Contacts of the helix formed by residues 238 - 260 (chain A) in PDB entry 4BKR
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 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS 3.5 11.0 - - - -
159A PRO* 4.0 4.3 - - - -
160A ILE* 3.6 9.5 - - - +
232A HIS 3.7 2.4 + - - -
233A ASP 3.7 11.7 - - - -
234A ILE 4.1 4.0 - - - -
235A TYR 2.9 10.7 + - - -
237A ASN* 1.3 81.4 - - - +
239A SER* 1.3 64.9 + - - -
240A ILE 3.3 2.7 - - - -
241A GLY 3.0 2.5 + - - -
242A ALA 3.0 17.2 + - - -
245A LYS* 5.3 0.2 + - - -
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ALA* 2.6 30.2 + - - +
158A LYS 2.9 25.1 + - - -
160A ILE* 3.8 11.6 - - - +
184A ALA* 4.1 19.3 - - - -
189A ILE* 4.6 8.5 - - - +
192A THR* 3.4 21.8 - - - +
238A GLY* 1.3 71.9 - - - -
240A ILE* 1.3 62.1 + - - +
242A ALA* 3.2 15.0 + - - +
243A ALA 3.3 8.1 + - - -
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER* 5.3 1.8 - - - +
157A LEU* 4.0 29.2 - - + -
192A THR* 3.8 12.3 - - + -
196A MET* 3.7 43.5 - - + -
234A ILE 3.9 6.3 - - - +
235A TYR* 3.6 59.0 - - + +
239A SER* 1.3 82.3 + - - +
241A GLY* 1.3 59.9 + - - +
243A ALA* 3.3 4.0 + - - +
244A LYS* 3.0 28.6 + - + +
282A ILE* 5.3 2.9 - - + -
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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
----------------------------------------------------------
235A TYR* 3.0 26.6 + - - -
236A TRP* 3.2 21.5 - - - -
238A GLY 3.0 2.3 + - - -
240A ILE* 1.3 74.7 - - - +
242A ALA* 1.3 55.3 + - - +
244A LYS* 3.6 8.1 - - - +
245A LYS* 2.7 40.8 + - - +
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Residues in contact with ALA 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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160A ILE* 4.4 6.5 - - + -
189A ILE* 3.9 25.8 - - + -
193A VAL* 3.8 10.8 - - + +
236A TRP 4.3 0.2 + - - -
238A GLY 3.0 11.5 + - - +
239A SER* 3.2 11.6 + - - +
241A GLY* 1.3 74.4 - - - +
243A ALA* 1.3 60.5 + - - +
245A LYS* 3.5 14.7 + - - +
246A ASP* 3.2 19.9 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A THR* 3.5 28.9 - - + +
193A VAL* 3.9 12.3 - - - +
196A MET* 3.6 26.5 - - + +
197A GLY* 3.4 10.4 - - - +
239A SER 3.3 4.9 + - - +
240A ILE 3.3 9.8 + - - +
241A GLY 3.1 0.2 - - - -
242A ALA* 1.3 78.1 - - - +
244A LYS* 1.3 65.5 + - - +
246A ASP* 3.0 18.9 + - - +
247A LEU* 3.4 3.3 + - - +
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Residues in contact with LYS 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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196A MET* 4.0 21.9 + - - +
223A PHE 3.0 16.6 + - - -
224A THR* 3.5 28.3 + - - +
235A TYR* 3.5 28.5 - - + +
236A TRP* 4.0 13.8 - - + -
240A ILE* 3.0 20.9 + - + +
241A GLY* 3.2 7.4 + - - +
243A ALA* 1.3 76.6 - - + +
245A LYS* 1.3 62.3 + - - +
247A LEU* 3.1 34.4 + - + +
248A ASP* 3.7 7.4 + - - +
268A VAL* 5.6 0.3 - - - +
1400A NAI 2.9 42.6 + - - -
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Residues in contact with LYS 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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160A ILE* 6.3 0.8 - - - +
236A TRP* 2.9 61.9 + - + +
237A ASN* 3.2 21.4 + - - +
238A GLY 5.3 0.2 + - - -
241A GLY 2.7 25.7 + - - +
242A ALA* 3.7 11.1 - - - +
243A ALA 3.2 0.2 - - - -
244A LYS* 1.3 73.6 - - - +
246A ASP* 1.3 61.3 + - - +
248A ASP* 3.1 27.4 + - - +
249A GLN* 3.7 9.2 + - - +
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Residues in contact with ASP 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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193A VAL* 3.9 22.0 - - + +
197A GLY* 3.6 3.2 - - - -
198A GLY 2.8 23.4 + - - -
199A GLU* 4.2 0.9 + - - +
242A ALA 3.2 12.2 + - - +
243A ALA 3.0 14.2 + - - +
245A LYS* 1.3 76.2 - - - +
247A LEU* 1.3 63.2 + - - +
249A GLN* 3.0 14.8 + - - +
250A LYS* 2.9 42.4 + - - +
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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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137A TYR* 5.6 3.8 - - + -
196A MET 4.3 3.6 - - - +
197A GLY 3.8 9.4 - - - +
198A GLY* 3.8 23.3 - - - -
201A TRP* 4.0 18.6 - - + -
222A ALA* 4.5 9.9 - - + -
223A PHE 3.8 16.6 - - - +
224A THR* 4.1 9.4 - - - -
243A ALA 3.4 6.5 + - - +
244A LYS* 3.1 39.5 + - + +
246A ASP* 1.3 77.2 - - - +
248A ASP* 1.3 57.7 + - - +
250A LYS* 3.9 4.6 - - - +
251A VAL* 3.0 33.6 + - - +
268A VAL* 3.5 19.3 - - + +
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Residues in contact with ASP 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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236A TRP* 3.7 14.7 - - - -
244A LYS 4.1 5.1 - - - +
245A LYS* 3.1 15.6 + - - +
247A LEU* 1.3 76.6 - - - +
249A GLN* 1.3 66.5 + - - +
251A VAL* 3.5 18.7 - - - +
252A LEU* 3.7 13.2 - - - +
268A VAL* 3.7 17.2 - - - +
327A GLU* 4.7 15.4 - - + +
329A ARG* 2.9 49.2 + - - +
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Residues in contact with GLN 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 LYS 4.1 9.6 - - - +
246A ASP* 3.0 19.0 + - - +
248A ASP* 1.3 90.0 + - - +
250A LYS* 1.3 65.3 + - + +
252A LEU* 4.1 24.5 + - - +
253A ALA* 4.5 4.2 + - - +
327A GLU* 5.9 1.0 + - - -
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Residues in contact with LYS 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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198A GLY* 3.4 26.7 - - - +
199A GLU* 3.7 21.7 + - - +
201A TRP* 4.4 9.6 - - + -
202A GLN* 3.3 33.0 - - - +
246A ASP* 2.9 43.7 + - - +
247A LEU 3.9 3.6 - - - +
249A GLN* 1.3 77.6 - - + +
251A VAL* 1.3 66.1 + - - +
252A LEU 2.9 4.6 + - - -
253A ALA* 3.1 16.1 + - - +
254A ILE* 3.2 18.3 + - + +
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Residues in contact with VAL 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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201A TRP* 3.9 14.8 - - + -
247A LEU 3.0 16.1 + - - +
248A ASP* 3.5 20.2 - - - +
250A LYS* 1.3 75.7 - - - +
252A LEU* 1.3 64.5 + - + +
254A ILE* 3.2 3.7 + - - +
255A ARG* 2.7 42.6 + - - +
266A ALA* 3.3 34.1 - - + +
267A ARG* 3.5 18.6 - - - +
268A VAL* 3.8 13.0 - - + +
327A GLU* 6.1 0.4 - - - +
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Residues in contact with LEU 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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248A ASP 3.7 16.4 - - - +
249A GLN* 4.2 21.3 - - - +
250A LYS 2.9 0.4 + - - -
251A VAL* 1.3 84.6 - - + +
253A ALA* 1.3 63.7 + - - +
255A ARG* 3.2 28.2 + - - +
256A GLU* 3.0 23.6 + - - +
327A GLU* 4.9 13.7 - - - +
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Residues in contact with ALA 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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202A GLN* 4.2 17.0 - - - +
249A GLN 4.5 4.1 + - - +
250A LYS* 3.1 9.4 + - - +
252A LEU* 1.3 78.5 - - - +
254A ILE* 1.3 62.9 + - - +
256A GLU* 3.3 20.3 - - - +
257A SER* 3.3 10.2 + - - -
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Residues in contact with ILE 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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201A TRP* 3.7 45.1 - - + +
202A GLN* 4.4 24.0 - - + +
205A ILE* 4.0 22.4 - - + -
220A THR* 3.5 29.2 - - + -
250A LYS* 3.2 17.4 + - + +
251A VAL* 3.7 5.6 - - - +
252A LEU 3.2 0.4 - - - -
253A ALA* 1.3 76.3 - - + +
255A ARG* 1.3 64.6 + - - +
257A SER* 2.7 22.5 + - - -
258A LEU* 3.3 10.2 - - + +
266A ALA* 3.7 4.0 - - + -
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Residues in contact with ARG 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 VAL* 2.7 33.9 + - - +
252A LEU* 3.6 26.0 - - - +
254A ILE* 1.3 73.3 - - - +
256A GLU* 1.3 62.9 + - - +
258A LEU* 3.4 1.1 + - - +
259A ALA* 3.0 32.8 + - + +
264A GLY 4.8 0.2 - - - +
265A ASP* 3.1 26.7 + - - +
266A ALA* 2.6 34.0 + - - +
267A ARG* 3.5 26.5 - - - +
268A VAL 5.0 0.6 - - - +
327A GLU 5.0 3.6 + - - -
328A GLY* 3.1 29.5 + - - -
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Residues in contact with GLU 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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252A LEU 3.0 12.7 + - - +
253A ALA* 3.3 14.6 - - - +
255A ARG* 1.3 79.1 - - - +
257A SER* 1.3 61.6 + - - +
259A ALA* 4.2 4.7 - - - +
260A ALA* 3.7 18.2 + - - +
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Residues in contact with SER 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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205A ILE* 4.7 2.4 - - - +
206A ASP* 6.1 0.4 - - - -
209A LEU* 4.2 21.9 - - - +
253A ALA 3.3 6.0 + - - -
254A ILE* 2.7 27.2 + - - +
256A GLU* 1.3 82.4 - - - +
258A LEU* 1.3 71.3 + - - +
260A ALA* 3.8 6.3 + - - +
261A HIS* 3.7 17.0 + - - +
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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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205A ILE* 4.6 6.1 - - + -
209A LEU* 4.8 8.3 - - + -
214A LEU* 4.2 26.5 - - + -
215A ALA 5.9 0.2 - - - +
218A ALA* 4.1 15.5 - - + +
219A GLN* 4.6 0.7 - - - -
220A THR* 3.8 25.8 - - + +
254A ILE* 3.3 19.6 + - + +
255A ARG 4.2 1.6 - - - +
257A SER* 1.3 85.9 - - - +
259A ALA* 1.3 60.1 + - - +
260A ALA 3.1 2.5 - - - -
261A HIS* 2.9 29.4 + - + +
264A GLY* 2.9 18.9 + - - -
265A ASP* 3.5 34.3 - - - +
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Residues in contact with ALA 259 (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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255A ARG* 3.0 22.5 + - + +
256A GLU* 4.2 5.6 - - - +
258A LEU* 1.3 77.5 - - - +
260A ALA* 1.3 59.6 + - - +
263A GLY* 3.3 19.2 + - - -
264A GLY 3.3 18.1 + - - +
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Residues in contact with ALA 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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216A GLU* 5.3 0.2 - - - +
256A GLU 3.7 10.9 + - - +
257A SER* 3.9 10.3 - - - +
258A LEU 3.1 0.2 - - - -
259A ALA* 1.3 78.3 - - - +
261A HIS* 1.3 56.8 + - - +
262A GLY 3.4 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