Contacts of the helix formed by residues 287 - 314 (chain E) in PDB entry 6C3P
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 ILE 287 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E ALA* 1.3 77.2 - - + +
288E TRP* 1.3 69.4 + - + +
289E GLN 3.1 2.2 - - - -
290E ALA* 3.1 11.3 + - + +
291E LEU* 2.9 27.1 + - + +
394E LYS* 6.3 1.6 - - - +
607E VAL* 3.6 30.5 - - + -
610E LEU* 4.5 20.2 - - + -
611E SER* 4.7 21.3 - - - +
614E LEU* 5.7 12.8 - - + -
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Residues in contact with TRP 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E ALA* 4.9 11.0 - - + +
287E ILE* 1.3 79.6 - - + +
289E GLN* 1.3 58.2 - - + +
291E LEU* 3.6 14.3 - - + +
292E SER* 2.9 33.5 + - - -
432E PHE* 6.6 0.2 - + - -
603E ALA 5.4 0.2 - - - -
604E LEU* 3.5 47.3 - - + -
607E VAL* 3.2 41.0 - - + +
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Residues in contact with GLN 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ALA* 5.4 3.8 - - + -
286E ALA 3.6 30.3 + - - +
287E ILE 3.1 0.8 - - - -
288E TRP* 1.3 78.3 - - + +
290E ALA* 1.3 58.9 + - - +
292E SER* 2.6 22.0 + - - -
293E HIS* 2.9 17.0 + - - +
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Residues in contact with ALA 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E GLU* 4.5 2.5 - - - +
269E ALA* 4.5 17.9 - - + +
272E ALA* 4.3 20.8 - - + +
286E ALA 4.1 1.5 + - - +
287E ILE* 3.1 14.8 + - + +
289E GLN* 1.3 75.5 - - - +
291E LEU* 1.3 65.8 + - - +
293E HIS* 3.7 6.5 - - - +
294E ALA* 2.9 26.3 + - - +
394E LYS* 6.0 4.0 - - - +
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Residues in contact with LEU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E ILE* 2.9 17.0 + - + +
288E TRP* 3.6 19.3 - - + +
290E ALA* 1.3 75.9 - - - +
292E SER* 1.3 67.0 + - - +
294E ALA* 3.0 6.3 + - - +
295E PHE* 2.9 49.5 + - + +
299E LEU* 5.2 2.7 - - + -
387E LEU* 3.7 40.2 - - + -
391E ILE* 5.8 1.6 - - + -
428E LEU* 6.4 0.7 - - + -
432E PHE* 4.1 23.3 - - + -
607E VAL* 6.6 0.4 - - + -
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Residues in contact with SER 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E TRP 2.9 17.2 + - - -
289E GLN* 2.6 26.2 + - - -
291E LEU* 1.3 78.7 - - - +
293E HIS* 1.3 63.3 + - - +
295E PHE 2.9 0.2 + - - -
296E GLY* 2.9 32.2 + - - +
299E LEU* 6.4 0.4 - - - -
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Residues in contact with HIS 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E GLU* 4.1 16.6 + - + +
271E ASP* 3.7 28.0 - - + +
272E ALA* 4.3 10.8 + - + +
275E ARG* 6.4 1.1 - - + -
289E GLN 2.9 15.9 + - - +
290E ALA* 3.7 7.2 - - - +
292E SER* 1.3 79.2 + - - +
294E ALA* 1.3 59.7 + - - +
296E GLY 5.1 0.3 + - - -
297E ARG* 5.6 3.6 + - - -
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Residues in contact with ALA 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E GLN* 4.8 7.9 - - + +
265E ARG* 4.8 9.0 - - + -
268E GLU* 3.4 24.9 - - + +
290E ALA 2.9 18.0 + - - +
291E LEU* 3.5 6.7 - - - +
293E HIS* 1.3 77.2 - - - +
295E PHE* 1.3 63.2 + - + +
297E ARG* 5.6 4.6 + - - +
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Residues in contact with PHE 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E LEU* 2.9 33.5 + - + +
292E SER 2.9 0.4 + - - -
294E ALA* 1.3 84.0 - - + +
296E GLY* 1.3 65.8 + - - +
297E ARG* 3.1 6.8 + - - -
298E ARG* 3.5 23.0 + - + +
299E LEU* 3.8 31.4 + - + -
383E THR* 3.2 53.4 - - + -
386E ASN* 4.6 13.5 - - + -
387E LEU* 4.8 15.3 - - + -
432E PHE* 4.9 7.6 - + - -
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Residues in contact with GLY 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E SER* 2.9 20.4 + - - -
295E PHE* 1.3 77.6 - - - +
297E ARG* 1.3 57.3 + - - +
298E ARG 3.3 0.2 - - - -
299E LEU* 3.3 13.9 + - - +
300E VAL* 2.9 37.0 + - - +
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Residues in contact with ARG 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E HIS 5.6 3.6 + - - -
294E ALA 5.6 5.1 + - - +
295E PHE* 4.7 4.5 - - - +
296E GLY* 1.3 77.5 - - - +
298E ARG* 1.3 63.3 + - + +
300E VAL* 3.1 13.3 - - + +
301E LEU* 2.9 29.3 + - - +
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Residues in contact with ARG 298 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E PHE* 3.5 17.0 + - + +
296E GLY 3.3 0.2 - - - -
297E ARG* 1.3 85.2 - - + +
299E LEU* 1.3 58.4 + - - +
301E LEU* 3.2 11.7 + - + +
302E SER* 3.0 23.9 + - - -
379E VAL* 3.5 19.1 - - + +
382E GLU* 3.1 35.5 + - - -
383E THR* 3.4 24.9 - - + +
386E ASN* 4.5 7.4 - - - +
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Residues in contact with LEU 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E LEU* 5.2 3.4 - - + -
292E SER* 6.4 0.7 - - - -
295E PHE* 3.8 35.0 - - + +
296E GLY* 3.3 13.3 + - - +
297E ARG 3.3 0.6 - - - -
298E ARG* 1.3 77.7 - - - +
300E VAL* 1.3 60.3 + - + +
302E SER* 3.2 6.2 + - - -
303E SER* 2.8 32.4 + - - +
380E ALA* 5.2 4.3 - - + -
383E THR* 3.8 28.5 - - + +
432E PHE* 4.0 16.2 - - + +
435E CYS* 3.7 35.8 - - + -
436E PRO* 4.8 1.7 - - + +
439E TRP* 5.9 1.8 - - + -
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Residues in contact with VAL 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E GLY* 2.9 23.0 + - - +
297E ARG* 3.1 22.2 - - + +
299E LEU* 1.3 77.8 - - + +
301E LEU* 1.3 53.1 + - - +
303E SER* 3.6 9.6 - - - -
304E THR* 2.6 39.3 + - - +
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Residues in contact with LEU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E ARG 2.9 14.4 + - - +
298E ARG* 3.3 13.5 - - + +
300E VAL* 1.3 75.9 - - - +
302E SER* 1.3 66.7 + - - +
304E THR* 3.2 8.5 + - - -
305E PHE* 3.0 59.7 + - + -
379E VAL* 3.8 18.6 - - + -
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Residues in contact with SER 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E ARG 3.0 8.7 + - - -
299E LEU* 3.6 9.2 - - - -
301E LEU* 1.3 75.9 - - - +
303E SER* 1.3 62.6 + - - +
305E PHE* 3.2 8.7 + - - +
306E ARG 3.0 7.1 + - - -
376E SER* 2.1 54.8 + - - -
379E VAL* 3.5 25.8 - - - -
380E ALA* 3.5 16.8 + - - +
436E PRO* 4.0 6.1 - - - +
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Residues in contact with SER 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E LEU* 2.8 21.5 + - - +
300E VAL* 3.6 10.6 - - - +
302E SER* 1.3 75.0 - - - +
304E THR* 1.3 55.1 + - - +
306E ARG* 2.6 26.3 + - - +
307E ILE* 2.8 27.9 + - - +
435E CYS* 5.7 0.5 - - - -
436E PRO* 3.4 30.8 + - - +
439E TRP* 4.6 15.7 - - - +
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Residues in contact with THR 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E VAL* 2.6 27.9 + - - +
301E LEU* 3.5 8.1 - - - -
303E SER* 1.3 71.4 - - - +
305E PHE* 1.3 69.4 + - + +
307E ILE* 3.9 9.9 - - + +
308E LEU* 2.9 32.5 + - + +
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Residues in contact with PHE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301E LEU* 3.0 47.6 + - + -
302E SER* 3.2 7.4 - - - +
304E THR* 1.3 81.8 - - + +
306E ARG* 1.3 56.7 + - - +
308E LEU* 3.9 5.3 - - + +
309E ALA* 2.9 31.6 + - - +
372E PHE* 4.0 10.9 - + + +
375E ALA* 3.4 36.1 - - + -
376E SER* 3.5 15.3 - - - +
379E VAL* 3.7 13.5 - - + -
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Residues in contact with ARG 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E SER 3.0 5.9 + - - +
303E SER* 2.6 17.8 + - - +
305E PHE* 1.3 72.7 - - - +
307E ILE* 1.3 56.2 + - - +
309E ALA* 3.4 3.3 + - - +
310E ASP* 2.9 40.0 + - - +
373E LEU* 3.9 23.2 + - - +
376E SER* 2.9 34.2 + - - +
377E TYR* 4.1 26.7 - - - +
433E PHE 5.2 2.6 + - - -
436E PRO* 3.8 17.0 - - + +
437E ASN* 3.6 34.7 + - - +
440E ALA* 3.5 24.9 - - + -
592E LEU* 5.6 4.0 - - - +
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Residues in contact with ILE 307 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E SER* 2.8 46.8 + - - +
304E THR* 3.9 10.3 - - + +
306E ARG* 1.3 70.1 - - - +
308E LEU* 1.3 67.2 + - - +
310E ASP* 2.5 22.7 - - - +
311E LEU* 2.9 22.6 + - + +
439E TRP* 4.6 4.7 - - + +
440E ALA* 4.0 28.3 - - + +
443E VAL* 4.2 33.0 - - + -
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Residues in contact with LEU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E THR* 2.9 24.1 + - + +
305E PHE* 3.9 5.2 - - + +
307E ILE* 1.3 77.8 - - - +
309E ALA* 1.3 67.2 + - - +
311E LEU* 3.8 6.0 - - - +
312E LEU* 2.9 28.1 + - + +
372E PHE* 3.6 34.1 - - + -
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Residues in contact with ALA 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E PHE 2.9 19.8 + - - +
306E ARG 3.5 4.3 - - - +
308E LEU* 1.3 75.5 - - - +
310E ASP* 1.3 58.0 + - - +
312E LEU* 2.8 18.4 + - - -
369E GLN* 2.2 52.0 + - - +
372E PHE* 3.8 14.1 - - + +
373E LEU* 3.6 18.4 - - + +
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Residues in contact with ASP 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ARG* 2.9 23.5 + - - +
307E ILE* 2.5 34.1 - - - +
309E ALA* 1.3 73.2 - - - +
311E LEU* 1.3 62.7 + - - +
313E GLY* 3.7 1.4 - - - -
314E PHE* 2.8 28.8 + - - +
369E GLN* 4.0 7.0 - - - +
373E LEU* 5.4 2.9 - - + -
440E ALA* 4.1 17.3 - - - +
443E VAL* 6.0 0.5 - - - +
444E GLN* 3.4 48.1 + - - +
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Residues in contact with LEU 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E ILE* 2.9 25.6 + - + +
308E LEU* 3.8 5.2 - - - +
310E ASP* 1.3 81.8 + - - +
312E LEU* 1.3 65.8 + - - +
314E PHE* 3.1 21.8 - - + +
315E ALA* 3.7 3.1 + - - +
443E VAL* 6.1 4.7 - - + -
444E GLN* 6.4 1.6 - - - +
447E VAL* 3.6 40.6 - - + -
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Residues in contact with LEU 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E LEU* 2.9 16.2 + - + +
309E ALA 2.8 14.1 + - - +
311E LEU* 1.3 67.1 - - - +
313E GLY* 1.3 54.2 + - - +
314E PHE 3.0 3.8 - - - -
315E ALA* 2.6 42.1 + - + +
365E ALA* 3.7 38.2 - - + +
368E LEU* 4.0 22.9 - - + -
369E GLN* 3.6 8.3 - - - +
372E PHE* 4.8 10.8 - - + -
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Residues in contact with GLY 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ALA 2.9 2.6 + - - -
310E ASP* 3.7 3.8 - - - -
312E LEU* 1.3 70.1 - - - +
314E PHE* 1.3 55.3 + - - +
315E ALA 3.0 0.2 - - - -
316E GLY* 2.9 23.2 + - - -
317E PRO* 4.2 2.3 - - - +
365E ALA* 5.8 2.5 - - - -
366E LEU* 5.0 10.5 - - - +
369E GLN* 2.8 38.6 - - - +
370E ARG* 5.8 0.4 - - - -
585E ILE* 4.9 9.7 - - - +
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Residues in contact with PHE 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E ASP 2.8 15.5 + - - +
311E LEU* 3.1 19.1 - - + +
312E LEU 2.9 0.6 + - - -
313E GLY* 1.3 72.1 - - - +
315E ALA* 1.3 56.4 + - - +
316E GLY 3.0 8.5 + - - -
317E PRO* 3.3 15.0 - - + +
318E LEU* 4.8 6.2 - - + +
444E GLN* 5.0 14.1 - - + -
447E VAL* 3.4 28.9 - - + -
448E GLY* 3.3 35.0 - - - -
451E LEU* 3.3 37.9 - - + +
582E LEU* 4.0 23.3 - - + +
585E ILE* 5.4 12.8 - - + -
586E LEU* 6.1 3.4 - - + -
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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
------------------------------------------------------------
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