Contacts of the helix formed by residues 153 - 179 (chain A) in PDB entry 5XRA
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 TYR 153 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 3.6 48.5 - - + -
144A SER* 3.1 36.8 + - - -
145A ARG* 5.1 5.2 - - + -
151A PRO* 3.8 30.9 - - + +
152A SER* 1.3 77.5 - - - +
154A HIS* 1.3 59.4 - - - +
155A PHE 3.4 2.0 - - - -
156A ILE* 4.0 20.2 - - + +
157A GLY* 2.8 26.9 + - - +
401A SER* 4.2 17.3 - - - -
403A ASP* 3.0 33.1 - - + +
404A LEU* 3.6 7.5 + - + -
604A OLA 3.8 5.4 - - - +
606A OLC 5.6 0.4 + - - -
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Residues in contact with HIS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 4.7 9.8 + - - -
152A SER* 3.3 31.7 - - - -
153A TYR* 1.3 76.2 - - - +
155A PHE* 1.3 63.3 + - - +
158A SER* 3.1 26.7 + - - -
230A ARG* 3.7 26.3 - - + +
233A ALA* 4.5 11.4 - - + -
234A VAL* 3.6 24.6 - - + +
237A PHE* 3.8 14.4 - + + -
604A OLA 3.3 19.9 + - - -
606A OLC 3.8 26.8 + - - +
608A CLR 3.3 14.5 + - - +
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A HIS* 1.3 76.9 - - - +
156A ILE* 1.3 78.5 + - + +
157A GLY 3.3 0.2 + - - -
158A SER* 3.4 2.3 + - - -
159A LEU* 3.0 30.1 + - + +
206A SER* 3.5 20.6 - - - -
207A LEU* 4.0 14.1 - - + -
210A ALA* 3.4 28.7 - - + -
237A PHE* 3.7 13.9 - + + -
397A TYR* 3.4 57.2 - + + -
606A OLC 3.8 21.0 + - - +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.1 22.2 - - + +
141A ILE* 4.2 11.0 - - + -
153A TYR* 3.7 22.7 + - + +
154A HIS 3.5 0.2 - - - -
155A PHE* 1.3 97.2 - - + +
157A GLY* 1.3 64.3 + - - +
159A LEU* 3.6 5.2 + - - +
160A ALA* 3.2 21.0 + - - +
397A TYR* 4.4 9.9 - - + +
398A ALA* 4.1 20.2 - - + +
401A SER* 3.8 31.2 - - - +
404A LEU* 5.4 2.5 - - + -
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.2 4.6 - - - +
141A ILE* 5.0 6.7 - - - -
153A TYR* 2.8 20.0 + - - +
156A ILE* 1.3 76.9 - - - +
158A SER* 1.3 64.1 + - - +
160A ALA* 3.1 15.4 + - - +
161A VAL* 3.1 20.7 + - - +
604A OLA 4.2 17.3 - - - -
608A CLR 4.5 3.8 - - - -
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A HIS 3.1 20.2 + - - -
155A PHE 3.9 0.7 - - - -
157A GLY* 1.3 73.5 - - - +
159A LEU* 1.3 62.5 + - - +
161A VAL* 3.2 2.3 + - - +
162A ALA* 3.0 22.5 + - - +
206A SER* 2.6 25.9 + - - -
237A PHE* 3.6 20.7 - - - -
241A TRP* 3.1 22.2 + - - +
608A CLR 3.9 23.4 - - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASN* 5.8 0.2 - - - +
155A PHE* 3.0 26.0 + - + +
156A ILE* 3.9 4.9 - - - +
158A SER* 1.3 76.6 + - - +
160A ALA* 1.3 63.4 + - - +
162A ALA* 3.4 2.6 + - - +
163A ASP* 3.0 36.1 + - - +
203A SER* 3.6 40.2 - - - +
206A SER* 4.0 10.5 + - - -
207A LEU* 4.1 12.6 - - + -
393A ASN* 3.8 35.4 - - + +
397A TYR* 3.9 23.3 - - + -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASN* 3.3 25.1 - - - +
137A VAL* 4.2 16.4 - - + -
138A LEU* 3.9 23.3 - - + -
156A ILE 3.2 11.2 + - - +
157A GLY* 3.1 9.7 + - - +
159A LEU* 1.3 76.5 - - - +
161A VAL* 1.3 59.2 + - - +
163A ASP 3.4 0.2 + - - -
164A LEU* 2.9 32.3 + - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.9 21.8 - - + -
157A GLY 3.1 17.6 + - - +
158A SER* 3.2 5.6 + - - +
160A ALA* 1.3 74.6 - - - +
162A ALA* 1.3 63.7 + - - +
164A LEU* 3.9 4.4 - - - +
165A LEU* 3.0 36.2 + - + +
241A TRP* 3.9 10.3 - - + -
604A OLA 4.0 31.4 - - + -
608A CLR 3.8 35.4 - - + -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER 3.0 16.3 + - - +
159A LEU* 3.8 5.4 - - - +
161A VAL* 1.3 77.8 - - - +
163A ASP* 1.3 57.5 + - - +
165A LEU* 5.0 0.7 - - - -
166A GLY* 3.0 26.2 + - - -
199A SER* 3.6 28.2 - - - +
200A PHE* 6.0 0.9 - - - -
202A ALA* 4.2 2.0 - - + +
203A SER* 3.8 21.3 - - - +
206A SER* 5.1 0.4 - - - +
241A TRP* 3.8 19.9 - - + -
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Residues in contact with ASP 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 4.6 0.3 - - - +
134A ASN* 3.7 24.2 - - - +
159A LEU* 3.0 23.2 + - - +
162A ALA* 1.3 73.8 - - - +
164A LEU* 1.3 63.1 + - - +
166A GLY* 5.1 0.2 - - - -
167A SER* 2.9 32.0 + - - +
200A PHE* 5.4 2.3 - - - -
203A SER* 3.0 28.0 + - - -
390A SER* 3.5 30.6 + - - +
393A ASN* 3.6 29.7 + - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 3.6 46.4 - - + +
134A ASN* 4.1 9.5 - - + +
135A LEU* 4.5 20.9 - - + +
138A LEU* 3.9 24.9 - - + -
160A ALA 2.9 18.6 + - - +
161A VAL* 3.9 4.0 - - - +
163A ASP* 1.3 76.7 - - - +
165A LEU* 1.3 68.5 + - + +
167A SER* 3.1 15.1 + - - -
168A VAL* 3.3 22.6 + - + +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 3.0 31.8 + - + +
162A ALA* 4.1 2.2 - - - +
164A LEU* 1.3 83.3 - - + +
166A GLY* 1.3 64.1 + - - +
168A VAL* 3.3 4.9 + - + +
169A ILE* 3.0 34.1 + - + +
199A SER* 4.2 11.2 - - - +
241A TRP* 4.8 6.7 - - + -
604A OLA 5.9 1.8 - - + -
608A CLR 3.8 51.1 - - + -
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 3.0 14.5 + - - -
163A ASP* 4.0 0.4 - - - -
165A LEU* 1.3 76.3 - - - +
167A SER* 1.3 56.3 + - - +
169A ILE* 3.4 2.3 + - - +
170A PHE* 2.8 34.0 + - - +
196A VAL* 4.9 2.0 - - - +
199A SER* 3.4 22.8 - - - -
200A PHE* 3.8 19.3 - - - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY* 4.7 4.5 - - - -
130A THR* 4.2 19.6 - - - +
131A VAL* 3.7 16.8 - - - +
163A ASP 2.9 21.0 + - - -
164A LEU* 3.1 7.8 + - - -
166A GLY* 1.3 75.7 - - - +
168A VAL* 1.3 60.8 + - - +
170A PHE* 4.4 0.2 - - - -
171A VAL* 2.9 36.3 + - - +
200A PHE* 4.4 2.9 - - - -
387A LEU* 4.0 26.5 - - - -
390A SER* 5.2 2.2 - - - -
605A OLC 5.7 0.2 - - - -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 3.5 26.7 - - + -
164A LEU* 3.3 22.4 + - + +
165A LEU* 3.3 7.7 + - + +
167A SER* 1.3 81.9 + - - +
169A ILE* 1.3 68.4 + - + +
171A VAL* 4.4 0.3 - - - +
172A TYR* 3.2 26.2 + - + +
605A OLC 4.6 21.7 - - + +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 3.0 23.0 + - + +
166A GLY* 4.0 2.5 - - - +
168A VAL* 1.3 78.8 - - + +
170A PHE* 1.3 64.0 + - - +
172A TYR* 4.0 2.3 - - - +
173A SER* 3.0 35.2 + - - +
192A LYS* 3.9 14.6 - - + +
195A GLY* 4.0 24.0 - - - +
196A VAL* 3.6 22.0 - - + +
199A SER* 4.4 5.2 - - - +
608A CLR 4.6 13.2 - - + -
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER* 5.0 0.9 - - - -
166A GLY 2.8 23.8 + - - +
167A SER* 3.9 2.7 - - - +
169A ILE* 1.3 74.7 - - - +
171A VAL* 1.3 62.7 + - - +
173A SER* 3.6 1.0 - - - -
174A PHE* 2.6 81.9 + + + +
196A VAL* 3.8 12.9 - - + +
200A PHE* 4.0 11.2 - + + -
383A SER* 3.9 18.6 - - - -
384A MET* 5.0 4.5 - - - -
386A CYS* 6.0 0.9 - - + -
387A LEU* 4.0 31.2 - - + -
602A 8D3 3.5 53.6 - + + +
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER* 3.7 17.5 - - - +
124A LEU* 3.9 28.3 - - + -
127A GLY* 4.0 11.4 - - - -
167A SER 2.9 25.1 + - - +
168A VAL 4.4 0.9 - - - +
170A PHE* 1.3 77.6 - - + +
172A TYR* 1.3 63.5 + - - +
174A PHE* 4.3 2.2 - - - -
175A ILE* 2.9 37.4 + - + +
387A LEU* 3.7 33.4 - - + -
605A OLC 4.2 17.5 - - + -
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Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 3.2 20.9 + - + +
169A ILE* 4.0 2.7 - - - +
170A PHE 3.2 0.8 - - - -
171A VAL* 1.3 79.6 - - - +
173A SER* 1.3 69.4 + - - +
175A ILE* 3.9 1.4 - - - +
176A ASP* 2.9 44.4 + - + +
182A ARG* 6.0 0.2 + - - -
192A LYS* 5.6 6.5 - - - -
605A OLC 3.4 73.4 + - + +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.0 24.7 + - - +
170A PHE 3.9 0.9 - - - -
172A TYR* 1.3 80.3 - - - +
174A PHE* 1.3 57.2 + - - +
176A ASP* 3.4 6.6 + - - +
177A PHE* 2.9 32.9 + - - +
192A LYS* 3.6 31.4 - - - +
196A VAL* 5.2 0.9 - - - -
602A 8D3 4.0 25.5 - - - +
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.6 30.7 - - + -
123A SER* 4.0 11.9 - - - +
170A PHE* 2.6 51.5 + + + +
171A VAL* 3.9 3.6 - - - +
173A SER* 1.3 70.9 - - - +
175A ILE* 1.3 64.2 + - + +
177A PHE* 3.4 1.7 + - - -
178A HIS* 3.0 54.9 + + - +
380A ALA* 3.5 28.3 - - + -
383A SER* 4.0 4.7 - - - -
384A MET* 4.2 10.1 - - - -
602A 8D3 3.6 40.3 - - + +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 4.2 4.5 - - + +
120A ALA* 3.6 38.6 - - + +
123A SER* 4.0 16.2 - - - +
124A LEU* 4.7 13.5 - - + -
171A VAL* 2.9 34.5 + - + +
172A TYR 4.0 1.8 - - - +
174A PHE* 1.3 74.9 - - + +
176A ASP* 1.3 58.6 + - - +
179A VAL* 2.9 39.1 + - + +
180A PHE* 3.4 16.9 - - + -
605A OLC 3.6 24.0 - - + +
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 2.9 34.0 + - + +
173A SER* 3.7 8.3 - - - +
175A ILE* 1.3 77.8 - - - +
177A PHE* 1.3 56.7 + - - +
180A PHE* 3.1 19.6 - - - +
181A HIS 3.1 21.7 + - - -
182A ARG* 3.1 45.6 + - + +
192A LYS* 4.2 9.7 + - - +
605A OLC 3.0 34.1 + - - +
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.9 15.0 - - + -
108A PHE* 3.4 37.5 - - + -
109A MET* 3.6 36.2 - - + +
173A SER 2.9 17.5 + - - +
174A PHE 4.1 1.8 - - - +
176A ASP* 1.3 76.8 - - - +
178A HIS* 1.3 74.3 + + - +
181A HIS* 3.2 24.9 + - - -
182A ARG* 3.9 18.8 - - + +
184A ASP* 6.1 0.4 - - - -
189A PHE* 4.5 18.2 - + + -
269A PRO* 4.3 5.4 - - + -
602A 8D3 3.5 36.1 - - + -
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE 3.6 23.1 - - - -
109A MET* 4.0 1.7 - - - -
110A VAL* 3.4 46.9 + - + +
116A GLN* 3.6 5.4 - - + +
119A ILE* 4.7 18.6 - - + -
174A PHE* 3.0 60.2 + + - +
177A PHE* 1.3 94.2 - + - +
179A VAL* 1.3 62.6 + - + +
181A HIS* 3.2 21.2 + - - -
380A ALA* 4.1 9.8 - - + +
602A 8D3 4.6 9.2 + - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 3.6 47.9 - - + +
119A ILE* 4.9 2.5 - - + -
120A ALA* 4.4 15.3 - - + +
175A ILE* 2.9 27.6 + - + +
178A HIS* 1.3 83.5 - - + +
180A PHE* 1.3 77.7 + - + +
181A HIS* 3.6 8.3 + - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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