Contacts of the helix formed by residues 164 - 191 (chain L) in PDB entry 5MQF
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 164 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466 G 5.2 1.1 - - - -
476 A 4.5 13.7 - - - -
486 A 6.2 0.7 - - - -
161L ASN 3.2 9.7 + - - -
162L THR* 3.1 6.9 - - - -
163L GLN* 1.3 79.1 - - - +
165L LYS* 1.3 61.8 + - - -
166L LYS* 3.2 3.6 - - - -
167L ALA* 3.4 1.0 + - - +
168L LYS* 2.9 28.0 + - - +
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Residues in contact with LYS 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466 G 3.7 30.8 + - - +
476 A 4.5 6.3 + - - +
164L GLY* 1.3 71.1 - - - -
166L LYS* 1.3 59.9 + - - +
168L LYS* 3.7 9.0 - - - +
169L ARG* 2.9 30.0 + - - +
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Residues in contact with LYS 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466 G 3.9 38.0 + - - +
163L GLN 5.4 2.5 - - - +
164L GLY* 3.2 1.7 - - - -
165L LYS* 1.3 78.0 - - - +
167L ALA* 1.3 57.3 + - - +
169L ARG* 3.4 4.6 + - - +
170L LYS* 2.9 27.6 + - - +
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Residues in contact with ALA 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L GLN* 3.7 37.4 + - + +
164L GLY 3.4 2.2 + - - -
166L LYS* 1.3 76.3 - - - +
168L LYS* 1.3 60.4 + - - +
170L LYS* 3.7 9.2 - - - +
171L ALA* 2.9 27.7 + - - +
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Residues in contact with LYS 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L GLY 2.9 18.7 + - - +
165L LYS* 3.7 10.3 - - + +
167L ALA* 1.3 77.3 - - - +
169L ARG* 1.3 58.4 + - - +
171L ALA* 3.2 5.8 + - - +
172L ARG* 2.9 29.5 + - - +
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Residues in contact with ARG 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466 G 4.9 5.8 - - - +
165L LYS 2.9 18.3 + - - +
166L LYS* 3.9 4.5 - - - +
168L LYS* 1.3 77.2 - - - +
170L LYS* 1.3 57.5 + - - +
172L ARG* 4.1 6.8 - - - +
173L GLU* 2.9 30.3 + - - +
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Residues in contact with LYS 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L LYS 2.9 18.7 + - - +
167L ALA* 3.7 10.3 - - - +
168L LYS 3.2 0.2 - - - -
169L ARG* 1.3 77.3 - - - +
171L ALA* 1.3 57.8 + - - +
173L GLU* 3.5 5.5 + - - +
174L LYS* 2.9 29.3 + - - +
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Residues in contact with ALA 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167L ALA 2.9 17.4 + - - +
168L LYS* 3.7 6.5 - - - +
170L LYS* 1.3 75.5 - - - +
172L ARG* 1.3 59.8 + - - +
174L LYS* 3.7 5.5 - - - +
175L GLN* 2.9 31.4 + - - +
205O LEU* 5.3 13.5 - - + -
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Residues in contact with ARG 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1795A GLU* 6.3 3.6 - - + -
459E PRO* 5.8 6.3 - - + +
168L LYS 2.9 17.1 + - - +
169L ARG* 4.1 6.5 - - - +
171L ALA* 1.3 76.1 - - - +
173L GLU* 1.3 59.0 + - - +
175L GLN* 4.3 3.8 - - - +
176L LEU* 2.9 33.3 + - - +
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Residues in contact with GLU 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L ARG 2.9 21.0 + - - +
170L LYS* 3.9 6.3 - - - +
171L ALA 3.2 0.2 - - - -
172L ARG* 1.3 76.3 - - - +
174L LYS* 1.3 59.3 + - - +
176L LEU* 4.5 3.4 - - - -
177L GLU* 2.8 32.1 + - - +
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Residues in contact with LYS 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L LYS 2.9 19.1 + - - +
171L ALA* 3.2 6.3 + - - +
173L GLU* 1.3 75.7 - - - +
175L GLN* 1.3 60.6 + - - +
177L GLU* 3.8 3.2 - - - +
178L GLU* 2.9 30.1 + - - +
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Residues in contact with GLN 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E PRO* 5.9 7.2 - - + +
171L ALA 2.9 17.2 + - - +
172L ARG* 4.3 3.6 - - - +
174L LYS* 1.3 72.8 - - - +
176L LEU* 1.3 61.6 + - - +
178L GLU* 3.4 5.0 + - - +
179L ALA* 2.9 30.5 + - - +
206O LEU* 5.6 9.4 - - + -
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Residues in contact with LEU 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E PRO* 5.2 19.0 - - + +
172L ARG 2.9 21.3 + - - +
173L GLU* 4.4 3.1 - - - +
175L GLN* 1.3 76.7 - - - +
177L GLU* 1.3 57.5 + - - +
179L ALA* 4.0 4.6 - - - +
180L ARG* 2.9 30.7 + - - +
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Residues in contact with GLU 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L GLU 2.8 23.1 + - - +
174L LYS* 4.0 4.5 - - - +
176L LEU* 1.3 75.2 - - - +
178L GLU* 1.3 60.9 + - - +
180L ARG* 3.8 4.5 - - - +
181L ARG* 2.9 30.1 + - - +
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Residues in contact with GLU 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L LYS 2.9 19.8 + - - +
175L GLN* 3.8 6.1 - - - +
177L GLU* 1.3 78.5 - - - +
179L ALA* 1.3 56.7 + - - +
181L ARG* 3.8 4.7 - - - +
182L LEU* 2.9 29.3 + - - +
209O PRO* 5.2 14.6 - - + -
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Residues in contact with ALA 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440E LYS* 5.3 10.7 - - + +
458E GLU 5.9 0.2 - - - +
459E PRO* 5.9 8.3 - - + -
460E SER* 5.9 1.6 - - - +
462E HIS* 4.8 20.4 - - + +
463E SER 5.4 0.2 + - - -
175L GLN 2.9 18.5 + - - +
176L LEU* 4.0 6.1 - - - +
178L GLU* 1.3 75.0 - - - +
180L ARG* 1.3 60.8 + - - +
182L LEU* 3.3 5.6 + - - +
183L ALA* 2.9 30.5 + - - +
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Residues in contact with ARG 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L LEU 2.9 20.2 + - - +
177L GLU* 4.0 4.5 - - - +
179L ALA* 1.3 76.4 - - - +
181L ARG* 1.3 58.5 + - - +
183L ALA* 4.1 5.0 - - - +
184L ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L GLU 2.9 19.5 + - - +
178L GLU* 3.9 5.8 - - - +
180L ARG* 1.3 74.2 - - - +
182L LEU* 1.3 61.1 + - - +
184L ALA* 4.6 3.1 - - - -
185L LEU* 2.9 34.4 + - + +
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Residues in contact with LEU 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E HIS* 5.4 4.5 - - + -
481E MET* 5.1 14.3 - - + +
178L GLU 2.9 19.0 + - - +
179L ALA* 3.3 6.9 + - - +
181L ARG* 1.3 77.4 - - - +
183L ALA* 1.3 50.0 + - - +
185L LEU* 4.8 1.3 - - - -
186L GLN* 2.5 37.0 + - - +
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Residues in contact with ALA 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438E ASP* 4.2 19.5 - - + +
440E LYS* 6.0 0.9 - - + -
462E HIS* 5.1 1.1 - - - +
463E SER* 3.7 35.8 - - - +
481E MET* 5.8 0.2 - - - -
179L ALA 2.9 16.8 + - - +
180L ARG* 4.1 4.3 - - - +
182L LEU* 1.3 76.1 - - - +
184L ALA* 1.3 60.2 + - - +
186L GLN* 3.3 5.6 - - - +
187L LYS* 2.9 31.9 + - - +
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Residues in contact with ALA 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L ARG 2.9 19.7 + - - +
181L ARG* 4.4 3.1 - - - +
183L ALA* 1.3 78.2 - - - +
185L LEU* 1.3 58.2 + - - +
187L LYS* 3.9 2.8 - - - +
188L ARG* 2.9 31.6 + - - +
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Residues in contact with LEU 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181L ARG* 2.9 22.0 + - + +
182L LEU* 4.7 1.8 - - - +
184L ALA* 1.3 74.2 - - - +
186L GLN* 1.3 59.0 + - - +
188L ARG* 3.9 7.0 - - - +
189L ARG* 2.9 30.8 + - - +
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Residues in contact with GLN 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463E SER* 5.4 3.6 - - - -
481E MET* 5.3 5.2 - - + -
508E ALA 5.4 0.7 - - - -
509E GLY* 3.2 41.2 - - - +
182L LEU 2.5 27.3 + - - +
183L ALA* 3.3 8.7 - - - +
184L ALA 3.2 0.2 - - - -
185L LEU* 1.3 76.0 - - - +
187L LYS* 1.3 59.1 + - - +
189L ARG* 3.0 7.6 + - - +
190L GLU* 2.9 25.5 + - - +
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Residues in contact with LYS 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E GLY 4.2 1.3 + - - -
183L ALA 2.9 18.8 + - - +
184L ALA* 4.4 2.5 - - - +
186L GLN* 1.3 74.9 - - - +
188L ARG* 1.3 57.5 + - - +
190L GLU* 3.3 8.9 + - - +
191L LEU* 2.9 29.3 + - - +
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Residues in contact with ARG 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L ALA 2.9 20.8 + - - +
185L LEU* 3.9 8.3 - - - +
187L LYS* 1.3 78.1 - - - +
189L ARG* 1.3 56.2 + - - +
191L LEU* 3.4 5.2 + - - +
192L ARG* 2.8 31.6 + - - +
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Residues in contact with ARG 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508E ALA 5.5 6.1 - - - +
509E GLY 6.2 0.4 - - - -
185L LEU 2.9 19.6 + - - +
186L GLN* 3.0 5.4 + - - +
188L ARG* 1.3 73.3 - - - +
190L GLU* 1.3 62.2 + - - +
192L ARG* 4.0 5.5 - - - +
193L ALA* 3.1 30.3 + - - +
216O ASP* 4.3 23.9 - - + +
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Residues in contact with GLU 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510E TYR* 4.2 28.6 - - + +
511E ALA 5.1 2.9 - - - +
186L GLN 2.9 12.3 + - - +
187L LYS* 3.3 12.8 + - - +
189L ARG* 1.3 80.3 - - - +
191L LEU* 1.3 59.2 + - - +
193L ALA* 3.8 4.5 + - - +
194L ALA* 3.7 18.4 + - - +
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Residues in contact with LEU 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L LYS 2.9 17.2 + - - +
188L ARG* 3.9 5.2 - - - +
190L GLU* 1.3 76.1 - - - +
192L ARG* 1.3 60.2 + - - +
194L ALA* 3.4 2.1 + - - -
195L GLY* 3.0 31.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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