Contacts of the helix formed by residues 312 - 337 (chain C) in PDB entry 5NTI
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ARG 3.6 1.8 + - - -
311C LYS* 1.3 76.8 - - - +
313C MET* 1.3 64.2 + - - +
314C TRP* 2.9 42.2 + - - -
315C GLU* 3.3 15.6 + - - +
316C MET* 3.2 19.4 + - - +
390C ALA* 4.7 0.2 - - - -
330D TYR* 4.9 4.4 + - - -
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Residues in contact with MET 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LYS 3.8 1.0 + - - -
312C SER* 1.3 73.4 - - - +
314C TRP* 1.3 63.3 + - - +
316C MET* 4.0 0.9 - - - +
317C TRP* 3.0 39.1 + - + -
390C ALA 3.4 24.0 + - - +
391C LEU 3.8 12.8 - - - +
392C GLY* 4.4 9.6 - - - +
486C PHE* 3.9 15.9 - - + -
489C LEU* 3.6 31.2 - - + -
490C HIS* 4.2 13.2 - - + -
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Residues in contact with TRP 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C SER* 2.9 29.7 + - - -
313C MET* 1.3 79.6 - - - +
315C GLU* 1.3 80.7 + - + +
317C TRP* 3.9 1.0 - - - +
318C GLU* 2.9 54.9 + - - +
486C PHE* 3.6 15.7 - - + -
490C HIS* 4.3 20.1 - + + -
493C VAL* 3.8 29.7 - - + +
326D GLU* 5.0 2.9 - - + -
329D GLN* 3.5 41.5 - - + -
330D TYR* 3.8 39.7 - + - -
333D GLU* 5.3 10.5 - - + -
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Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LYS* 2.8 46.0 + - + +
312C SER* 3.3 18.8 + - - +
314C TRP* 1.3 99.1 - - + +
316C MET* 1.3 57.1 + - - +
318C GLU* 3.3 4.7 - - - +
319C ARG* 2.9 29.5 + - - +
286D GLN* 3.1 21.4 + - - +
326D GLU* 4.0 16.4 - - - +
330D TYR* 2.8 31.7 + - + -
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Residues in contact with MET 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C TYR* 3.8 31.6 - - + +
311C LYS* 4.1 13.0 - - + +
312C SER 3.2 6.6 + - - +
313C MET 4.1 1.8 - - - +
315C GLU* 1.3 76.6 - - - +
317C TRP* 1.3 58.4 + - - +
319C ARG* 3.2 10.7 + - - +
320C CYS* 2.9 51.6 + - - -
378C PHE* 4.2 5.6 - - + -
387C LEU* 3.6 24.9 - - + +
388C PHE* 3.8 17.7 - - + -
390C ALA* 3.9 31.4 - - + +
391C LEU* 3.7 18.6 - - + +
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Residues in contact with TRP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C MET* 3.0 25.5 + - + +
314C TRP 3.9 0.2 - - - +
316C MET* 1.3 74.5 - - - +
318C GLU* 1.3 53.5 + - - +
320C CYS* 3.3 1.5 + - - +
321C ALA* 2.8 37.9 + - - +
391C LEU* 2.9 40.9 + - + +
393C CYS* 4.2 11.9 - - + -
479C HIS* 4.6 3.4 - + - -
482C ARG* 3.6 20.6 - - + -
483C LEU* 3.6 40.2 - - + -
486C PHE* 3.4 39.2 - + + +
498C PHE* 3.8 15.0 - + + -
502C TYR* 3.2 27.4 - + - -
601C C3S 3.7 31.4 - - + -
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TRP* 2.9 24.5 + - - +
315C GLU* 3.3 6.1 - - - +
316C MET 3.3 0.2 - - - -
317C TRP* 1.3 75.6 - - - +
319C ARG* 1.3 63.2 + - - +
321C ALA* 3.5 1.7 + - - +
322C HIS* 3.1 18.5 + - - +
493C VAL* 3.1 17.5 - - - +
497C ALA* 3.2 21.6 - - + +
498C PHE* 3.6 21.2 - - + -
499C PRO* 5.1 2.3 - - + +
322D HIS* 3.4 20.7 - - + +
325D THR* 5.3 0.5 - - - +
326D GLU* 3.4 18.6 + - - +
329D GLN* 2.5 46.0 + - - +
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Residues in contact with ARG 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C TYR* 3.7 16.7 + - - -
311C LYS* 3.1 29.0 - - - +
315C GLU* 2.9 16.8 + - - +
316C MET* 3.2 11.9 + - - +
318C GLU* 1.3 77.5 - - - +
320C CYS* 1.3 60.9 + - - +
322C HIS* 3.4 3.1 + - - +
323C HIS* 3.2 37.3 + - + +
378C PHE* 4.6 3.8 - - + -
379C GLU* 3.2 41.0 + - - +
286D GLN* 3.1 30.5 - - - +
287D LEU* 6.0 1.6 - - - +
322D HIS* 3.7 12.6 - - + +
323D HIS* 4.7 11.9 + - + -
326D GLU* 3.3 18.6 + - - +
379D GLU* 6.1 2.8 - - - +
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Residues in contact with CYS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C MET* 2.9 49.0 + - - +
317C TRP 3.8 1.6 - - - +
319C ARG* 1.3 73.1 - - - +
321C ALA* 1.3 57.5 + - - +
323C HIS* 3.3 5.1 + - - -
324C LEU* 2.9 30.0 + - - +
378C PHE* 4.4 4.9 - - - -
388C PHE* 3.9 23.1 - - - -
391C LEU* 4.0 13.7 - - + -
601C C3S 3.6 36.9 - - + +
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TRP* 2.8 21.5 + - + +
318C GLU 3.9 3.8 - - - +
320C CYS* 1.3 73.0 - - - +
322C HIS* 1.3 53.2 + - - +
324C LEU* 3.5 2.6 + - - +
325C THR* 2.7 37.9 + - - -
498C PHE* 3.8 24.0 - - + -
499C PRO* 4.3 5.8 - - + -
502C TYR* 3.8 33.0 - - + -
601C C3S 4.2 2.4 - - + +
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Residues in contact with HIS 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU 3.1 17.8 + - - +
319C ARG 3.7 4.0 - - - +
320C CYS 3.2 0.2 - - - -
321C ALA* 1.3 73.3 - - - +
323C HIS* 1.3 83.9 + + - +
325C THR* 3.2 3.8 + - - -
326C GLU* 2.9 47.3 + - - +
499C PRO* 3.8 19.1 - - + +
318D GLU* 3.3 44.1 + - + +
319D ARG* 3.6 13.2 - - - -
322D HIS* 3.7 35.8 + + + +
497D ALA 5.0 3.2 + - - -
499D PRO* 6.3 0.2 - - - +
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Residues in contact with HIS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLN* 5.5 0.2 + - - -
319C ARG* 3.2 25.2 + - + +
320C CYS 3.8 1.6 - - - +
322C HIS* 1.3 88.3 - + - +
324C LEU* 1.3 56.8 + - - +
326C GLU* 3.4 10.5 + - - +
327C ALA 3.1 21.5 + - - -
378C PHE* 3.6 28.0 - + + -
379C GLU* 2.8 37.5 + - + +
601C C3S 3.5 35.2 - - + +
319D ARG* 3.5 32.7 + - - -
323D HIS* 4.9 3.1 - + - -
379D GLU* 3.9 2.2 - - - -
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C CYS 2.9 16.8 + - - +
321C ALA 3.7 4.9 - - - +
323C HIS* 1.3 74.7 - - - +
325C THR* 1.3 60.9 + - - +
327C ALA* 3.2 5.1 + - - +
328C ILE* 2.8 41.2 + - + +
358C MET* 3.7 41.1 - - + -
361C VAL* 3.8 25.1 - - + -
362C LEU* 6.2 0.4 - - + -
479C HIS* 4.2 7.4 - - + +
502C TYR* 3.7 26.9 - - + -
506C PHE* 4.4 3.1 - - + -
601C C3S 4.1 31.3 - - + +
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Residues in contact with THR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ALA 2.7 23.2 + - - -
322C HIS 3.2 5.6 + - - -
324C LEU* 1.3 74.3 - - - +
326C GLU* 1.3 57.7 + - - +
328C ILE* 3.2 11.0 + - - +
329C GLN* 2.9 41.3 + - - +
499C PRO* 3.3 31.5 - - + +
501C LEU* 4.0 27.8 - - + -
502C TYR* 3.4 14.9 - - - +
318D GLU* 4.7 1.3 - - - +
497D ALA* 4.6 6.3 - - + -
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLN* 2.9 32.6 + - - +
322C HIS* 2.9 41.0 + - - +
323C HIS* 3.4 14.4 + - - +
325C THR* 1.3 76.7 - - - +
327C ALA* 1.3 61.4 + - - +
329C GLN* 3.3 19.4 + - - +
330C TYR* 3.3 21.2 + - + -
314D TRP* 5.0 4.0 - - + -
315D GLU* 3.8 24.8 - - + +
318D GLU* 3.8 14.5 + - - +
319D ARG* 3.3 29.3 + - - -
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLN* 3.7 9.1 + - - +
323C HIS 3.1 7.5 + - - +
324C LEU 3.6 7.4 - - - +
326C GLU* 1.3 75.8 - - - +
328C ILE* 1.3 61.6 + - - +
330C TYR* 3.3 7.8 + - - +
331C VAL* 3.1 24.8 + - - +
361C VAL* 4.2 20.9 - - + -
364C ARG* 4.7 2.6 + - - -
601C C3S 3.7 39.0 - - + +
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Residues in contact with ILE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C LEU* 2.8 33.0 + - + +
325C THR* 3.6 8.3 - - - +
327C ALA* 1.3 74.6 - - - +
329C GLN* 1.3 59.7 + - - +
331C VAL* 3.1 8.4 + - - +
332C VAL* 2.9 33.7 + - + +
357C ALA* 4.1 19.5 - - + +
358C MET* 5.0 2.2 - - - +
361C VAL* 3.9 16.6 - - + -
501C LEU* 4.0 14.6 - - + -
502C TYR* 5.6 1.3 - - + -
505C LEU* 3.9 22.4 - - + -
506C PHE* 3.7 37.2 - - + -
501R LEU* 5.9 0.9 - - + -
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Residues in contact with GLN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C THR* 2.9 21.8 + - - +
326C GLU* 3.3 10.9 + - - +
328C ILE* 1.3 76.4 - - - +
330C TYR* 1.3 60.9 + - - +
332C VAL* 3.5 10.7 + - - +
333C GLU* 3.2 22.5 + - - +
501C LEU* 4.3 15.5 - - + -
314D TRP* 3.4 26.1 - - + -
318D GLU* 2.7 41.6 + - - +
493D VAL* 4.5 11.9 - - - +
496D ALA* 6.0 1.3 - - - +
497D ALA* 3.7 15.4 - - - +
504R LEU* 5.0 17.9 - - + +
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Residues in contact with TYR 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLU 5.3 2.0 - - - -
284C THR* 3.2 41.1 - - + +
285C CYS 4.0 5.8 - - - -
286C GLN* 3.7 41.8 + - + +
326C GLU* 3.3 21.6 + - + -
327C ALA* 3.3 12.0 + - - +
328C ILE 3.2 0.6 - - - -
329C GLN* 1.3 74.7 - - - +
331C VAL* 1.3 60.8 + - - +
333C GLU* 3.2 10.5 + - + +
334C PHE* 3.0 22.7 + - - +
364C ARG* 4.0 7.0 - - - +
601C C3S 5.0 1.6 - - - +
312D SER* 5.0 1.6 + - - -
314D TRP* 3.9 25.0 - + - -
315D GLU* 2.6 31.0 + - + -
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ALA 3.1 15.4 + - - +
328C ILE* 3.4 9.6 - - - +
330C TYR* 1.3 73.5 - - - +
332C VAL* 1.3 64.8 + - - +
334C PHE* 3.0 14.9 + - + +
335C ALA* 2.9 21.0 + - - +
353C LEU* 4.3 11.0 - - + -
357C ALA* 4.1 17.9 - - + +
360C VAL* 3.8 41.3 - - + -
361C VAL* 3.8 19.1 - - + -
364C ARG* 4.2 13.5 - - - +
425C LEU* 5.4 2.0 - - + -
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Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ILE* 2.9 29.0 + - + +
329C GLN* 3.6 12.6 - - - +
331C VAL* 1.3 75.1 - - - +
333C GLU* 1.3 63.1 + - - +
335C ALA* 3.3 4.2 + - - +
336C LYS* 3.1 30.4 + - + +
353C LEU* 4.2 33.4 - - + -
357C ALA* 5.7 0.4 - - + -
501C LEU* 5.3 0.4 - - + -
501R LEU* 4.2 16.4 - - + -
504R LEU* 4.2 30.5 - - + +
505R LEU* 4.4 10.0 - - + +
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C THR* 3.7 16.6 - - + -
329C GLN 3.2 11.3 + - - +
330C TYR* 3.2 17.0 + - + +
332C VAL* 1.3 77.9 - - - +
334C PHE* 1.3 63.7 - - - +
336C LYS* 3.1 30.6 + - - +
337C ARG* 3.0 51.6 + - - +
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Residues in contact with PHE 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL* 4.0 8.1 - - + -
280C SER* 3.8 7.7 - - - -
281C TYR* 3.6 35.0 - + + -
284C THR* 3.3 29.5 - - - +
330C TYR 3.0 7.0 + - - +
331C VAL* 3.0 15.0 + - + +
333C GLU* 1.3 74.0 - - - +
335C ALA* 1.3 59.7 + - - +
337C ARG* 3.4 4.2 + - - +
338C LEU* 3.0 55.2 + - + +
360C VAL* 5.2 9.0 - - + -
364C ARG* 3.7 14.1 - - - +
418C ALA 3.9 9.6 - - - -
421C THR* 3.9 22.4 - - - -
422C ALA* 4.2 13.0 - - + -
425C LEU* 4.5 9.2 - - + -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C VAL 2.9 11.8 + - - +
332C VAL 3.4 9.2 - - - +
334C PHE* 1.3 74.4 - - - +
336C LYS* 1.3 65.2 + - - +
338C LEU* 3.1 21.9 + - - +
341C PHE* 3.2 40.2 - - + +
353C LEU* 4.0 12.8 - - + -
425C LEU* 3.9 22.0 - - + -
505R LEU* 5.2 0.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C VAL* 3.1 22.6 + - + +
333C GLU* 3.1 31.9 + - - +
335C ALA* 1.3 76.2 - - - +
337C ARG* 1.3 62.5 + - + +
338C LEU 3.2 2.8 + - - +
342C MET* 3.4 34.2 - - + +
504R LEU 2.8 28.5 + - - +
505R LEU* 3.7 35.2 + - + -
506R GLY* 5.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C SER* 4.7 3.5 + - - -
280C SER* 2.9 31.3 + - - +
283C GLU* 2.8 47.9 + - - +
284C THR* 3.7 15.7 - - - -
333C GLU* 3.0 45.4 + - - +
334C PHE 3.6 1.1 - - - +
336C LYS* 1.3 76.3 - - + +
338C LEU* 1.3 60.9 + - - +
339C SER 3.5 1.9 + - - -
----------------------------------------------------------
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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