Contacts of the helix formed by residues 244 - 268 (chain A) in PDB entry 4YCV
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 ASN 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LYS 4.3 5.3 - - - +
227A LEU* 4.4 24.3 + - - +
228A LYS* 4.5 8.7 - - - +
233A ARG* 4.2 12.3 - - - +
240A ASP* 2.8 40.9 + - - +
241A LEU 3.8 9.1 - - - +
242A LEU 4.9 0.7 - - - -
243A ILE* 1.3 88.9 - - - +
245A GLU* 1.3 64.1 + - - +
246A SER* 4.2 15.8 + - - +
247A SER* 3.8 5.8 + - - +
248A ARG 3.9 4.3 + - - -
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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
----------------------------------------------------------
158A GLY* 5.1 12.8 - - - +
241A LEU 5.3 0.9 - - - -
242A LEU 5.9 0.2 - - - -
243A ILE 3.7 4.0 + - - -
244A ASN* 1.3 72.8 - - - +
246A SER* 1.3 68.8 + - - +
248A ARG* 2.9 27.3 + - + +
249A HIS* 2.9 47.0 + - - +
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 4.2 13.4 + - - +
245A GLU* 1.3 85.9 + - - +
247A SER* 1.3 55.7 + - - +
249A HIS* 3.6 4.5 + - - +
250A THR* 2.5 37.3 + - - -
567A LYS* 4.6 13.1 + - - -
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 4.6 3.5 + - - -
237A ARG* 4.0 4.7 + - - -
240A ASP* 2.5 42.3 + - - -
241A LEU* 4.2 3.8 - - - -
244A ASN* 3.8 5.4 + - - +
245A GLU 3.1 0.4 - - - -
246A SER* 1.3 80.8 + - - +
248A ARG* 1.3 66.6 + - - +
250A THR* 3.1 8.3 + - - -
251A PHE* 2.9 41.5 + - - -
567A LYS* 4.8 5.6 + - - +
572A ASP 5.2 2.3 + - - -
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Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 3.7 30.3 + - - +
158A GLY* 3.8 21.9 - - - +
241A LEU* 3.7 31.4 - - + +
244A ASN 3.9 5.3 + - - +
245A GLU* 2.9 22.2 + - + +
247A SER* 1.3 78.6 - - - +
249A HIS* 1.3 64.7 + - - +
251A PHE* 3.1 4.8 + - - +
252A VAL* 3.0 41.4 + - + +
271B PHE* 5.9 4.9 - - - -
317B GLY 5.1 0.8 + - - -
318B GLY* 2.6 37.2 + - - -
319B ILE* 3.8 19.4 - - - +
320B ASP 5.7 0.2 - - - +
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Residues in contact with HIS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 2.9 37.0 + - - +
246A SER* 3.8 5.8 - - - +
248A ARG* 1.3 77.9 - - - +
250A THR* 1.3 63.8 + - - +
252A VAL* 3.3 13.4 + - + +
253A THR* 2.9 38.9 + - - -
256A LYS* 6.2 2.3 + - - -
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Residues in contact with THR 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER 2.5 23.1 + - - -
247A SER* 3.2 12.8 - - - +
249A HIS* 1.3 78.0 + - - +
251A PHE* 1.3 60.4 + - + +
253A THR* 3.3 4.6 + - - -
254A ARG* 2.9 23.2 + - - +
561A THR* 4.9 0.7 - - + -
565A THR* 3.6 35.3 + - + +
567A LYS* 3.0 23.4 + - - +
572A ASP 3.9 20.2 - - - +
573A VAL* 4.2 12.1 - - + -
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Residues in contact with PHE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ARG* 3.6 32.5 - - - -
241A LEU* 3.7 21.8 - - + -
247A SER* 2.9 32.0 + - - +
248A ARG* 3.1 3.8 + - - +
250A THR* 1.3 74.7 - - + +
252A VAL* 1.3 67.4 + - - +
254A ARG* 3.0 20.5 + - + +
255A THR* 3.0 17.3 + - - +
572A ASP 3.6 16.6 - - - -
573A VAL 3.5 19.7 - - - -
574A ILE 3.5 6.5 - - - -
575A LEU* 3.5 50.5 - - + -
271B PHE* 4.0 11.5 - - + -
273B VAL* 6.4 0.4 - - + -
319B ILE* 6.2 2.7 - - + -
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 3.0 41.4 + - + +
249A HIS* 3.5 16.4 - - + +
251A PHE* 1.3 75.3 - - - +
253A THR* 1.3 64.5 + - - +
255A THR* 3.0 15.1 + - - -
256A LYS* 3.1 38.1 + - + +
271B PHE* 3.4 30.7 - - + -
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A HIS* 2.9 30.2 + - - -
250A THR* 3.3 10.5 - - - -
252A VAL* 1.3 77.7 - - - +
254A ARG* 1.3 62.9 + - - +
256A LYS* 3.3 14.7 + - - +
257A ILE* 2.9 37.4 + - + +
372A LEU* 4.3 19.7 - - + +
373A PHE* 5.6 2.9 - - + -
564A LEU 4.9 6.1 - - - +
565A THR* 3.7 21.1 - - + +
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Residues in contact with ARG 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 THR* 2.9 12.1 + - + +
251A PHE* 3.0 19.0 + - + +
253A THR* 1.3 76.7 - - - +
255A THR* 1.3 63.2 + - - +
257A ILE* 3.1 7.2 + - - +
258A ILE* 3.0 33.7 + - + +
327A LYS* 4.6 3.2 - - - +
343A THR* 3.4 12.9 + - - -
557A ILE* 4.9 2.3 - - + +
558A ASP* 2.5 39.7 + - - +
561A THR* 3.7 31.5 + - + +
573A VAL* 2.5 47.2 + - - +
574A ILE* 4.1 5.4 - - - +
575A LEU* 6.2 2.7 - - - -
274B GLU* 2.7 37.8 + - - +
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Residues in contact with THR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE 3.0 9.7 + - - +
252A VAL 3.0 13.0 + - - -
254A ARG* 1.3 84.4 - - + +
256A LYS* 1.3 57.8 + - - +
258A ILE* 3.9 15.7 - - + +
259A ASN* 2.9 37.2 + - - +
271B PHE* 3.1 25.5 - - + -
272B GLU* 3.0 37.0 - - + +
273B VAL* 4.6 6.1 - - + -
274B GLU* 5.7 1.6 - - + +
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Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A HIS* 6.2 1.8 - - - -
252A VAL* 3.1 38.4 + - + +
253A THR* 3.8 12.2 + - - +
255A THR* 1.3 76.1 + - - +
257A ILE* 1.3 60.0 + - - +
259A ASN* 3.6 13.9 - - + +
260A PHE* 2.9 28.2 + - - +
368A LEU* 4.9 0.5 - - - +
371A HIS* 4.7 20.0 + - + -
372A LEU* 4.0 27.1 + - + +
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Residues in contact with ILE 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 THR* 2.9 26.6 + - + +
254A ARG* 3.2 7.2 - - - +
256A LYS* 1.3 77.4 - - - +
258A ILE* 1.3 59.7 + - - +
260A PHE* 3.3 2.6 + - - +
261A LEU* 2.9 29.9 + - + +
364A PHE* 5.1 4.3 - - + -
368A LEU* 4.3 22.2 - - + +
372A LEU* 4.0 18.4 - - + -
557A ILE* 4.7 11.7 - - + -
560A ILE* 4.9 8.7 - - + -
561A THR* 3.8 35.4 - - + +
564A LEU* 3.8 28.9 - - + -
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Residues in contact with ILE 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 ARG* 3.0 24.6 + - + +
255A THR* 3.9 13.2 - - + +
257A ILE* 1.3 76.6 - - - +
259A ASN* 1.3 57.6 - - - +
261A LEU* 3.2 8.0 + - - +
262A ARG* 2.9 53.2 + - - +
325A ILE* 4.2 20.4 - - + -
343A THR* 5.3 1.8 - - + -
557A ILE* 3.9 25.8 - - + -
272B GLU* 6.0 1.3 - - - +
274B GLU* 3.1 34.1 - - + +
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Residues in contact with ASN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A THR* 2.9 28.8 + - - +
256A LYS* 3.6 15.1 - - + +
258A ILE* 1.3 77.9 - - - +
260A PHE* 1.3 57.5 + - - +
262A ARG* 3.3 9.6 + - - +
263A ASN* 2.9 41.8 + - - +
262B ARG* 5.6 2.3 - - - -
266B ASN* 4.5 18.2 + - - +
272B GLU* 4.4 13.7 - - - +
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Residues in contact with PHE 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 LYS 2.9 20.3 + - - +
257A ILE 3.7 2.9 - - - +
259A ASN* 1.3 76.4 - - - +
261A LEU* 1.3 56.7 + - - +
263A ASN* 4.6 5.2 - - + -
264A PHE* 2.8 67.7 + + - +
364A PHE* 3.7 15.3 - + - -
367A GLN* 3.8 10.5 - - + -
368A LEU* 3.5 53.2 - - + -
371A HIS* 4.0 37.2 - + + +
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Residues in contact with LEU 261 (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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257A ILE* 2.9 18.5 + - + +
258A ILE* 3.5 5.8 - - - +
260A PHE* 1.3 77.4 - - - +
262A ARG* 1.3 58.1 + - - +
264A PHE* 3.3 3.2 + - - +
265A LEU* 2.9 49.3 + - + +
325A ILE* 4.4 8.5 - - + -
345A CYS* 3.6 33.7 - - + -
360A TRP* 4.1 11.7 - - + -
364A PHE* 3.8 32.3 - - + -
555A LEU* 3.9 18.8 - - + -
557A ILE* 3.7 21.1 - - + -
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Residues in contact with ARG 262 (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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258A ILE* 2.9 37.3 + - - +
259A ASN* 3.7 9.2 + - - +
261A LEU* 1.3 76.6 - - - +
263A ASN* 1.3 63.4 + - - +
265A LEU* 3.5 3.9 + - - +
266A ASN* 2.9 44.6 + - - +
272A GLU* 2.3 49.4 + - - -
323A TYR* 3.7 10.5 - - - +
325A ILE* 4.0 25.2 + - + +
259B ASN* 5.3 2.2 - - - -
262B ARG* 3.2 47.6 - - - +
272B GLU* 3.9 10.9 + - - -
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Residues in contact with ASN 263 (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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259A ASN* 2.9 31.1 + - - +
260A PHE* 4.0 7.0 - - + +
262A ARG* 1.3 78.4 - - - +
264A PHE* 1.3 66.9 + - - +
266A ASN* 3.7 7.5 - - - +
267A GLU* 2.9 45.6 + - - +
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Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 2.8 46.9 + + + +
261A LEU* 3.3 8.5 - - - +
263A ASN* 1.3 77.8 - - - +
265A LEU* 1.3 60.9 + - - +
267A GLU* 3.7 9.5 + - - +
268A ARG* 2.2 63.5 + - - +
360A TRP* 4.0 25.1 - + - -
363A ASP* 3.8 10.1 - - + -
364A PHE* 3.3 49.8 - + + -
367A GLN* 3.2 26.0 - - - -
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Residues in contact with LEU 265 (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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261A LEU* 2.9 25.9 + - + +
262A ARG 3.8 4.0 - - - +
264A PHE* 1.3 75.0 - - - +
266A ASN* 1.3 64.7 + - - +
268A ARG* 3.0 12.4 + - - +
270A PHE* 3.2 54.2 + - + +
323A TYR* 3.5 36.8 - - + -
345A CYS* 3.8 22.9 - - - -
347A PHE* 4.1 11.7 - - + -
360A TRP* 3.4 31.4 - - + +
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Residues in contact with ASN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ARG* 2.9 30.2 + - - +
263A ASN* 3.2 8.9 + - - +
265A LEU* 1.3 74.5 - - - +
267A GLU* 1.3 63.1 + - + +
269A GLY* 3.1 15.2 + - - -
270A PHE 4.1 10.8 - - - +
272A GLU* 5.1 0.7 + - - +
323A TYR* 2.5 36.4 + - - -
259B ASN* 4.6 19.0 + - - +
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 2.9 35.1 + - + +
264A PHE* 3.9 9.9 - - - +
265A LEU 3.2 0.2 - - - -
266A ASN* 1.3 76.2 - - + +
268A ARG* 1.3 66.7 + - + +
269A GLY 3.3 1.6 + - - -
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 2.2 86.2 + - - +
265A LEU 3.0 8.9 + - - +
267A GLU* 1.3 86.6 + - - +
269A GLY* 1.3 60.5 + - - +
270A PHE* 3.3 15.5 - - + -
321A LYS* 3.4 21.4 - - + +
349A TRP* 5.9 5.2 - - + -
360A TRP* 4.2 23.3 - - - +
363A ASP* 5.4 2.8 + - - +
367A GLN* 4.5 8.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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