Contacts of the helix formed by residues 171 - 203 (chain A) in PDB entry 2LCK
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 GLY 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 2.7 37.9 + - - +
168A ARG 5.0 1.1 - - - -
169A GLU 3.6 1.0 - - - -
170A GLU* 1.3 76.8 - - - +
172A ILE* 1.3 65.4 + - - +
173A ARG* 3.4 1.8 - - - -
174A GLY* 3.6 4.9 + - - -
175A LEU* 3.9 8.7 + - - +
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 5.9 3.1 - - - +
171A GLY* 1.3 69.8 - - - -
173A ARG* 1.3 76.7 + - + +
174A GLY 3.1 2.0 - - - -
175A LEU* 2.9 26.4 + - - +
176A TRP* 3.1 27.3 + - + +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU 5.1 3.6 - - - +
171A GLY 3.4 0.2 - - - -
172A ILE* 1.3 88.1 - - + +
174A GLY* 1.3 63.7 + - - +
175A LEU 3.2 0.3 + - - -
176A TRP* 3.3 24.5 + - - +
177A LYS* 3.4 12.7 + - - -
251A HIS* 5.0 15.6 + - - -
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Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 2.5 34.4 + - - -
170A GLU* 3.2 37.7 + - - +
171A GLY 3.6 6.7 + - - -
172A ILE 3.1 1.6 - - - -
173A ARG* 1.3 79.5 - - - +
175A LEU* 1.3 49.8 + - - +
177A LYS* 3.1 19.4 + - - +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.6 31.2 - - + +
140A VAL* 5.6 1.6 - - + -
143A ARG* 2.8 38.2 + - - +
163A TYR* 3.4 52.5 - - + +
166A ILE* 6.1 4.3 - - + -
167A ALA* 6.1 2.7 - - + -
171A GLY 3.9 6.9 + - - +
172A ILE* 2.9 16.7 + - - +
174A GLY* 1.3 74.3 - - - +
176A TRP* 1.3 68.8 + - + +
178A GLY 4.2 0.7 + - - -
179A THR* 4.2 4.0 + - - -
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Residues in contact with TRP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 3.1 29.1 + - + +
173A ARG* 3.3 21.3 + - - +
175A LEU* 1.3 90.6 - - + +
177A LYS* 1.3 66.2 + - - +
178A GLY 3.0 3.5 + - - -
179A THR* 3.2 30.5 + - + +
180A SER* 2.9 29.3 + - - +
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 3.3 6.7 - - - +
170A GLU* 3.8 14.0 + - - +
173A ARG 3.4 7.6 + - - -
174A GLY* 3.1 32.6 + - - +
175A LEU 3.0 1.0 - - - -
176A TRP* 1.3 79.5 - - - +
178A GLY* 1.3 56.6 + - - +
180A SER* 3.9 1.2 + - - -
181A PRO* 3.3 17.0 - - - +
247A LEU* 3.6 36.3 - - + -
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 5.2 4.9 - - - -
143A ARG* 3.9 6.8 - - - +
177A LYS* 1.3 76.2 - - - +
179A THR* 1.3 67.4 + - - +
180A SER 3.3 2.5 - - - -
181A PRO* 3.0 9.5 - - - +
182A ASN* 2.8 37.5 + - - -
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN* 2.8 37.1 + - - +
139A VAL* 4.8 8.3 - - - +
175A LEU 4.2 6.4 + - - -
176A TRP* 3.2 51.2 + - + +
178A GLY* 1.3 76.9 - - - +
180A SER* 1.3 77.7 + - - +
182A ASN* 3.3 10.5 + - - +
183A VAL* 3.3 25.9 + - - +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TRP* 2.9 20.6 + - - +
177A LYS* 3.9 1.2 + - - -
179A THR* 1.3 83.4 - - - +
181A PRO* 1.3 73.1 - - - +
183A VAL* 3.2 17.1 + - - +
184A ALA* 3.4 9.9 + - - +
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Residues in contact with PRO 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS 3.3 17.7 - - - +
178A GLY* 3.0 25.4 - - - +
180A SER* 1.3 92.1 - - - +
182A ASN* 1.3 60.3 + - - +
184A ALA* 3.1 10.8 + - + +
185A ARG* 2.8 29.3 + - - +
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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
----------------------------------------------------------
135A GLN* 5.2 8.4 + - + +
138A ASP* 5.9 4.6 - - - +
139A VAL* 5.5 9.7 - - - +
178A GLY* 2.8 36.7 + - - +
179A THR* 3.4 10.4 - - - +
181A PRO* 1.3 78.1 - - - +
183A VAL* 1.3 63.1 + - - +
185A ARG* 3.2 9.5 + - - +
186A ASN* 3.2 28.4 + - - +
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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
----------------------------------------------------------
128A ALA* 5.6 9.9 - - + -
131A VAL* 4.6 18.8 - - + -
135A GLN* 4.1 15.7 - - - +
179A THR* 3.3 14.8 + - + +
180A SER* 3.2 9.5 + - - +
181A PRO 3.2 0.2 - - - -
182A ASN* 1.3 76.0 - - - +
184A ALA* 1.3 64.0 + - - +
186A ASN* 3.2 20.5 + - + +
187A ALA* 3.2 13.4 + - + +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER 3.4 6.3 + - - +
181A PRO* 3.1 16.1 + - + +
183A VAL* 1.3 82.3 - - - +
185A ARG* 1.3 61.8 + - - +
187A ALA* 3.2 8.9 + - - +
188A ILE* 3.2 23.5 + - - +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO 2.8 13.4 + - - +
182A ASN* 3.2 15.0 + - - +
184A ALA* 1.3 77.6 - - - +
186A ASN* 1.3 68.6 + - - +
188A ILE* 2.8 28.8 - - + +
189A VAL* 3.2 28.9 - - - +
235A VAL* 5.7 4.6 - - - +
236A ASP* 5.9 1.0 + - - -
239A LYS* 3.7 33.7 - - - +
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Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY 6.3 2.2 - - - -
131A VAL* 3.7 25.9 - - + +
182A ASN* 3.2 15.6 + - - +
183A VAL* 3.2 12.6 + - + +
185A ARG* 1.3 88.7 - - - +
187A ALA* 1.3 58.5 + - - +
189A VAL* 2.8 26.0 - - - +
190A ASN* 3.3 11.1 + - - +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 3.2 8.1 + - + +
184A ALA* 3.2 12.4 + - - +
186A ASN* 1.3 80.4 - - - +
188A ILE* 1.3 58.7 + - - +
190A ASN* 3.4 5.7 + - - +
191A CYS* 2.8 31.0 + - - +
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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 ALA 3.2 11.5 + - - +
185A ARG* 2.8 38.8 - - + +
187A ALA* 1.3 72.5 - - - +
189A VAL* 1.3 57.0 + - + +
191A CYS* 3.1 12.5 + - + +
192A ALA* 2.6 45.3 + - + +
235A VAL* 4.6 20.2 - - + -
239A LYS* 6.2 1.1 - - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 3.2 39.9 - - - +
186A ASN* 2.8 34.1 - - - +
188A ILE* 1.3 76.2 - - + +
190A ASN* 1.3 56.2 + - + +
192A ALA* 3.2 7.9 + - - +
193A GLU* 2.4 41.1 + - - +
235A VAL* 5.1 12.3 - - + -
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Residues in contact with ASN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 5.1 12.4 - - - -
120A LEU* 3.8 25.9 + - - +
123A GLY* 4.7 15.9 - - - +
124A SER* 4.6 11.9 + - - -
186A ASN 3.3 13.6 + - - +
187A ALA* 3.7 5.3 + - - +
188A ILE 3.3 0.4 - - - -
189A VAL* 1.3 81.8 - - + +
191A CYS* 1.3 61.2 + - - +
193A GLU* 3.0 10.9 + - - +
194A LEU* 2.9 27.9 + - - +
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Residues in contact with CYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 5.4 3.8 - - - -
187A ALA 2.8 19.3 + - - +
188A ILE* 3.4 15.5 - - + +
190A ASN* 1.3 82.4 - - - +
192A ALA* 1.3 62.5 + - - +
194A LEU* 3.5 12.0 + - - +
195A VAL* 3.6 12.7 + - - +
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 2.6 30.5 + - + +
189A VAL* 3.3 9.6 - - - +
191A CYS* 1.3 72.9 - - - +
193A GLU* 1.3 54.8 + - - +
195A VAL* 2.7 28.7 - - - +
196A THR* 2.8 19.7 + - - +
235A VAL* 5.4 8.1 - - + -
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Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 5.9 3.1 - - + +
189A VAL* 2.4 27.1 + - - +
190A ASN* 3.0 15.7 + - - +
192A ALA* 1.3 73.2 - - - +
194A LEU* 1.3 55.8 + - - +
196A THR* 4.3 10.9 - - - +
197A TYR* 2.6 54.9 + - + +
200A ILE* 5.7 2.9 - - - +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.3 32.1 - - + +
116A ILE* 3.5 41.0 - - + +
120A LEU* 3.5 45.3 - - + -
190A ASN* 2.9 17.2 + - - +
191A CYS 4.0 4.7 - - - +
192A ALA 3.4 0.4 - - - -
193A GLU* 1.3 71.7 - - - +
195A VAL* 1.3 72.2 - - + +
197A TYR* 3.9 2.5 - - + +
198A ASP* 3.4 18.2 + - - +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A CYS 3.6 7.9 + - - +
192A ALA* 2.7 34.8 - - - +
194A LEU* 1.3 85.6 - - + +
196A THR* 1.3 67.1 + - - +
198A ASP* 3.7 13.3 + - - +
199A LEU* 3.8 13.1 - - + +
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA* 2.8 24.1 + - - +
193A GLU* 3.6 13.9 - - - +
195A VAL* 1.3 79.8 - - - +
197A TYR* 1.3 65.4 + - - +
199A LEU* 3.1 31.5 + - + +
200A ILE* 3.7 10.9 + - + +
228A THR* 5.4 7.9 - - - +
231A ILE* 4.5 20.4 - - + +
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.9 37.7 - + - +
108A THR* 4.9 15.6 + - - +
119A ARG* 4.8 10.9 + - - -
193A GLU* 2.6 36.5 + - + +
194A LEU* 3.9 6.5 - - - +
196A THR* 1.3 70.0 - - - +
198A ASP* 1.3 69.3 + - - +
200A ILE* 2.7 51.1 + - + +
201A LYS* 3.4 43.4 + - + +
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 5.3 11.2 - - + +
194A LEU 3.4 9.8 + - - +
195A VAL* 3.8 11.9 - - - +
196A THR 3.2 0.4 - - - -
197A TYR* 1.3 88.1 - - + +
199A LEU* 1.3 70.5 + - + +
201A LYS* 3.4 21.0 + - - +
202A ASP* 3.6 21.6 + - - +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.8 17.3 - - + +
196A THR* 3.1 21.3 + - + +
198A ASP* 1.3 86.7 - - + +
200A ILE* 1.3 63.9 + - + +
202A ASP* 3.5 21.3 + - - +
203A THR* 3.5 11.3 + - - -
231A ILE* 6.5 0.9 - - + -
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 5.7 3.1 - - - +
196A THR* 3.7 10.1 + - + +
197A TYR* 2.7 57.4 - - + +
199A LEU* 1.3 75.1 - - + +
201A LYS* 1.3 55.2 + - + +
203A THR* 2.8 33.8 + - - +
205A LEU* 4.1 3.7 - - - +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 5.7 4.3 - - - +
197A TYR* 3.4 44.2 + - + +
198A ASP* 3.4 15.0 + - - +
199A LEU 3.3 0.4 - - - -
200A ILE* 1.3 79.1 - - + +
202A ASP* 1.3 67.6 + - - +
205A LEU* 2.8 57.0 + - + +
206A LYS* 4.6 0.5 - - - -
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 3.6 24.1 + - - +
199A LEU* 3.5 15.3 + - - +
200A ILE 3.3 0.8 - - - -
201A LYS* 1.3 82.4 - - - +
203A THR* 1.3 63.8 + - + +
204A LEU 3.9 1.2 + - - -
205A LEU 4.4 1.2 + - - -
206A LYS* 4.5 13.2 + - - +
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU 3.5 13.7 + - - -
200A ILE* 2.8 23.2 + - - +
201A LYS 3.2 0.4 - - - -
202A ASP* 1.3 78.5 - - + +
204A LEU* 1.3 67.8 + - - +
205A LEU* 3.0 10.3 + - - +
----------------------------------------------------------
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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