Contacts of the helix formed by residues 154 - 176 (chain B) in PDB entry 5K58
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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153B THR* 1.3 71.9 - - - +
155B GLU* 1.3 60.3 + - - +
156B THR* 3.0 19.8 + - - -
157B LEU* 3.2 29.2 + - + +
158B LEU* 2.8 33.4 + - - +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ARG* 4.1 8.2 - - + +
140B MET* 3.1 43.7 - - + +
141B ARG* 3.8 12.6 - - + +
144B ARG* 4.0 25.3 + - - +
151B TYR* 3.1 39.9 + - - +
153B THR 3.5 8.2 - - - +
154B ASP* 1.3 76.4 + - - +
156B THR* 1.3 60.8 + - - +
158B LEU* 4.8 1.8 - - - -
159B ALA* 2.9 28.6 + - - +
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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
----------------------------------------------------------
180A TYR* 6.2 0.2 - - - +
133B GLU* 6.0 2.9 - - - +
137B ARG* 3.4 35.3 + - - +
154B ASP* 3.0 9.7 + - - -
155B GLU* 1.3 76.3 - - - +
157B LEU* 1.3 61.2 + - - +
159B ALA* 3.4 5.7 - - + +
160B SER* 3.0 31.6 + - - -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASP* 4.0 33.2 - - + +
188A ALA* 3.6 38.4 - - + +
189A ARG* 3.7 20.0 + - + +
192A LEU* 4.4 15.7 - - + -
153B THR* 5.6 0.4 - - - -
154B ASP* 3.2 33.8 + - + +
156B THR* 1.3 76.5 - - - +
158B LEU* 1.3 63.0 + - - +
160B SER* 2.9 19.4 + - - -
161B GLN* 3.1 13.0 + - - +
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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
----------------------------------------------------------
192A LEU* 3.8 25.7 - - + +
140B MET* 3.8 15.9 - - + -
151B TYR* 4.1 19.5 - - + -
153B THR* 3.9 19.7 - - - +
154B ASP 2.8 19.3 + - - +
155B GLU* 4.2 3.4 - - - +
157B LEU* 1.3 71.2 - - - +
159B ALA* 1.3 65.3 + - - +
161B GLN* 3.5 1.0 + - + +
162B ILE* 3.0 42.2 + - + +
196B GLN* 3.8 26.0 - - + +
197B LEU* 3.6 27.6 - - + -
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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 GLU* 4.2 12.6 - - + +
136B LEU* 3.6 10.0 - - + +
137B ARG* 3.9 21.1 - - + +
140B MET* 2.9 21.7 - - + +
155B GLU 2.9 21.4 + - - +
156B THR* 3.4 10.5 - - + +
157B LEU 3.2 0.2 - - - -
158B LEU* 1.3 78.6 - - - +
160B SER* 1.3 64.7 + - - +
162B ILE* 3.2 11.3 + - - +
163B LEU* 3.3 8.1 + - - +
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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
----------------------------------------------------------
169A MET* 6.0 1.6 - - - -
180A TYR* 3.6 21.3 + - - -
189A ARG* 3.0 19.7 + - - -
133B GLU* 3.3 26.4 + - - +
156B THR* 3.0 12.5 + - - -
157B LEU* 2.9 12.8 + - - -
159B ALA* 1.3 76.6 - - - +
161B GLN* 1.3 63.5 + - - +
163B LEU* 2.7 24.3 + - - +
164B ALA* 2.9 14.2 + - - +
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Residues in contact with GLN 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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165A PHE* 3.1 30.9 - - - +
189A ARG* 3.4 39.6 + - - +
192A LEU* 4.0 15.0 - - + +
193A ILE* 3.2 27.9 - - - +
157B LEU 3.2 13.7 - - - +
158B LEU* 3.6 8.7 - - - +
160B SER* 1.3 81.6 + - - +
162B ILE* 1.3 60.3 + - + +
164B ALA* 3.6 17.7 - - - +
165B PHE* 3.7 8.7 + - - +
196B GLN* 3.8 25.6 - - - +
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Residues in contact with ILE 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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88B LEU* 4.0 14.8 - - + -
92B VAL* 3.8 27.8 - - + -
136B LEU* 4.3 10.5 - - + -
140B MET* 3.9 12.8 - - + -
158B LEU* 3.0 28.5 - - + +
159B ALA 3.2 5.8 + - - +
160B SER 3.1 0.6 - - - -
161B GLN* 1.3 74.8 - - - +
163B LEU* 1.3 65.5 + - - +
165B PHE* 3.6 8.2 + - + +
166B CYS* 3.4 21.8 + - - -
193B ILE* 3.6 22.9 - - + +
196B GLN* 3.1 27.6 - - - +
197B LEU* 5.6 2.2 - - + -
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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
----------------------------------------------------------
172A ARG* 5.9 0.7 - - - +
175A ARG* 3.9 10.5 - - - +
95B LEU* 4.6 5.8 - - + -
129B PHE* 4.2 18.2 - - + +
132B ILE* 4.1 26.5 - - + -
133B GLU* 3.3 33.9 - - + +
136B LEU* 4.6 7.1 - - + +
159B ALA 3.3 6.6 + - - +
160B SER 2.7 14.3 + - - +
162B ILE* 1.3 72.7 - - - +
164B ALA* 1.3 53.2 + - - +
166B CYS* 2.8 14.7 + - + +
167B GLU* 2.7 63.0 + - + +
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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 4.4 1.1 - - - -
165A PHE* 3.7 22.7 - - + +
168A GLY* 3.1 21.9 - - - -
169A MET* 3.8 24.0 - - + -
160B SER 2.9 9.6 + - - +
161B GLN 3.6 11.9 - - - +
163B LEU* 1.3 76.0 - - - +
165B PHE* 1.3 56.9 + - - +
167B GLU* 3.1 3.4 + - - +
168B GLY* 2.9 24.6 + - - -
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Residues in contact with PHE 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 GLN* 3.1 38.8 - - - -
164A ALA* 3.6 28.3 - - + -
165A PHE* 4.6 5.2 - - + +
92B VAL* 4.8 0.2 - - + -
96B LEU* 4.2 14.4 - - + -
161B GLN 3.7 8.3 + - - +
162B ILE* 3.6 10.7 + - + +
163B LEU 3.3 0.2 - - - -
164B ALA* 1.3 78.5 - - - +
166B CYS* 1.3 67.9 + - - +
169B MET* 3.0 65.4 + - + +
186B PHE* 6.0 0.2 - + - -
189B ARG* 3.8 17.9 - - + -
193B ILE* 3.8 29.2 - - + -
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Residues in contact with CYS 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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92B VAL* 3.6 38.6 - - - -
95B LEU* 3.5 26.5 - - + -
96B LEU* 3.7 17.3 - - + +
162B ILE* 3.4 15.0 + - - +
163B LEU* 2.8 15.8 + - + +
165B PHE* 1.3 82.2 - - - +
167B GLU* 1.3 58.7 + - - +
168B GLY 3.3 2.2 + - - -
169B MET 4.4 0.7 - - - -
170B LEU* 3.2 31.9 + - - +
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Residues in contact with GLU 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* 4.1 15.9 - - - +
171A SER* 3.9 21.6 + - - +
172A ARG* 4.5 0.9 + - - +
175A ARG* 2.4 48.5 + - - -
95B LEU* 6.1 0.4 - - + -
110B THR* 5.4 1.7 - - - +
129B PHE* 3.0 38.5 - - + -
163B LEU* 2.7 26.8 + - + +
164B ALA* 3.1 4.9 + - - +
166B CYS* 1.3 77.9 - - - +
168B GLY* 1.3 58.4 + - - +
170B LEU* 4.8 4.8 - - + +
171B SER* 3.3 24.6 + - - -
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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* 3.5 24.9 - - - -
167A GLU* 4.3 1.3 - - - -
168A GLY* 3.8 5.2 - - - -
164B ALA 2.9 7.6 + - - -
165B PHE 3.8 0.4 - - - -
166B CYS 3.3 0.2 - - - -
167B GLU* 1.3 78.5 - - - +
169B MET* 1.3 56.0 + - - +
170B LEU 3.2 1.6 - - - -
171B SER* 2.7 20.8 + - - -
172B ARG* 2.8 30.6 + - - +
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Residues in contact with MET 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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160A SER 4.6 0.2 - - - +
164A ALA* 4.4 8.4 - - - +
96B LEU* 4.4 18.8 - - + -
165B PHE* 3.0 53.8 + - + +
166B CYS 4.4 1.1 + - - +
168B GLY* 1.3 75.0 - - - +
170B LEU* 1.3 56.5 + - - +
172B ARG* 3.8 22.3 + - - +
173B PHE* 3.1 23.4 + - - +
180B TYR 4.4 8.0 - - - +
181B ARG 4.6 3.6 - - - +
182B PRO* 3.2 40.2 - - + +
184B ASP 5.4 0.9 - - - +
189B ARG* 3.7 28.3 - - - +
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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
----------------------------------------------------------
95B LEU* 4.8 22.2 - - + -
96B LEU* 4.7 7.6 - - + +
99B GLY* 3.7 22.7 - - - +
106B THR* 3.3 23.1 - - - +
109B LEU* 4.5 21.5 - - + -
110B THR* 4.1 10.1 - - + -
129B PHE* 5.9 3.4 - - + -
166B CYS 3.2 23.2 + - - +
167B GLU* 4.8 5.8 - - + +
168B GLY 3.2 0.6 - - - -
169B MET* 1.3 76.0 - - + +
171B SER* 1.3 62.4 + - - +
172B ARG 3.3 0.4 - - - -
173B PHE* 3.1 6.6 - - + +
174B VAL* 3.1 33.3 + - - +
182B PRO* 4.1 15.5 - - + -
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS* 6.2 3.4 - - - -
167A GLU* 3.6 21.9 + - - +
171A SER* 5.2 7.0 - - - -
110B THR* 3.9 16.1 - - - +
112B HIS* 5.1 4.7 - - - -
167B GLU 3.3 18.0 + - - -
168B GLY* 2.7 23.0 + - - -
170B LEU* 1.3 77.4 - - - +
172B ARG* 1.3 60.2 + - - +
174B VAL* 3.7 1.6 + - - +
175B ARG* 3.1 34.8 + - - +
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Residues in contact with ARG 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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133A GLU* 3.7 21.6 + - - -
160A SER* 3.8 29.5 + - - +
163A LEU* 4.0 10.3 - - - +
164A ALA* 4.3 19.1 - - - +
167A GLU* 3.0 35.6 + - - +
168B GLY 2.8 20.0 + - - +
169B MET* 4.0 20.3 - - - +
171B SER* 1.3 74.7 - - - +
173B PHE* 1.3 65.8 + - - +
175B ARG* 3.2 16.4 + - - +
176B SER* 3.6 12.8 + - - -
180B TYR* 3.9 51.2 + - + +
189B ARG* 5.8 0.4 - - - +
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Residues in contact with PHE 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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99B GLY 3.7 23.1 - - - -
100B GLU* 3.9 20.2 - - + -
103B PRO* 4.7 4.9 - - + -
106B THR* 3.9 17.9 - - + -
169B MET 3.1 17.0 + - - +
170B LEU* 3.1 12.8 - - + +
171B SER 3.2 0.2 - - - -
172B ARG* 1.3 80.5 - - - +
174B VAL* 1.3 61.0 + - - +
176B SER 3.4 3.8 + - - -
178B PHE* 2.8 83.2 + + + -
179B LYS 4.0 1.0 + - - -
180B TYR 3.6 8.5 - - - +
181B ARG* 3.5 29.8 - - + -
182B PRO* 3.5 17.9 - - + -
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Residues in contact with VAL 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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106B THR* 3.6 24.2 - - + +
107B ARG* 3.8 37.8 + - + +
110B THR* 3.6 21.3 - - + -
112B HIS* 3.6 24.9 - - + +
170B LEU 3.1 16.6 + - - +
171B SER 4.2 2.2 - - - +
173B PHE* 1.3 75.0 - - - +
175B ARG* 1.3 64.8 + - - +
177B GLU* 2.8 22.9 + - - +
178B PHE* 4.3 9.0 - - + -
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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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109A LEU 5.4 3.4 - - - -
110A THR* 5.4 8.7 - - - +
122A GLN* 4.3 22.0 - - - +
125A ILE* 5.4 2.5 - - - -
126A ASN* 3.2 39.7 + - - +
129A PHE* 3.7 36.8 - - - +
163A LEU* 5.2 1.6 - - - +
167A GLU* 2.8 42.0 + - - -
112B HIS* 5.0 12.5 - - + -
171B SER* 3.1 22.6 + - - +
172B ARG* 3.2 24.6 + - - +
173B PHE 3.3 0.2 - - - -
174B VAL* 1.3 79.1 - - - +
176B SER* 1.3 59.0 + - - +
177B GLU* 3.4 3.0 + - - +
180B TYR* 4.8 10.5 - - - -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 4.7 6.5 + - - +
172B ARG 3.6 11.1 + - - -
173B PHE 3.4 3.1 + - - -
174B VAL 2.9 1.2 + - - -
175B ARG* 1.3 80.0 - - - +
177B GLU* 1.3 68.4 + - - +
178B PHE 3.2 1.6 - - - -
179B LYS* 3.0 30.9 + - - +
180B TYR* 3.9 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) + - + + + + + -
------------------------------------------------------------
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