Contacts of the helix formed by residues 169 - 195 (chain A) in PDB entry 4P9U
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 GLU 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLU* 5.2 3.7 - - - +
167A LYS* 3.0 5.2 + - - -
168A ASP* 1.3 92.5 + - - +
170A LEU* 1.3 67.3 + - - +
171A LYS 3.4 0.4 - - - -
172A ARG* 3.7 17.5 - - + +
173A GLN* 3.0 39.5 + - + +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLU 4.6 3.6 - - - +
167A LYS* 2.8 39.0 + - + +
169A GLU* 1.3 83.6 + - - +
171A LYS* 1.3 62.7 + - - +
173A GLN* 4.6 5.3 - - - +
174A GLU* 3.3 25.8 + - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A HIS* 2.9 42.3 + - + -
162A LYS* 4.0 22.8 + - - +
167A LYS* 2.8 16.1 + - + +
170A LEU* 1.3 74.2 - - - +
172A ARG* 1.3 66.4 + - - +
174A GLU* 3.1 8.2 + - - +
175A ILE* 3.0 50.2 + - + +
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLN* 2.5 54.1 + - - +
159A GLN* 4.6 12.9 + - - +
160A HIS* 3.9 28.5 - - + +
168A ASP* 3.0 26.9 + - - +
169A GLU* 3.7 15.5 - - - +
170A LEU 3.3 0.2 - - - -
171A LYS* 1.3 81.6 - - - +
173A GLN* 1.3 58.1 + - + +
175A ILE* 3.3 2.1 + - - -
176A LEU* 2.9 55.1 + - + +
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 3.2 51.8 - - + +
143A SER* 4.1 10.4 + - - +
169A GLU* 3.0 29.3 + - + +
170A LEU* 4.6 6.3 - - - +
171A LYS 3.3 0.8 - - - -
172A ARG* 1.3 78.4 - - + +
174A GLU* 1.3 63.3 + - - +
176A LEU* 3.5 22.0 - - + +
177A ILE* 2.9 34.7 + - + +
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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
----------------------------------------------------------
142A PRO* 5.8 4.7 - - - +
170A LEU 3.3 18.2 + - - +
171A LYS* 3.1 9.3 + - - +
173A GLN* 1.3 78.1 - - - +
175A ILE* 1.3 68.0 + - + +
177A ILE* 3.1 21.1 + - - +
178A ALA* 3.0 22.0 + - - +
221A SER* 5.1 10.2 - - - +
223A PRO* 6.0 0.9 - - - +
226A ARG* 4.7 13.2 + - - -
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLN* 3.1 41.1 - - - +
160A HIS* 4.9 1.1 - - + +
171A LYS* 3.0 48.2 + - + +
172A ARG* 3.6 1.3 - - - +
174A GLU* 1.3 77.0 - - + +
176A LEU* 1.3 55.7 + - - +
178A ALA* 3.4 6.6 + - - +
179A LYS* 2.9 40.8 + - + +
217A SER* 5.1 7.9 - - - +
221A SER* 5.9 2.2 - - - -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LYS* 2.9 37.9 - - + +
157A ILE* 5.0 0.4 - - - -
158A GLN* 3.6 36.6 - - + +
172A ARG* 2.9 51.3 + - - +
173A GLN* 3.5 27.6 - - + +
174A GLU 3.1 0.2 - - - -
175A ILE* 1.3 78.4 - - - +
177A ILE* 1.3 56.0 + - + +
179A LYS* 3.1 5.4 + - + +
180A THR 2.9 24.9 + - - -
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA* 4.6 22.0 - - + +
138A LEU* 5.7 5.2 - - + -
140A ASN 6.0 0.7 - - - +
142A PRO* 5.1 22.2 - - + +
144A TRP* 6.1 3.4 - - + -
156A LYS* 4.8 0.7 - - - +
173A GLN 2.9 18.6 + - - +
174A GLU* 3.1 24.9 + - - +
176A LEU* 1.3 74.5 - - + +
178A ALA* 1.3 67.0 + - - +
180A THR* 3.1 16.0 - - + +
181A PHE* 3.0 22.5 + - + +
226A ARG* 3.7 37.5 - - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU 3.0 9.8 + - - +
175A ILE* 3.6 9.0 - - - +
176A LEU 3.3 0.2 - - - -
177A ILE* 1.3 76.1 - - - +
179A LYS* 1.3 58.3 + - - +
182A ASN* 3.0 30.1 + - - +
216A GLY 4.0 0.2 - - - +
217A SER* 3.1 28.3 - - - +
220A PHE* 3.2 37.1 + - - +
221A SER* 3.6 10.8 - - - +
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU 5.7 1.1 - - - +
156A LYS* 4.4 17.8 - - + +
157A ILE 3.2 31.5 + - - +
158A GLN* 3.6 19.9 - - + +
175A ILE* 2.9 34.1 + - + +
176A LEU* 3.4 10.5 - - + +
178A ALA* 1.3 78.2 - - - +
180A THR* 1.3 56.0 + - - +
182A ASN* 3.5 5.8 + - - +
183A PHE* 2.9 26.6 + - - +
217A SER* 3.8 28.9 - - - +
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA* 4.4 21.5 - - + -
144A TRP* 3.9 10.4 - - - +
153A TYR* 5.4 3.9 + - - -
156A LYS* 3.1 31.8 - - - +
176A LEU 2.9 8.2 + - - +
177A ILE* 3.1 26.0 - - + +
179A LYS* 1.3 73.7 - - - +
181A PHE* 1.3 69.0 + - + +
183A PHE* 3.0 9.4 + - - +
184A TYR* 3.0 45.1 + - + -
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A CYS* 3.7 18.4 - - - -
137A ALA* 6.2 0.7 - - + -
138A LEU* 3.5 33.0 - - + -
177A ILE* 3.0 16.1 + - + +
178A ALA 4.0 2.7 - - - +
180A THR* 1.3 80.7 - - + +
182A ASN* 1.3 58.6 + - - +
184A TYR* 3.4 5.7 + - - +
185A ASP* 2.9 24.9 + - - +
220A PHE* 3.5 28.5 - + + -
226A ARG* 3.2 38.1 - - + -
229A ALA* 3.4 25.4 - - + -
230A MET* 3.6 16.8 - - + -
233A TYR* 3.8 16.4 - + - -
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ALA 3.0 17.9 + - - +
179A LYS* 3.6 7.7 + - - +
181A PHE* 1.3 74.9 - - - +
183A PHE* 1.3 68.5 + - - +
185A ASP* 3.6 0.2 - - - +
186A TYR* 2.9 23.9 + - - +
212A TYR* 3.2 29.1 - - - +
213A ASP* 2.9 38.3 + - - +
216A GLY* 3.2 27.6 - - - -
217A SER* 4.0 4.6 + - - +
220A PHE* 3.5 12.3 - - + -
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Residues in contact with PHE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO 4.7 3.1 - - - -
153A TYR* 3.8 29.2 - + - -
155A GLU* 3.7 46.9 - - + -
156A LYS* 5.4 5.2 - - + -
179A LYS 2.9 16.5 + - - +
180A THR* 3.1 13.0 - - - +
182A ASN* 1.3 81.5 - - - +
184A TYR* 1.3 78.5 + + - +
186A TYR* 3.6 5.4 + - - +
187A MET* 3.0 55.6 + - + +
209A LYS* 6.2 1.3 - - - -
213A ASP* 5.3 1.3 - - - -
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASN* 4.5 7.6 - - - -
131A VAL* 3.8 19.2 - - + +
134A SER* 3.4 46.2 + - - -
135A CYS* 3.8 25.8 - - - -
144A TRP* 4.3 5.0 - + - -
148A ILE* 3.9 9.0 - - - +
153A TYR* 2.6 28.0 + + - -
180A THR* 3.0 41.4 + - - +
181A PHE 4.0 1.1 - - - +
183A PHE* 1.3 86.2 - + - +
185A ASP* 1.3 60.4 + - - +
187A MET* 3.3 28.3 + - + +
188A LEU* 2.9 28.2 + - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 3.6 7.7 + - - -
181A PHE 2.9 16.6 + - - +
182A ASN* 3.6 4.7 - - - +
184A TYR* 1.3 76.5 - - - +
186A TYR* 1.3 62.0 + - - +
188A LEU* 3.1 5.4 + - - +
189A PHE* 3.0 39.4 + - - -
212A TYR* 2.8 33.9 + - - -
220A PHE* 3.6 26.3 - - + -
233A TYR* 2.3 38.3 + - - +
255A TYR* 4.5 5.5 + - - -
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Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ASN 2.9 16.8 + - - +
183A PHE* 3.8 4.7 - - - +
185A ASP* 1.3 76.3 + - - +
187A MET* 1.3 70.6 + - + +
189A PHE* 3.4 1.0 + - - +
190A GLN* 2.9 48.4 + - + +
205A PHE* 3.1 46.2 + + + -
206A ASN* 3.4 14.2 + - - -
209A LYS* 3.5 44.8 - - + +
212A TYR* 3.5 40.8 - + + -
213A ASP* 4.3 9.0 - - - +
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Residues in contact with MET 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 5.9 1.1 - - + +
130A ASN* 4.2 19.1 - - - +
131A VAL* 4.7 7.2 - - + -
183A PHE* 3.0 48.0 + - + +
184A TYR* 3.4 24.2 - - + +
186A TYR* 1.3 82.5 - - + +
188A LEU* 1.3 62.0 + - - +
190A GLN* 4.9 1.3 - - - -
191A ARG* 2.9 75.4 + - - +
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 4.3 2.0 - - + -
127A ILE* 5.9 2.9 - - + -
128A MET* 4.7 19.1 - - + +
131A VAL* 3.8 30.2 - - + +
184A TYR 2.9 13.1 + - - +
185A ASP* 3.1 10.7 + - - +
187A MET* 1.3 75.9 - - - +
189A PHE* 1.3 87.7 + - + +
191A ARG* 4.1 1.9 - - - +
192A LEU* 2.9 49.5 + - + +
233A TYR* 3.6 35.9 - - + -
236A LEU* 4.3 12.3 - - + -
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 3.6 38.4 - - + -
109A SER* 3.6 14.6 - - - -
112A PHE* 3.7 8.1 - + - -
113A MET* 3.6 24.9 - - + -
185A ASP* 3.0 32.1 + - - +
186A TYR 4.2 1.6 - - - +
188A LEU* 1.3 92.4 - - + +
190A GLN* 1.3 57.7 + - - +
192A LEU* 4.7 1.6 - - - -
193A ALA* 2.9 29.4 + - - +
205A PHE* 3.4 22.4 - + + -
212A TYR* 3.1 24.0 - - + +
232A PHE* 3.7 28.7 - + - -
233A TYR* 4.7 1.6 - + - -
255A TYR* 4.7 3.8 - + - -
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Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 2.9 48.8 + - + +
187A MET* 4.3 1.2 - - - +
189A PHE* 1.3 75.4 - - - +
191A ARG* 1.3 77.1 + - - +
193A ALA* 2.9 21.8 + - - +
194A PHE* 3.0 34.1 + - + -
202A GLY 4.1 6.1 - - - +
205A PHE* 3.7 19.0 - - + -
206A ASN* 3.1 23.6 + - - -
76B GLU* 3.2 24.9 + - - +
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 6.1 0.4 - - - +
127A ILE* 3.6 36.9 - - + +
187A MET* 2.9 66.3 + - - +
188A LEU* 5.0 0.2 - - - -
190A GLN* 1.3 89.2 + - - +
192A LEU* 1.3 60.8 + - - +
194A PHE* 3.4 4.6 + - - +
195A HIS* 2.8 37.3 + - + +
76B GLU* 5.7 4.2 + - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.6 13.8 - - + +
113A MET* 4.1 19.3 - - + -
116A ALA* 3.6 23.7 - - + +
117A PHE* 4.2 11.0 - - + -
124A ALA* 3.8 30.5 - - + -
127A ILE* 3.9 15.3 - - + -
128A MET* 4.0 26.5 - - + -
188A LEU* 2.9 41.0 + - + +
189A PHE* 3.9 3.8 - - - +
191A ARG* 1.3 78.0 - - - +
193A ALA* 1.3 61.5 + - - +
195A HIS* 3.4 11.1 + - + +
196A SER 3.8 1.4 + - - -
236A LEU* 5.0 0.9 - - + -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.4 16.4 - - + -
189A PHE 2.9 19.0 + - - +
190A GLN 2.9 8.1 + - - +
192A LEU* 1.3 76.9 - - - +
194A PHE* 1.3 56.4 + - - +
195A HIS 3.5 0.2 - - - -
196A SER* 2.9 18.6 + - - -
198A ASN 3.6 1.7 - - - +
201A TYR* 3.4 37.4 - - + +
202A GLY* 3.5 6.3 + - - +
205A PHE* 3.6 15.3 - - + -
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLN* 3.0 36.0 + - - +
191A ARG* 4.0 6.3 - - - +
192A LEU 3.2 0.2 - - - -
193A ALA* 1.3 76.5 - - - +
195A HIS* 1.3 62.3 + - + +
196A SER 3.0 10.0 + - - -
197A GLY* 3.5 10.7 + - - -
198A ASN 4.6 3.8 + - - +
199A GLN* 3.6 34.3 - - + -
202A GLY* 3.4 20.2 - - - -
203A LEU* 3.7 13.0 - - + -
206A ASN* 3.1 27.6 - - - -
75B MET* 3.1 29.2 - - + -
76B GLU* 4.1 8.3 - - - -
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Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TYR 4.6 0.2 - - - +
116A ALA* 3.2 24.6 - - + -
119A LEU* 5.0 1.0 - - - +
120A ASN* 3.5 37.4 + - + +
123A SER* 3.7 34.4 - - - -
124A ALA* 5.6 1.1 - - + -
126A ARG* 4.2 13.9 + - - -
127A ILE* 4.7 11.6 - - + +
191A ARG* 2.8 32.2 + - + +
192A LEU* 3.4 9.7 + - + +
194A PHE* 1.3 80.2 - - + +
196A SER* 1.3 58.3 + - - +
197A GLY 3.3 2.2 - - - +
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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