Contacts of the helix formed by residues 155 - 178 (chain B) in PDB entry 3EUP
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 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A TYR* 4.7 7.0 - - - -
188A GLU* 4.3 8.5 - - - +
153B ASP 3.3 4.9 + - - +
154B THR* 1.3 70.0 - - - +
156B VAL* 1.3 63.9 + - - +
157B THR* 3.6 6.9 + - - -
158B LYS* 3.3 45.2 + - + +
159B ILE* 3.0 26.2 + - + +
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Residues in contact with VAL 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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138B VAL* 3.8 42.4 - - + +
141B ILE* 3.8 31.4 - - + +
142B LYS* 4.3 17.0 - - + -
145B ILE* 3.9 16.6 - - + -
154B THR* 3.1 20.1 + - - +
155B ASP* 1.3 73.2 + - - +
157B THR* 1.3 59.7 + - - +
159B ILE* 3.4 1.4 + - - -
160B ALA* 3.0 27.0 + - - +
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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
----------------------------------------------------------
185A TYR* 3.3 39.7 - - + +
134B LYS* 3.3 29.5 + - - +
138B VAL* 4.7 3.3 - - - +
155B ASP* 3.3 6.0 + - - -
156B VAL* 1.3 76.9 - - - +
158B LYS* 1.3 64.8 + - - +
160B ALA* 3.2 1.6 + - - +
161B PHE* 3.0 36.1 + - + -
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Residues in contact with LYS 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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185A TYR* 3.7 27.0 - - + +
188A GLU* 3.3 38.2 + - + +
189A SER* 3.5 19.1 - - - +
192A ASP* 2.6 31.2 + - - +
155B ASP* 3.2 35.5 + - - +
157B THR* 1.3 80.3 - - - +
159B ILE* 1.3 71.3 + - - +
161B PHE* 3.6 1.0 + - - +
162B SER* 2.8 28.9 + - - -
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 5.6 0.7 - - - +
141B ILE* 3.9 18.4 - - + -
154B THR* 4.0 7.9 - - + -
155B ASP* 3.0 18.2 + - + +
156B VAL* 3.4 4.0 + - - +
158B LYS* 1.3 88.1 - - + +
160B ALA* 1.3 57.8 + - - +
162B SER* 3.1 5.0 + - - -
163B MET* 2.8 37.7 + - + +
193B LEU* 3.6 28.9 - - + +
194B ILE* 3.9 25.1 - - + -
197B ILE* 3.6 32.8 - - + -
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Residues in contact with ALA 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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134B LYS* 3.9 20.9 - - + +
137B LEU* 3.7 28.3 - - + +
138B VAL* 4.1 8.5 - - + -
141B ILE* 4.2 7.2 - - + +
156B VAL 3.0 18.1 + - - +
157B THR 3.2 3.8 + - - +
159B ILE* 1.3 78.0 - - - +
161B PHE* 1.3 64.7 + - - +
163B MET* 3.2 5.7 + - - +
164B ILE* 3.2 25.1 + - - +
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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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173A ILE* 3.6 27.2 - - + +
182A TYR* 3.5 47.6 - + + +
185A TYR* 3.7 19.3 - + + -
186A VAL* 4.0 15.3 - - + -
130B ILE* 4.3 11.0 - - + -
131B LEU* 3.8 16.6 - - + -
134B LYS* 3.6 45.3 - - + -
157B THR* 3.0 30.4 + - + +
158B LYS 4.2 2.2 - - - +
160B ALA* 1.3 76.2 - - - +
162B SER* 1.3 57.8 - - - +
164B ILE* 3.3 10.5 + - + +
165B ALA* 3.0 23.0 + - - +
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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 LEU* 4.3 5.5 - - - +
185A TYR 3.7 7.8 + - - -
186A VAL* 4.0 4.5 - - - -
189A SER* 2.5 38.6 + - - -
158B LYS 2.8 22.9 + - - -
159B ILE* 3.7 4.0 - - - -
161B PHE* 1.3 71.7 - - - +
163B MET* 1.3 60.6 + - - +
165B ALA* 3.3 7.2 + - - +
166B LEU* 2.9 34.0 + - - +
193B LEU* 3.9 15.9 - - - -
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Residues in contact with MET 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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86B LEU* 3.4 44.9 - - + +
89B TYR* 3.9 10.8 - - + -
133B TRP* 5.6 0.7 - - + -
137B LEU* 3.6 34.1 - - + -
141B ILE* 4.5 6.1 - - - -
159B ILE* 2.8 24.6 + - - +
160B ALA* 3.4 7.2 - - - +
162B SER* 1.3 73.6 - - - +
164B ILE* 1.3 66.4 + - - +
166B LEU* 3.2 3.1 + - - +
167B VAL* 2.9 30.0 + - + +
190B LEU* 3.8 26.2 - - + -
193B LEU* 4.0 4.2 - - + +
194B ILE* 3.8 22.0 - - + -
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Residues in contact with ILE 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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173A ILE* 3.9 11.7 - - + -
130B ILE* 3.7 38.4 - - + +
133B TRP* 3.7 38.8 - - + -
134B LYS* 3.6 42.8 - - + +
137B LEU* 3.7 9.2 - - + -
160B ALA 3.2 12.9 + - - +
161B PHE* 3.3 10.5 + - + +
163B MET* 1.3 76.1 - - - +
165B ALA* 1.3 60.0 + - - +
167B VAL* 3.3 0.7 + - - +
168B GLU* 2.9 40.2 + - + +
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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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165A ALA 3.5 7.3 - - - +
166A LEU* 4.3 4.3 - - + +
169A GLY* 3.7 23.8 - - - -
173A ILE* 4.2 3.1 - - + -
186A VAL* 3.3 37.5 - - + -
161B PHE 3.0 12.6 + - - +
162B SER 3.6 7.2 - - - +
163B MET 3.2 0.2 - - - -
164B ILE* 1.3 77.5 - - - +
166B LEU* 1.3 56.8 + - - +
168B GLU* 5.0 0.4 - - - -
169B GLY* 2.8 28.9 + - - -
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Residues in contact with LEU 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* 4.2 8.7 - - - +
165A ALA* 4.4 2.5 - - + -
166A LEU* 3.7 31.4 - - + -
162B SER* 2.9 19.9 + - - +
163B MET 3.6 3.8 - - - +
165B ALA* 1.3 74.3 - - - +
167B VAL* 1.3 60.0 + - - +
170B ALA* 2.8 32.6 + - - +
186B VAL* 3.3 25.3 - - + +
187B PHE* 6.1 0.4 - - - -
189B SER* 4.2 15.7 - - - +
190B LEU* 3.7 37.9 - - + +
193B LEU* 3.9 20.6 - - + -
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Residues in contact with VAL 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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89B TYR* 3.7 44.4 - - + +
92B MET* 6.3 0.7 - - + -
93B TYR* 6.2 0.9 - - + -
101B PHE* 6.0 2.0 - - + -
133B TRP* 4.2 14.1 - - + -
163B MET* 2.9 21.8 + - + +
164B ILE 3.9 2.7 - - - +
166B LEU* 1.3 75.0 - - - +
168B GLU* 1.3 73.8 + - - +
170B ALA* 3.3 7.1 + - - +
171B ILE* 3.0 38.5 + - + +
187B PHE* 4.6 10.5 - - + -
190B LEU* 3.9 16.8 - - + -
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Residues in contact with GLU 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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169A GLY* 5.1 2.7 - - - -
172A LEU* 3.5 28.5 - - + +
65B TRP* 5.4 0.3 - - - -
101B PHE* 6.0 0.2 - - - -
106B CYS* 3.1 33.2 - - - +
108B LEU* 4.4 4.6 - - + +
109B LEU* 3.7 22.8 + - + +
133B TRP* 3.4 32.6 - - + -
164B ILE* 2.9 25.5 + - + +
165B ALA* 4.2 2.9 - - - +
167B VAL* 1.3 84.5 - - - +
169B GLY* 1.3 56.3 + - - +
171B ILE* 3.3 10.8 + - - +
172B LEU* 3.0 26.3 + - - +
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Residues in contact with GLY 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 ALA* 3.7 26.0 - - - -
168A GLU* 5.1 2.7 - - - -
169A GLY* 4.7 5.5 - - - -
165B ALA 2.8 22.3 + - - -
166B LEU 3.7 0.2 - - - -
168B GLU* 1.3 69.6 - - - +
170B ALA* 1.3 65.0 + - - +
172B LEU* 3.3 8.4 + - - +
173B ILE* 3.0 28.1 + - - +
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Residues in contact with ALA 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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165A ALA* 4.0 0.8 - - - +
166B LEU 2.8 19.8 + - - +
167B VAL 3.3 5.6 + - - +
169B GLY* 1.3 76.6 - - - +
171B ILE* 1.3 62.6 + - - +
173B ILE* 3.2 3.0 + - - +
174B HIS* 3.0 18.5 + - - +
183B SER* 3.4 15.8 - - - +
186B VAL* 3.6 27.6 - - + -
187B PHE* 3.7 30.1 - - + -
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Residues in contact with ILE 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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93B TYR* 3.6 54.5 - - + +
101B PHE* 4.2 10.3 - - + -
106B CYS* 4.1 19.5 - - + +
109B LEU* 3.6 20.2 - - + -
167B VAL* 3.0 27.7 + - + +
168B GLU* 3.6 25.6 - - - +
169B GLY 3.3 0.2 - - - -
170B ALA* 1.3 76.1 - - - +
172B LEU* 1.3 55.8 + - - +
174B HIS* 3.2 2.3 + - - +
175B ARG* 2.8 44.0 + - - +
187B PHE* 5.0 2.2 - - + -
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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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108A LEU* 3.8 15.3 - - + -
109A LEU* 3.4 39.7 - - + +
112A THR* 3.5 35.4 - - + +
113A ILE* 4.5 7.0 - - + -
130A ILE* 5.2 3.6 - - + -
168A GLU* 3.4 32.5 - - + -
109B LEU* 4.2 7.6 - - + +
168B GLU 3.0 13.1 + - - +
169B GLY* 3.5 10.3 - - - +
171B ILE* 1.3 75.7 - - - +
173B ILE* 1.3 65.1 + - + +
175B ARG* 3.2 3.5 + - - -
176B ALA* 2.9 23.7 + - - +
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Residues in contact with ILE 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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130A ILE* 4.3 11.9 - - + -
161A PHE* 3.5 39.3 - - + +
164A ILE* 3.9 24.2 - - + -
165A ALA 4.0 5.2 - - - +
169B GLY 3.0 21.2 + - - +
170B ALA* 3.7 4.0 - - - +
172B LEU* 1.3 78.1 - - + +
174B HIS* 1.3 54.9 + - - +
176B ALA* 3.3 3.7 + - - -
177B THR* 2.7 44.7 + - + +
182B TYR* 3.7 30.5 - - + -
183B SER* 4.0 7.4 - - - +
186B VAL* 3.8 16.4 - - + -
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Residues in contact with HIS 174 (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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93B TYR* 2.8 38.4 - + + +
97B ASP* 5.5 0.4 - - - -
170B ALA 3.0 10.2 + - - +
171B ILE 3.5 6.1 - - - +
173B ILE* 1.3 78.1 - - - +
175B ARG* 1.3 65.5 + - + +
177B THR* 4.0 3.8 - - - -
178B LYS* 2.7 44.9 + - + +
179B ASN 4.0 2.6 + - - -
180B ARG* 3.5 55.4 + - + +
183B SER* 3.6 19.3 - - - +
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Residues in contact with ARG 175 (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 THR* 3.7 12.8 - - + -
113A ILE* 5.7 2.0 - - + -
116A ASP* 2.7 39.5 + - + +
117A ASP* 2.8 31.3 + - - -
123A ARG* 3.4 16.1 - - - +
203A SO4 4.8 1.6 - - - -
93B TYR* 3.0 33.2 + - - +
104B GLY* 3.3 24.4 + - - +
105B GLY* 3.6 16.0 - - - +
106B CYS 5.3 0.9 - - - +
109B LEU* 5.3 5.4 - - - -
110B ASN* 5.5 1.6 - - - -
171B ILE* 2.8 36.2 + - - +
172B LEU* 3.2 1.5 + - - +
174B HIS* 1.3 80.9 + - + +
176B ALA* 1.3 60.7 + - - +
178B LYS* 4.3 6.6 + - - +
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Residues in contact with ALA 176 (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 THR* 3.5 24.4 - - - +
123A ARG* 2.8 27.3 + - - +
126A ALA* 4.8 1.3 - - - -
127A GLY* 3.3 20.3 + - - +
130A ILE* 4.1 25.6 - - + -
172B LEU* 2.9 18.0 + - + +
173B ILE 3.8 2.9 - - - +
175B ARG* 1.3 77.0 - - - +
177B THR* 1.3 60.2 + - + +
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Residues in contact with THR 177 (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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123A ARG* 3.7 10.2 + - - +
127A GLY* 4.3 7.9 - - - -
130A ILE* 4.0 25.8 - - + -
131A LEU* 4.2 15.9 - - + -
173B ILE* 2.7 25.7 + - + +
174B HIS 3.8 0.2 + - - -
176B ALA* 1.3 81.9 - - - +
178B LYS* 1.3 65.5 + - - +
179B ASN* 3.1 19.0 + - - +
182B TYR* 3.5 33.8 - - + -
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Residues in contact with LYS 178 (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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116A ASP* 3.0 29.9 + - - +
117A ASP* 4.8 4.2 + - - -
120A ASP* 6.0 1.8 - - - -
123A ARG* 3.9 39.1 - - - +
174B HIS* 2.7 32.7 + - + +
175B ARG* 4.5 6.7 + - - +
177B THR* 1.3 71.8 - - - +
179B ASN* 1.3 56.0 + - - +
180B ARG* 4.1 1.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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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