B ILE* 4.1 18.8 - - + -
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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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165A HIS* 5.2 2.9 - - + +
169A LEU* 3.4 33.4 - - + -
108B TRP* 4.1 19.7 - - + -
109B ARG* 3.6 26.7 - - - +
165B HIS* 2.8 40.3 + - + +
166B GLY* 3.9 3.8 - - - +
168B VAL* 1.3 72.3 - - - +
170B LEU* 1.3 70.3 + - + +
172B LEU* 4.1 0.5 - - - +
173B GLU* 3.0 63.0 + - + +
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Residues in contact with LEU 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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112A PHE* 3.8 20.6 - - + -
161A PHE* 3.9 15.9 - - + -
162A SER* 3.7 23.3 - - - +
165A HIS* 3.7 33.4 - - + +
166B GLY 3.0 13.7 + - - +
169B LEU* 1.3 83.5 - - + +
171B GLY* 1.3 61.4 + - - +
173B GLU* 4.5 5.6 - - - +
174B ASN* 3.4 2.1 + - - -
175B ARG* 3.2 43.0 + - + +
177B SER* 3.8 16.4 - - - +
178B GLY* 4.0 17.4 - - - -
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Residues in contact with GLY 171 (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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167B ILE 3.0 20.1 + - - -
168B VAL 3.7 0.2 - - - -
169B LEU 3.2 0.2 - - - -
170B LEU* 1.3 77.4 - - - +
172B LEU* 1.3 56.9 + - - +
174B ASN* 3.2 27.5 + - - -
178B GLY* 4.6 1.4 - - - -
179B VAL 3.5 24.5 - - - +
180B PRO* 5.8 0.2 - - - +
181B GLY* 4.7 3.5 + - - -
184B LEU* 3.8 15.2 - - - +
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Residues in contact with LEU 172 (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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117A ARG* 3.9 11.1 + - - -
98B LEU* 4.1 2.2 - - + +
101B ALA* 3.4 44.4 - - + +
102B ARG* 3.7 35.0 - - + +
108B TRP* 4.2 12.3 - - + -
168B VAL* 2.8 32.4 + - + +
169B LEU 4.3 1.6 - - - +
171B GLY* 1.3 70.8 - - - +
173B GLU* 1.3 61.2 + - + +
174B ASN* 3.2 8.1 + - - +
181B GLY* 5.9 0.4 - - - -
184B LEU* 3.8 20.6 - - + -
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 4.8 6.5 - - - +
117A ARG* 3.3 22.2 + - - +
108B TRP* 6.2 2.2 - - + -
109B ARG* 4.5 13.5 + - - -
169B LEU* 3.0 45.8 + - + +
170B LEU* 4.5 3.8 - - - +
172B LEU* 1.3 75.2 - - + +
174B ASN* 1.3 67.8 - - - +
175B ARG* 3.3 34.8 + - + +
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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