Contacts of the helix formed by residues 169 - 195 (chain A) in PDB entry 1KYZ
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 ASP 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 3.7 7.1 - - - +
165A TYR* 2.6 46.5 + - + +
166A HIS* 3.5 4.9 + - - +
167A GLY 3.5 0.4 - - - -
168A THR* 1.3 83.7 + - - +
170A PRO* 1.3 60.2 - - - +
171A ARG* 3.3 15.8 + - - +
172A PHE* 3.0 27.1 + - + +
173A ASN* 2.8 28.6 + - - +
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Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A HIS 5.2 0.4 - - - +
167A GLY 5.5 1.8 - - - +
168A THR 3.9 5.6 - - - +
169A ASP* 1.3 86.6 - - - +
171A ARG* 1.3 60.7 + - + +
173A ASN* 3.6 8.2 - - + +
174A LYS* 2.9 36.3 + - + +
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Residues in contact with ARG 171 (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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133A ASP* 2.7 44.0 + - - -
134A LYS* 3.9 26.6 - - - +
135A VAL* 3.6 18.4 - - - +
169A ASP* 3.3 11.1 + - - +
170A PRO* 1.3 83.5 - - + +
172A PHE* 1.3 70.7 - - - +
174A LYS* 3.3 5.7 + - - +
175A VAL* 3.2 36.2 + - + +
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Residues in contact with PHE 172 (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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130A MET* 4.9 1.6 - - + -
133A ASP* 3.6 27.1 - - + -
135A VAL* 3.8 20.4 - - + -
136A LEU* 3.6 44.6 - - + -
154A PHE* 5.3 1.8 - + - -
165A TYR* 4.0 14.6 - + - -
166A HIS* 3.7 33.2 - + - -
169A ASP* 3.0 25.2 + - + +
171A ARG* 1.3 87.4 - - - +
173A ASN* 1.3 58.7 + - - +
175A VAL* 3.0 7.2 + - + -
176A PHE* 2.7 51.7 + + + +
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Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A HIS* 3.7 37.5 - - - +
169A ASP 2.8 18.8 + - - +
170A PRO* 3.6 9.1 + - + +
172A PHE* 1.3 78.2 - - - +
174A LYS* 1.3 68.2 + - - +
176A PHE* 3.6 5.3 - - - +
177A ASN* 3.0 55.6 + - - +
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 2.9 25.3 + - + +
171A ARG* 3.7 6.7 - - - +
172A PHE 3.2 0.6 - - - -
173A ASN* 1.3 83.9 - - - +
175A VAL* 1.3 68.3 + - + +
177A ASN* 3.4 7.5 + - - +
178A LYS* 3.0 32.5 + - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 4.8 1.3 - - - +
129A LEU* 3.7 18.4 - - + +
130A MET* 3.7 30.6 - - + +
133A ASP* 4.2 10.3 - - + +
171A ARG* 3.2 31.2 + - + +
172A PHE* 3.0 11.8 + - + +
174A LYS* 1.3 77.4 - - + +
176A PHE* 1.3 63.8 + - - +
178A LYS* 3.4 5.1 + - - +
179A GLY* 3.0 19.4 + - - -
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A MET* 2.6 42.8 - - + +
163A PHE* 4.6 11.4 - + - -
166A HIS* 3.1 35.7 - + + +
172A PHE* 2.7 36.1 + + + +
173A ASN 3.6 3.6 - - - +
175A VAL* 1.3 74.2 - - - +
177A ASN* 1.3 72.4 + - - +
180A MET* 3.0 31.9 + - + +
366A FER 3.6 57.9 - + - -
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Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A HIS* 5.6 0.2 - - - -
173A ASN* 3.0 48.7 + - - +
174A LYS* 3.8 10.6 - - - +
176A PHE* 1.3 86.6 - - - +
178A LYS* 1.3 53.9 + - - +
180A MET* 3.7 4.0 - - - +
181A SER* 2.7 39.2 + - - -
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 6.2 1.6 - - - +
121A GLY 5.9 2.5 - - - +
126A ALA* 4.0 12.3 - - + -
129A LEU* 6.4 2.7 - - + -
174A LYS* 3.0 23.3 + - - +
175A VAL* 3.8 5.4 - - - +
177A ASN* 1.3 76.8 - - - +
179A GLY* 1.3 58.6 + - - +
181A SER* 4.1 5.2 - - - -
182A ASP* 2.9 47.1 + - - +
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA* 3.7 25.9 - - - +
127A LEU* 3.3 10.0 - - - +
130A MET* 3.1 18.2 - - - -
175A VAL 3.0 11.7 + - - -
178A LYS* 1.3 76.4 - - - +
180A MET* 1.3 56.0 + - - +
182A ASP* 4.1 0.7 - - - +
183A HIS* 3.1 29.8 + - - +
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Residues in contact with MET 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 5.1 4.5 - - - -
130A MET* 3.6 17.7 - - + +
176A PHE* 3.0 42.4 + - + +
177A ASN* 3.9 4.0 - - - +
179A GLY* 1.3 74.3 - - - +
181A SER* 1.3 60.4 + - - +
183A HIS* 3.8 6.9 - - - +
184A SER* 2.9 31.0 + - - -
266A TRP* 4.7 20.8 - - + -
269A HIS* 6.3 2.2 - - + +
366A FER 4.3 35.2 - - + +
1698A SAH 5.6 10.5 - - + -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASN 2.7 24.1 + - - -
178A LYS* 3.7 6.7 - - - -
180A MET* 1.3 72.6 - - - +
182A ASP* 1.3 66.0 + - - +
184A SER* 3.3 5.6 + - - -
185A THR* 2.9 36.6 + - - -
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLY 3.7 5.8 - - - +
122A VAL* 3.2 30.1 - - + +
123A SER 2.8 40.3 + - - +
124A ILE* 5.9 0.4 - - - -
126A ALA* 3.8 12.0 - - + +
127A LEU* 6.1 0.4 - - + -
178A LYS* 2.9 31.2 + - - +
179A GLY 4.1 0.7 - - - +
181A SER* 1.3 80.8 + - - +
183A HIS* 1.3 57.3 + - - +
185A THR* 3.3 2.3 + - - -
186A ILE* 2.9 37.1 + - - +
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Residues in contact with HIS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 5.0 6.7 - - + +
127A LEU* 3.8 31.5 - - + +
179A GLY 3.1 19.5 + - - +
180A MET* 3.8 10.1 - - - +
182A ASP* 1.3 77.8 - - - +
184A SER* 1.3 61.8 + - - +
186A ILE* 3.5 4.9 + - + +
187A THR* 3.0 39.0 + - - -
266A TRP* 3.3 33.9 - + + -
316A ILE* 5.3 9.9 - - + -
354A PHE 5.9 1.4 + - - -
356A THR* 5.5 1.0 + - - -
366A FER 4.9 12.4 + - - -
24E MET* 3.7 26.0 - - + +
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET 2.9 18.8 + - - -
181A SER* 3.5 6.1 - - - -
183A HIS* 1.3 76.5 - - - +
185A THR* 1.3 54.8 + - - +
187A THR* 3.2 1.9 + - - -
188A MET* 2.8 39.0 + - - +
214A VAL* 3.6 14.0 - - - +
265A LYS* 2.7 25.4 + - - +
266A TRP* 3.8 12.7 - - - -
1698A SAH 3.4 11.3 + - - -
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Residues in contact with THR 185 (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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118A ASN* 5.7 1.8 - - - +
122A VAL* 4.3 23.9 - - + +
181A SER* 2.9 24.2 + - - -
182A ASP* 3.6 8.2 - - - -
184A SER* 1.3 77.1 - - - +
186A ILE* 1.3 65.1 + - + +
188A MET* 3.9 4.4 - - - +
189A LYS* 3.1 27.4 + - + +
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Residues in contact with ILE 186 (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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114A TYR* 4.2 10.1 - - + +
118A ASN* 4.6 9.0 - - - +
122A VAL* 3.4 27.4 - - + +
123A SER* 4.8 8.3 - - - +
124A ILE* 4.1 25.6 - - + +
182A ASP 2.9 22.8 + - - +
183A HIS* 3.9 4.0 - - + +
185A THR* 1.3 78.7 - - + +
187A THR* 1.3 62.6 + - - +
189A LYS* 3.8 5.0 + - - +
190A LYS* 3.4 19.4 + - - +
354A PHE* 3.9 27.4 - - + -
20E ASN* 4.7 0.4 - - - +
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A HIS* 3.0 34.2 + - - -
184A SER 3.7 2.0 - - - -
186A ILE* 1.3 76.3 - - - +
188A MET* 1.3 61.0 + - - +
190A LYS* 3.2 6.4 + - - +
191A ILE* 2.9 47.2 + - + +
265A LYS* 4.4 4.9 - - - -
266A TRP* 3.7 17.3 - - + -
353A ALA 4.5 5.2 - - - +
354A PHE* 5.1 9.7 + - - +
356A THR* 3.9 24.4 + - + +
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Residues in contact with MET 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A SER* 2.8 22.5 + - - +
185A THR* 3.9 4.7 - - - +
187A THR* 1.3 72.2 - - - +
189A LYS* 1.3 55.7 + - - +
191A ILE* 2.9 13.8 + - + +
192A LEU* 2.7 54.2 + - + +
198A PHE* 5.1 0.2 - - + -
214A VAL* 3.8 29.2 - - + +
217A THR* 4.8 13.9 - - + +
218A ILE* 4.0 29.6 - - + -
263A PHE* 4.0 12.3 - - + -
265A LYS* 3.6 31.9 - - - -
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A THR* 3.1 17.0 + - + +
186A ILE* 4.0 5.6 - - - +
188A MET* 1.3 78.7 - - - +
190A LYS* 1.3 63.9 + - - +
192A LEU* 3.6 9.3 + - - +
193A GLU* 3.3 41.2 + - + +
217A THR* 5.7 1.9 - - - +
221A LYS* 5.1 2.5 + - - +
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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
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186A ILE 3.4 11.2 + - - +
187A THR* 3.2 8.6 + - - +
188A MET 3.2 0.4 - - - -
189A LYS* 1.3 76.4 - - + +
191A ILE* 1.3 65.0 - - - +
193A GLU* 3.1 25.6 + - - +
194A THR* 3.1 45.0 + - - +
352A ASN 5.9 0.2 + - - -
353A ALA* 3.7 21.4 - - + +
354A PHE* 3.7 48.0 - - + +
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Residues in contact with ILE 191 (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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187A THR* 2.9 34.8 + - + +
188A MET* 2.9 28.9 + - + +
190A LYS* 1.3 72.6 - - - +
192A LEU* 1.3 55.7 + - - +
193A GLU 2.8 7.5 + - - -
194A THR* 2.9 6.8 + - - -
195A TYR* 2.8 42.1 + - + -
198A PHE* 4.3 17.0 - - + -
263A PHE* 4.8 1.8 - - + -
265A LYS* 4.6 1.1 - - + -
296A ALA* 4.2 13.2 - - + -
353A ALA* 3.7 15.5 - - + -
356A THR* 4.5 3.1 - - + -
358A ILE* 3.6 35.0 - - + -
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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
----------------------------------------------------------
188A MET* 2.7 35.6 + - + +
189A LYS* 4.0 6.5 - - - +
191A ILE* 1.3 72.4 - - - +
193A GLU* 1.3 58.1 + - - +
195A TYR 4.2 9.7 - - - +
196A THR* 5.7 2.4 - - - +
198A PHE* 3.8 30.3 - - + -
217A THR* 3.4 43.7 - - + +
218A ILE* 4.4 9.2 - - + -
221A LYS* 3.7 38.0 + - + +
222A TYR* 4.3 20.9 + - + -
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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
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189A LYS* 3.3 42.7 + - + +
190A LYS* 3.1 33.2 + - + +
191A ILE 2.9 0.6 - - - -
192A LEU* 1.3 82.8 - - - +
194A THR* 1.3 63.8 + - + +
195A TYR 5.4 0.4 - - - -
196A THR* 5.5 4.7 - - - +
221A LYS* 4.6 10.8 - - - +
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LYS* 3.1 35.7 + - - +
191A ILE* 2.9 7.0 + - - -
193A GLU* 1.3 82.3 - - + +
195A TYR* 1.3 63.3 + - - +
196A THR* 3.8 7.2 + - - +
351A CYS* 4.0 36.6 + - + +
352A ASN 5.0 4.9 - - - +
353A ALA* 4.0 13.3 + - + +
358A ILE* 5.5 1.4 - - - +
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Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 2.8 29.4 + - + +
192A LEU 4.2 6.5 - - - +
194A THR* 1.3 74.2 + - - +
196A THR* 1.3 61.9 + - - +
197A GLY* 3.3 35.1 - - - -
198A PHE* 3.4 36.3 - + - -
222A TYR* 4.2 4.3 + - - -
292A LYS* 4.0 3.6 + - - -
294A ILE* 3.7 38.4 - - + +
350A HIS* 3.6 39.0 - + + -
351A CYS* 5.8 2.5 - - + +
358A ILE* 3.7 28.9 - - + -
360A GLU* 3.3 17.1 + - + +
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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