Contacts of the helix formed by residues 235 - 260 (chain A) in PDB entry 4DJH
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 PHE 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 6.1 0.2 - - + -
231A PHE* 3.3 36.4 + + - +
233A PHE 3.2 2.2 + - - -
234A ALA* 1.3 82.0 - - - +
236A VAL* 1.3 76.9 + - + +
237A ILE 3.4 1.1 - - - -
238A PRO* 3.3 3.5 - - - +
239A VAL* 2.9 55.0 + - + +
283A PHE* 5.9 4.0 - + - -
284A VAL* 5.0 6.5 - - + -
287A TRP* 4.6 2.9 - - + -
288A THR* 3.2 45.5 - - + -
291A HIS* 3.6 32.5 - + + +
292A ILE* 5.7 2.9 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.0 47.8 + - + +
232A ILE* 3.3 21.7 + - + +
235A PHE* 1.3 81.6 - - + +
237A ILE* 1.3 73.0 + - + +
239A VAL* 4.2 1.1 - - - +
240A LEU* 3.1 43.7 + - + +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 2.9 32.6 + - + +
233A PHE* 3.9 33.4 - - + +
236A VAL* 1.3 80.1 - - + +
238A PRO* 1.3 74.1 - - + +
240A LEU* 3.7 2.7 - - - +
241A ILE* 2.8 49.1 + - + +
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Residues in contact with PRO 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.5 28.5 - - + +
147A PHE* 4.9 6.7 - - + -
150A THR* 3.3 24.5 - - + +
233A PHE 3.1 28.5 - - - +
235A PHE 3.3 19.1 - - - +
237A ILE* 1.3 93.3 - - + +
239A VAL* 1.3 49.8 - - - +
241A ILE* 3.2 8.0 + - + +
242A ILE* 2.7 41.6 + - - +
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 4.5 13.2 - - + -
235A PHE* 2.9 54.8 + - + +
236A VAL* 4.2 1.8 - - - +
238A PRO* 1.3 72.9 - - - +
240A LEU* 1.3 62.4 + - + +
242A ILE* 3.3 9.3 + - + +
243A ILE* 2.9 44.0 + - + +
283A PHE* 5.9 0.2 - - + -
284A VAL* 4.0 31.0 - - + -
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Residues in contact with LEU 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 VAL* 3.1 41.0 + - + +
237A ILE* 3.7 2.9 - - - +
239A VAL* 1.3 75.0 - - + +
241A ILE* 1.3 68.2 + - + +
243A ILE* 3.0 19.7 + - + +
244A VAL* 2.8 32.8 + - + +
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Residues in contact with ILE 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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150A THR* 3.6 22.9 - - + -
154A VAL* 5.0 11.7 - - + -
237A ILE* 2.8 42.0 + - + +
238A PRO* 3.4 9.9 - - + +
240A LEU* 1.3 73.8 - - + +
242A ILE* 1.3 57.5 + - - +
244A VAL* 3.4 8.8 + - - +
245A CYS* 2.8 27.5 + - + +
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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
----------------------------------------------------------
146A ILE* 4.5 9.9 - - + -
149A LEU* 4.2 10.5 - - + +
150A THR* 3.5 42.8 - - + +
153A SER* 4.0 7.0 - - - +
238A PRO 2.7 24.8 + - - +
239A VAL* 3.5 10.1 - - + +
241A ILE* 1.3 73.0 - - - +
243A ILE* 1.3 58.9 + - + +
245A CYS* 2.7 33.1 + - - +
246A TYR* 2.9 22.6 + - + -
280A VAL* 3.8 32.5 - - + -
284A VAL* 5.8 1.6 - - + -
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Residues in contact with ILE 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 VAL* 2.9 35.4 + - + +
240A LEU* 3.4 21.3 - - + +
242A ILE* 1.3 75.3 - - + +
244A VAL* 1.3 64.5 + - + +
246A TYR* 3.2 5.6 + - - +
247A THR* 2.8 40.8 + - + +
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Residues in contact with VAL 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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240A LEU* 2.8 24.0 + - + +
241A ILE* 3.5 10.1 - - - +
243A ILE* 1.3 74.4 - - + +
245A CYS* 1.3 64.8 + - - +
247A THR* 3.0 16.6 + - - -
248A LEU* 3.1 36.0 + - + +
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Residues in contact with CYS 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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153A SER* 3.4 39.9 - - - -
154A VAL* 3.6 19.7 - - - -
157A TYR* 3.3 27.6 - - - -
241A ILE* 2.8 15.9 + - + +
242A ILE* 2.7 24.1 + - - +
244A VAL* 1.3 73.5 - - - +
246A TYR* 1.3 55.0 + - + +
248A LEU* 5.9 0.2 - - - -
249A MET* 3.1 26.4 + - - +
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Residues in contact with TYR 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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153A SER* 3.2 28.9 + - - -
156A ARG* 4.6 1.4 - - - +
242A ILE* 2.9 27.0 + - + +
243A ILE* 3.2 6.7 + - - +
245A CYS* 1.3 78.3 - - - +
247A THR* 1.3 67.8 + - - +
248A LEU 3.0 1.6 - - - -
249A MET* 2.8 38.7 + - + +
250A ILE* 2.9 25.1 + - + +
273A THR* 4.1 6.8 + - + -
276A VAL* 3.0 33.1 + - - +
277A LEU* 3.3 54.0 + - + -
280A VAL* 4.9 2.9 - - + -
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Residues in contact with THR 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 ILE* 2.8 34.0 + - + +
244A VAL* 3.0 17.5 + - - -
246A TYR* 1.3 74.1 - - + +
248A LEU* 1.3 62.4 + - - +
250A ILE* 3.2 30.7 - - + +
251A LEU* 3.3 12.5 - - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 3.5 31.2 - - + +
244A VAL* 3.1 35.3 + - + +
245A CYS* 5.9 0.2 - - - -
246A TYR 3.0 0.8 - - - -
247A THR* 1.3 83.7 + - - +
249A MET* 1.3 60.7 + - - +
251A LEU* 3.0 22.1 + - + +
252A ARG* 2.9 29.8 + - - +
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Residues in contact with MET 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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153A SER 3.8 4.9 - - - +
156A ARG* 3.2 45.5 - - + +
157A TYR* 3.2 18.6 - - + +
160A VAL* 4.0 15.7 - - + -
245A CYS* 3.1 24.8 + - - +
246A TYR* 2.8 28.1 + - + +
248A LEU* 1.3 77.2 - - - +
250A ILE* 1.3 58.5 + - + +
252A ARG* 3.3 6.4 + - - +
253A LEU* 2.9 34.0 + - + +
273A THR* 3.4 29.2 - - - -
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Residues in contact with ILE 250 (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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246A TYR* 2.9 19.6 + - + +
247A THR* 3.2 21.5 - - + +
249A MET* 1.3 78.2 - - + +
251A LEU* 1.3 69.5 + - + +
253A LEU* 3.5 14.2 + - + +
254A LYS* 3.0 37.2 + - + +
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Residues in contact with LEU 251 (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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247A THR 3.3 17.3 - - - +
248A LEU* 3.0 27.7 + - + +
250A ILE* 1.3 88.2 - - + +
252A ARG* 1.3 59.5 + - - +
254A LYS* 3.2 10.7 + - + +
255A SER* 2.8 30.7 + - - -
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Residues in contact with ARG 252 (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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157A TYR* 3.3 68.4 + - - +
158A ILE* 4.1 8.1 - - - +
160A VAL* 3.2 20.6 - - + +
161A CYS* 2.7 45.3 - - - +
162A HIS* 4.9 2.6 + - - -
248A LEU 2.9 10.8 + - - +
249A MET* 3.7 6.7 - - - +
251A LEU* 1.3 75.7 - - + +
253A LEU* 1.3 58.4 + - - +
255A SER* 3.3 8.2 + - - -
256A VAL* 2.8 33.3 + - - +
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Residues in contact with LEU 253 (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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160A VAL* 3.5 31.6 - - + -
249A MET* 2.9 34.7 + - + +
250A ILE* 3.6 15.7 - - + +
251A LEU 3.1 0.2 - - - -
252A ARG* 1.3 73.2 - - - +
254A LYS* 1.3 60.9 + - + +
256A VAL* 3.1 11.7 + - + +
257A ARG* 2.8 32.0 + - - +
269A LEU* 5.3 7.4 - - + -
273A THR* 5.4 7.0 - - + -
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Residues in contact with LYS 254 (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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250A ILE* 3.0 26.3 + - + +
251A LEU* 3.5 14.8 - - + +
253A LEU* 1.3 76.2 - - + +
255A SER* 1.3 61.3 + - - +
257A ARG* 3.4 23.5 + - - +
258A LEU* 3.3 29.1 - - + +
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Residues in contact with SER 255 (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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251A LEU 2.8 16.6 + - - -
252A ARG* 3.5 9.2 - - - -
254A LYS* 1.3 77.1 - - - +
256A VAL* 1.3 57.9 + - - +
258A LEU* 3.5 4.9 + - - +
259A LEU* 3.1 31.0 + - - +
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Residues in contact with VAL 256 (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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160A VAL* 4.0 23.1 - - + +
161A CYS* 4.7 14.1 - - - -
252A ARG 2.8 18.6 + - - +
253A LEU* 3.1 13.2 + - + +
255A SER* 1.3 76.6 - - - +
257A ARG* 1.3 62.3 + - - +
258A LEU 3.2 0.2 - - - -
259A LEU* 4.5 2.9 - - - +
260A SER* 2.9 36.5 + - - +
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Residues in contact with ARG 257 (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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253A LEU 2.8 15.6 + - - +
254A LYS* 3.4 21.7 + - - +
255A SER 3.3 0.2 - - - -
256A VAL* 1.3 79.3 - - + +
258A LEU* 1.3 75.9 + - + +
260A SER* 3.9 4.4 + - - -
1094A VAL* 3.6 5.5 - - - +
1155A THR 5.2 1.6 - - - -
1156A GLY 4.0 11.7 - - - +
1157A THR* 3.8 29.6 - - + -
1158A TRP* 3.5 19.4 + - - -
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Residues in contact with LEU 258 (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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254A LYS* 3.3 23.6 + - + +
255A SER* 4.0 6.5 - - - +
256A VAL 3.2 0.2 - - - -
257A ARG* 1.3 94.1 - - + +
259A LEU* 1.3 58.9 + - + +
260A SER 3.4 0.9 - - - -
261A GLY 3.3 6.1 - - - +
1092A ASP* 5.0 10.5 - - + +
1093A ALA* 4.1 29.6 - - + +
1094A VAL* 3.8 17.7 - - + +
1156A GLY 5.3 1.1 - - - +
1158A TRP* 3.0 21.0 + - - -
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER* 3.1 19.9 + - - +
256A VAL* 3.9 2.9 - - - -
258A LEU* 1.3 77.1 - - + +
260A SER* 1.3 61.9 + - - +
261A GLY* 3.2 5.8 + - - +
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Residues in contact with SER 260 (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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256A VAL* 2.9 27.2 + - - -
257A ARG* 3.9 4.7 + - - -
258A LEU 3.4 0.2 - - - -
259A LEU* 1.3 78.5 - - - +
261A GLY* 1.3 56.4 + - - +
263A ARG* 2.8 44.2 + - - +
1005A GLU* 4.3 2.9 - - - +
1158A TRP* 3.4 20.8 + - - +
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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
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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