Contacts of the helix formed by residues 226 - 249 (chain A) in PDB entry 2QW4
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 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A SER 2.8 19.9 + - - -
223A ARG 3.0 9.3 + - - -
225A LEU* 1.3 69.2 - - - +
227A LYS* 1.3 58.5 + - - +
228A LEU 3.3 0.2 - - - -
229A PRO* 2.9 21.3 - - - +
230A GLU* 3.2 20.0 - - - +
64C PHE* 4.3 10.9 - - - +
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Residues in contact with LYS 227 (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 LEU* 5.9 1.6 - - + -
158A PHE* 4.2 17.2 - - + -
161A SER* 2.5 35.6 + - - -
162A LEU* 4.0 26.2 - - + -
165A LEU* 3.8 27.1 - - + +
175A LEU* 5.1 5.4 - - + -
223A ARG 4.6 2.7 - - - -
224A LEU* 2.9 26.9 + - + +
226A GLY* 1.3 75.9 - - - +
228A LEU* 1.3 71.3 + - + +
230A GLU* 2.8 45.3 + - - +
231A LEU* 3.0 11.7 + - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 5.0 0.3 - - - +
118A LEU* 6.2 0.2 - - + -
175A LEU* 3.3 41.1 - - + -
178A LEU* 5.0 12.1 - - + -
179A VAL* 3.6 27.1 - - + +
225A LEU* 3.1 33.1 + - + +
227A LYS* 1.3 75.2 - - + +
229A PRO* 1.3 66.2 - - + +
231A LEU* 3.4 21.4 - - + +
232A ARG* 3.6 14.6 + - - -
64C PHE* 5.0 11.2 - - + -
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Residues in contact with PRO 229 (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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225A LEU 3.8 3.8 - - - +
226A GLY* 2.9 31.2 - - - +
228A LEU* 1.3 80.9 - - + +
230A GLU* 1.3 58.1 + - + +
231A LEU 3.0 1.6 - - - -
232A ARG* 2.7 32.8 + - + +
233A THR* 3.4 8.1 + - - -
64C PHE* 3.7 33.0 - - + -
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Residues in contact with GLU 230 (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 PHE* 4.1 14.6 - - + -
161A SER* 3.7 4.5 + - - -
226A GLY* 3.2 20.9 - - - +
227A LYS* 2.8 47.4 + - - +
229A PRO* 1.3 73.4 - - + +
231A LEU* 1.3 63.3 + - - +
232A ARG 3.1 1.0 + - - -
233A THR* 3.3 22.1 + - - -
234A LEU* 3.5 12.7 + - - +
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Residues in contact with LEU 231 (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 GLU* 3.5 37.5 - - + +
117A ILE* 3.7 28.5 - - + -
118A LEU* 3.9 22.9 - - + -
158A PHE* 3.8 25.0 - - + -
179A VAL* 4.2 20.4 - - + -
227A LYS 3.0 9.9 + - - +
228A LEU* 3.4 17.7 - - + +
229A PRO 3.0 0.2 - - - -
230A GLU* 1.3 76.9 - - - +
232A ARG* 1.3 59.8 + - - +
234A LEU* 3.4 9.8 + - + +
235A CYS* 3.3 21.2 + - - -
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Residues in contact with ARG 232 (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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110A SER 5.1 0.4 + - - -
114A GLU* 2.8 47.0 + - - -
182A THR* 5.3 5.1 + - - +
183A ASP 5.7 0.6 + - - -
184A ARG* 3.2 25.6 - - - +
228A LEU 3.6 10.3 + - - -
229A PRO* 2.7 24.9 + - + +
231A LEU* 1.3 70.9 - - - +
233A THR* 1.3 63.1 + - - +
235A CYS* 3.3 14.6 + - + +
236A THR* 3.3 15.1 + - - -
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Residues in contact with THR 233 (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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229A PRO 3.5 7.3 + - - -
230A GLU* 3.5 14.3 + - - -
232A ARG* 1.3 76.6 - - - +
234A LEU* 1.3 62.1 + - - +
236A THR* 3.0 31.3 - - + -
237A GLN* 3.3 20.7 + - + +
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Residues in contact with LEU 234 (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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117A ILE* 3.8 22.7 - - + -
151A TRP* 3.2 24.9 + - - +
154A SER* 3.6 40.8 - - - +
155A ILE* 3.7 14.1 - - + +
158A PHE* 3.5 45.5 - - + -
230A GLU 3.5 10.9 + - - +
231A LEU* 3.4 12.1 + - - +
232A ARG 3.2 0.6 - - - -
233A THR* 1.3 82.3 - - + +
235A CYS* 1.3 61.3 + - - +
236A THR 3.4 0.2 + - - -
237A GLN* 3.4 10.7 + - - +
238A GLY 3.2 6.6 + - - -
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Residues in contact with CYS 235 (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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113A LEU* 3.8 15.7 - - + +
114A GLU* 3.4 39.3 - - - -
117A ILE* 3.6 18.8 - - - -
231A LEU 3.3 16.6 - - - -
232A ARG* 3.3 9.6 + - + +
233A THR 3.3 0.4 - - - -
234A LEU* 1.3 74.6 - - - +
236A THR* 1.3 52.9 + - - +
238A GLY* 3.0 3.3 + - - -
239A LEU* 2.8 44.5 + - + +
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Residues in contact with THR 236 (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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232A ARG 3.3 12.2 + - - -
233A THR* 3.0 18.3 + - + +
235A CYS* 1.3 75.1 - - - +
237A GLN* 1.3 60.6 + - + +
239A LEU* 3.0 15.8 + - - +
240A GLN* 2.9 43.0 + - + +
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Residues in contact with GLN 237 (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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150A ASP* 4.7 1.0 - - - +
151A TRP* 3.9 23.9 + - + +
154A SER* 3.1 37.0 + - - -
233A THR* 3.3 25.6 + - + +
234A LEU* 3.4 14.6 + - - +
236A THR* 1.3 76.5 - - + +
238A GLY* 1.3 57.2 + - - +
240A GLN* 3.3 20.6 - - - +
241A ARG* 2.8 28.6 + - - +
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Residues in contact with GLY 238 (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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113A LEU* 4.7 2.0 - - - -
151A TRP* 3.4 38.1 - - - -
234A LEU 3.2 4.9 + - - -
235A CYS 3.0 8.5 + - - -
237A GLN* 1.3 76.4 - - - +
239A LEU* 1.3 59.2 + - - +
241A ARG* 3.2 3.3 + - - +
242A ILE* 2.8 36.6 + - - +
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Residues in contact with LEU 239 (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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113A LEU* 3.6 21.1 - - + +
235A CYS* 2.8 31.4 + - + +
236A THR* 3.0 10.3 + - - +
238A GLY* 1.3 68.8 - - - +
240A GLN* 1.3 56.3 + - - +
242A ILE* 2.8 11.3 + - + +
243A PHE* 2.6 36.0 + - - +
260A ILE* 5.4 4.5 - - + +
261A PHE* 4.0 35.5 - - + +
263A ASP 5.9 2.7 - - - +
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Residues in contact with GLN 240 (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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236A THR* 2.9 28.0 + - + +
237A GLN* 3.3 32.0 + - - +
239A LEU* 1.3 73.1 - - + +
241A ARG* 1.3 61.8 + - - +
243A PHE* 3.1 10.1 + - - +
244A TYR* 2.9 24.0 + - - +
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Residues in contact with ARG 241 (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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67A GLU* 3.7 12.0 + - - +
75A PHE* 4.8 3.1 - - + -
145A ALA 3.9 0.2 + - - -
146A ARG 3.1 26.3 + - - -
147A GLY* 2.7 22.7 + - - -
148A PHE 3.5 17.6 - - - +
149A GLY* 3.2 24.9 - - - +
151A TRP* 4.3 14.4 - - + +
237A GLN 2.8 20.4 + - - +
238A GLY 3.5 5.2 - - - +
239A LEU 3.2 0.2 - - - -
240A GLN* 1.3 72.8 - - - +
242A ILE* 1.3 62.4 + - - +
244A TYR* 3.3 38.1 + - - +
245A LEU* 3.0 38.0 + - - +
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Residues in contact with ILE 242 (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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75A PHE* 4.3 21.1 - - + -
76A TYR* 4.6 15.7 + - + +
79A LEU* 5.3 5.4 - - + -
112A PHE* 6.4 0.7 - - + -
113A LEU* 4.7 13.9 - - + -
151A TRP* 5.7 1.1 - - + -
238A GLY 2.8 21.8 + - - +
239A LEU* 2.8 24.2 + - + +
241A ARG* 1.3 71.5 - - - +
243A PHE* 1.3 57.4 + - - +
245A LEU* 3.3 8.1 + - - +
246A LYS* 2.8 32.4 + - + +
253A PRO* 5.7 2.9 - - + -
257A ILE* 4.6 20.4 - - + +
258A ASP* 6.1 1.1 - - - +
260A ILE* 6.2 2.9 - - + -
261A PHE* 3.6 31.2 - - + -
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Residues in contact with PHE 243 (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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239A LEU 2.6 16.4 + - - +
240A GLN* 3.2 13.0 - - - +
242A ILE* 1.3 73.0 - - - +
244A TYR* 1.3 59.3 + - - +
246A LYS* 2.9 22.2 + - + +
247A LEU* 3.0 50.7 + - + +
261A PHE* 3.8 27.0 - + + -
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Residues in contact with TYR 244 (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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66A LYS* 4.1 14.0 + - - +
67A GLU* 2.5 41.1 + - - -
240A GLN 2.9 17.9 + - - +
241A ARG* 3.3 32.1 + - - +
243A PHE* 1.3 74.8 - - + +
245A LEU* 1.3 69.0 + - + +
247A LEU* 3.4 12.4 + - + +
248A GLU* 3.0 31.7 + - - -
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Residues in contact with LEU 245 (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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67A GLU* 4.6 6.5 - - + +
72A VAL* 3.7 36.7 - - + +
75A PHE* 3.7 32.5 - - + -
76A TYR* 3.7 16.7 + - - +
147A GLY* 4.1 2.9 - - - +
241A ARG* 3.0 47.4 + - - +
242A ILE* 3.7 5.2 - - - +
244A TYR* 1.3 90.9 - - + +
246A LYS* 1.3 59.1 + - - +
247A LEU 3.1 5.6 - - - -
248A GLU* 4.3 2.6 - - - +
249A ASP* 3.3 21.9 + - - +
250A LEU* 4.6 3.4 + - + -
251A VAL 5.2 2.4 - - - +
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Residues in contact with LYS 246 (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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76A TYR* 4.5 1.5 + - - +
242A ILE* 2.8 19.6 + - + +
243A PHE* 2.9 11.6 + - + +
245A LEU* 1.3 76.3 - - - +
247A LEU* 1.3 62.7 + - + +
249A ASP* 3.6 23.1 - - - +
253A PRO* 4.5 17.9 - - + -
258A ASP* 2.7 32.3 + - - +
261A PHE* 4.2 19.9 - - + -
262A MET* 3.1 35.0 - - - +
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Residues in contact with LEU 247 (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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243A PHE* 3.0 52.5 + - + +
244A TYR* 3.8 11.7 - - + +
246A LYS* 1.3 82.7 - - + +
248A GLU* 1.3 56.9 + - - +
249A ASP* 2.7 21.0 + - - +
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Residues in contact with GLU 248 (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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244A TYR* 3.0 24.7 + - - -
245A LEU* 4.5 1.8 - - - +
247A LEU* 1.3 74.4 - - - +
249A ASP* 1.3 62.6 + - - +
250A LEU* 3.1 13.8 + - - +
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Residues in contact with ASP 249 (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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245A LEU 3.3 15.3 + - - +
246A LYS* 3.6 25.4 - - - +
247A LEU 2.7 12.0 - - - +
248A GLU* 1.3 74.5 - - - +
250A LEU* 1.3 73.2 + - - +
251A VAL 4.3 6.4 - - - +
252A PRO* 5.1 1.5 - - - +
253A PRO* 4.9 6.1 - - - +
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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