Contacts of the helix formed by residues 334 - 362 (chain A) in PDB entry 3RFU
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 ARG 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A MET* 6.3 2.5 - - - -
205A GLU* 3.6 27.1 + - - -
209A ARG* 3.0 50.5 - - - +
332A ILE* 4.2 11.0 + - + +
333A GLN* 1.3 76.1 + - - +
335A LEU* 1.3 67.0 + - - +
336A ALA* 3.3 9.3 + - + +
337A ASP* 3.4 32.9 + - - +
338A THR* 3.6 14.0 + - - +
390A THR* 5.6 10.0 - - + +
412A GLU* 5.1 5.2 + - - -
415A GLU* 5.0 10.2 + - - +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN 4.9 5.2 - - - +
334A ARG* 1.3 74.0 - - - +
336A ALA* 1.3 59.3 + - - +
338A THR* 2.7 24.1 + - + +
339A VAL* 2.8 20.0 - - + +
390A THR* 5.8 1.1 + - - +
675A MET* 3.9 29.4 - - + -
678A ILE* 4.2 18.2 - - + -
679A ARG* 3.9 23.3 - - + +
682A LEU* 3.9 14.6 - - + -
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 4.6 18.2 - - + -
334A ARG* 3.2 6.4 - - + +
335A LEU* 1.3 79.7 - - - +
337A ASP* 1.3 61.8 + - - +
339A VAL* 3.2 8.4 - - - +
340A SER* 2.7 38.8 + - - +
386A LEU* 5.0 7.2 - - + +
390A THR* 4.5 12.8 + - - +
682A LEU* 4.2 20.8 - - + +
686A PHE* 6.1 0.2 - - - -
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Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU 3.3 15.0 - - - +
147A ASN* 3.4 22.1 + - + +
148A MET* 3.4 36.9 + - - +
149A PHE* 5.5 2.7 - - - -
333A GLN* 4.5 11.0 - - - +
334A ARG* 3.4 33.7 + - - +
335A LEU 3.3 0.4 - - - -
336A ALA* 1.3 78.2 - - - +
338A THR* 1.3 58.1 + - - +
341A GLY 3.0 18.2 + - - -
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Residues in contact with THR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU 5.3 0.2 - - - -
333A GLN* 3.8 29.4 - - + +
334A ARG 3.6 6.5 + - - +
335A LEU* 2.7 30.9 + - - +
337A ASP* 1.3 75.3 - - - +
339A VAL* 1.3 57.9 + - - +
340A SER 3.1 0.9 - - - -
341A GLY* 2.7 22.3 + - - -
342A TRP* 3.1 12.1 + - - +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU 2.8 24.9 - - - +
336A ALA* 3.2 18.2 - - - +
338A THR* 1.3 77.2 + - - +
340A SER* 1.3 56.9 + - - +
342A TRP* 3.4 11.1 + - + +
343A PHE* 3.0 26.6 + - + +
682A LEU* 4.5 11.4 - - + -
686A PHE* 4.0 32.8 - - + -
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Residues in contact with SER 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN 3.8 3.4 - - - -
148A MET* 3.7 29.7 - - - -
151A LEU* 4.3 9.9 - - - -
336A ALA 2.7 23.4 + - - -
339A VAL* 1.3 74.0 - - - +
341A GLY* 1.3 63.9 + - - +
343A PHE* 3.9 7.9 - - - -
344A VAL* 2.9 34.0 + - - +
386A LEU* 3.8 9.7 - - - +
686A PHE* 3.7 17.0 - - - -
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Residues in contact with GLY 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.4 36.7 + - - +
337A ASP 3.0 7.2 + - - -
338A THR* 2.7 12.7 + - - -
340A SER* 1.3 79.1 - - - +
342A TRP* 1.3 54.3 + - - -
345A PRO* 3.1 22.7 - - - +
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Residues in contact with TRP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A THR 3.1 8.6 + - - +
339A VAL* 3.8 11.2 - - + +
341A GLY* 1.3 75.3 - - - +
343A PHE* 1.3 82.8 + + + +
345A PRO* 2.9 17.9 - - + +
346A ALA* 3.1 34.5 + - + +
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Residues in contact with PHE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.3 26.7 - - + -
339A VAL* 3.0 19.1 + - + +
340A SER* 3.6 8.1 - - - +
342A TRP* 1.3 96.3 - + + +
344A VAL* 1.3 64.1 + - - +
346A ALA* 2.8 16.0 + - + +
347A VAL* 2.9 39.4 + - + +
381A ALA* 3.6 32.5 - - + -
686A PHE* 3.5 32.1 - + + -
689A ASN* 5.8 0.4 - - + -
690A VAL* 4.7 27.4 - - + -
693A VAL* 5.1 4.7 - - + -
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.6 22.0 - - + -
147A ASN 4.6 0.7 - - - +
150A THR* 3.5 24.2 - - - +
151A LEU* 3.6 34.3 - - + +
154A MET* 4.8 10.0 - - - +
340A SER 2.9 20.5 + - - +
343A PHE* 1.3 72.5 - - - +
345A PRO* 1.3 73.9 - - + +
347A VAL* 3.5 5.0 + - - +
348A ILE* 3.0 40.3 + - + +
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Residues in contact with PRO 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.5 17.3 - - + -
341A GLY 3.1 23.6 - - - +
342A TRP* 2.9 20.6 - - - +
344A VAL* 1.3 91.6 - - + +
346A ALA* 1.3 61.9 + - - +
348A ILE* 3.3 8.5 + - + +
349A LEU* 3.0 22.2 + - - +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TRP* 3.1 41.2 + - + +
343A PHE* 2.8 15.7 + - + +
345A PRO* 1.3 75.0 - - - +
347A VAL* 1.3 62.2 + - + +
349A LEU* 3.1 12.8 + - - +
350A VAL* 3.0 26.7 + - + +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 5.1 0.4 - - + -
154A MET* 5.3 2.0 - - + -
343A PHE* 2.9 57.1 + - + +
344A VAL* 3.8 6.3 - - - +
346A ALA* 1.3 74.7 - - + +
348A ILE* 1.3 57.7 + - - +
350A VAL* 3.3 9.1 + - + +
351A ALA* 3.0 26.3 + - - +
377A VAL* 3.8 20.8 - - + +
378A LEU* 3.9 14.6 - - + -
381A ALA* 3.5 23.6 - - + -
693A VAL* 5.3 3.1 - - + -
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Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 4.5 12.1 - - - -
344A VAL* 3.0 33.1 + - + +
345A PRO* 3.7 7.4 - - + +
346A ALA 3.2 0.2 - - - -
347A VAL* 1.3 74.0 - - - +
349A LEU* 1.3 68.6 + - - +
351A ALA* 3.2 7.6 + - + +
352A VAL* 3.0 33.6 + - + +
378A LEU* 4.4 15.7 - - + -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PRO 3.0 12.9 + - - +
346A ALA* 3.3 12.1 - - - +
348A ILE* 1.3 79.0 - - - +
350A VAL* 1.3 64.6 + - + +
352A VAL* 3.4 6.1 + - + +
353A LEU* 3.0 55.7 + - + +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA* 3.0 19.7 + - + +
347A VAL* 3.6 9.9 - - - +
349A LEU* 1.3 79.5 - - + +
351A ALA* 1.3 63.1 + - - +
353A LEU* 3.3 9.2 + - + +
354A SER* 3.0 30.3 + - - +
377A VAL* 3.9 20.2 - - + -
693A VAL* 4.6 15.5 - - + -
694A PRO* 6.0 0.7 - - + -
697A ALA* 4.6 8.5 - - + -
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL 3.0 12.9 + - - +
348A ILE* 3.5 12.1 - - + +
350A VAL* 1.3 76.4 - - - +
352A VAL* 1.3 64.3 + - + +
354A SER* 3.1 6.9 + - - -
355A PHE* 3.0 20.3 + - - +
374A ALA* 3.8 24.2 - - + +
377A VAL* 3.4 30.3 - - + -
378A LEU* 4.4 8.3 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 3.0 30.4 + - + +
349A LEU* 3.9 7.6 - - + +
351A ALA* 1.3 76.7 - - + +
353A LEU* 1.3 67.3 + - + +
355A PHE* 3.0 22.3 + - + +
356A ILE* 3.0 28.2 + - + +
374A ALA* 5.6 0.2 - - - -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.0 48.1 + - + +
350A VAL* 3.8 7.9 - - + +
352A VAL* 1.3 78.6 - - + +
354A SER* 1.3 58.2 + - - +
356A ILE* 3.2 19.2 + - + +
357A VAL* 3.0 34.6 + - + +
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL* 3.0 15.3 + - - +
351A ALA* 3.4 11.0 - - - -
353A LEU* 1.3 77.1 - - - +
355A PHE* 1.3 56.8 + - - +
357A VAL* 3.8 6.2 - - - +
358A TRP* 3.0 37.9 + - - -
373A ALA* 4.3 20.4 - - - -
377A VAL* 5.5 0.6 - - - +
697A ALA* 3.2 34.4 + - - +
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ALA 3.0 12.1 + - - +
352A VAL* 3.0 16.8 + - + +
354A SER* 1.3 76.5 - - - +
356A ILE* 1.3 59.4 + - + +
358A TRP* 4.3 0.2 - - - +
359A ALA* 2.8 48.0 + - + +
367A LEU* 4.5 21.5 - - + -
370A GLY* 3.4 34.7 + - - +
371A LEU* 3.5 21.3 - - + -
374A ALA* 4.8 5.2 - - + -
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A VAL* 3.0 29.5 + - + +
353A LEU* 3.2 20.8 + - + +
354A SER 3.1 0.2 - - - -
355A PHE* 1.3 86.3 - - + +
357A VAL* 1.3 62.0 + - + +
359A ALA* 4.1 4.5 - - - -
360A LEU* 3.0 53.2 + - + +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.0 22.4 + - + +
354A SER* 3.3 7.8 + - - +
356A ILE* 1.3 81.7 - - + +
358A TRP* 1.3 62.8 + - + +
360A LEU* 5.3 0.2 - - - -
361A LEU* 3.1 35.7 + - + +
362A GLY* 3.1 17.0 + - - -
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Residues in contact with TRP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A SER* 3.0 27.9 + - - +
357A VAL* 1.3 82.1 - - + +
359A ALA* 1.3 62.7 + - - +
362A GLY* 2.8 41.0 + - - +
363A PRO* 5.0 3.1 - - + -
364A GLN* 4.2 10.3 - - - -
367A LEU* 4.8 9.7 - - - +
369A TYR* 3.3 51.3 - + + +
370A GLY* 3.5 20.9 - - - +
373A ALA* 3.8 19.9 - - + +
697A ALA 3.2 24.8 + - - -
698A GLY* 4.7 12.2 + - - -
701A TYR* 3.3 40.8 - + - -
706A LEU* 6.0 0.4 - - + -
707A LEU* 4.8 7.0 - - + -
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 2.8 41.6 + - + +
356A ILE* 4.0 5.6 - - - +
357A VAL 3.3 0.2 - - - -
358A TRP* 1.3 81.4 - - - +
360A LEU* 1.3 70.8 + - + +
362A GLY 4.5 0.3 + - - -
367A LEU* 4.5 23.0 - - + +
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 3.0 41.3 + - + +
359A ALA* 1.3 89.7 - - + +
361A LEU* 1.3 63.6 + - + +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 3.1 35.1 + - + +
360A LEU* 1.3 81.9 - - + +
362A GLY* 1.3 53.4 + - - +
363A PRO* 2.7 36.2 - - + +
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Residues in contact with GLY 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL 3.1 3.2 + - - -
358A TRP* 2.8 44.3 + - - +
359A ALA 4.5 0.4 + - - +
360A LEU 3.7 0.6 - - - -
361A LEU* 1.3 73.6 - - - +
363A PRO* 1.3 60.6 - - - +
364A GLN* 2.8 24.9 + - - +
365A PRO* 4.5 1.7 - - - +
367A LEU* 6.1 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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il