Contacts of the helix formed by residues 173 - 194 (chain A) in PDB entry 4UAL
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 PRO 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A PHE* 4.5 9.4 - - + -
171A LYS 4.3 3.1 - - - +
172A LEU* 1.3 88.5 - - + +
174A GLU* 1.3 60.7 + - - +
175A ASP* 4.4 7.6 - - + +
176A MET* 2.9 30.4 + - + +
177A ALA* 2.8 24.7 + - - +
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Residues in contact with GLU 174 (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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172A LEU 3.8 0.8 + - - -
173A PRO* 1.3 72.2 - - - +
175A ASP* 1.3 65.3 + - - +
177A ALA* 4.0 1.1 - - - +
178A ARG* 2.9 40.4 + - - +
275A LEU* 3.6 23.5 - - + +
308A ASP 4.1 4.7 - - - +
309A VAL* 3.5 10.9 - - - +
310A SER* 2.6 52.3 + - - -
313A ALA* 3.6 11.8 - - - +
341A PHE* 3.7 14.9 - - + -
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Residues in contact with ASP 175 (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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173A PRO* 3.2 6.5 - - + +
174A GLU* 1.3 79.0 - - - +
176A MET* 1.3 63.0 - - + +
178A ARG* 3.1 29.0 + - - +
179A PHE* 3.7 14.2 + - - +
356A PRO* 5.4 1.4 - - - +
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Residues in contact with MET 176 (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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164A LEU* 4.5 1.1 - - + -
168A PHE* 3.8 27.8 - - + -
172A LEU* 3.8 26.7 - - + -
173A PRO* 2.9 33.4 + - + +
175A ASP* 1.3 78.6 - - + +
177A ALA* 1.3 59.8 - - - +
179A PHE* 2.9 21.8 + - - +
180A TYR* 3.3 40.4 + - + +
356A PRO* 3.8 28.7 - - + +
357A TYR* 4.4 9.4 - - + -
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Residues in contact with ALA 177 (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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172A LEU* 4.4 8.1 - - + -
173A PRO 2.8 15.0 + - - +
174A GLU* 4.0 2.2 - - - +
176A MET* 1.3 73.7 - - - +
178A ARG* 1.3 59.0 + - - +
180A TYR* 3.9 0.8 - - - +
181A ILE* 2.8 43.8 + - + +
271A MET* 6.0 0.2 - - + -
274A MET* 3.6 26.7 - - + -
275A LEU* 3.8 25.4 - - + -
341A PHE* 4.5 4.7 - - + -
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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
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174A GLU* 2.9 31.8 + - - +
175A ASP* 3.1 42.6 + - - +
177A ALA* 1.3 77.5 - - - +
179A PHE* 1.3 57.2 + - - +
182A GLY* 2.9 25.3 + - - -
341A PHE* 2.8 50.6 + - + +
342A PHE* 3.6 30.1 - - + +
343A GLU 4.8 7.5 + - - -
345A LEU* 4.2 20.1 - - + +
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Residues in contact with PHE 179 (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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175A ASP 3.7 6.2 + - - +
176A MET 2.9 10.2 + - - +
178A ARG* 1.3 83.1 - - - +
180A TYR* 1.3 85.3 + + - +
182A GLY* 3.8 0.5 - - - -
183A GLU* 3.0 66.2 + - - +
212A GLY 3.7 8.1 - - - -
213A HIS* 3.4 12.8 - + - -
345A LEU* 5.3 4.7 - - + -
350A ILE* 4.2 12.3 - - + +
353A LEU* 3.2 36.8 - - + -
354A GLU 4.9 0.2 - - - -
355A ALA* 3.8 12.3 - - + -
356A PRO* 3.4 27.8 - - + -
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Residues in contact with TYR 180 (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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161A LEU* 4.2 14.1 - - + -
164A LEU* 3.3 24.4 - - + +
172A LEU* 3.6 28.7 - - + -
176A MET* 3.3 32.2 + - + -
177A ALA* 4.1 1.1 - - - +
179A PHE* 1.3 101.2 - + - +
181A ILE* 1.3 61.2 + - - +
183A GLU* 3.4 4.4 + - - +
184A MET* 2.9 35.1 + - - +
208A LEU* 4.0 13.8 - - + +
212A GLY 3.9 10.9 + - - -
214A ILE* 4.0 15.4 - - + +
274A MET* 3.6 18.8 - - + -
356A PRO* 3.9 9.3 - - + +
357A TYR* 3.5 24.4 + - - +
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Residues in contact with ILE 181 (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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177A ALA* 2.8 29.6 + - + +
178A ARG 4.3 1.8 - - - +
180A TYR* 1.3 73.2 - - - +
182A GLY* 1.3 54.9 + - - +
184A MET* 3.3 7.7 + - - +
185A VAL* 2.8 33.9 + - + +
267A LEU* 4.1 32.1 - - + -
270A CYS* 4.7 1.3 - - + -
271A MET* 3.8 49.6 - - + +
274A MET* 3.6 27.6 - - + -
316A LEU* 4.8 2.7 - - + -
336A PHE* 6.2 0.2 - - + -
341A PHE* 4.7 2.7 - - + -
342A PHE* 3.8 19.7 - - + -
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Residues in contact with GLY 182 (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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178A ARG 2.9 19.3 + - - -
179A PHE 3.8 0.7 - - - -
181A ILE* 1.3 75.9 - - - +
183A GLU* 1.3 63.2 + - - +
185A VAL* 3.2 4.6 + - - +
186A LEU* 3.1 24.9 + - - +
342A PHE* 3.7 16.0 - - - -
345A LEU* 4.2 5.8 - - - -
347A TRP* 3.5 15.3 - - - -
350A ILE* 4.5 4.0 - - - -
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Residues in contact with GLU 183 (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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135A TRP* 3.7 29.0 - - + -
179A PHE* 3.0 40.0 + - + +
180A TYR 3.9 2.7 - - - +
182A GLY* 1.3 75.4 - - - +
184A MET* 1.3 63.5 + - - +
186A LEU* 3.0 6.0 + - - +
187A ALA* 2.9 22.3 + - - +
213A HIS* 2.5 33.6 + - - +
214A ILE* 2.9 45.3 + - + +
350A ILE* 3.5 21.5 - - + +
351A ARG* 4.2 0.7 - - - +
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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
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161A LEU* 4.0 17.7 - - + -
180A TYR 2.9 21.5 + - - +
181A ILE* 3.6 14.4 - - - +
183A GLU* 1.3 75.8 - - - +
185A VAL* 1.3 65.7 + - - +
187A ALA* 4.4 2.2 - - - +
188A ILE* 2.8 34.4 + - + +
201A ILE* 3.8 25.4 - - + -
202A LYS 5.3 0.2 - - - +
206A VAL* 3.8 30.5 - - + -
214A ILE* 3.9 18.4 - - + -
216A LEU* 5.7 2.7 - - + -
267A LEU* 3.7 26.7 - - + -
270A CYS* 4.2 15.3 - - - -
274A MET* 4.7 1.3 - - - -
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Residues in contact with VAL 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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181A ILE* 2.8 26.2 + - + +
182A GLY* 3.2 10.1 + - - +
184A MET* 1.3 76.6 - - - +
186A LEU* 1.3 58.6 + - - +
189A ASP* 2.9 32.1 + - - +
264A TRP* 3.6 10.5 - - + -
267A LEU* 3.8 22.0 - - + +
333A ILE* 3.6 24.2 - - + -
336A PHE* 3.8 43.5 - - + -
342A PHE* 4.5 4.9 - - + -
347A TRP* 4.1 7.0 - - + -
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Residues in contact with LEU 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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135A TRP* 3.4 40.6 - - + +
182A GLY 3.1 14.0 + - - +
183A GLU* 3.0 7.4 + - - +
185A VAL* 1.3 76.6 - - - +
187A ALA* 1.3 60.7 + - - +
189A ASP* 3.9 2.4 - - - +
190A SER* 3.2 22.5 + - - -
333A ILE* 3.9 18.8 - - + -
337A LYS* 5.2 3.8 - - - +
347A TRP* 3.7 37.5 - - + +
350A ILE* 3.6 21.1 - - + -
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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
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135A TRP* 3.8 34.7 - - + +
136A ILE* 5.1 0.9 - - + +
183A GLU 2.9 15.0 + - - +
184A MET* 3.9 3.4 - - - +
186A LEU* 1.3 75.3 - - - +
188A ILE* 1.3 64.9 + - + +
190A SER* 2.8 20.6 + - - -
191A ILE* 3.4 10.0 + - - +
214A ILE* 4.2 14.8 - - + -
216A LEU* 4.2 17.4 - - + +
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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
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184A MET* 2.8 28.1 + - + +
187A ALA* 1.3 72.4 - - + +
189A ASP* 1.3 64.4 + - - +
191A ILE* 3.1 15.6 + - + +
192A HIS* 3.1 38.4 + - + +
198A HIS* 6.3 0.7 - - + -
201A ILE* 4.0 43.3 - - + -
216A LEU* 4.5 9.2 - - + -
263A ASP* 4.0 12.1 - - + +
264A TRP* 3.6 22.4 - - + -
267A LEU* 4.1 25.1 - - + -
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Residues in contact with ASP 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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185A VAL 2.9 21.0 + - - +
186A LEU 3.9 4.3 - - - +
188A ILE* 1.3 77.8 - - - +
190A SER* 1.3 57.8 + - - +
192A HIS* 3.3 9.1 + - - +
193A GLN* 2.9 50.1 + - - +
264A TRP* 3.9 8.4 - - + -
332A GLY* 4.2 10.1 + - - -
333A ILE* 3.6 42.5 + - + +
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Residues in contact with SER 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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132A ASP* 3.7 37.5 + - - +
135A TRP* 4.1 5.3 - - - +
136A ILE* 4.5 1.7 - - - +
186A LEU 3.2 13.5 + - - -
187A ALA* 2.8 20.2 + - - -
189A ASP* 1.3 77.9 - - - +
191A ILE* 1.3 67.9 + - - +
193A GLN* 3.5 9.0 + - - +
194A LEU* 3.5 22.9 + - - +
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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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127A VAL* 3.9 24.9 - - + -
131A GLY* 5.8 1.6 - - - -
136A ILE* 3.9 22.0 - - + -
187A ALA 3.6 12.1 - - - +
188A ILE* 3.1 8.9 + - + +
190A SER* 1.3 78.9 + - - +
192A HIS* 1.3 68.0 + - + +
194A LEU* 3.0 20.0 + - + +
196A TYR* 3.3 42.5 + - + +
198A HIS* 4.4 20.0 - - + +
216A LEU* 4.0 18.6 - - + -
219A PHE* 3.9 5.2 - - + -
222A CYS* 4.7 6.3 - - - -
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Residues in contact with HIS 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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188A ILE* 3.1 25.1 + - + +
189A ASP* 3.7 13.1 + - - +
191A ILE* 1.3 80.7 - - + +
193A GLN* 1.3 61.1 + - - +
195A HIS* 2.9 23.6 + - - -
196A TYR 3.2 19.7 - - - -
225A MET* 4.3 7.7 - - + +
260A PRO* 3.4 40.8 - - + +
263A ASP* 2.7 27.5 + - + -
264A TRP* 3.5 29.9 + - - -
329A GLY 5.4 0.8 + - - -
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Residues in contact with GLN 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 ASP* 2.9 41.9 + - - +
190A SER* 3.9 9.4 - - - +
191A ILE 3.2 0.2 - - - -
192A HIS* 1.3 80.3 - - - +
194A LEU* 1.3 60.2 + - - +
195A HIS* 3.2 16.9 + - - -
332A GLY* 4.8 10.8 + - - -
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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
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19A TRP* 6.3 0.9 - - + -
127A VAL* 4.1 24.9 - - + -
130A ASN* 3.3 30.3 - - + +
131A GLY* 3.8 26.9 - - - +
190A SER 3.5 12.9 + - - +
191A ILE* 3.0 14.0 + - + +
193A GLN* 1.3 77.5 - - - +
195A HIS* 1.3 76.8 + - - +
196A TYR* 3.6 24.3 - - + -
224A LYS* 3.9 5.4 + - - -
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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