Contacts of the helix formed by residues 153 - 182 (chain A) in PDB entry 1YDI
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 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.8 2.3 - - - +
152A GLU* 1.3 86.5 - - + +
154A MET* 1.3 58.5 + - - +
155A GLU* 3.4 15.6 + - - +
156A ASP* 3.0 35.6 + - - +
157A LEU* 2.9 26.7 + - - +
213A VAL* 3.5 8.2 - - - +
217A ASN* 4.3 5.8 - - - +
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Residues in contact with MET 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A THR* 1.3 74.7 - - - +
155A GLU* 1.3 71.1 + - - +
157A LEU* 3.2 26.6 + - - +
158A VAL* 3.0 31.4 + - + +
210A LYS* 4.3 13.2 - - + +
213A VAL* 3.3 33.5 - - + +
214A THR* 3.6 25.1 - - - +
217A ASN* 5.1 0.8 - - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A THR* 3.5 15.2 + - - +
154A MET* 1.3 84.0 + - - +
156A ASP* 1.3 65.5 + - - +
158A VAL* 3.3 9.9 + - - +
159A THR* 3.3 23.2 + - - -
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL 4.8 7.4 - - - +
151A VAL* 3.9 18.6 - - + +
152A GLU 4.9 0.5 + - - -
153A THR* 3.0 30.9 + - - +
155A GLU* 1.3 76.5 - - - +
157A LEU* 1.3 60.0 + - - +
159A THR* 3.2 10.6 + - - -
160A TYR* 2.8 30.3 + - - +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.5 9.1 - - + +
153A THR 2.9 13.8 + - - +
154A MET* 3.2 24.0 + - - +
156A ASP* 1.3 77.2 - - - +
158A VAL* 1.3 63.1 + - + +
160A TYR* 3.2 4.3 + - + -
161A THR* 2.9 24.4 + - + +
206A ILE* 4.4 22.2 - - + +
209A MET* 3.9 40.2 - - + +
210A LYS* 3.6 40.8 - - + +
213A VAL* 4.6 2.0 - - + -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 3.0 23.1 + - + +
155A GLU* 3.6 9.6 - - - +
156A ASP 3.3 0.2 - - - -
157A LEU* 1.3 76.9 - - + +
159A THR* 1.3 64.0 + - - +
161A THR* 3.2 9.2 - - + +
162A LYS* 3.0 58.7 + - + +
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 5.2 2.7 - - - +
155A GLU 3.3 10.9 + - - -
156A ASP* 3.2 14.3 + - - -
158A VAL* 1.3 79.2 - - - +
160A TYR* 1.3 64.4 + - - +
162A LYS* 3.3 7.0 + - - +
163A ASN* 2.8 40.5 + - - +
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Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 2.8 62.4 + + - -
145A LEU* 3.5 14.2 - - - +
147A VAL* 4.0 7.2 - - + -
148A ALA* 3.6 22.7 - - + +
151A VAL* 3.8 22.7 - - + -
156A ASP 2.8 17.9 + - - +
157A LEU* 3.2 7.4 + - + +
159A THR* 1.3 76.9 - - - +
161A THR* 1.3 60.1 + - - +
163A ASN* 3.0 2.6 + - - +
164A LEU* 2.8 55.1 + - + +
205A LEU* 4.6 0.7 - - + -
206A ILE* 4.4 7.6 - - + -
209A MET* 3.6 28.5 - - + -
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 2.9 20.2 + - + +
158A VAL* 3.2 17.3 - - + +
160A TYR* 1.3 74.7 - - - +
162A LYS* 1.3 67.8 - - + +
164A LEU* 4.6 2.0 - - - +
165A GLY* 3.0 29.5 + - - -
166A PRO* 4.0 0.3 - - - +
206A ILE* 3.8 41.0 - - + +
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Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 3.0 41.3 + - + +
159A THR* 3.7 6.7 - - - +
160A TYR 3.2 0.4 - - - -
161A THR* 1.3 82.4 - - + +
163A ASN* 1.3 61.3 + - - +
166A PRO* 3.2 24.5 - - - +
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Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 3.5 29.6 + - + +
159A THR* 2.8 32.5 + - - +
160A TYR 3.0 1.6 + - - +
162A LYS* 1.3 83.0 - - - +
164A LEU* 1.3 65.5 + - - +
165A GLY 3.2 1.3 - - - -
166A PRO* 3.7 3.9 - - - +
167A GLY* 3.3 18.0 + - - -
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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
----------------------------------------------------------
141A ILE* 4.2 22.9 - - + -
144A TYR* 3.8 24.4 - - + -
145A LEU* 4.0 17.9 - - + -
160A TYR* 2.8 47.9 + - + +
161A THR* 4.5 2.9 - - - +
163A ASN* 1.3 72.0 - - - +
165A GLY* 1.3 60.0 + - - +
167A GLY* 3.3 1.2 + - - -
168A MET* 2.9 43.7 + - + +
202A LEU* 3.6 29.6 - - + -
205A LEU* 4.0 5.4 - - + -
206A ILE* 4.8 1.6 - - + -
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 3.0 16.0 + - - -
164A LEU* 1.3 78.3 - - - +
166A PRO* 1.3 69.5 - - - +
168A MET* 3.3 3.5 + - - +
169A THR* 3.1 24.8 + - - -
202A LEU* 4.4 17.2 - - - +
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Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR 4.0 1.3 - - - +
162A LYS* 3.2 29.4 - - - +
163A ASN 3.7 3.8 - - - +
165A GLY* 1.3 89.0 - - - +
167A GLY* 1.3 65.3 + - - +
169A THR* 3.2 8.3 + - - +
170A LYS* 3.0 23.6 + - - +
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 5.0 1.6 - - - +
141A ILE* 3.6 21.2 - - - +
163A ASN 3.3 12.5 + - - -
164A LEU* 3.7 3.6 - - - -
165A GLY 3.2 0.8 - - - -
166A PRO* 1.3 79.7 - - - +
168A MET* 1.3 55.9 + - - +
170A LYS* 3.3 8.0 + - - +
171A MET* 3.0 27.2 + - - +
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Residues in contact with MET 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 4.0 14.4 - - + +
164A LEU* 2.9 35.5 + - + +
165A GLY 3.3 4.2 + - - +
167A GLY* 1.3 72.2 - - - +
169A THR* 1.3 61.0 + - - +
171A MET* 3.4 19.1 + - - +
172A ALA* 2.8 32.5 + - + +
195A MET* 4.3 9.4 - - + -
198A VAL* 3.5 23.8 - - + -
199A LYS* 5.1 7.6 - - + -
202A LEU* 4.1 24.9 - - + -
237A MET* 3.8 29.2 - - + -
241A ILE* 5.4 0.2 - - + -
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Residues in contact with THR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY 3.1 14.9 + - - -
166A PRO* 3.2 12.9 + - - +
168A MET* 1.3 78.6 - - - +
170A LYS* 1.3 57.3 + - - +
172A ALA* 3.7 6.3 - - - +
173A LYS* 3.0 30.1 + - + +
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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
----------------------------------------------------------
137A VAL* 4.6 17.5 - - + -
166A PRO 3.0 12.9 + - - +
167A GLY* 3.6 10.1 - - - +
169A THR* 1.3 75.6 - - - +
171A MET* 1.3 66.0 + - - +
173A LYS* 3.2 23.3 + - + +
174A MET* 3.0 52.3 + - + +
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Residues in contact with MET 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE* 6.1 0.2 - - + -
137A VAL* 4.0 18.1 - - + +
138A CYS* 4.1 33.7 - - - -
141A ILE* 4.0 21.1 - - + -
167A GLY 3.0 13.6 + - - +
168A MET* 3.6 23.3 - - - +
170A LYS* 1.3 77.3 - - - +
172A ALA* 1.3 62.5 + - - +
174A MET* 3.2 6.7 + - + +
175A ILE* 3.0 32.4 + - + +
195A MET* 3.1 37.0 - - + -
198A VAL* 4.0 7.9 - - + -
241A ILE* 4.3 14.8 - - + -
244A ILE* 4.6 4.9 - - + -
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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 MET* 2.8 21.9 + - + +
169A THR* 3.7 7.0 - - - +
171A MET* 1.3 71.6 - - - +
173A LYS* 1.3 58.1 + - - +
175A ILE* 3.3 2.1 + - - +
176A ASP* 2.8 30.8 + - - +
195A MET* 3.8 32.2 - - + +
199A LYS* 6.3 2.0 - - + -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A THR* 3.0 19.4 + - + +
170A LYS* 3.6 23.2 - - + +
172A ALA* 1.3 77.4 - - - +
174A MET* 1.3 62.4 + - + +
176A ASP* 3.3 5.8 + - - +
177A GLU* 2.9 52.0 + - + +
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 4.0 15.9 - - + +
134A ILE* 4.0 44.9 - - + +
137A VAL* 3.6 37.7 - - + -
170A LYS* 3.0 39.6 + - - +
171A MET* 3.2 7.4 + - - +
173A LYS* 1.3 77.4 - - + +
175A ILE* 1.3 59.1 + - - +
177A GLU* 3.9 11.0 - - - +
178A ARG* 3.0 28.6 + - - +
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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
----------------------------------------------------------
134A ILE* 3.6 27.4 - - + -
138A CYS* 4.5 2.9 - - - -
171A MET* 3.0 20.0 + - + +
172A ALA 3.7 3.6 - - - +
174A MET* 1.3 74.4 - - - +
176A ASP* 1.3 60.5 + - - +
178A ARG* 3.2 2.7 + - - +
179A GLN* 2.9 30.8 + - + +
191A LEU* 4.1 37.6 - - + +
192A VAL* 5.6 1.1 - - - -
195A MET* 4.1 25.1 - - + -
244A ILE* 3.7 26.7 - - + -
248A LEU* 4.0 10.3 - - + -
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA 2.8 16.9 + - - +
173A LYS* 3.7 7.0 - - - +
175A ILE* 1.3 76.0 - - - +
177A GLU* 1.3 64.5 + - + +
179A GLN* 3.0 28.9 + - - +
180A GLN* 3.2 39.8 + - - +
192A VAL* 5.7 0.7 - - - +
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LYS* 2.9 54.9 + - + +
174A MET* 3.9 9.8 - - - +
176A ASP* 1.3 77.8 - - + +
178A ARG* 1.3 63.3 + - - +
180A GLN* 3.4 18.7 + - - +
181A GLU* 3.5 15.1 + - - +
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Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS* 3.5 20.8 + - - -
6A THR* 3.9 7.8 - - - +
127A ASP* 2.9 43.8 + - - -
130A GLU* 5.4 4.6 - - - +
131A VAL* 3.3 23.3 - - - +
134A ILE* 3.9 19.3 - - + +
174A MET 3.0 19.6 + - - +
175A ILE* 3.2 6.5 + - - +
177A GLU* 1.3 74.5 - - - +
179A GLN* 1.3 68.0 + - - +
181A GLU* 2.9 21.6 + - - +
182A LEU* 3.3 32.2 + - + +
191A LEU* 4.8 1.1 - - + -
248A LEU* 3.8 28.3 + - + +
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ILE* 2.9 20.8 + - + +
176A ASP* 3.0 33.0 + - - +
178A ARG* 1.3 73.3 - - - +
180A GLN* 1.3 76.2 + - - +
181A GLU 3.2 1.0 + - - -
182A LEU* 3.2 19.0 + - - -
188A ARG* 2.9 68.3 + - - +
191A LEU* 4.2 20.2 - - + +
192A VAL* 3.8 24.4 - - + +
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 4.2 10.9 + - - +
176A ASP* 3.2 39.8 + - - +
177A GLU* 3.6 14.0 - - - +
178A ARG 3.1 0.8 - - - -
179A GLN* 1.3 88.4 - - - +
181A GLU* 1.3 61.5 + - + +
182A LEU 4.4 2.6 - - - +
188A ARG* 4.0 16.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 3.2 17.8 - - + -
7A ARG* 2.8 44.9 + - - +
8A THR* 2.9 43.2 + - - -
177A GLU 3.5 10.0 + - - +
178A ARG* 2.9 18.8 + - - +
180A GLN* 1.3 80.1 - - - +
182A LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS* 3.9 24.5 - - + +
6A THR* 4.5 1.3 - - + -
7A ARG* 4.4 6.9 + - - -
178A ARG* 3.5 46.0 - - + +
179A GLN* 3.2 10.8 + - - +
180A GLN 4.4 2.8 - - - +
181A GLU* 1.3 80.6 - - - +
183A THR* 1.3 61.6 + - - +
184A HIS* 4.3 5.4 - - + +
187A HIS* 4.3 19.3 - - + +
188A ARG* 3.6 29.2 + - + -
191A LEU* 3.7 30.3 - - + -
247A VAL 5.9 2.2 - - - +
248A LEU* 6.1 1.3 - - + -
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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