Contacts of the helix formed by residues 154 - 176 (chain B) in PDB entry 2I10
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 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA* 4.8 4.5 - - - +
188A LEU* 5.1 2.2 - - + +
152B GLY 3.2 5.1 + - - +
153B THR* 1.3 71.9 - - - +
155B CYS* 1.3 58.2 + - - +
156B THR* 3.2 9.5 + - - -
157B ALA* 3.1 34.1 + - + +
158B LEU* 3.0 28.1 + - - +
202B PGE 5.1 0.4 - - - -
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Residues in contact with CYS 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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137B LEU* 3.4 16.3 - - + +
140B PHE* 3.7 31.7 - - + -
141B GLU* 5.1 0.7 - - - -
144B LEU* 3.6 31.4 - - - -
149B LEU* 4.3 9.6 - - - -
153B THR* 3.0 16.5 + - - -
154B ASP* 1.3 72.5 + - - +
156B THR* 1.3 60.7 + - - +
158B LEU* 4.3 1.3 - - - -
159B ALA* 2.9 31.0 + - - +
202B PGE 4.7 3.7 + - - +
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 3.4 36.2 - - + +
133B ARG* 4.7 13.2 + - - +
137B LEU* 4.0 14.6 - - - +
154B ASP* 3.6 8.1 - - - +
155B CYS* 1.3 77.0 - - - +
157B ALA* 1.3 65.1 + - - +
159B ALA* 3.6 3.2 + - - +
160B ARG* 3.2 22.0 + - - +
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 4.7 6.3 - - - -
184A ALA* 3.6 28.0 - - + -
185A ALA* 4.1 3.6 - - - +
188A LEU* 3.8 12.6 - - + +
154B ASP* 3.1 33.6 + - + +
156B THR* 1.3 78.6 - - - +
158B LEU* 1.3 59.1 + - - +
160B ARG* 3.4 7.7 + - - +
161B TYR* 2.9 27.7 + - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.8 14.3 - - + +
140B PHE* 3.5 29.4 - - + -
149B LEU* 4.3 6.1 - - + -
153B THR* 3.8 23.8 - - + -
154B ASP 3.0 18.3 + - - +
155B CYS 3.9 2.0 - - - +
156B THR 3.3 0.2 - - - -
157B ALA* 1.3 74.3 - - - +
159B ALA* 1.3 59.4 + - - +
161B TYR* 3.3 5.3 + - + +
162B VAL* 3.0 31.7 + - - +
192B VAL* 3.7 37.7 - - + +
193B VAL* 4.0 14.8 - - + -
194B PRO* 4.3 12.6 - - + -
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 4.3 15.0 - - + +
136B VAL* 4.1 18.6 - - + +
137B LEU* 3.9 22.2 - - + -
140B PHE* 3.6 8.4 - - + -
155B CYS 2.9 18.0 + - - +
156B THR 3.7 5.2 - - - +
158B LEU* 1.3 72.5 - - - +
160B ARG* 1.3 64.7 + - - +
162B VAL* 3.2 4.6 + - - +
163B MSE 3.1 28.4 + - - +
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLU* 2.6 44.9 + - + -
177A ALA* 3.6 18.5 - - - +
178A PRO* 3.5 1.8 - - - +
181A GLU* 2.8 48.9 + - + +
182A LEU* 4.6 6.1 - - + +
185A ALA* 4.4 7.6 - - + -
129B ARG* 3.3 2.8 - - - +
133B ARG* 3.5 15.4 - - - +
156B THR 3.2 11.3 + - - +
157B ALA 3.6 9.4 - - - +
159B ALA* 1.3 74.9 - - - +
161B TYR* 1.3 67.0 + - - +
163B MSE 3.3 14.0 + - - +
164B ALA* 3.0 23.8 + - + +
201B NPO 2.8 57.1 + - - -
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.4 22.6 + + - -
165A ALA* 5.6 2.2 - - + -
169A LEU* 6.0 0.7 - - + -
185A ALA* 3.9 21.7 - - + +
188A LEU* 4.3 4.7 - - + -
189A ALA* 3.8 26.2 - - + -
85B VAL* 6.0 0.2 - - + -
89B LEU* 5.7 2.0 - - + -
157B ALA 2.9 14.4 + - - +
158B LEU* 3.6 15.5 - - + +
159B ALA 3.2 0.2 - - - -
160B ARG* 1.3 77.4 - - - +
162B VAL* 1.3 68.6 + - + +
164B ALA* 3.3 7.1 + - + +
165B ALA* 2.8 40.6 + - + +
189B ALA* 2.6 46.6 + - - +
192B VAL* 3.4 29.8 - - + +
193B VAL* 5.2 2.7 - - + -
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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
----------------------------------------------------------
85B VAL* 4.1 34.1 - - + -
88B PHE* 4.9 7.6 - - + -
89B LEU* 4.6 5.4 - - + -
132B MSE 6.2 1.8 - - + -
136B VAL* 4.5 17.9 - - + -
140B PHE* 4.1 20.6 - - + -
158B LEU 3.0 20.8 + - - +
159B ALA 3.2 7.6 + - - +
161B TYR* 1.3 82.0 - - + +
163B MSE 1.3 58.3 + - + +
165B ALA* 3.3 7.0 + - - +
166B VAL* 3.1 36.6 + - + +
193B VAL* 4.2 7.9 - - + -
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Residues in contact with MSE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLU* 3.5 12.3 - - - +
129B ARG* 3.2 59.2 - - - +
130B GLU* 4.4 2.5 - - - +
132B MSE 3.7 30.1 - - + -
133B ARG* 3.5 39.5 - - + -
136B VAL* 6.0 2.0 - - + -
159B ALA 3.1 18.6 + - - +
160B ARG* 3.6 22.7 - - - +
162B VAL* 1.3 75.3 - - + +
164B ALA* 1.3 61.7 + - - +
166B VAL* 3.3 2.5 + - - +
167B TYR* 2.8 34.9 + - + -
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Residues in contact with ALA 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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164A ALA 4.2 1.2 - - - +
165A ALA* 5.1 2.9 - - - +
168A GLY* 3.1 34.4 - - - +
169A LEU* 3.9 24.5 - - + +
172A GLU* 4.0 8.1 - - + +
160B ARG* 3.0 13.9 + - + +
161B TYR* 3.5 11.9 - - + +
163B MSE 1.3 76.0 - - - +
165B ALA* 1.3 56.6 + - - +
167B TYR* 4.6 0.7 - - - -
168B GLY* 2.9 27.0 + - - -
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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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161A TYR* 5.8 1.1 - - + -
164A ALA* 5.0 6.3 - - - +
165A ALA* 5.8 2.5 - - - +
89B LEU* 4.3 12.3 - - + -
161B TYR* 2.8 33.9 + - + +
162B VAL* 3.6 6.7 - - - +
163B MSE 3.2 0.2 - - - -
164B ALA* 1.3 74.9 - - - +
166B VAL* 1.3 57.0 + - - +
168B GLY* 3.8 0.6 - - - -
169B LEU* 2.9 37.3 + - + +
189B ALA* 4.2 24.9 - - + -
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Residues in contact with VAL 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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66B CYS* 3.7 31.2 - - + +
88B PHE* 3.5 24.0 - - + -
89B LEU* 3.5 23.3 - - + -
92B ARG* 4.2 10.5 - - + -
96B PHE* 3.6 13.1 - - + -
132B MSE 4.7 7.9 - - + -
162B VAL* 3.1 19.0 + - + +
163B MSE 3.3 8.0 + - - +
165B ALA* 1.3 75.9 - - - +
167B TYR* 1.3 63.0 + - + +
169B LEU* 3.5 3.2 + - - +
170B SER* 3.0 24.6 + - - -
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Residues in contact with TYR 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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168A GLY* 4.3 2.7 - - - -
171A VAL* 3.9 30.7 - - + -
172A GLU* 3.2 27.6 - - + -
66B CYS* 3.8 25.6 - - + -
67B GLU* 2.5 29.4 + - - -
105B CYS* 4.0 5.6 - - - -
107B THR* 3.5 21.8 - - + -
108B VAL* 3.8 3.6 - - + +
129B ARG* 3.1 20.2 + - - +
132B MSE 3.2 23.4 - - + +
163B MSE 2.8 25.4 + - + +
164B ALA* 4.1 3.8 - - - +
166B VAL* 1.3 76.1 - - + +
168B GLY* 1.3 57.6 + - - +
170B SER* 3.2 6.8 + - - -
171B VAL* 3.0 31.7 + - - +
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Residues in contact with GLY 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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164A ALA* 3.0 33.5 - - - -
167A TYR* 4.4 2.9 - - - +
168A GLY* 3.5 9.3 - - - -
164B ALA 2.9 12.9 + - - -
167B TYR* 1.3 74.5 - - - +
169B LEU* 1.3 62.5 + - - +
171B VAL* 3.3 5.7 + - - +
172B GLU* 3.0 28.2 + - - +
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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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161A TYR* 6.5 0.4 - - + -
164A ALA* 3.8 11.8 - - + +
89B LEU* 4.3 21.3 - - + +
92B ARG* 6.0 0.2 - - + -
93B VAL* 4.0 15.0 - - + -
96B PHE* 4.0 7.0 - - + -
165B ALA* 2.9 28.1 + - + +
166B VAL* 3.9 5.2 - - - +
168B GLY* 1.3 76.1 - - - +
170B SER* 1.3 55.9 + - - +
172B GLU* 3.4 1.9 + - - +
173B ALA* 3.0 25.6 + - - +
182B LEU* 3.4 50.0 - - + +
185B ALA* 4.2 7.6 - - + +
186B ALA* 3.8 29.8 - - + +
189B ALA* 5.1 2.9 - - + -
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Residues in contact with SER 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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66B CYS* 3.8 8.7 - - - -
96B PHE* 3.5 29.1 - - - -
104B GLY* 3.5 3.1 - - - -
105B CYS* 3.0 31.6 + - - +
108B VAL* 3.9 2.9 - - - +
166B VAL 3.0 14.4 + - - -
167B TYR 3.2 10.7 + - - -
169B LEU* 1.3 77.3 - - - +
171B VAL* 1.3 56.7 + - - +
173B ALA* 3.3 2.3 + - - +
174B ALA* 2.9 30.7 + - - +
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Residues in contact with VAL 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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107A THR* 3.1 43.5 - - - +
108A VAL* 4.4 2.5 - - + -
129A ARG* 4.3 5.6 - - - +
167A TYR* 3.7 34.1 - - + -
171A VAL* 4.2 7.9 - - + -
108B VAL* 3.7 22.9 - - + -
167B TYR 3.0 17.6 + - - +
168B GLY 3.3 7.8 + - - +
170B SER* 1.3 76.9 - - - +
172B GLU* 1.3 61.3 + - - +
174B ALA* 3.3 7.6 + - - +
175B SER* 2.9 28.5 + - - +
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Residues in contact with GLU 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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129A ARG* 2.0 37.1 + - - +
160A ARG* 2.8 37.6 + - - -
163A MSE 3.5 13.4 - - - +
164A ALA* 3.9 18.6 - - + +
167A TYR* 3.1 21.5 - - + -
168B GLY 3.0 20.1 + - - +
169B LEU 3.8 0.4 - - - +
170B SER 3.3 0.2 - - - -
171B VAL* 1.3 74.4 - - - +
173B ALA* 1.3 62.6 + - - +
175B SER* 3.2 9.5 + - - -
176B GLY 3.2 0.5 + - - -
177B ALA* 3.1 23.8 + - + +
182B LEU* 3.6 22.0 - - + -
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Residues in contact with ALA 173 (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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96B PHE* 3.5 39.3 - - + +
97B THR* 4.2 7.2 - - + +
100B GLY* 4.0 14.0 + - - -
101B GLN 4.6 1.1 - - - -
169B LEU 3.0 17.9 + - - +
170B SER 3.6 3.6 - - - +
171B VAL 3.3 0.2 - - - -
172B GLU* 1.3 76.4 - - - +
174B ALA* 1.3 56.4 + - - +
176B GLY* 3.0 20.3 + - - -
177B ALA* 4.1 4.6 + - - +
182B LEU* 3.5 16.4 - - + +
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 3.8 10.3 - - + -
109A GLN* 4.5 3.9 + - - -
100B GLY 3.9 4.2 - - - +
101B GLN 3.1 23.3 + - - +
102B PRO* 3.3 28.5 - - - +
104B GLY* 3.4 22.4 - - - +
170B SER 2.9 16.5 + - - +
171B VAL 3.3 6.5 + - - +
173B ALA* 1.3 75.0 - - - +
175B SER* 1.3 60.1 + - - +
176B GLY 3.6 0.5 + - - -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR 4.0 5.5 + - - -
108A VAL* 4.7 0.9 - - - -
109A GLN* 2.9 35.2 + - - +
129A ARG* 3.4 39.6 + - - -
171B VAL 2.9 16.3 + - - -
172B GLU 3.2 2.9 + - - -
173B ALA 3.1 0.8 - - - -
174B ALA* 1.3 78.1 - - - +
176B GLY* 1.3 59.9 + - - +
177B ALA 3.6 0.7 - - - -
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLY* 5.3 6.7 - - - -
173B ALA 3.0 11.9 + - - -
174B ALA 3.2 1.4 - - - -
175B SER* 1.3 81.5 - - - +
177B ALA* 1.3 68.5 + - - +
178B PRO* 3.4 5.0 - - - +
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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