Contacts of the helix formed by residues 312 - 338 (chain D) in PDB entry 5NTN
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 SER 312 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C TYR* 4.8 1.7 + - - -
310D ARG 3.6 2.2 + - - -
311D LYS* 1.3 78.8 - - - +
313D MET* 1.3 64.8 + - - +
314D TRP* 3.0 36.2 + - - -
315D GLU* 3.2 19.0 + - - +
316D MET* 3.1 21.8 + - - +
390D ALA* 4.6 0.2 - - - -
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Residues in contact with MET 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D LYS 3.8 1.0 + - - -
312D SER* 1.3 73.8 - - - +
314D TRP* 1.3 62.2 + - - +
316D MET* 3.5 0.9 + - - +
317D TRP* 3.0 39.2 + - + -
390D ALA* 3.5 27.3 + - - +
391D LEU 3.9 13.2 - - - +
392D GLY* 4.5 8.7 - - - +
486D PHE* 3.8 20.2 - - + -
489D LEU* 5.2 11.7 - - + -
490D HIS* 4.2 17.5 - - + +
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Residues in contact with TRP 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C GLU* 4.8 2.9 - - + -
329C GLN* 3.4 36.8 - - + -
330C TYR* 3.7 44.9 - + - -
312D SER* 3.0 28.1 + - - -
313D MET* 1.3 79.3 - - - +
315D GLU* 1.3 80.2 + - + +
317D TRP* 3.8 0.9 - - - +
318D GLU* 2.9 50.1 + - - +
486D PHE* 3.7 19.9 - - + -
490D HIS* 4.5 15.3 - + + -
493D VAL* 3.9 26.5 - - + -
498D PHE* 4.6 1.2 - - - -
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Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLN* 5.3 2.6 - - - +
326C GLU* 3.8 27.1 - - - +
330C TYR* 2.4 30.2 + - - +
311D LYS* 3.1 37.7 + - + +
312D SER* 3.2 20.3 + - - +
314D TRP* 1.3 97.0 - - + +
316D MET* 1.3 57.5 + - - +
318D GLU* 3.3 3.6 + - + +
319D ARG* 2.9 46.7 + - - +
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Residues in contact with MET 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D TYR* 3.6 38.4 - - + +
311D LYS* 4.2 13.6 - - + +
312D SER 3.1 16.6 + - - +
313D MET 4.1 2.2 - - - +
315D GLU* 1.3 75.2 - - - +
317D TRP* 1.3 58.3 + - - +
319D ARG* 3.5 9.1 + - - +
320D CYS* 3.1 36.7 + - - -
378D PHE* 3.8 26.0 - - + -
387D LEU 3.7 17.0 - - - +
388D PHE* 4.0 15.5 - - + +
390D ALA* 4.2 17.9 - - + -
391D LEU* 3.7 21.8 - - + +
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Residues in contact with TRP 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D MET* 3.0 32.2 + - + +
314D TRP 3.9 0.2 - - - +
316D MET* 1.3 73.2 - - - +
318D GLU* 1.3 60.7 + - - +
320D CYS* 3.8 1.4 - - - +
321D ALA* 2.8 32.2 + - - +
391D LEU* 2.9 40.5 + - + +
393D CYS* 4.2 18.4 - - - -
479D HIS* 4.8 4.3 - + - -
482D ARG* 3.7 32.5 - - + -
483D LEU* 3.7 22.4 - - + -
486D PHE* 3.4 50.3 - + + +
498D PHE* 3.7 4.7 - + + -
502D TYR* 3.4 26.2 - - - -
601D 98H 3.5 23.6 - - + -
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C HIS* 3.9 20.6 + - + +
325C THR* 4.6 2.1 - - - +
326C GLU* 4.1 12.4 + - - +
329C GLN* 2.6 43.8 + - - +
499C PRO* 6.1 0.2 - - - +
314D TRP* 2.9 26.8 + - - +
315D GLU* 3.5 6.1 - - - +
317D TRP* 1.3 76.5 - - - +
319D ARG* 1.3 62.9 + - - +
321D ALA* 3.4 1.7 + - - +
322D HIS* 3.1 23.4 + - - +
493D VAL* 3.4 14.9 - - - +
497D ALA* 3.4 16.8 - - + +
498D PHE* 3.5 21.7 - - + -
499D PRO* 5.5 1.2 - - - +
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Residues in contact with ARG 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 5.8 4.2 - - - +
322C HIS* 4.0 15.3 - - - +
323C HIS* 5.9 7.1 + - + -
326C GLU* 3.4 30.1 + - - +
601C 98H 6.3 1.0 - - - +
308D TYR* 4.5 2.2 + - - -
311D LYS* 3.6 28.8 - - - +
315D GLU* 2.9 45.6 + - - +
316D MET* 3.7 12.8 - - - +
318D GLU* 1.3 75.3 - - - +
320D CYS* 1.3 63.9 + - - +
322D HIS* 3.3 5.0 + - - +
323D HIS* 3.0 30.0 + - + +
378D PHE* 5.1 0.7 - - + -
379D GLU* 3.0 42.7 + - - +
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Residues in contact with CYS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D MET* 3.1 22.9 + - - +
317D TRP 4.0 1.6 - - - +
319D ARG* 1.3 76.9 - - - +
321D ALA* 1.3 60.9 + - - +
323D HIS* 3.3 6.2 + - - +
324D LEU* 2.8 32.9 + - - +
378D PHE* 4.1 19.5 - - - -
388D PHE* 4.2 12.6 - - - -
391D LEU* 4.1 14.8 - - + -
601D 98H 3.8 46.6 - - + +
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Residues in contact with ALA 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D TRP 2.8 19.4 + - - +
318D GLU 3.7 4.3 - - - +
320D CYS* 1.3 75.5 - - - +
322D HIS* 1.3 55.8 + - - +
325D THR* 2.8 37.8 + - - -
498D PHE* 3.6 24.5 - - + -
499D PRO* 4.3 6.5 - - + -
502D TYR* 3.6 34.8 - - + +
601D 98H 3.9 1.2 - - - -
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Residues in contact with HIS 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU* 3.8 39.8 + - + +
319C ARG* 3.8 26.1 - - - +
322C HIS* 3.2 40.0 - + + +
323C HIS* 5.1 1.7 + - - -
379C GLU* 5.4 0.2 + - - -
497C ALA 5.5 2.0 + - - -
318D GLU 3.1 12.9 + - - +
319D ARG 3.3 6.7 + - - +
321D ALA* 1.3 76.3 - - - +
323D HIS* 1.3 84.9 + + - +
325D THR* 3.2 4.0 + - - -
326D GLU* 3.0 32.4 + - + +
499D PRO* 4.2 16.5 - - + +
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Residues in contact with HIS 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ARG* 5.8 8.5 + - + -
322C HIS* 5.4 0.9 - + - -
323C HIS* 5.2 9.0 - - - -
379C GLU* 5.6 4.5 - - - -
286D GLN* 5.1 1.2 + - - -
319D ARG* 3.0 25.0 + - - +
320D CYS* 3.9 3.6 - - - +
322D HIS* 1.3 97.1 + + - +
324D LEU* 1.3 62.6 + - - +
326D GLU* 3.4 12.3 + - - +
327D ALA* 3.1 23.0 + - - +
378D PHE* 3.8 19.5 - + - -
379D GLU* 2.6 42.1 + - + +
601D 98H 3.3 30.5 + - + +
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Residues in contact with LEU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D CYS 2.8 21.2 + - - +
321D ALA 3.9 4.0 - - - +
323D HIS* 1.3 73.2 - - - +
325D THR* 1.3 56.9 + - - +
327D ALA* 3.3 3.4 + - - +
328D ILE* 2.8 44.9 + - + +
358D MET* 3.6 30.5 - - + -
361D VAL* 3.9 23.6 - - + -
479D HIS* 3.6 35.2 - - + +
502D TYR* 4.0 4.0 - - + -
506D PHE* 4.0 11.0 - - + -
601D 98H 3.6 28.6 - - + +
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Residues in contact with THR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU* 4.6 1.3 - - - +
497C ALA* 4.3 9.4 - - + -
321D ALA 2.8 22.3 + - - -
322D HIS* 3.6 4.5 - - - -
324D LEU* 1.3 75.6 - - - +
326D GLU* 1.3 57.6 + - - +
328D ILE* 3.1 10.5 + - - +
329D GLN* 2.8 44.6 + - - +
499D PRO* 3.4 24.2 - - + +
501D LEU* 4.4 19.1 - - + -
502D TYR* 3.4 25.2 - - - +
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Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TRP* 4.9 4.5 - - + -
315C GLU* 3.5 29.6 - - + +
318C GLU* 4.3 7.2 + - - +
319C ARG* 3.1 47.0 + - - +
286D GLN* 3.0 22.4 + - - +
322D HIS* 3.0 21.6 + - + +
323D HIS* 3.6 14.8 + - - +
325D THR* 1.3 74.6 - - - +
327D ALA* 1.3 61.7 + - - +
329D GLN* 3.1 29.1 + - - +
330D TYR* 3.3 19.0 - - + -
601D 98H 5.1 0.9 - - - +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D GLN* 3.8 25.5 - - - +
323D HIS 3.1 14.3 + - - +
324D LEU* 3.3 9.2 + - - +
326D GLU* 1.3 76.2 - - - +
328D ILE* 1.3 62.0 + - - +
330D TYR* 3.2 14.7 + - - +
331D VAL* 3.2 14.9 + - - +
361D VAL* 3.9 28.5 - - + -
364D ARG* 4.8 2.6 + - - -
601D 98H 4.8 11.2 - - + -
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Residues in contact with ILE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D LEU* 2.8 30.2 + - + +
325D THR* 3.5 7.6 - - - +
327D ALA* 1.3 71.9 - - - +
329D GLN* 1.3 60.6 + - - +
331D VAL* 3.0 10.3 + - - +
332D VAL* 2.9 32.7 + - + +
357D ALA* 4.0 21.1 - - + +
358D MET 4.8 2.0 - - - +
361D VAL* 3.9 15.7 - - + -
501D LEU* 4.2 13.7 - - + -
502D TYR* 6.3 0.4 - - - -
505D LEU* 3.8 24.5 - - + -
506D PHE* 3.5 38.4 - - + -
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Residues in contact with GLN 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TRP* 3.6 23.0 - - + -
318C GLU* 2.5 43.3 + - - +
493C VAL* 4.3 9.9 - - - +
496C ALA* 5.7 1.3 - - - +
497C ALA* 3.6 12.2 - - - +
325D THR* 2.8 28.3 + - - +
326D GLU* 3.1 14.8 + - - +
328D ILE* 1.3 76.5 - - - +
330D TYR* 1.3 56.7 + - - +
332D VAL* 3.4 10.2 + - - +
333D GLU* 3.1 31.2 + - - +
501D LEU* 4.5 15.5 - - + -
504S LEU* 5.4 12.5 - - + +
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Residues in contact with TYR 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C SER* 4.1 6.2 + - - -
314C TRP* 3.6 32.7 - + - -
315C GLU* 2.4 35.5 + - - +
283D GLU 5.7 1.3 - - - -
284D THR* 3.5 36.2 - - + +
286D GLN* 3.6 44.5 + - + +
326D GLU* 3.3 24.3 + - + -
327D ALA 3.2 8.8 + - - +
329D GLN* 1.3 74.6 - - - +
331D VAL* 1.3 59.9 + - - +
333D GLU* 3.3 8.8 + - + +
334D PHE* 2.9 27.0 + - - +
364D ARG* 3.7 8.1 - - - +
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Residues in contact with VAL 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ALA 3.2 13.6 + - - +
328D ILE* 3.0 9.3 + - - +
330D TYR* 1.3 74.9 - - - +
332D VAL* 1.3 64.4 + - - +
334D PHE* 3.2 12.1 + - + +
335D ALA* 3.0 21.8 + - - +
353D LEU* 4.2 10.8 - - + -
357D ALA* 4.1 16.4 - - - +
360D VAL* 3.7 44.4 - - + -
361D VAL* 3.7 20.9 - - + -
364D ARG* 4.3 10.5 - - - -
425D LEU* 5.1 2.5 - - + -
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ILE* 2.9 31.0 + - + +
329D GLN* 3.5 10.8 - - - +
331D VAL* 1.3 74.6 - - - +
333D GLU* 1.3 61.3 + - - +
335D ALA* 3.3 4.0 + - - +
336D LYS* 3.0 44.8 + - + +
353D LEU* 4.3 18.6 - - + -
357D ALA* 5.7 0.2 - - + -
501D LEU* 5.2 1.1 - - + -
501S LEU* 4.4 19.5 - - + -
504S LEU* 4.2 30.1 - - + -
505S LEU* 4.4 12.1 - - + -
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Residues in contact with GLU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TRP* 5.6 8.1 - - + -
284D THR* 3.7 15.5 - - + -
329D GLN 3.1 15.8 + - - +
330D TYR* 3.7 13.7 - - + +
331D VAL 3.2 0.2 - - - -
332D VAL* 1.3 76.9 - - - +
334D PHE* 1.3 65.8 + - - +
336D LYS* 3.0 38.4 + - - +
337D ARG* 3.1 43.4 + - - +
504S LEU* 5.4 5.9 - - - +
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Residues in contact with PHE 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D VAL* 4.2 7.6 - - + -
280D SER* 4.0 7.2 - - - -
281D TYR* 3.8 34.3 - + + -
284D THR* 3.4 25.7 - - - +
330D TYR 2.9 12.5 + - - +
331D VAL* 3.2 12.6 - - + +
333D GLU* 1.3 74.5 - - - +
335D ALA* 1.3 63.3 + - - +
337D ARG* 3.2 6.2 + - - +
338D LEU* 3.2 35.3 + - + +
360D VAL* 4.9 10.3 - - + -
364D ARG* 3.7 13.0 - - - +
418D ALA 3.9 9.4 - - - -
421D THR* 3.6 28.9 - - - -
422D ALA* 3.9 24.7 - - + -
425D LEU* 4.6 12.3 - - + -
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Residues in contact with ALA 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D VAL 3.0 11.8 + - - +
332D VAL 3.4 9.0 - - - +
334D PHE* 1.3 77.4 - - - +
336D LYS* 1.3 61.5 + - + +
338D LEU* 3.1 23.1 + - - +
341D PHE* 3.4 39.5 - - + -
342D MET* 3.9 0.7 - - - +
353D LEU* 4.0 13.9 - - + -
425D LEU* 3.9 22.7 - - + -
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Residues in contact with LYS 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D VAL* 3.0 27.8 + - + +
333D GLU* 3.0 39.1 + - - +
334D PHE 3.3 0.2 - - - -
335D ALA* 1.3 76.9 - - - +
337D ARG* 1.3 60.9 + - + +
338D LEU 3.3 0.4 - - - -
339D SER* 5.8 0.2 - - - -
342D MET* 3.3 37.1 - - + +
504S LEU* 2.9 30.0 + - - +
505S LEU* 3.8 23.6 - - + +
----------------------------------------------------------
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Residues in contact with ARG 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D SER* 4.8 2.4 + - - -
280D SER* 3.0 25.9 + - - +
283D GLU* 3.1 46.5 + - - +
284D THR* 3.6 29.1 - - - +
333D GLU* 3.1 26.8 + - - +
334D PHE 3.2 3.3 + - - +
336D LYS* 1.3 75.8 - - + +
338D LEU* 1.3 58.4 + - - +
339D SER* 3.4 7.3 + - - -
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Residues in contact with LEU 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D LEU* 6.5 0.4 - - + -
276D SER* 4.3 3.6 - - - +
277D VAL* 3.8 34.1 - - + +
280D SER* 3.6 20.4 - - - +
334D PHE* 3.2 35.1 + - + +
335D ALA 3.1 12.3 + - - +
336D LYS 3.3 0.2 - - - -
337D ARG* 1.3 74.8 - - - +
339D SER* 1.3 66.0 - - - +
340D GLY* 3.3 4.0 - - - +
341D PHE* 2.9 26.0 + - + +
342D MET* 3.2 11.3 + - - +
422D ALA* 4.3 12.6 - - + -
425D LEU* 4.5 15.9 - - + -
426D ILE* 5.1 7.6 - - + -
442D LEU* 6.5 0.2 - - + -
446D LEU* 5.8 1.6 - - + -
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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