Contacts of the helix formed by residues 159 - 192 (chain A) in PDB entry 2YPT
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 THR 159 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.5 8.3 - - - -
157A GLN 4.0 1.3 + - - +
158A GLN* 1.3 74.9 - - - +
160A LEU* 1.3 67.0 + - - +
161A GLY* 3.2 6.7 + - - +
162A PHE* 3.3 26.1 + - + +
163A PHE* 3.1 18.7 + - - +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 6.0 3.3 - - + +
147A PHE* 3.6 23.1 - - + -
159A THR* 1.3 75.6 + - - +
161A GLY* 1.3 55.8 + - - +
163A PHE* 3.6 2.1 + - - +
164A MET* 3.0 34.7 + - + +
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Residues in contact with GLY 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A THR* 3.2 7.7 + - - -
160A LEU* 1.3 76.0 - - - +
162A PHE* 1.4 54.1 + - - +
164A MET* 3.4 5.9 + - - +
165A LYS* 2.8 42.2 + - - +
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLN* 3.3 22.4 - - + -
159A THR* 3.3 28.7 + - + +
161A GLY* 1.4 70.2 - - - +
163A PHE* 1.3 59.7 + - - +
165A LYS* 4.0 6.1 - - + +
166A ASP* 2.9 51.7 + - - +
169A LYS* 5.0 4.7 - - - -
223A PHE 4.1 10.3 - - - -
224A ASP* 5.2 0.9 - - - -
259A LYS* 4.8 17.7 - - + -
260A ARG* 3.7 46.4 - - + -
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.5 19.1 - - + -
142A SER* 3.2 28.7 - - - -
143A LEU* 3.6 46.4 - - + -
146A THR* 3.6 29.4 - - + -
147A PHE* 3.6 13.7 - + + -
158A GLN* 3.5 24.7 + - - +
159A THR 3.1 16.2 + - - +
160A LEU 3.7 2.9 - - - +
162A PHE* 1.3 76.9 - - - +
164A MET* 1.3 63.1 + - - +
166A ASP* 3.8 3.1 - - - +
167A ALA* 3.0 30.3 + - + +
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Residues in contact with MET 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.6 5.8 - - + -
143A LEU* 5.2 2.0 - - + -
160A LEU* 3.0 22.4 + - + +
161A GLY* 3.7 4.9 - - - +
163A PHE* 1.3 83.2 - - + +
165A LYS* 1.4 65.2 - - + +
167A ALA* 3.2 13.5 + - - +
168A ILE* 3.2 25.4 + - + +
91B LEU* 3.7 30.1 - - + +
94B LEU* 3.9 24.0 - - + +
95B PHE* 3.7 51.1 - - + +
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLY 2.8 24.0 + - - +
162A PHE* 4.0 6.1 - - + +
164A MET* 1.4 71.2 - - - +
166A ASP* 1.3 57.0 + - - +
168A ILE* 3.7 9.9 + - + +
169A LYS* 3.0 41.8 + - - +
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 2.9 31.0 + - + +
163A PHE* 3.8 6.1 - - - +
165A LYS* 1.3 74.4 - - - +
167A ALA* 1.3 57.9 + - - +
169A LYS* 3.0 31.7 + - - +
170A LYS* 2.9 34.8 + - - +
223A PHE* 3.7 11.2 - - - +
260A ARG* 2.8 45.8 + - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.0 21.5 - - + -
163A PHE* 3.0 21.7 + - + +
164A MET* 3.2 9.6 + - - +
166A ASP* 1.3 75.9 - - - +
168A ILE* 1.4 56.3 + - - +
170A LYS* 4.0 4.1 - - - +
171A PHE* 3.0 29.3 + - - +
95B PHE* 3.8 18.9 - - + -
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Residues in contact with ILE 168 (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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164A MET* 3.2 34.0 + - + +
165A LYS* 4.0 8.7 - - + +
167A ALA* 1.4 71.7 - - - +
169A LYS* 1.4 56.2 + - - +
171A PHE* 3.2 2.5 + - + +
172A VAL* 2.8 53.4 + - + +
94B LEU 4.5 6.1 - - - +
95B PHE* 3.7 45.5 - - + +
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Residues in contact with LYS 169 (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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162A PHE* 5.0 6.2 - - - -
165A LYS* 3.0 32.8 + - - +
166A ASP* 3.0 32.9 + - - +
168A ILE* 1.4 74.7 - - - +
170A LYS* 1.4 57.7 + - - +
172A VAL* 3.5 4.8 + - - +
173A VAL* 3.1 34.9 + - + +
222A LEU* 3.5 27.5 + - + +
223A PHE* 3.8 22.7 + - + +
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Residues in contact with LYS 170 (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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166A ASP* 2.9 22.0 + - - +
167A ALA* 4.0 5.2 - - - +
169A LYS* 1.4 69.3 - - - +
171A PHE* 1.4 55.9 + - - +
173A VAL* 3.5 1.7 + - - +
174A THR* 2.6 39.7 + - - +
223A PHE* 3.6 21.9 - - + -
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 3.6 26.7 - - - -
132A LEU* 3.9 19.5 - - + -
135A ALA* 3.8 20.2 - - + -
167A ALA 3.0 20.5 + - - +
168A ILE* 3.6 5.2 - - + +
170A LYS* 1.4 75.3 - - - +
172A VAL* 1.4 68.8 + - + +
174A THR* 3.4 9.5 - - + -
175A GLN* 3.2 54.2 + - + +
95B PHE* 3.7 26.0 - + + -
100B TYR* 3.9 31.4 - + - -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 2.8 38.6 + - + +
169A LYS* 3.8 5.6 - - - +
171A PHE* 1.4 76.3 - - + +
173A VAL* 1.3 69.1 + - + +
175A GLN* 3.3 9.8 + - - +
176A CYS* 3.2 36.8 + - - -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LYS* 3.1 19.2 + - + +
170A LYS 3.9 3.4 - - - +
172A VAL* 1.3 74.9 - - + +
174A THR* 1.4 64.4 + - - +
176A CYS* 3.4 9.4 + - + +
177A ILE* 3.3 41.3 + - + +
219A ILE* 3.9 23.6 - - + -
222A LEU* 4.6 15.3 - - + -
223A PHE* 4.0 18.2 - - + -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 5.7 3.4 - - + -
170A LYS* 2.6 28.1 + - - +
171A PHE* 3.4 12.5 - - + -
172A VAL 3.2 0.2 - - - -
173A VAL* 1.4 73.4 - - - +
175A GLN* 1.4 64.0 - - - +
177A ILE* 3.2 8.2 + - - +
178A LEU* 2.8 46.8 + - + +
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Residues in contact with GLN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.5 25.5 - - + +
131A THR* 3.1 30.9 + - - -
171A PHE* 3.2 37.6 + - + +
172A VAL* 3.3 7.6 + - - +
174A THR* 1.4 91.6 - - - +
176A CYS* 1.3 58.8 + - - +
177A ILE 3.1 0.2 - - - -
178A LEU* 4.1 8.1 - - - +
179A LEU* 2.9 50.5 + - + +
100B TYR* 3.7 9.6 + - - +
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Residues in contact with CYS 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 VAL* 3.2 31.5 + - - +
173A VAL* 3.7 12.6 - - + +
174A THR 3.4 0.2 - - - -
175A GLN* 1.3 76.4 - - - +
177A ILE* 1.3 60.8 + - + +
179A LEU* 5.5 0.2 - - - -
180A PRO* 3.4 21.5 - - - +
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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
----------------------------------------------------------
173A VAL* 3.3 33.2 + - + +
174A THR* 3.2 8.3 + - - +
175A GLN 3.1 0.2 - - - -
176A CYS* 1.3 80.8 - - + +
178A LEU* 1.4 63.3 + - - +
179A LEU 3.6 0.4 - - - -
180A PRO* 3.3 7.4 - - - +
181A VAL* 3.3 35.7 - - + +
207A VAL* 6.4 0.2 - - + -
219A ILE* 3.9 28.7 - - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.8 32.8 - - + +
131A THR* 3.9 24.2 - - + +
174A THR* 2.8 24.6 + - + +
175A GLN* 3.9 16.2 - - - +
177A ILE* 1.4 77.7 - - - +
179A LEU* 1.3 63.7 + - + +
181A VAL* 4.0 2.4 - - - +
182A SER* 2.9 41.8 + - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.6 34.0 - - + +
127A LEU* 5.3 3.1 - - + -
128A LEU* 3.6 47.6 - - + +
175A GLN* 2.9 42.5 + - + +
176A CYS* 5.5 0.2 - - - -
178A LEU* 1.3 81.0 - - + +
180A PRO* 1.4 63.1 - - + +
182A SER* 4.8 0.7 - - - -
183A SER* 2.8 28.7 + - - -
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Residues in contact with PRO 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A CYS* 3.4 24.0 - - - +
177A ILE* 3.3 14.1 - - - +
179A LEU* 1.4 93.4 - - + +
181A VAL* 1.4 61.1 + - + +
183A SER* 2.8 19.3 + - - +
184A LEU* 3.1 27.5 + - + +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.3 30.7 + - + +
178A LEU* 4.1 2.9 - - - +
180A PRO* 1.4 75.3 - - + +
182A SER* 1.4 59.4 + - - +
184A LEU* 3.5 1.5 + - + -
185A LEU* 2.9 30.5 + - + +
203A PHE* 3.4 18.7 - - + -
204A THR* 6.2 2.9 - - + -
207A VAL* 3.9 37.7 - - + -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 4.5 4.9 - - - -
127A LEU* 3.4 27.5 - - - +
178A LEU* 2.9 27.7 + - - +
179A LEU 4.0 2.5 - - - -
181A VAL* 1.4 75.6 - - - +
183A SER* 1.3 55.0 + - - +
185A LEU* 3.1 11.2 + - - +
186A LEU* 2.8 46.2 + - - +
385A LEU* 5.1 4.7 - - - +
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 4.0 26.4 - - - +
124A LEU* 3.7 21.2 - - - +
179A LEU 2.8 17.5 + - - -
180A PRO* 2.8 24.6 + - - +
182A SER* 1.3 74.0 - - - +
184A LEU* 1.4 60.9 + - - +
186A LEU* 3.8 0.6 + - - -
187A TYR* 3.3 22.3 + - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PRO* 3.1 29.6 + - + +
181A VAL* 4.9 0.7 - - + +
183A SER* 1.4 75.3 + - - +
185A LEU* 1.4 64.4 + - - +
187A TYR* 3.4 14.5 - - + +
188A ILE* 3.3 28.3 + - + +
203A PHE* 3.5 30.1 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 2.9 21.5 + - + +
182A SER* 3.1 11.0 + - - +
184A LEU* 1.4 74.6 - - - +
186A LEU* 1.4 64.1 + - + +
188A ILE* 3.3 14.3 + - - +
189A ILE* 3.3 23.5 + - + +
200A ALA* 4.1 11.7 - - + +
203A PHE* 3.7 17.7 - - + -
204A THR* 3.8 30.1 - - + -
360A PHE* 4.1 12.1 - - + -
385A LEU* 6.4 0.7 - - + -
388A LEU* 4.2 28.0 - - + -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 5.2 0.9 - - - +
120A ILE* 4.0 20.6 - - + +
123A SER* 3.8 28.0 - - - +
124A LEU* 5.0 3.1 - - + -
127A LEU* 6.2 0.2 - - + -
182A SER* 2.8 32.8 + - - +
183A SER* 4.0 8.3 - - - +
185A LEU* 1.4 73.2 - - + +
187A TYR* 1.4 56.8 + - - +
189A ILE* 3.5 8.4 + - - +
190A LYS* 3.1 34.1 + - + +
384A THR* 3.8 17.0 - - + +
385A LEU* 3.6 47.8 - - + +
388A LEU* 4.4 7.6 - - + -
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 6.3 1.3 - - + -
120A ILE* 4.0 20.2 - - + +
183A SER 3.3 17.8 + - - +
184A LEU* 3.4 17.5 - - + +
186A LEU* 1.4 78.3 - - - +
188A ILE* 1.3 61.7 + - + +
190A LYS* 4.8 1.3 - - - -
191A ILE* 2.8 76.7 + - + +
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 3.3 17.7 + - + +
185A LEU* 3.3 7.5 + - - +
187A TYR* 1.3 85.3 - - + +
189A ILE* 1.3 55.9 - - - +
191A ILE* 5.1 0.7 - - - -
192A GLY* 2.9 30.6 + - - +
196A PHE* 4.1 4.9 - - - +
199A TYR* 3.8 18.8 - - + +
200A ALA* 3.5 33.7 - - + +
203A PHE* 3.6 40.8 - - + -
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.3 36.6 + - + +
186A LEU* 3.9 5.4 - - - +
187A TYR 3.4 0.2 - - - -
188A ILE* 1.3 77.1 - - - +
190A LYS* 1.3 60.0 + - - +
192A GLY 3.2 14.6 - - - +
196A PHE* 3.7 37.7 - - + +
200A ALA* 4.1 19.1 - - + -
360A PHE* 4.7 2.5 - - + -
363A PHE* 4.3 10.8 - - + -
367A ILE* 4.4 7.4 - - + -
384A THR* 3.7 22.0 - - + -
388A LEU* 4.1 28.9 - - + -
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Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 5.0 18.8 - - + +
119A GLU* 4.3 10.3 - - - +
120A ILE* 5.2 9.6 - - + -
186A LEU* 3.1 22.0 + - + +
187A TYR* 4.0 3.8 - - - +
189A ILE* 1.3 76.5 - - - +
191A ILE* 1.4 64.1 - - + +
192A GLY 4.2 1.7 - - - +
384A THR* 3.6 26.0 - - - +
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 4.6 23.8 - - + -
120A ILE* 6.3 0.2 - - + -
187A TYR* 2.8 64.5 + - + +
188A ILE* 5.1 0.9 - - - -
190A LYS* 1.4 75.8 - - + +
192A GLY* 1.3 65.5 + - - +
193A GLY 4.0 0.2 + - - -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 2.9 21.0 + - - +
189A ILE 3.2 15.9 - - - +
190A LYS 4.2 1.7 - - - +
191A ILE* 1.3 81.4 - - - +
193A GLY* 1.3 58.5 + - - -
196A PHE* 3.5 10.7 - - - +
199A TYR* 4.4 12.6 - - - -
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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