Contacts of the helix formed by residues 232 - 255 (chain A) in PDB entry 1KEK
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 ALA 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER 5.7 1.1 - - - +
102A GLY 5.6 1.8 - - - +
104A LEU* 4.1 30.5 - - + -
228A GLY 4.6 1.0 + - - -
229A ARG 4.2 7.8 + - - +
230A GLU 3.2 1.0 - - - -
231A ALA* 1.3 78.8 - - - +
233A ASN* 1.3 63.7 + - - +
234A PRO* 3.2 2.2 - - - -
235A TYR* 3.0 19.6 + - - +
236A TYR* 3.5 17.9 - - + -
331B LYS* 5.9 1.8 - - - +
661B ALA* 3.9 15.7 + - - +
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Residues in contact with ASN 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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230A GLU* 2.9 37.6 + - - +
232A ALA* 1.3 75.5 - - - +
234A PRO* 1.3 64.8 - - + +
236A TYR* 3.0 11.2 + - - +
237A LEU* 2.8 32.9 + - + +
331B LYS* 3.2 36.2 - - - +
396B ASP* 4.2 1.7 - - - +
398B VAL* 5.8 0.2 - - + -
399B THR* 2.9 29.6 + - + +
401B THR* 4.7 4.2 - - - +
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Residues in contact with PRO 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU 4.6 0.2 - - - +
231A ALA 3.4 11.0 - - - +
232A ALA 3.2 5.8 - - - -
233A ASN* 1.3 97.3 - - + +
235A TYR* 1.3 69.2 + - + +
237A LEU* 3.3 14.6 + - + +
238A LYS* 3.3 38.2 + - + +
398B VAL* 3.5 29.4 - - + -
399B THR* 4.1 3.8 - - + -
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Residues in contact with TYR 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.9 35.2 - - + -
163A SER* 3.7 19.1 - - - +
164A ASN* 4.4 14.8 - - + -
165A VAL* 4.1 6.6 - - + +
231A ALA 4.6 1.8 - - - -
232A ALA* 3.0 16.1 + - - +
234A PRO* 1.3 87.2 - - + +
236A TYR* 1.3 60.8 + - + +
238A LYS* 3.3 9.6 + - + +
239A VAL* 3.1 26.8 + - - +
661B ALA* 3.5 25.1 - - + +
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 3.7 17.8 + - - -
104A LEU* 4.4 10.5 - - + +
137A GLY* 2.7 37.1 + - - -
138A PHE 5.4 1.1 - - - -
165A VAL* 3.8 21.1 - - + +
232A ALA* 3.5 30.3 - - + -
233A ASN* 3.0 10.6 + - - +
235A TYR* 1.3 77.5 - - + +
237A LEU* 1.3 66.7 + - + +
239A VAL* 3.5 5.6 + - + +
240A PRO* 3.4 18.2 - - - +
307A PRO* 4.0 23.1 - - + +
331B LYS* 5.4 4.3 - - - -
333B PRO* 3.7 33.9 - - + +
334B GLY* 4.2 13.0 - - - +
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASN* 2.8 18.5 + - + +
234A PRO* 3.6 9.6 - - + +
235A TYR 3.2 0.2 - - - -
236A TYR* 1.3 80.5 - - + +
238A LYS* 1.3 61.4 + - + +
240A PRO* 3.6 11.9 - - - +
241A GLY 5.2 0.5 + - - -
399B THR* 3.6 33.0 - - + -
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Residues in contact with LYS 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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234A PRO* 3.3 25.3 + - - +
235A TYR* 3.3 8.9 + - + +
236A TYR 3.3 0.2 - - - -
237A LEU* 1.3 76.4 - - + +
239A VAL* 1.4 65.4 + - - +
240A PRO* 3.4 2.0 - - - -
241A GLY* 3.3 4.9 + - - +
242A ILE* 3.2 38.2 + - + +
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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
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139A ALA* 4.4 2.7 - - + -
163A SER* 4.1 13.0 - - - +
165A VAL* 3.5 31.4 - - + -
167A PHE* 4.3 20.6 - - + -
235A TYR 3.1 17.4 + - - +
236A TYR* 3.5 8.9 + - - +
238A LYS* 1.4 76.5 - - - +
240A PRO* 1.3 70.9 - - + +
242A ILE* 3.1 8.6 + - + +
243A VAL* 2.8 27.2 + - + +
304A LEU* 4.7 1.1 - - + -
307A PRO* 3.4 30.3 - - + -
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Residues in contact with PRO 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 TYR 3.4 16.2 - - - +
237A LEU* 3.6 9.4 - - - +
238A LYS 3.4 4.0 - - - -
239A VAL* 1.3 96.4 - - + +
241A GLY* 1.3 55.5 + - - +
243A VAL* 3.3 2.4 + - - +
244A ALA* 2.9 30.8 + - - +
260A LEU* 3.9 15.1 - - + +
304A LEU* 4.1 14.8 - - + -
307A PRO* 4.4 9.4 - - + -
309A VAL* 3.5 35.0 - - + -
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Residues in contact with GLY 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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237A LEU 5.2 0.4 + - - -
238A LYS* 3.3 7.1 + - - +
239A VAL 3.2 0.6 - - - -
240A PRO* 1.3 80.7 - - - +
242A ILE* 1.3 54.8 + - - +
244A ALA* 3.4 7.0 + - - +
245A GLU* 2.9 31.1 + - - +
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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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159A ALA* 3.8 22.7 - - + +
162A GLU* 3.6 27.6 - - + +
163A SER* 3.7 28.5 - - - -
238A LYS* 3.2 29.5 + - + +
239A VAL* 3.1 8.2 + - - +
241A GLY* 1.3 71.4 - - - +
243A VAL* 1.3 67.6 + - - +
245A GLU* 3.3 9.1 + - - +
246A TYR* 2.9 51.6 + - + -
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.5 2.5 - - + -
155A VAL* 4.0 12.0 - - + +
159A ALA* 4.0 10.1 - - + -
167A PHE* 3.5 36.6 - - + -
239A VAL* 2.8 19.3 + - + +
240A PRO 3.6 7.9 - - - +
242A ILE* 1.3 77.1 - - - +
244A ALA* 1.3 56.8 + - - +
246A TYR* 3.2 2.6 + - - +
247A MET* 2.8 46.7 + - + +
260A LEU* 3.8 18.8 - - + -
304A LEU* 4.1 19.7 - - + -
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Residues in contact with ALA 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 PRO 2.9 21.1 + - - +
241A GLY* 3.5 9.0 - - - +
243A VAL* 1.3 74.0 - - - +
245A GLU* 1.3 64.0 + - - +
247A MET* 3.4 10.1 + - - +
248A GLN* 3.1 38.5 + - - +
258A TYR 5.3 0.2 - - - +
259A LYS* 6.3 0.9 - - - +
260A LEU* 4.0 17.2 - - + +
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Residues in contact with GLU 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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162A GLU* 2.9 25.0 - - - +
241A GLY 2.9 16.9 + - - +
242A ILE* 3.6 14.4 - - - +
244A ALA* 1.3 77.2 - - - +
246A TYR* 1.3 74.8 + - - +
248A GLN* 3.1 14.7 + - - +
249A LYS* 2.7 66.3 + - + +
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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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155A VAL* 4.1 20.9 - - + +
158A LEU* 3.6 46.2 + - + -
159A ALA* 4.0 8.5 - - - -
162A GLU* 2.6 27.1 + - - +
194A LEU* 3.4 24.0 + - + -
196A ASN* 3.5 18.4 + - - +
242A ILE* 2.9 41.3 + - + +
243A VAL 3.9 2.9 - - - +
245A GLU* 1.3 88.8 + - - +
247A MET* 1.3 65.7 + - - +
249A LYS* 3.8 21.9 + - + +
250A VAL* 2.9 29.3 + - - +
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Residues in contact with MET 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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141A LEU* 4.0 4.7 - - + -
152A MET* 3.9 21.5 - - + -
155A VAL* 4.2 17.3 - - + -
243A VAL* 2.8 36.6 + - + +
244A ALA* 3.4 9.9 - - - +
246A TYR* 1.3 77.2 - - - +
248A GLN* 1.3 62.6 + - - +
250A VAL* 3.9 2.2 - - - +
251A ALA* 3.0 24.4 + - - +
256A ARG 4.7 1.7 - - - +
258A TYR* 3.6 34.1 + - + +
259A LYS* 3.6 35.2 - - - +
260A LEU* 4.1 7.2 - - + +
303A ARG* 3.8 18.2 - - + -
304A LEU 5.2 0.2 - - - +
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Residues in contact with GLN 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 ALA* 3.1 29.1 + - - +
245A GLU* 3.1 13.5 + - - +
247A MET* 1.3 80.1 - - + +
249A LYS* 1.3 57.5 + - + +
251A ALA* 3.3 7.6 + - - +
252A SER* 3.0 27.4 + - - -
258A TYR 5.4 4.4 + - - +
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Residues in contact with LYS 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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162A GLU* 4.8 1.8 + - - -
194A LEU* 4.4 28.4 + - + +
245A GLU* 2.7 51.5 + - + +
246A TYR* 3.2 30.2 + - + +
248A GLN* 1.3 74.8 - - + +
250A VAL* 1.4 66.2 + - - +
252A SER* 2.6 26.9 + - - +
253A LEU* 3.4 8.8 + - - +
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Residues in contact with VAL 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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151A ASP* 4.7 22.0 - - + +
154A LEU* 3.9 31.2 - - + -
155A VAL* 4.0 16.8 - - + -
158A LEU* 4.3 8.5 - - + -
186A LEU* 4.8 1.8 - - + -
194A LEU* 4.2 14.1 - - + -
246A TYR 2.9 20.8 + - - +
247A MET* 3.9 3.1 - - - +
249A LYS* 1.4 76.3 - - + +
251A ALA* 1.3 58.5 + - - +
253A LEU* 2.9 22.3 + - - +
254A THR* 2.9 31.0 + - + +
256A ARG 5.3 2.7 - - - +
258A TYR* 5.7 3.1 - - + -
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Residues in contact with ALA 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 MET 3.0 16.5 + - - +
248A GLN* 3.5 9.2 - - - +
249A LYS 3.2 0.2 - - - -
250A VAL* 1.3 75.3 - - - +
252A SER* 1.3 59.6 + - - +
253A LEU 3.1 2.7 - - - -
254A THR* 3.6 2.9 - - - -
255A GLY* 2.7 29.3 + - - -
256A ARG 3.2 27.3 + - - +
257A SER* 3.8 20.2 - - - +
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Residues in contact with SER 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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194A LEU* 5.8 0.5 - - - +
248A GLN 3.0 13.0 + - - -
249A LYS* 2.6 23.2 + - - -
251A ALA* 1.3 76.6 - - - +
253A LEU* 1.3 67.3 + - - +
255A GLY 5.0 0.3 + - - -
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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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3A LYS* 3.3 24.1 - - - +
186A LEU* 4.2 17.7 - - + +
190A ASP* 4.1 33.9 - - + +
193A SER* 4.6 3.4 - - - +
194A LEU* 3.7 36.8 - - + -
249A LYS 3.8 8.5 - - - +
250A VAL 2.9 8.3 + - - +
252A SER* 1.3 87.5 - - - +
254A THR* 1.3 59.7 + - + +
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Residues in contact with THR 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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3A LYS* 3.0 25.6 + - - +
151A ASP* 4.6 1.0 + - - +
184A GLU* 3.8 10.0 - - - +
186A LEU* 3.9 23.6 - - + -
250A VAL* 2.9 25.6 + - + +
251A ALA* 3.6 3.3 - - - -
253A LEU* 1.3 81.5 - - - +
255A GLY* 1.3 62.5 + - - +
256A ARG* 2.9 59.5 + - - +
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Residues in contact with GLY 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 ALA 2.7 22.8 + - - -
252A SER 4.7 0.4 + - - -
253A LEU 3.7 0.6 - - - -
254A THR* 1.3 73.1 - - - +
256A ARG* 1.4 61.2 + - - +
257A SER* 3.8 5.7 + - - -
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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