Contacts of the helix formed by residues 248 - 274 (chain A) in PDB entry 5AVL
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 GLU 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 1.3 77.1 - - - +
249A ALA* 1.3 65.5 + - - +
250A ARG 3.1 2.0 + - - -
251A GLN* 3.3 8.5 + - + +
252A GLN* 3.0 24.4 + - - +
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 5.0 2.9 - - - +
248A GLU* 1.3 77.4 - - - +
250A ARG* 1.3 54.3 + - - +
252A GLN* 3.5 7.5 + - - +
253A ARG* 3.0 51.6 + - - +
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 3.2 52.0 + - + +
248A GLU 3.1 0.2 - - - -
249A ALA* 1.3 75.8 - - - +
251A GLN* 1.3 60.8 + - - +
253A ARG* 3.5 20.9 + - - +
254A PHE* 3.2 26.5 + - - +
327A ALA 3.5 16.0 + - - -
328A LYS* 3.9 21.9 + - - +
330A GLY* 3.5 17.8 + - - -
331A LEU 5.4 0.2 + - - -
431A GLN* 5.2 3.2 - - - +
433A LYS* 3.2 32.0 + - - +
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Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 3.8 9.4 + - - +
248A GLU* 3.3 10.7 + - + +
250A ARG* 1.3 79.1 - - + +
252A GLN* 1.3 59.6 + - - +
254A PHE* 3.4 27.8 - - - -
255A ALA* 3.1 26.9 + - - +
432A ASP 4.2 5.9 + - - +
433A LYS* 3.4 32.4 - - - +
434A LYS 4.7 8.5 + - - +
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 5.8 13.2 - - + +
237A PRO* 5.9 4.9 - - - +
248A GLU 3.0 16.7 + - - +
249A ALA* 3.9 7.9 - - - +
250A ARG 3.3 0.2 - - - -
251A GLN* 1.3 76.2 - - - +
253A ARG* 1.3 58.8 + - - +
255A ALA* 3.1 8.8 + - + +
256A HIS* 2.9 29.3 + - - +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TRP* 3.6 49.7 - - + -
249A ALA* 3.0 38.0 + - - +
250A ARG* 3.5 27.8 + - - +
252A GLN* 1.3 70.8 - - - +
254A PHE* 1.3 65.6 + - - +
256A HIS* 3.5 5.2 + - - +
257A PHE* 3.4 21.1 + - - +
328A LYS* 3.0 63.2 + - - +
329A ALA* 4.2 3.1 - - - +
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Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ARG 3.2 15.0 + - - +
251A GLN* 3.4 31.4 - - - +
253A ARG* 1.3 77.9 - - - +
255A ALA* 1.3 67.5 + - + +
257A PHE* 3.2 4.4 + - + +
258A THR* 3.0 43.7 + - + +
329A ALA* 3.4 25.6 + - - +
330A GLY* 4.4 4.5 - - - -
331A LEU* 5.4 0.2 - - + -
428A LEU* 4.2 12.3 - - + -
433A LYS* 4.2 28.9 - - + +
434A LYS 3.7 25.1 - - - -
435A LEU* 4.3 9.0 - - + -
436A PRO* 5.3 0.7 - - + -
501A 4KQ 3.7 27.6 - + - -
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 5.7 0.9 - - - +
251A GLN* 3.1 13.7 + - - +
252A GLN* 3.1 15.5 + - + +
254A PHE* 1.3 82.9 - - + +
256A HIS* 1.3 56.6 + - - +
258A THR* 2.7 23.2 + - - +
259A GLU* 3.0 29.6 + - - +
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Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 3.6 23.3 - - + +
236A THR* 2.9 38.0 + - - +
237A PRO 3.4 17.3 - - - +
238A TRP* 3.7 24.8 - + + +
252A GLN 2.9 14.6 + - - +
253A ARG* 4.0 4.9 - - - +
254A PHE 3.4 0.2 - - - -
255A ALA* 1.3 74.3 - - - +
257A PHE* 1.3 60.4 - - - +
259A GLU* 3.7 7.5 + - - +
260A LEU* 3.3 27.9 + - + +
319A PHE* 4.4 21.4 - + - -
321A TYR* 3.1 28.5 + - - -
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Residues in contact with PHE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TRP* 5.6 0.2 - - + -
253A ARG 3.4 10.1 + - - +
254A PHE* 3.2 10.0 + - + +
255A ALA 3.1 0.4 - - - -
256A HIS* 1.3 75.9 - - + +
258A THR* 1.3 65.9 + - - +
260A LEU* 3.3 18.4 + - + +
261A ALA 3.3 8.5 + - - -
315A PHE* 4.1 8.5 - + - -
321A TYR* 3.8 35.0 - + - -
326A PHE* 3.9 31.2 - + - -
329A ALA* 3.6 25.8 - - + +
331A LEU* 3.8 28.3 - - + -
501A 4KQ 3.3 56.5 - + + +
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Residues in contact with THR 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 PHE* 3.0 43.4 + - + +
255A ALA* 2.7 25.3 + - - -
257A PHE* 1.3 74.3 - - - +
259A GLU* 1.3 58.0 + - - +
261A ALA* 3.4 1.1 + - - -
262A ILE* 3.0 32.4 + - - +
435A LEU* 4.7 0.9 - - + -
436A PRO* 3.8 24.0 - - + +
439A LEU* 3.5 17.4 - - + +
501A 4KQ 3.9 21.3 - - + -
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 4.0 14.8 - - + +
236A THR* 2.8 39.5 + - - +
255A ALA* 3.0 27.4 + - - +
256A HIS* 3.8 6.3 - - - +
257A PHE 3.2 0.2 - - - -
258A THR* 1.3 77.1 + - - +
260A LEU* 1.3 64.5 + - - +
262A ILE* 3.2 16.9 + - + +
263A VAL* 3.0 28.4 + - - +
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Residues in contact with LEU 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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235A VAL* 4.6 17.0 - - + -
256A HIS* 3.3 22.1 + - + +
257A PHE* 3.3 15.6 + - + +
259A GLU* 1.3 76.9 - - - +
261A ALA* 1.3 59.0 + - - +
263A VAL* 3.5 9.0 + - + +
264A SER* 2.9 26.9 + - - -
315A PHE* 4.5 10.8 - - + -
316A LEU* 3.6 31.9 - - + -
319A PHE* 5.5 4.9 - - + -
321A TYR* 3.7 29.4 - - + +
501A 4KQ 3.6 32.3 - - + -
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Residues in contact with ALA 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 PHE 3.3 3.6 + - - +
258A THR 3.6 8.1 - - - +
259A GLU 3.3 0.4 - - - -
260A LEU* 1.3 75.1 - - - +
262A ILE* 1.3 55.8 + - - +
264A SER* 2.9 3.5 + - - -
265A VAL* 2.8 36.7 + - - +
298A MET* 3.4 15.5 - - + +
439A LEU* 3.8 19.7 - - + -
443A TRP* 4.4 2.2 - - + -
501A 4KQ 3.5 37.1 - - + +
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Residues in contact with ILE 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 THR* 3.0 20.1 + - - +
259A GLU* 3.2 21.3 + - + +
261A ALA* 1.3 75.2 - - - +
263A VAL* 1.3 63.5 + - + +
265A VAL* 3.2 13.2 + - - +
266A GLN* 3.0 30.9 + - - +
436A PRO* 3.7 26.7 - - + -
438A LEU* 3.9 25.4 - - + +
439A LEU* 3.9 19.5 - - + -
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Residues in contact with VAL 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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235A VAL* 4.4 22.2 - - + -
259A GLU* 3.0 18.3 + - + +
260A LEU* 3.5 13.0 - - + +
262A ILE* 1.3 75.8 - - + +
264A SER* 1.3 65.3 + - - +
266A GLN* 3.1 26.8 + - - +
267A GLU* 3.1 27.9 + - + +
316A LEU* 5.3 13.2 - - + -
501A 4KQ 5.5 4.0 - - + -
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Residues in contact with SER 264 (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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260A LEU 2.9 16.1 + - - -
261A ALA 2.9 8.2 + - - -
263A VAL* 1.3 77.7 - - - +
265A VAL* 1.3 62.5 + - - +
267A GLU* 2.9 13.0 + - - +
268A ILE* 2.9 34.7 + - - +
298A MET* 3.5 22.0 - - - +
301A GLU* 5.4 3.6 - - - +
501A 4KQ 3.6 32.6 - - - -
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Residues in contact with VAL 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 ALA 2.8 21.4 + - - +
262A ILE 3.2 7.2 + - - +
264A SER* 1.3 73.0 - - - +
266A GLN* 1.3 62.2 + - - +
268A ILE* 3.2 10.0 + - + +
269A VAL* 3.0 28.1 + - + +
294A ALA* 5.0 6.1 - - + -
298A MET* 3.5 18.3 - - + +
438A LEU* 3.8 29.2 - - + -
439A LEU* 4.0 11.9 - - + -
442A ILE* 4.0 22.0 - - + -
690B LEU* 4.5 7.9 - - + -
693B LEU* 4.4 7.2 - - + -
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Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 3.0 42.7 + - - +
263A VAL* 3.1 17.3 + - + +
265A VAL* 1.3 75.0 - - - +
267A GLU* 1.3 58.0 + - + +
269A VAL* 3.2 4.2 + - - +
270A ASP* 3.0 38.8 + - - +
438A LEU* 5.1 1.3 - - + -
693B LEU* 3.8 38.2 - - + +
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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 VAL* 3.1 26.8 + - + +
264A SER* 2.9 13.4 + - - +
266A GLN* 1.3 76.3 - - + +
268A ILE* 1.3 52.6 + - + +
270A ASP* 3.3 9.6 + - - +
271A PHE* 2.8 35.9 + - - +
301A GLU* 5.6 3.5 - - - +
305A ARG* 5.8 0.3 + - - -
316A LEU* 6.0 1.6 - - - +
501A 4KQ 4.4 22.1 - - - +
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Residues in contact with ILE 268 (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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264A SER* 2.9 38.6 + - - +
265A VAL* 3.5 12.1 - - + +
267A GLU* 1.3 70.2 - - + +
269A VAL* 1.3 59.9 + - + +
271A PHE* 3.7 8.5 - - + +
272A ALA* 3.0 27.4 + - - +
290A LEU* 4.0 20.0 - - + -
293A SER* 5.2 0.2 - - - +
294A ALA* 3.6 38.4 - - + +
297A VAL* 3.8 37.0 - - + -
298A MET* 4.0 5.2 - - + +
301A GLU* 6.1 0.7 - - + -
364A ILE* 4.9 4.7 - - + +
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Residues in contact with VAL 269 (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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265A VAL* 3.0 19.4 + - + +
266A GLN 3.2 7.8 + - - +
268A ILE* 1.3 72.6 - - + +
270A ASP* 1.3 71.3 - - - +
272A ALA* 2.9 12.5 + - - +
273A LYS* 2.9 32.4 + - - +
290A LEU* 3.9 13.9 - - + -
690B LEU* 3.8 29.6 - - + -
693B LEU* 3.8 30.7 - - + +
694B LEU* 3.8 21.0 - - + +
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLN* 3.0 28.4 + - - +
267A GLU* 3.6 8.0 - - - +
269A VAL* 1.3 81.0 - - - +
271A PHE* 1.3 61.7 + - - +
273A LYS* 3.3 26.1 + - - +
274A GLN* 3.3 20.9 + - - +
693B LEU 5.3 0.7 - - - +
696B GLU* 5.7 0.9 - - - +
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.6 22.9 - - + -
220A ALA* 4.0 18.6 - - + +
221A GLN* 3.5 41.7 - - + -
267A GLU 2.8 20.4 + - - +
268A ILE* 3.7 8.7 - - - +
269A VAL 3.2 0.2 - - - -
270A ASP* 1.3 73.1 - - - +
272A ALA* 1.3 62.8 + - - +
274A GLN* 3.2 21.0 + - - +
275A LEU* 3.4 32.8 + - + +
357A ALA* 4.1 18.2 - - + -
360A ILE* 3.6 30.5 - - + -
361A ALA 4.5 0.7 - - - -
364A ILE* 4.2 9.0 - - + -
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Residues in contact with ALA 272 (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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268A ILE 3.0 16.7 + - - +
269A VAL* 2.9 6.9 + - - +
271A PHE* 1.3 71.7 - - - +
273A LYS* 1.3 58.8 + - - +
274A GLN 3.0 4.7 - - - -
275A LEU* 2.9 31.5 + - + +
278A PHE* 3.2 52.8 - - + +
290A LEU* 3.8 12.3 - - + -
364A ILE* 4.6 3.4 - - + -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 2.9 26.3 + - - +
270A ASP* 3.6 23.1 + - - +
271A PHE 3.2 0.2 - - - -
272A ALA* 1.3 77.9 - - - +
274A GLN* 1.3 58.8 + - + +
275A LEU 3.8 3.6 + - - +
278A PHE* 4.4 1.6 - - - -
279A LEU* 3.3 49.7 + - + +
693B LEU 3.6 20.6 + - - -
694B LEU* 3.7 25.5 + - + +
696B GLU* 3.2 33.7 + - - +
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LYS* 3.3 31.8 + - - +
217A LEU* 4.8 3.8 - - + +
220A ALA* 4.1 35.2 + - + +
270A ASP 3.3 17.3 - - - +
271A PHE 3.4 8.1 - - - +
272A ALA 3.0 0.4 - - - -
273A LYS* 1.3 78.9 - - + +
275A LEU* 1.3 62.0 + - - +
276A PRO* 3.3 9.7 - - - +
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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
------------------------------------------------------------
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