Contacts of the helix formed by residues 345 - 369 (chain B) in PDB entry 1I0E
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 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LYS* 3.0 39.1 + - - +
109B ASP* 3.6 20.1 - - - +
289B THR* 4.1 3.1 - - - -
343B GLY 4.0 1.0 + - - -
344B SER* 1.3 74.8 - - - +
346B GLU* 1.3 60.2 + - - +
347B VAL* 3.4 4.0 + - - +
348B GLU* 3.2 34.3 + - - +
349B GLN* 2.9 30.0 + - - +
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B THR* 3.6 27.6 + - - +
109B ASP 3.1 26.7 - - - +
110B LEU* 3.9 15.7 - - + +
135B ARG* 4.1 14.4 + - - -
250B PHE* 4.2 8.1 - - + -
253B PHE* 5.1 1.9 - - - -
279B TYR* 4.4 1.4 - - - -
289B THR* 3.0 45.7 - - - +
291B LEU* 3.9 22.7 - - + +
345B SER* 1.3 72.6 - - - +
347B VAL* 1.3 57.5 + - - +
349B GLN* 3.2 5.1 + - - +
350B VAL* 2.9 34.9 + - - +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 3.2 29.1 + - - +
111B ASN 3.1 27.4 - - - +
114B ASN* 3.3 35.4 - - + +
115B LEU* 3.8 8.9 - - + +
250B PHE* 3.7 22.9 - - + -
345B SER* 3.4 3.4 + - - +
346B GLU* 1.3 75.5 - - - +
348B GLU* 1.3 73.9 + - + +
350B VAL* 3.3 1.2 + - - +
351B GLN* 2.8 26.8 + - - +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LYS* 2.9 32.2 - - - +
343B GLY 5.3 0.6 - - - +
344B SER* 4.3 12.0 - - - -
345B SER* 3.2 28.3 + - - +
347B VAL* 1.3 80.5 - - + +
349B GLN* 1.3 58.4 + - - +
351B GLN* 2.9 10.3 - - - +
352B LEU* 2.9 38.8 + - + +
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Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B THR* 2.8 23.6 + - - +
291B LEU* 3.9 11.2 - - + +
338B ASN* 3.4 24.3 - - + +
340B ASP* 3.0 27.8 + - + +
341B ARG* 3.6 10.3 + - - -
344B SER* 2.9 48.0 + - - -
345B SER 2.9 13.6 + - - +
346B GLU* 3.4 4.4 - - - +
347B VAL 3.1 0.2 - - - -
348B GLU* 1.3 73.2 - - - +
350B VAL* 1.3 68.1 + - - +
352B LEU* 3.0 18.8 + - + +
353B VAL* 2.9 17.0 + - - +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.1 10.3 - - + -
131B VAL* 4.9 5.4 - - + -
246B MET* 4.0 25.8 - - + -
250B PHE* 3.4 52.0 - - + -
291B LEU* 4.1 17.0 - - + -
293B GLY* 5.4 2.5 - - - -
346B GLU 2.9 19.0 + - - +
347B VAL 3.9 2.9 - - - +
349B GLN* 1.3 70.7 - - - +
351B GLN* 1.3 55.7 + - - +
353B VAL* 2.8 37.6 + - + +
354B VAL* 3.1 9.9 + - + +
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Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN 4.0 4.0 + - - -
115B LEU* 3.6 12.6 - - - +
116B LYS* 2.7 61.3 - - - +
347B VAL* 2.8 15.4 + - - +
348B GLU* 2.9 19.1 - - - +
350B VAL* 1.3 72.5 - - - +
352B LEU* 1.3 56.3 + - + +
353B VAL 2.5 17.3 + - - -
354B VAL* 2.8 18.9 + - - +
355B ASP* 3.2 40.4 + - - +
380B GLN* 5.4 1.6 - - - +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU 4.7 0.7 - - - +
316B ARG* 3.8 36.6 - - + +
317B LEU* 3.6 11.1 - - + +
338B ASN* 5.4 3.6 - - + -
340B ASP* 5.4 3.1 - - - +
348B GLU* 2.9 36.3 + - + +
349B GLN* 3.4 12.8 - - + +
351B GLN* 1.3 75.8 - - + +
353B VAL* 1.3 59.3 + - + +
356B GLY 3.7 1.4 + - - -
379B ALA 4.8 1.3 - - - -
380B GLN* 4.0 19.3 - - - +
381B LYS* 2.4 59.7 - - - +
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET* 4.8 7.9 - - + -
293B GLY* 3.9 26.5 - - - +
294B GLY* 4.3 10.8 - - - +
295B VAL* 5.1 0.2 - - + -
317B LEU* 4.4 7.6 - - + -
336B VAL 4.6 4.5 - - - +
338B ASN* 3.8 24.0 - - + +
349B GLN 2.9 19.7 - - - +
350B VAL* 2.9 18.6 - - + +
351B GLN 2.5 9.7 + - - -
352B LEU* 1.3 74.9 - - - +
354B VAL* 1.3 57.9 + - + +
355B ASP 3.5 0.2 - - - -
357B VAL* 2.8 48.7 + - + +
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.4 9.4 - - + -
118B GLY* 3.3 34.8 - - - +
121B LEU* 4.7 11.3 - - + +
246B MET* 4.0 26.5 - - + -
350B VAL 3.3 16.8 - - - +
351B GLN* 2.8 19.1 + - - +
353B VAL* 1.3 72.8 - - - +
355B ASP* 1.3 85.1 + - - +
357B VAL* 3.7 4.2 - - - +
358B LYS* 2.8 39.5 + - + +
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Residues in contact with ASP 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS 4.7 1.2 - - - +
118B GLY 5.1 0.2 + - - -
351B GLN* 3.2 31.0 + - - +
354B VAL* 1.3 96.1 - - - +
356B GLY* 1.3 64.5 + - - +
358B LYS* 3.1 17.5 + - - +
359B LEU 3.1 17.5 + - - -
380B GLN* 3.9 15.9 + - - +
381B LYS* 3.1 41.5 - - + +
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Residues in contact with GLY 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 3.6 4.3 - - - +
317B LEU* 4.2 4.0 - - - -
352B LEU 3.7 5.4 + - - -
353B VAL 3.6 2.0 + - - -
354B VAL 3.3 0.6 - - - -
355B ASP* 1.3 79.4 - - - +
357B VAL* 1.3 60.4 + - - +
359B LEU* 3.2 6.2 + - - +
360B MET* 3.0 26.3 + - - +
381B LYS* 2.7 40.3 - - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.7 24.0 - - + -
126B VAL* 4.3 2.9 - - + -
295B VAL* 3.5 25.4 - - + -
297B VAL* 3.7 25.6 - - + -
317B LEU* 4.7 4.2 - - + +
336B VAL* 5.1 9.0 - - + -
353B VAL* 2.8 40.4 + - + +
354B VAL 3.7 2.9 - - - +
356B GLY* 1.3 70.0 - - - +
358B LYS* 1.3 66.3 + - - +
360B MET* 3.0 19.4 + - + +
361B VAL* 3.0 19.1 + - + +
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Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLY 4.6 6.3 - - - +
119B ASP* 2.8 34.4 + - - +
121B LEU* 4.4 21.8 - - + -
354B VAL* 2.8 29.0 + - + +
355B ASP* 3.1 24.4 + - - +
357B VAL* 1.3 74.3 - - - +
359B LEU* 1.3 57.1 + - - +
361B VAL* 3.5 6.2 + - - +
362B GLU* 3.0 34.4 + - + +
381B LYS* 4.6 8.5 - - - +
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.1 10.8 - - + -
355B ASP 3.1 5.1 + - - -
356B GLY 3.6 8.7 - - - +
357B VAL 3.1 0.8 - - - -
358B LYS* 1.3 74.6 - - - +
360B MET* 1.3 67.6 + - - +
362B GLU* 4.3 13.9 - - + +
363B MET* 2.9 56.7 + - + +
374B ASP 5.0 5.4 - - - +
375B ASP* 5.1 0.2 - - - -
376B MET* 3.4 32.8 - - + -
381B LYS* 3.5 37.0 - - + +
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Residues in contact with MET 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL* 5.4 2.9 - - + -
299B LEU* 3.5 32.0 - - + +
302B LEU* 3.4 21.1 - - + +
308B PHE* 3.7 11.7 - - + -
311B ILE* 4.6 8.3 - - - -
312B LEU* 3.4 31.4 - - + -
315B LEU* 3.9 20.6 - - - -
317B LEU* 5.0 3.4 - - + -
336B VAL* 5.0 10.8 - - + -
356B GLY 3.0 22.4 + - - +
357B VAL* 3.0 17.7 + - + +
359B LEU* 1.3 78.0 - - - +
361B VAL* 1.3 56.7 + - + +
363B MET* 3.5 2.2 - - - +
364B GLU* 2.8 29.0 + - - +
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 5.6 1.8 - - + -
122B ASP* 4.0 13.5 - - + +
125B TYR* 3.6 44.9 - - + -
126B VAL* 4.7 8.1 - - + -
297B VAL* 5.1 1.8 - - + -
299B LEU* 4.9 6.5 - - + -
357B VAL* 3.0 27.3 + - + +
358B LYS* 3.8 7.0 - - - +
360B MET* 1.3 75.7 - - + +
362B GLU* 1.3 68.1 + - - +
363B MET 2.9 2.0 + - - -
364B GLU* 3.1 6.0 + - - +
365B LYS* 2.8 37.6 + - + +
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B LYS* 3.0 20.9 + - + +
359B LEU* 3.8 15.4 - - + +
361B VAL* 1.3 74.8 - - - +
363B MET* 1.3 64.0 + - - +
365B LYS* 3.6 11.6 - - + +
366B LYS* 3.2 28.7 + - - +
381B LYS* 4.9 9.2 + - - -
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Residues in contact with MET 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 3.4 27.4 - - + -
311B ILE* 3.9 31.9 - - + -
359B LEU* 2.9 59.7 + - + +
360B MET* 3.5 1.1 - - - +
362B GLU* 1.3 73.5 - - - +
364B GLU* 1.3 70.9 + - - +
365B LYS 2.9 1.3 - - - -
366B LYS* 2.6 17.4 + - - -
367B LEU* 2.9 16.4 + - - +
373B ILE* 4.1 26.7 - - + -
374B ASP 4.0 19.1 - - - +
375B ASP* 4.2 10.3 - - + -
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TYR* 4.0 17.0 - - + -
298B LYS* 3.7 3.0 - - - +
299B LEU* 3.2 21.0 - - + -
300B ALA* 2.6 31.5 + - - +
301B HIS* 3.1 12.0 + - - +
302B LEU* 2.6 35.6 + - + +
360B MET 2.8 21.7 + - - +
361B VAL* 3.5 6.5 - - - +
363B MET* 1.3 71.7 - - - +
365B LYS* 1.3 62.2 + - - +
367B LEU* 3.1 21.4 + - - +
368B GLU* 3.1 23.4 + - - +
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP* 2.9 29.3 + - - +
125B TYR* 3.3 31.2 - - + +
361B VAL* 2.8 28.6 + - + +
362B GLU* 3.6 10.1 - - + +
363B MET 2.7 3.6 + - - -
364B GLU* 1.3 69.1 - - - +
366B LYS* 1.3 56.0 + - + +
367B LEU 2.9 4.5 - - - -
368B GLU* 2.5 41.6 + - - +
369B LYS* 3.0 12.8 + - - +
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Residues in contact with LYS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLU* 3.2 18.7 + - - +
363B MET* 2.6 13.2 + - - +
365B LYS* 1.3 75.3 - - + +
367B LEU* 1.3 58.2 + - - +
368B GLU 3.2 0.4 + - - -
369B LYS* 3.5 13.5 + - - +
371B GLN* 3.1 48.3 + - + +
372B SER 4.1 15.4 + - - +
373B ILE* 4.1 17.4 - - + +
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B HIS* 4.0 32.9 + - + +
302B LEU* 4.6 8.1 - - + +
305B HIS* 4.5 15.5 - - + -
363B MET* 2.9 24.4 + - + +
364B GLU* 3.1 14.1 - - - +
365B LYS 2.8 0.8 + - - -
366B LYS* 1.3 77.1 - - - +
368B GLU* 1.3 62.5 + - - +
369B LYS 3.1 2.0 + - - -
370B GLY* 3.4 11.3 + - - -
371B GLN 4.4 11.7 - - - +
373B ILE* 3.4 42.8 - - + -
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TYR* 2.6 42.6 + - - -
301B HIS* 4.8 12.7 - - + +
364B GLU* 3.1 13.8 + - + +
365B LYS* 2.5 34.8 + - - +
367B LEU* 1.3 72.1 - - - +
369B LYS* 1.3 73.4 + - + +
370B GLY 3.5 1.6 + - - -
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Residues in contact with LYS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LYS* 3.0 31.7 + - - +
366B LYS* 3.5 9.1 + - - +
367B LEU 3.1 0.6 - - - -
368B GLU* 1.3 93.0 - - + +
370B GLY* 1.3 66.8 + - - +
371B GLN* 2.8 33.3 + - - +
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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