Contacts of the helix formed by residues 162 - 187 (chain A) in PDB entry 2ADU
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 SER 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU 3.5 7.2 + - - -
159A ASP 3.3 3.6 + - - -
161A ALA* 1.3 77.4 - - - +
163A GLU* 1.3 63.0 + - - +
164A GLU 3.3 2.7 - - - -
165A ILE* 3.1 35.9 + - - +
166A TRP* 3.1 42.0 + - - -
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Residues in contact with GLU 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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131A LYS* 4.5 5.5 - - - -
159A ASP* 3.6 21.8 + - - +
160A GLN* 3.2 45.8 + - - +
161A ALA 3.3 4.2 + - - -
162A SER* 1.3 77.4 - - - +
164A GLU* 1.3 59.3 + - + +
166A TRP* 3.4 6.1 + - - +
167A ASN* 2.9 31.8 + - + +
170A ARG* 3.0 32.4 + - - -
465A ARG* 5.3 1.1 + - - -
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA 5.0 1.2 + - - +
162A SER 3.3 0.8 - - - -
163A GLU* 1.3 78.3 - - + +
165A ILE* 1.3 63.3 + - + +
167A ASN* 3.6 8.2 + - - +
168A ASP* 3.0 32.8 + - - +
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 3.1 30.9 + - - +
164A GLU* 1.3 77.2 - - + +
166A TRP* 1.3 76.2 + - + +
168A ASP* 3.1 17.9 + - - +
169A PHE* 3.1 35.2 + - + -
259A ARG* 3.9 35.6 - - - +
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Residues in contact with TRP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASP* 3.2 40.5 + - - -
162A SER* 3.1 31.6 + - - -
163A GLU* 3.7 12.6 - - - +
165A ILE* 1.3 91.2 - - + +
167A ASN* 1.3 63.8 + - - +
169A PHE* 2.9 13.7 + + - +
170A ARG* 2.9 46.5 + - - +
358A GLY* 4.1 25.6 - - - -
360A VAL* 4.6 7.2 - - + -
463A LEU* 3.8 33.8 - - + +
464A LEU 5.2 0.2 - - - -
465A ARG* 3.7 33.0 - - + +
466A PRO* 4.4 7.4 - - + -
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Residues in contact with ASN 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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127A GLY 2.8 23.5 + - - +
128A VAL* 3.7 6.2 - - - +
129A PHE* 3.0 37.0 + - - +
163A GLU* 2.9 20.9 + - + +
164A GLU* 3.6 9.8 + - - +
166A TRP* 1.3 78.1 - - - +
168A ASP* 1.3 61.9 + - - +
170A ARG* 3.2 16.5 + - - +
171A GLU* 3.0 26.5 + - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 3.0 23.3 + - - +
165A ILE* 3.1 11.2 + - - +
167A ASN* 1.3 78.0 + - - +
169A PHE* 1.3 67.8 + - - +
171A GLU* 3.3 8.3 + - - +
172A ALA* 3.1 22.9 + - - +
256A ILE* 3.4 34.8 - - + +
257A SER* 4.2 13.3 + - - -
259A ARG* 3.7 21.1 + - + +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 3.1 46.0 + - + -
166A TRP* 2.9 12.0 + + - +
168A ASP* 1.3 78.0 - - - +
170A ARG* 1.3 56.7 + - - +
172A ALA* 3.2 4.3 + - - -
173A ALA* 2.9 22.7 + - - +
259A ARG* 3.7 34.3 - - + -
260A ILE 3.4 26.9 - - - -
261A ILE* 3.4 20.9 - - + +
333A ILE* 5.0 4.3 - - + -
334A GLY 6.4 1.3 - - - -
360A VAL* 3.6 37.5 - - + -
461A THR* 4.9 0.4 - - + -
463A LEU* 3.8 26.9 - - + -
472A VAL* 4.0 6.3 - - + -
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 6.1 2.0 - - - +
129A PHE* 3.5 19.6 + - + +
130A PRO 3.1 26.4 - - - +
131A LYS* 3.4 32.8 - - - +
163A GLU* 3.0 24.9 + - - -
166A TRP* 2.9 37.5 + - - +
167A ASN* 3.5 18.4 + - - +
168A ASP 3.2 0.4 - - - -
169A PHE* 1.3 74.7 - - - +
171A GLU* 1.3 60.3 + - - +
173A ALA* 3.1 2.6 + - - +
174A GLU* 2.9 30.5 + - - +
177A ARG* 4.1 2.8 + - - -
463A LEU* 5.3 0.6 - - - +
465A ARG* 3.7 12.9 - - - +
470A GLU* 3.1 32.8 + - - +
472A VAL* 3.8 19.7 - - + -
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 4.1 8.2 - - + +
121A CYS* 3.5 28.6 + - - +
129A PHE* 3.3 45.4 - - + +
167A ASN* 3.0 12.4 + - - +
168A ASP* 3.8 7.2 - - - +
170A ARG* 1.3 75.5 - - - +
172A ALA* 1.3 64.1 + - - +
174A GLU* 3.4 4.0 + - - +
175A ALA* 3.2 20.8 + - - +
207A LEU 5.7 0.7 - - - +
208A ILE* 5.1 5.8 - - + +
209A LYS* 6.1 0.5 - - - +
256A ILE* 3.5 39.9 - - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP 3.1 12.7 + - - +
169A PHE 3.5 3.8 - - - +
171A GLU* 1.3 78.6 - - - +
173A ALA* 1.3 55.6 + - - +
175A ALA* 3.4 1.9 + - - +
176A HIS* 3.0 16.1 + - - +
208A ILE* 4.0 9.9 - - - -
254A THR* 2.7 40.3 + - - +
255A HIS* 4.1 4.9 - - - -
256A ILE* 4.2 4.3 - - + -
259A ARG 4.1 8.1 - - - +
261A ILE* 3.3 21.5 - - + -
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE 2.9 13.0 + - - +
170A ARG 3.1 7.8 + - - +
172A ALA* 1.3 73.6 - - - +
174A GLU* 1.3 55.1 + - - +
175A ALA 3.1 1.3 - - - -
176A HIS* 3.0 7.9 + - - +
177A ARG* 2.7 45.8 + - - +
180A ARG* 5.2 0.2 + - - -
261A ILE* 3.5 11.6 - - + +
472A VAL* 3.2 37.0 - - + +
473A SER* 4.1 4.0 - - - +
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Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 3.5 30.6 - - + +
124A TYR* 4.3 21.3 + - + -
130A PRO* 4.5 11.9 - - + +
170A ARG 2.9 16.2 + - - +
171A GLU* 3.7 1.1 - - - +
173A ALA* 1.3 76.0 - - - +
175A ALA* 1.3 62.3 + - - +
177A ARG* 2.9 34.5 + - - +
178A GLN* 2.5 56.2 + - - +
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Residues in contact with ALA 175 (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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120A ILE* 3.7 20.6 - - + +
171A GLU 3.2 13.0 + - - +
172A ALA 3.4 9.4 - - - +
173A ALA 3.1 0.2 - - - -
174A GLU* 1.3 77.6 - - - +
176A HIS* 1.3 57.3 + - - +
178A GLN* 3.9 1.4 - - - +
179A VAL* 3.0 36.8 + - + +
204A SER 5.4 0.4 - - - +
207A LEU* 4.5 4.5 - - + -
208A ILE* 3.8 31.6 - - + +
254A THR* 4.3 7.0 - - + -
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Residues in contact with HIS 176 (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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172A ALA 3.0 13.5 + - - +
173A ALA* 3.0 10.4 + - - +
175A ALA* 1.3 77.2 - - - +
177A ARG* 1.3 61.7 + - - +
179A VAL 3.4 0.2 + - - -
180A ARG* 3.0 48.6 + - - +
252A PHE* 2.8 69.1 + + - -
253A GLY* 4.4 1.6 - - - -
254A THR* 4.1 5.1 + - - +
261A ILE* 4.0 21.5 - - + -
263A CYS* 2.9 40.3 + - + +
264A ALA* 5.1 0.2 - - - -
478A TYR* 4.0 2.2 - - - -
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO* 4.4 18.3 + - - +
131A LYS 5.4 2.1 + - - -
132A GLY* 4.8 4.9 - - - -
170A ARG* 4.1 3.6 + - - +
173A ALA* 2.7 23.4 + - - +
174A GLU* 2.9 52.6 + - - +
175A ALA 3.4 0.2 - - - -
176A HIS* 1.3 73.5 - - - +
178A GLN* 1.3 63.2 + - + +
180A ARG* 3.4 35.1 + - - +
181A LYS* 3.3 24.3 + - - +
472A VAL 2.8 26.9 + - - -
473A SER 3.8 2.4 - - - +
474A ARG 3.1 24.1 + - - -
475A GLY* 3.8 9.0 - - - -
476A ASP 5.3 0.7 - - - +
477A ASP* 4.6 2.0 - - - +
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Residues in contact with GLN 178 (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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112A GLN* 2.8 41.1 + - + +
116A PRO* 4.4 6.3 - - + +
120A ILE* 3.6 17.6 - - - +
123A LEU* 4.1 11.3 - - - +
124A TYR* 5.4 1.4 + - - -
174A GLU* 2.5 39.5 + - - +
177A ARG* 1.3 75.1 - - + +
179A VAL* 1.3 66.1 + - - +
181A LYS* 3.5 12.6 + - - +
182A TYR* 3.2 22.5 + - - +
207A LEU* 3.6 15.6 - - + +
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Residues in contact with VAL 179 (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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175A ALA* 3.0 28.9 + - + +
176A HIS 3.8 3.6 - - - +
177A ARG 3.4 0.2 - - - -
178A GLN* 1.3 77.6 - - - +
180A ARG* 1.3 57.6 + - - +
182A TYR* 3.2 6.1 + - - +
183A VAL* 3.0 30.4 + - + +
200A LEU* 3.8 30.7 - - + +
203A CYS* 4.0 16.8 - - + -
204A SER* 3.6 31.2 - - - +
207A LEU* 4.1 8.3 - - + -
252A PHE* 3.6 24.0 - - + -
254A THR* 5.5 0.2 - - + -
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS* 3.0 45.6 + - - +
177A ARG* 3.4 21.8 - - - +
179A VAL* 1.3 74.6 - - - +
181A LYS* 1.3 63.2 + - - +
183A VAL* 3.2 10.3 + - - +
184A MET* 2.9 37.8 + - + +
252A PHE* 4.0 8.1 - - + -
263A CYS* 3.1 13.5 - - - -
265A PHE* 3.8 20.8 - - + -
460A HIS* 4.2 0.6 - - - -
473A SER* 2.9 29.7 + - - -
475A GLY* 3.3 16.2 - - - +
477A ASP* 2.8 39.0 + - - +
478A TYR* 3.5 23.1 + - + -
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Residues in contact with LYS 181 (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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177A ARG 3.3 14.3 + - - +
178A GLN* 3.9 12.3 - - - +
179A VAL 3.3 0.6 - - - -
180A ARG* 1.3 80.6 - - - +
182A TYR* 1.3 63.2 + - - +
184A MET* 3.3 19.5 + - + +
185A SER* 3.3 17.8 + - - -
476A ASP* 4.6 20.2 - - - +
477A ASP* 5.2 2.7 - - + +
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Residues in contact with TYR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 4.9 4.7 - - - -
115A PRO* 4.2 19.5 - - + +
116A PRO* 3.5 29.8 - - + -
178A GLN 3.2 12.9 + - - +
179A VAL* 3.2 10.7 + - - +
180A ARG 3.1 0.2 - - - -
181A LYS* 1.3 74.7 - - - +
183A VAL* 1.3 62.4 + - + +
185A SER* 2.6 36.4 + - - -
186A TRP* 3.1 39.7 - + - -
199A LYS* 3.4 32.3 + - + +
203A CYS* 3.6 34.3 - - + -
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.0 18.9 + - + +
180A ARG* 3.4 10.1 - - - +
182A TYR* 1.3 77.6 - - + +
184A MET* 1.3 58.4 + - - +
185A SER 2.9 0.9 + - - -
186A TRP* 3.0 23.1 + - + -
187A ILE* 2.8 51.5 + - + +
196A ILE* 5.2 1.3 - - + -
200A LEU* 3.5 43.7 - - + -
250A ILE* 5.0 3.8 - - + -
252A PHE* 5.4 0.2 - - + -
265A PHE* 4.5 14.4 - - + -
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Residues in contact with MET 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ARG* 2.9 33.0 + - + +
181A LYS* 3.3 24.5 - - + +
182A TYR 3.3 0.2 - - - -
183A VAL* 1.3 71.8 - - - +
185A SER* 1.3 60.6 + - - +
187A ILE* 4.1 14.5 - - + +
188A LYS* 4.6 5.4 + - - -
265A PHE* 3.8 32.1 - - + -
267A VAL* 5.6 1.3 - - + -
477A ASP* 3.3 38.8 - - + +
478A TYR* 5.2 3.1 - - + -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LYS 3.3 10.8 + - - -
182A TYR* 2.6 27.8 + - - -
184A MET* 1.3 80.2 - - - +
186A TRP* 1.3 66.3 + - - +
188A LYS* 3.5 12.7 + - - -
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Residues in contact with TRP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 3.1 57.5 + + - -
183A VAL* 3.0 26.9 + - + -
185A SER* 1.3 86.9 - - - +
187A ILE* 1.3 94.8 + - + +
188A LYS* 3.0 18.2 + - - +
191A MET* 3.6 37.4 - - + +
196A ILE* 3.5 36.8 - - + -
199A LYS* 3.3 38.1 - - + -
200A LEU* 4.1 5.8 - - + -
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 2.8 28.7 + - + +
184A MET* 4.1 14.2 - - - +
186A TRP* 1.3 84.1 - - + +
188A LYS* 1.3 76.8 + - - +
191A MET* 4.3 0.4 - - - -
196A ILE* 4.0 20.6 - - + -
242A LEU* 3.8 21.1 - - + -
248A CYS* 4.9 3.8 - - - -
250A ILE* 4.4 18.4 - - + -
267A VAL* 3.8 42.4 - - + -
269A PHE* 3.6 8.7 - - + -
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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