Contacts of the helix formed by residues 179 - 205 (chain A) in PDB entry 1M5I
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 SER 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PRO* 5.4 2.5 - - - +
180A LEU* 1.3 61.8 + - - +
181A GLN* 3.8 6.6 + - - +
182A THR* 3.1 34.1 + - - -
183A ASP* 3.3 28.8 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A SER* 1.3 72.1 - - - +
181A GLN* 1.3 61.4 + - - +
183A ASP* 3.4 7.3 + - + +
184A MET* 2.8 63.3 + - + +
187A ARG* 5.3 1.1 - - - +
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 6.5 0.2 - - + -
173A PRO* 6.3 2.0 - - + -
179A SER* 4.2 6.1 - - - +
180A LEU* 1.3 77.2 - - - +
182A THR* 1.3 67.2 + - - +
184A MET* 3.0 11.6 + - - +
185A THR* 2.8 40.4 + - - -
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 3.7 23.1 - - + +
173A PRO* 3.5 34.4 - - - +
179A SER* 3.1 23.3 + - - +
181A GLN* 1.3 81.5 - - - +
183A ASP* 1.3 58.5 + - - +
185A THR* 3.8 4.8 - - - -
186A ARG* 2.8 58.3 + - - +
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A SER 3.3 19.5 + - - +
180A LEU* 3.6 7.9 - - + +
181A GLN 3.1 0.4 - - - -
182A THR* 1.3 76.0 - - - +
184A MET* 1.3 67.7 + - - +
186A ARG* 3.3 21.0 + - - +
187A ARG* 3.0 60.4 + - - +
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Residues in contact with MET 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 2.8 47.6 + - + +
181A GLN* 3.3 13.5 - - - +
183A ASP* 1.3 76.8 - - - +
185A THR* 1.3 63.6 - - - +
187A ARG* 3.2 37.6 + - - +
188A GLN* 3.2 20.5 + - - +
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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
----------------------------------------------------------
168A ARG* 6.0 2.2 - - - +
172A LEU* 3.6 27.4 - - + -
181A GLN* 2.8 35.4 + - - -
182A THR* 3.8 4.5 - - - -
184A MET* 1.3 75.5 - - - +
186A ARG* 1.3 64.2 + - - +
188A GLN* 3.2 8.0 + - + +
189A LEU* 3.0 40.1 + - + +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.9 33.7 + - + +
172A LEU* 3.9 20.9 + - + +
173A PRO 6.1 0.6 - - - -
182A THR* 2.8 44.1 + - - +
183A ASP* 3.3 21.6 + - - +
185A THR* 1.3 72.4 - - - +
187A ARG* 1.3 60.0 + - + +
189A LEU 3.6 0.2 + - - -
190A GLU* 2.8 56.8 + - + +
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Residues in contact with ARG 187 (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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180A LEU* 5.3 1.6 - - - +
183A ASP* 3.0 49.1 + - - +
184A MET* 3.2 36.2 - - - +
186A ARG* 1.3 76.1 - - + +
188A GLN* 1.3 61.1 + - - +
190A GLU* 3.9 14.7 - - - +
191A TYR* 3.0 29.6 + - - +
194A ARG* 5.4 1.2 + - - -
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Residues in contact with GLN 188 (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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184A MET 3.2 12.9 + - - +
185A THR* 3.2 13.2 + - + +
187A ARG* 1.3 79.5 - - - +
189A LEU* 1.3 58.8 + - + +
191A TYR* 3.3 22.9 + - - +
192A GLU* 2.9 63.9 + - - +
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Residues in contact with LEU 189 (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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165A LEU* 3.9 16.0 - - + +
168A ARG* 2.9 60.6 - - + +
169A ILE* 3.6 34.9 - - + +
172A LEU* 4.7 1.3 - - + -
185A THR* 3.0 33.0 + - + +
186A ARG 3.9 0.4 - - - +
188A GLN* 1.3 76.4 - - + +
190A GLU* 1.3 59.6 + - - +
192A GLU* 3.3 14.6 + - - +
193A ALA* 2.9 29.8 + - - +
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Residues in contact with GLU 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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169A ILE* 3.5 18.0 - - + +
186A ARG* 2.8 42.1 + - - +
187A ARG* 3.9 16.7 - - - +
189A LEU* 1.3 72.8 - - - +
191A TYR* 1.3 60.6 + - - +
193A ALA* 3.4 7.5 + - - +
194A ARG* 3.0 45.8 + - - +
197A ARG* 4.9 1.0 + - - -
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Residues in contact with TYR 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 ARG 3.0 18.9 + - - +
188A GLN* 3.3 28.3 - - - +
190A GLU* 1.3 77.8 - - - +
192A GLU* 1.3 62.8 + - + +
194A ARG* 2.9 45.2 + - - +
195A GLN* 3.0 49.3 + - + +
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Residues in contact with GLU 192 (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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165A LEU* 3.8 23.8 - - + +
168A ARG* 4.0 7.9 + - - -
188A GLN* 2.9 50.1 + - - +
189A LEU* 3.5 16.8 - - - +
191A TYR* 1.3 83.2 - - + +
193A ALA* 1.3 59.9 + - - +
195A GLN* 3.1 10.1 + - - +
196A ILE* 3.1 27.2 + - + +
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Residues in contact with ALA 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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162A LEU* 3.8 17.2 - - + +
165A LEU* 3.7 22.0 - - + +
169A ILE* 6.3 1.1 - - + -
189A LEU 2.9 17.7 + - - +
190A GLU* 3.7 8.1 - - - +
191A TYR 3.2 0.2 - - - -
192A GLU* 1.3 76.3 - - - +
194A ARG* 1.3 57.4 + - - +
196A ILE* 3.5 0.8 + - - -
197A ARG* 2.5 41.0 + - - +
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Residues in contact with ARG 194 (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 ARG 5.4 0.8 + - - -
190A GLU* 3.0 33.8 + - - +
191A TYR* 2.9 35.9 + - - +
193A ALA* 1.3 76.4 - - - +
195A GLN* 1.3 71.6 + - - +
197A ARG* 3.4 17.6 + - + +
198A VAL* 3.1 31.6 + - + +
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Residues in contact with GLN 195 (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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191A TYR* 3.0 64.7 + - + +
192A GLU* 3.1 8.7 + - - +
194A ARG* 1.3 90.1 - - - +
196A ILE* 1.3 58.8 + - + +
198A VAL* 3.1 14.0 + - - +
199A ALA* 3.0 30.0 + - - +
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Residues in contact with ILE 196 (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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158A TYR* 4.1 19.2 - - + +
161A GLN* 4.0 36.8 - - + +
162A LEU* 3.3 29.4 - - + -
165A LEU* 3.5 31.6 - - + -
192A GLU* 3.1 12.7 + - + +
193A ALA 3.8 0.7 - - - +
194A ARG 3.3 0.2 - - - -
195A GLN* 1.3 77.4 - - + +
197A ARG* 1.3 60.8 + - - +
199A ALA* 4.1 5.7 - - - +
200A MET* 3.4 21.8 + - - +
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Residues in contact with ARG 197 (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 LEU* 4.1 23.8 - - + -
190A GLU 4.9 1.0 + - - -
193A ALA* 2.5 53.1 + - - +
194A ARG* 3.4 17.9 - - + +
195A GLN 3.1 0.6 - - - -
196A ILE* 1.3 75.6 - - - +
198A VAL* 1.3 65.6 + - + +
200A MET* 3.5 8.6 + - + +
201A GLU* 3.2 24.4 + - - +
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Residues in contact with VAL 198 (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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194A ARG* 3.1 21.7 + - + +
195A GLN* 3.1 17.7 + - - +
197A ARG* 1.3 75.0 - - + +
199A ALA* 1.3 65.8 + - - +
201A GLU* 3.4 5.5 + - - +
202A GLU* 3.1 44.5 + - + +
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Residues in contact with ALA 199 (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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158A TYR* 4.3 12.8 - - + +
195A GLN 3.0 16.3 + - - +
196A ILE* 4.3 6.5 - - - +
198A VAL* 1.3 76.8 - - - +
200A MET* 1.3 57.9 + - - +
202A GLU* 3.5 13.2 + - - +
203A GLN* 3.1 34.6 + - + +
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Residues in contact with MET 200 (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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155A LYS* 3.8 13.0 - - + -
158A TYR* 3.6 43.7 - - + -
159A TYR* 3.5 40.8 - - + +
162A LEU* 4.9 4.9 - - - -
196A ILE 3.4 17.3 + - - +
197A ARG* 3.7 10.5 - - - +
198A VAL 3.2 0.4 - - - -
199A ALA* 1.3 78.2 - - - +
201A GLU* 1.3 55.7 + - - +
203A GLN* 3.0 1.0 + - - +
204A LEU* 2.5 60.7 + - + +
205A GLY 5.4 1.3 - - - +
210A MET* 4.3 6.7 - - + -
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Residues in contact with GLU 201 (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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197A ARG 3.2 14.9 + - - +
198A VAL* 3.4 4.5 + - - +
200A MET* 1.3 76.2 - - - +
202A GLU* 1.3 61.7 + - + +
205A GLY* 2.9 49.0 + - - +
206A THR* 3.4 33.1 - - + +
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Residues in contact with GLU 202 (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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198A VAL* 3.1 36.8 + - + +
199A ALA* 3.7 14.2 - - - +
201A GLU* 1.3 78.9 - - + +
203A GLN* 1.3 64.3 + - + +
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Residues in contact with GLN 203 (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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154A GLU* 3.8 18.2 + - - +
158A TYR* 3.2 28.1 + - + +
199A ALA* 3.1 22.6 + - + +
200A MET* 3.0 4.4 + - - +
202A GLU* 1.3 85.9 - - + +
204A LEU* 1.3 66.5 + - + +
205A GLY 3.6 0.4 - - - -
213A ARG* 5.6 0.2 + - - -
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Residues in contact with LEU 204 (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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151A GLU* 3.9 26.2 - - + +
154A GLU* 3.3 31.0 - - + +
155A LYS* 3.7 18.4 - - + +
158A TYR* 3.9 11.4 - - + -
200A MET* 2.5 52.0 + - + +
203A GLN* 1.3 81.2 - - + +
205A GLY* 1.3 63.5 + - - +
209A ASP* 4.0 0.2 - - - +
210A MET* 3.6 20.9 - - - +
213A ARG* 3.0 29.1 + - - +
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Residues in contact with GLY 205 (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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200A MET* 4.1 2.1 - - - +
201A GLU* 2.9 37.6 + - - +
202A GLU 4.6 0.4 - - - -
203A GLN 3.6 1.0 - - - -
204A LEU* 1.3 78.7 - - - +
206A THR* 1.3 69.2 + - - +
209A ASP* 3.5 12.6 - - - -
210A MET* 5.0 1.2 - - - +
213A ARG* 4.2 3.3 - - - +
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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
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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) + - + + + + + -
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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