Contacts of the helix formed by residues 318 - 345 (chain D) in PDB entry 2CX9
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 PHE 318 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ARG* 4.9 4.5 - - + -
246D ASP* 3.7 35.2 - - + -
247D GLY 4.5 2.2 - - - -
250D ILE* 4.0 12.6 - - + -
308D ALA* 4.2 3.8 - - - +
311D LEU* 3.8 19.3 - - + -
312D LYS* 3.5 53.8 - - + -
315D GLY 6.3 0.2 - - - -
316D ARG 3.2 15.7 - - - -
317D PRO* 1.3 75.5 - - + +
319D THR* 1.3 64.2 + - - +
320D LEU 3.4 1.8 - - - -
321D GLU* 3.2 14.4 - - + +
322D ALA* 2.8 29.8 + - + +
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Residues in contact with THR 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ASP* 2.7 38.2 + - - +
249D ARG* 5.2 1.1 - - - +
317D PRO* 5.4 0.2 - - - +
318D PHE* 1.3 79.2 + - - +
320D LEU* 1.3 63.5 - - - +
322D ALA* 4.1 1.4 - - - +
323D ALA* 3.1 24.3 + - - +
378D VAL* 4.0 18.8 - - + -
382D ARG* 3.1 40.4 + - - +
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU* 5.0 8.3 - - - +
319D THR* 1.3 80.0 - - - +
321D GLU* 1.3 77.4 + - - +
323D ALA* 3.4 5.1 + - - +
324D GLN* 2.9 52.2 + - - +
378D VAL* 5.4 1.3 - - - -
379D ILE* 3.6 44.9 - - + +
382D ARG* 4.2 24.3 - - + +
383D LEU* 4.6 14.8 - - + +
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Residues in contact with GLU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU* 5.6 1.0 - - - +
304D LEU* 4.5 2.6 - - - +
307D LYS* 3.9 25.1 + - + +
308D ALA* 3.7 15.8 - - + +
311D LEU* 3.3 31.9 - - + +
317D PRO 3.6 4.8 - - - +
318D PHE* 3.2 22.4 + - - +
319D THR 3.3 0.2 - - - -
320D LEU* 1.3 95.9 + - - +
322D ALA* 1.3 64.0 + - - +
324D GLN* 3.7 12.3 - - - +
325D ALA* 3.0 24.9 + - - +
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D ASP* 3.3 31.4 - - - +
249D ARG* 4.0 10.1 - - + +
250D ILE* 3.9 13.7 - - + -
308D ALA* 3.8 10.0 - - - +
318D PHE* 2.8 27.3 + - + +
319D THR 4.1 2.2 - - - +
321D GLU* 1.3 73.5 - - - +
323D ALA* 1.3 58.9 + - - +
325D ALA* 3.4 2.4 + - - +
326D LYS* 3.0 31.2 + - - +
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Residues in contact with ALA 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ARG* 4.7 7.4 - - - +
319D THR 3.1 18.5 + - - +
320D LEU 3.7 3.8 - - - +
322D ALA* 1.3 75.1 - - - +
324D GLN* 1.3 65.1 + - - +
326D LYS* 4.6 1.6 - - - -
327D LEU* 3.0 27.2 + - - +
375D LEU* 3.9 26.3 - - + +
378D VAL* 4.3 13.5 - - + -
379D ILE* 4.0 19.0 - - + +
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Residues in contact with GLN 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA* 3.9 7.8 - - - +
296B THR* 3.5 39.1 + - + +
299B GLU* 3.7 37.4 - - - +
304D LEU* 4.4 10.1 - - + +
307D LYS* 4.9 2.0 - - - +
320D LEU* 2.9 48.1 + - + +
321D GLU* 3.7 17.8 - - - +
322D ALA 3.3 0.2 - - - -
323D ALA* 1.3 75.9 - - - +
325D ALA* 1.3 57.2 + - - +
327D LEU* 3.8 0.2 - - - +
328D PHE* 2.9 33.3 + - - +
379D ILE* 3.9 14.4 - - + +
383D LEU* 5.3 0.5 - - - +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 5.7 1.1 - - - -
253D ALA* 3.8 4.5 - - + -
301D ALA 5.0 0.9 - - - +
304D LEU* 3.7 17.4 - - - +
305D TYR* 3.6 39.0 - - + +
308D ALA* 4.6 1.6 - - + -
321D GLU 3.0 18.5 + - - +
322D ALA* 3.7 6.3 - - - +
324D GLN* 1.3 77.1 - - - +
326D LYS* 1.3 57.0 + - - +
328D PHE* 4.0 0.3 - - - +
329D ALA* 2.8 35.0 + - - +
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Residues in contact with LYS 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ARG* 3.6 31.4 - - + +
252D ILE* 3.9 17.7 - - + -
253D ALA* 3.7 11.0 - - - +
322D ALA 3.0 18.1 + - - +
323D ALA 4.0 2.9 - - - +
325D ALA* 1.3 72.6 - - - +
327D LEU* 1.3 57.3 + - - +
330D SER* 2.7 37.1 + - - +
365D THR 2.8 27.8 + - - +
366D ARG* 3.9 10.3 + - - +
368D GLY 2.9 21.9 + - - -
369D GLU* 4.2 7.2 - - - -
370D GLY 2.6 27.5 + - - -
371D THR 4.7 0.4 - - - -
372D SER* 4.7 0.4 + - - +
375D LEU* 3.4 14.9 - - + +
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Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA 5.2 2.5 - - - +
293B GLU* 5.2 6.1 - - + -
296B THR* 4.2 15.7 - - + +
323D ALA 3.0 18.4 + - - +
324D GLN 3.8 1.3 - - - +
326D LYS* 1.3 76.7 - - - +
328D PHE* 1.3 63.9 + - - +
330D SER* 2.9 18.4 + - - -
331D GLU* 3.1 26.4 + - + +
372D SER* 3.5 37.9 - - - +
375D LEU* 3.7 12.3 - - + +
376D LYS* 4.0 27.4 - - + -
379D ILE* 3.8 22.0 - - + -
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Residues in contact with PHE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR* 3.9 16.2 - - + -
297B GLU* 4.5 18.8 - - + -
300B ALA* 4.8 1.1 - - + -
328B PHE* 3.5 39.9 - + - -
297D GLU* 3.2 39.0 - - + -
300D ALA* 3.6 9.0 - - + -
301D ALA* 3.6 19.7 - - + -
304D LEU* 3.6 19.7 - - + -
324D GLN 2.9 18.1 + - - +
325D ALA 4.0 0.2 - - - +
327D LEU* 1.3 80.2 - - - +
329D ALA* 1.3 56.8 + - - +
331D GLU* 4.0 2.7 - - - +
332D ALA* 2.9 38.0 + - + +
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Residues in contact with ALA 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ALA* 3.4 33.2 - - + +
256D ALA* 3.7 3.1 - - + -
257D VAL* 3.9 5.6 - - + -
298D LEU* 5.3 0.5 - - - +
301D ALA* 3.6 26.4 - - + +
325D ALA 2.8 21.6 + - - +
326D LYS 4.3 0.2 - - - +
328D PHE* 1.3 74.7 - - - +
330D SER* 1.3 54.7 + - - +
332D ALA* 3.3 0.4 + - - -
333D ALA* 2.7 39.0 + - - +
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Residues in contact with SER 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ALA* 3.8 5.0 - - - +
326D LYS* 2.7 26.7 + - - +
327D LEU* 2.9 14.9 + - - -
329D ALA* 1.3 76.6 - - - +
331D GLU* 1.3 64.7 + - - +
333D ALA* 4.0 0.2 - - - +
334D VAL* 3.1 31.0 + - - +
365D THR* 3.2 46.5 + - - -
366D ARG* 3.7 11.2 - - - +
372D SER* 4.2 1.9 + - - -
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Residues in contact with GLU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D LEU* 3.1 31.2 + - + +
328D PHE* 4.0 3.4 - - - +
330D SER* 1.3 81.5 + - - +
332D ALA* 1.3 62.8 + - - +
334D VAL* 4.0 1.6 - - - +
335D LYS* 3.2 25.5 + - - +
366D ARG* 2.9 35.4 + - - +
372D SER* 2.8 29.9 + - - +
373D GLU* 5.3 0.2 - - - +
376D LYS* 4.9 8.5 + - - -
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D ALA* 6.0 0.7 - - - -
297D GLU* 3.7 43.1 - - + +
298D LEU* 4.8 5.6 - - + +
301D ALA* 4.9 2.0 - - + -
328D PHE* 2.9 31.3 + - + +
329D ALA* 3.8 3.6 - - - +
331D GLU* 1.3 77.9 - - - +
333D ALA* 1.3 57.3 + - - +
335D LYS* 3.2 5.3 + - - +
336D ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ALA* 3.1 37.2 - - + +
257D VAL 4.5 0.2 - - - +
260D GLY* 4.1 12.3 - - - +
298D LEU* 4.3 7.9 - - + +
329D ALA 2.7 22.1 + - - +
330D SER 4.0 2.0 - - - +
332D ALA* 1.3 72.8 - - - +
334D VAL* 1.3 58.1 - - + +
336D ALA* 3.3 2.6 + - - +
337D CYS* 2.9 35.3 + - - -
362D ALA* 4.8 7.0 - - + -
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Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C ASP* 5.2 1.1 - - - +
330D SER 3.1 19.1 + - - +
331D GLU 4.0 2.0 - - - +
333D ALA* 1.3 75.5 - - + +
335D LYS* 1.3 57.4 + - - +
337D CYS* 3.4 4.9 + - - -
338D ASP* 3.0 24.7 + - + +
359D TRP* 3.4 27.2 - - + +
362D ALA* 3.4 34.1 - - + +
363D ARG* 3.9 10.1 - - - -
365D THR* 4.2 0.4 - - - +
366D ARG* 3.4 37.7 - - + +
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Residues in contact with LYS 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D GLU* 4.0 21.0 + - - +
297D GLU* 4.6 20.0 + - - +
331D GLU 3.2 14.2 + - - +
332D ALA* 3.4 10.8 - - - +
333D ALA 3.2 0.2 - - - -
334D VAL* 1.3 74.7 - - - +
336D ALA* 1.3 65.3 + - - +
338D ASP* 3.2 6.8 + - - +
339D GLU* 3.0 49.8 + - - +
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Residues in contact with ALA 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D GLY 4.3 16.2 - - - +
263D ALA* 4.3 3.0 - - - +
264D LEU* 5.3 3.4 + - + -
294D ALA* 3.8 31.0 - - + -
298D LEU* 4.4 10.3 - - + -
332D ALA 2.9 16.1 + - - +
333D ALA* 3.6 5.6 - - - +
335D LYS* 1.3 76.2 - - - +
337D CYS* 1.3 58.7 + - - +
339D GLU* 3.3 5.9 + - - +
340D ALA* 2.9 28.2 + - - +
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Residues in contact with CYS 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D LEU 3.9 13.2 - - - -
260D GLY* 4.2 2.2 - - - -
263D ALA* 3.7 24.9 - - + -
333D ALA 2.9 24.6 + - - +
334D VAL* 3.6 6.3 - - - +
336D ALA* 1.3 78.7 - - - +
338D ASP* 1.3 61.7 + - - +
340D ALA* 3.3 3.3 + - - +
341D ILE* 3.2 26.7 + - - +
355D VAL 4.5 1.4 - - - +
358D TYR* 3.7 23.8 - - + -
359D TRP* 3.6 23.1 - - + +
362D ALA* 3.9 9.9 - - - -
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Residues in contact with ASP 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C VAL* 5.0 1.0 - - - +
359C TRP* 3.6 16.0 - - - -
363C ARG* 2.7 49.4 + - - -
366C ARG* 2.7 31.3 + - - -
334D VAL* 3.0 17.4 + - + +
335D LYS* 3.2 7.8 + - - +
337D CYS* 1.3 77.6 - - - +
339D GLU* 1.3 64.5 + - + +
341D ILE* 3.3 4.8 + - - +
342D GLN* 3.1 7.4 + - - +
359D TRP* 3.7 12.9 + - + +
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ARG* 4.6 11.7 + - - -
290D LYS* 2.7 58.9 + - + +
335D LYS* 3.0 44.5 + - - +
336D ALA* 3.7 7.9 - - - +
337D CYS 3.3 0.2 - - - -
338D ASP* 1.3 75.4 - - + +
340D ALA* 1.3 60.2 + - - +
342D GLN* 3.2 7.2 + - - +
343D ILE* 2.8 36.8 + - + +
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Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ALA* 3.7 33.9 - - + +
264D LEU* 5.5 0.2 - - - -
267D ALA* 4.2 14.6 - - + -
336D ALA 2.9 13.5 + - - +
337D CYS 3.4 9.6 - - - +
338D ASP 3.2 0.2 - - - -
339D GLU* 1.3 74.2 - - - +
341D ILE* 1.3 64.3 + - - +
343D ILE* 3.3 2.5 + - - +
344D LEU* 3.1 28.9 + - - +
355D VAL* 4.0 14.6 - - + -
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU* 4.6 7.0 - - + -
359C TRP* 4.3 14.8 - - + -
363C ARG* 3.7 21.8 - - + +
367C ILE* 4.3 8.1 - - + +
337D CYS 3.2 9.8 + - - +
338D ASP* 3.4 11.0 - - - +
339D GLU 3.3 0.2 - - - -
340D ALA* 1.3 76.1 - - - +
342D GLN* 1.3 63.8 + - - +
344D LEU 3.3 2.1 + - - -
345D GLY 3.1 21.5 + - - +
348D GLY* 3.7 20.7 - - - +
349D TYR* 5.2 1.8 - - + -
355D VAL* 3.7 28.7 - - + +
356D GLU* 4.1 9.6 - - - -
359D TRP* 3.7 32.8 - - + -
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Residues in contact with GLN 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ARG* 3.0 30.0 + - - +
366C ARG* 3.0 38.7 + - - +
367C ILE* 3.6 8.9 - - - +
371C THR* 4.3 6.7 - - - +
372C SER* 3.9 7.9 + - - +
373C GLU* 2.8 42.4 + - - +
290D LYS* 4.4 9.0 - - - +
338D ASP 3.1 13.0 + - - +
339D GLU* 3.4 15.3 - - - +
340D ALA 3.2 0.2 - - - -
341D ILE* 1.3 78.0 - - - +
343D ILE* 1.3 58.3 + - - +
345D GLY* 2.9 19.8 + - - -
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Residues in contact with ILE 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D ALA* 3.9 35.7 - - + +
270D TYR* 3.9 7.5 - - + -
271D ALA* 4.7 0.2 - - + -
281D ILE* 3.8 31.1 - - + +
287D VAL* 4.4 22.4 - - + +
290D LYS* 3.7 36.1 - - + +
291D LEU* 4.1 14.6 - - + +
339D GLU* 2.8 24.0 + - + +
340D ALA* 3.3 5.4 + - - +
342D GLN* 1.3 75.7 - - - +
344D LEU* 1.3 61.8 + - - +
345D GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D TYR* 3.4 28.5 - - + -
267D ALA* 4.7 6.5 - - - -
270D TYR* 3.4 51.7 + - + -
340D ALA 3.1 16.0 + - - +
343D ILE* 1.3 77.0 - - - +
345D GLY* 1.3 62.6 + - - +
346D GLY 3.4 2.3 + - - -
347D TYR* 3.4 23.9 + - + +
348D GLY* 3.6 17.7 - - - +
353D TYR* 4.3 12.3 - - + -
355D VAL* 3.2 30.1 - - + -
----------------------------------------------------------
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Residues in contact with GLY 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ILE* 3.2 33.6 - - - +
371C THR* 5.2 7.0 - - - -
341D ILE 3.1 3.5 + - - -
342D GLN 2.9 18.1 + - - -
343D ILE 3.1 1.0 - - - -
344D LEU* 1.3 74.8 - - - +
346D GLY* 1.3 67.5 + - - -
348D GLY* 3.0 10.7 + - - -
349D TYR 3.7 0.5 + - - -
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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).
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