Contacts of the helix formed by residues 361 - 385 (chain A) in PDB entry 4C48
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 ASN 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 3.9 8.7 + - - +
359A LEU* 2.9 14.2 + - - +
360A GLN* 1.3 98.1 + - - +
362A PHE* 1.3 77.2 + - + +
363A ARG* 3.1 6.0 + - + +
364A ALA* 3.1 23.5 + - + +
365A THR* 3.2 15.8 + - - +
417A GLU* 5.7 1.0 - - - +
498A LYS* 5.5 6.9 - - + +
500A ILE* 5.6 5.5 - - - +
509A LYS* 4.6 12.7 + - - +
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Residues in contact with PHE 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 5.2 2.6 - - + -
356A TYR* 3.5 23.6 - - + -
361A ASN* 1.3 80.2 - - + +
363A ARG* 1.3 91.0 + - + +
365A THR* 2.7 21.6 + - - -
366A LEU* 3.2 20.4 - - + +
498A LYS* 6.5 1.8 - - + -
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Residues in contact with ARG 363 (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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361A ASN* 3.1 5.0 + - + +
362A PHE* 1.3 97.9 - - + +
364A ALA* 1.3 68.0 + - - +
366A LEU* 3.2 24.8 + - + +
367A ILE* 3.5 8.6 - - - +
495A THR 3.4 10.1 + - - -
496A MET* 2.5 57.8 + - + +
497A LEU* 4.5 2.6 + - - -
498A LYS* 4.1 34.2 - - + +
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 3.9 34.9 - - + +
361A ASN* 3.1 19.0 + - + +
363A ARG* 1.3 78.5 - - - +
365A THR* 1.3 62.2 + - - +
367A ILE* 3.1 28.8 + - - +
368A PRO* 3.2 9.9 - - - +
413A VAL* 5.5 0.9 - - - +
417A GLU* 5.9 1.8 - - - +
497A LEU* 4.5 15.0 - - + +
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 3.2 26.0 - - - +
355A MET* 3.5 15.2 - - + +
356A TYR* 3.3 44.8 - - + +
359A LEU* 5.2 0.9 - - + -
361A ASN 3.2 12.5 + - - +
362A PHE* 2.7 26.7 + - - -
364A ALA* 1.3 72.2 - - + +
366A LEU* 1.3 60.3 + - - +
367A ILE 3.3 0.4 - - - -
368A PRO* 3.5 10.3 - - - +
369A THR* 2.8 26.2 + - - +
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 5.0 7.2 - - + -
362A PHE* 3.2 27.1 + - + +
363A ARG* 3.2 13.4 + - + +
365A THR* 1.3 82.1 + - - +
367A ILE* 1.3 62.0 + - - +
369A THR* 2.4 21.0 + - - +
370A ILE* 3.0 33.9 + - + +
496A MET* 4.4 9.4 - - + -
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Residues in contact with ILE 367 (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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363A ARG 3.5 15.0 - - - +
364A ALA* 3.1 25.7 + - - +
366A LEU* 1.3 78.7 - - - +
368A PRO* 1.3 68.9 - - + +
369A THR 3.3 0.2 + - - -
370A ILE* 3.4 3.3 + - - +
371A ALA* 3.4 18.2 + - - +
413A VAL* 3.9 25.4 - - + -
489A THR* 4.4 10.8 - - - +
492A LEU* 3.9 32.3 - - + +
493A CYS* 4.4 3.8 - - - +
496A MET* 3.7 33.4 - - + -
497A LEU* 4.0 24.7 - - + -
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Residues in contact with PRO 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 5.5 4.3 - - + -
355A MET* 3.6 28.9 - - + -
359A LEU* 5.3 0.4 - - + -
364A ALA 3.2 14.8 - - - +
365A THR* 3.5 7.6 - - - +
367A ILE* 1.3 94.0 - - + +
369A THR* 1.3 64.6 + - - +
371A ALA* 3.4 13.6 + - + +
372A VAL* 3.5 18.9 + - - +
406A VAL 5.3 0.2 - - - +
409A ALA* 4.6 10.8 - - + +
410A ILE* 3.7 22.7 - - + -
413A VAL* 4.0 20.4 - - + -
489A THR* 5.6 0.2 - - - +
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Residues in contact with THR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 4.6 17.8 - - + +
351A VAL* 4.8 7.4 - - + -
352A PHE* 3.3 39.7 - - + +
355A MET* 5.5 0.9 - - + -
365A THR 2.8 17.3 + - - +
366A LEU* 2.4 32.1 + - - +
368A PRO* 1.3 76.3 - - + +
370A ILE* 1.3 60.0 + - - +
371A ALA 3.3 0.5 + - - -
372A VAL* 3.3 7.0 + - - +
373A PRO* 2.8 26.0 - - - +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 5.1 20.4 - - + -
20A MET* 6.6 0.4 - - - -
366A LEU* 3.0 42.6 + - + +
367A ILE* 3.9 4.0 - - - +
369A THR* 1.3 78.1 + - - +
371A ALA* 1.3 62.4 + - - +
373A PRO* 3.1 20.5 - - + +
374A VAL* 3.4 16.5 - - + +
488A LEU* 4.9 3.8 - - + -
492A LEU* 4.5 13.5 - - + -
496A MET* 3.9 21.3 - - + -
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE 3.4 9.8 + - - +
368A PRO 3.8 8.7 - - - +
369A THR 3.2 1.0 - - - -
370A ILE* 1.3 81.3 - - - +
372A VAL* 1.3 62.6 + - - +
374A VAL* 3.7 3.6 + - - +
375A VAL* 3.3 26.0 + - + +
405A LEU* 5.5 0.2 - - - -
409A ALA* 4.3 11.9 - - + -
484A VAL* 4.5 6.6 - - + +
485A ALA* 6.0 0.7 - - - -
488A LEU* 4.3 19.3 - - + -
489A THR* 3.8 22.9 - - - +
492A LEU* 5.0 0.9 - - + -
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 3.8 21.3 - - + -
351A VAL* 5.6 5.6 - - + -
368A PRO 3.5 11.4 + - - +
369A THR* 3.3 6.8 + - - +
371A ALA* 1.3 75.7 - - + +
373A PRO* 1.4 77.1 - - + +
375A VAL* 3.0 5.5 + - - +
376A LEU* 3.0 38.4 + - + +
402A ILE* 5.2 6.1 - - + -
405A LEU* 3.6 27.3 - - + +
406A VAL* 3.7 28.3 - - + +
409A ALA* 5.8 2.0 - - + -
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Residues in contact with PRO 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 5.8 5.8 - - + -
348A ILE* 4.5 9.9 - - + -
369A THR 2.8 27.1 - - - +
370A ILE* 3.1 17.9 - - + +
372A VAL* 1.4 83.3 - - + +
374A VAL* 1.3 61.8 + - + +
376A LEU* 3.0 27.9 + - + +
377A LEU* 3.0 30.1 + - + +
2044A LMT 6.2 3.4 - - + -
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Residues in contact with VAL 374 (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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16A ALA* 4.0 37.2 - - + +
19A ILE* 3.6 10.4 - - + +
20A MET* 4.4 17.9 - - + +
370A ILE* 3.4 23.1 - - + +
371A ALA 3.7 8.1 - - - +
372A VAL 3.1 0.6 + - - -
373A PRO* 1.3 76.2 - - + +
375A VAL* 1.3 63.8 + - - +
377A LEU* 3.9 7.1 - - - +
378A GLY* 3.2 18.5 + - - -
480A LEU* 5.0 0.3 - - - +
484A VAL* 4.3 22.1 - - + +
488A LEU* 4.1 16.2 - - + -
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA* 3.3 11.9 + - + +
372A VAL 3.0 6.6 + - - +
374A VAL* 1.3 77.7 - - - +
376A LEU* 1.3 59.8 + - - +
378A GLY 3.0 2.6 + - - -
379A THR* 3.0 28.3 + - - +
405A LEU* 3.3 38.1 - - + +
477A ALA 3.3 24.2 - - - +
480A LEU* 3.1 14.7 - - + +
481A SER* 3.6 13.5 - - - +
484A VAL* 3.3 29.4 - - + -
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Residues in contact with LEU 376 (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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344A LEU* 3.9 40.6 - - + -
348A ILE* 4.4 2.5 - - + -
372A VAL* 3.0 36.5 + - + +
373A PRO* 3.0 17.0 + - + +
375A VAL* 1.3 79.9 - - - +
377A LEU* 1.3 83.3 + - + +
379A THR* 3.2 23.1 + - - -
380A PHE* 3.8 15.3 + - + -
398A MET* 4.4 14.3 - - + +
402A ILE* 4.3 15.0 - - + -
405A LEU* 4.8 6.1 - - + -
2044A LMT 4.9 15.3 - - + -
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Residues in contact with LEU 377 (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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19A ILE 3.1 30.1 - - - +
20A MET* 3.3 40.2 - - + +
23A GLY* 3.2 24.2 - - - -
24A GLY* 4.7 3.1 - - - +
373A PRO* 3.0 30.9 + - + +
374A VAL 3.9 6.7 - - - +
376A LEU* 1.3 79.7 - - + +
378A GLY* 1.3 77.3 + - - +
379A THR 3.0 2.5 - - - -
380A PHE* 2.8 32.3 + - + +
2044A LMT 5.2 13.7 - - + -
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Residues in contact with GLY 378 (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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19A ILE* 3.5 31.8 - - - +
374A VAL 3.2 1.9 + - - -
375A VAL 3.0 9.9 + - - -
377A LEU* 1.3 84.4 - - - +
379A THR* 1.3 60.1 + - - +
381A ALA* 3.2 20.7 - - - +
382A VAL* 3.4 5.9 + - - +
480A LEU* 3.6 15.0 - - - +
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Residues in contact with THR 379 (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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375A VAL 3.0 14.4 + - - -
376A LEU* 3.2 14.7 + - - -
377A LEU 3.0 0.4 - - - -
378A GLY* 1.3 74.1 - - - +
380A PHE* 1.3 65.9 + - - +
382A VAL* 3.2 1.0 + - - +
383A LEU* 3.1 39.1 + - + +
398A MET* 5.5 8.4 - - + +
473A THR* 3.8 8.3 - - + +
476A SER* 3.1 28.3 - - - +
477A ALA* 3.5 31.2 - - + +
480A LEU* 3.7 8.4 - - - +
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Residues in contact with PHE 380 (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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23A GLY 3.8 13.5 - - - +
26A ALA* 3.6 8.2 - - + +
27A ILE* 3.6 29.6 - - + -
30A LEU* 4.7 5.8 - - + +
376A LEU* 4.1 9.0 - - + -
377A LEU* 2.8 41.4 + - + +
379A THR* 1.3 72.3 - - - +
381A ALA* 1.3 63.5 + - - +
383A LEU* 3.8 10.2 - - + +
384A ALA* 2.9 27.9 + - - +
390A ILE* 3.8 28.3 - - + -
395A MET* 4.1 12.8 - - + -
398A MET* 3.5 39.5 - - + -
2044A LMT 4.8 13.2 - - + -
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 5.1 1.3 - - + +
22A ALA* 3.9 33.7 - - + -
23A GLY* 3.9 3.4 - - - +
26A ALA* 3.6 11.8 - - - +
377A LEU 3.4 1.4 + - - -
378A GLY* 3.2 14.7 + - - +
379A THR 3.1 0.6 - - - -
380A PHE* 1.3 82.4 - - - +
382A VAL* 1.3 63.2 + - + +
384A ALA* 3.4 3.8 - - - +
385A ALA* 3.2 19.6 + - - +
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY 3.4 3.8 + - - +
379A THR 3.2 4.8 + - - +
381A ALA* 1.3 79.6 - - + +
383A LEU* 1.3 58.0 + - - +
385A ALA* 3.1 20.8 + - + +
386A PHE* 3.2 34.6 + - + -
476A SER* 4.1 19.1 - - - -
480A LEU* 3.6 29.8 - - + -
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Residues in contact with LEU 383 (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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30A LEU* 4.0 11.9 - - + -
379A THR* 3.1 41.0 + - + +
380A PHE* 3.8 14.8 - - + +
382A VAL* 1.3 74.2 - - - +
384A ALA* 1.3 63.2 + - - +
385A ALA 3.3 0.2 - - - -
386A PHE* 3.6 9.3 + - - +
387A GLY 3.5 2.1 + - - -
388A PHE* 3.0 56.6 + - + +
389A SER 3.8 16.4 - - - +
390A ILE* 5.2 1.6 - - - -
394A THR* 5.1 5.8 - - + -
398A MET* 4.8 7.4 - - + -
472A ILE* 4.6 13.7 - - + -
473A THR* 4.3 17.0 - - + +
476A SER* 4.9 3.8 - - - +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.1 14.4 - - + +
30A LEU* 3.6 31.5 - - + +
380A PHE 2.9 21.2 + - - +
381A ALA 3.4 5.6 - - - +
383A LEU* 1.3 76.4 - - - +
385A ALA* 1.3 58.1 + - - +
386A PHE 3.2 0.2 - - - -
387A GLY* 3.0 20.4 + - - -
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA 3.2 9.5 + - - +
382A VAL* 3.1 15.9 + - + +
384A ALA* 1.3 78.8 - - - +
386A PHE* 1.3 63.5 + - + +
387A GLY 3.5 0.4 - - - -
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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