Contacts of the helix formed by residues 413 - 444 (chain A) in PDB entry 3R29
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 GLY 413 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLN* 3.1 1.4 - - - +
412A PRO* 1.3 82.0 - - - +
414A ARG* 1.3 55.0 + - - +
415A PHE* 3.0 4.5 - - - -
416A ALA* 2.9 10.2 + - - +
417A LYS* 2.6 38.9 + - - +
397B TYR* 4.1 17.7 + - - -
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Residues in contact with ARG 414 (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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360A MET* 2.6 41.3 + - + +
361A GLN 3.0 25.1 + - - -
362A MET* 3.9 0.6 - - - +
366A GLU* 2.6 44.0 + - - +
404A CYS* 4.2 9.0 - - + -
408A TYR* 3.2 40.4 + - + -
411A GLN* 3.0 46.1 + - - +
413A GLY* 1.3 76.9 - - - +
415A PHE* 1.3 56.2 + - - +
417A LYS* 3.4 9.9 - - - +
418A LEU* 2.8 39.3 + - + +
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Residues in contact with PHE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TYR* 3.6 32.8 - + + -
400A LEU* 3.9 23.1 - - + -
401A GLU* 3.4 47.1 - - + -
404A CYS* 4.1 18.9 - - + +
412A PRO 5.4 1.5 - - - +
413A GLY 2.9 1.2 + - - -
414A ARG* 1.3 77.1 - - - +
416A ALA* 1.3 63.9 + - - +
418A LEU* 3.4 3.2 + - - +
419A LEU* 3.0 40.8 + - + +
401B GLU* 5.5 1.6 - - - -
413B GLY* 6.5 0.2 - - - -
415B PHE* 4.7 15.0 - + - -
416B ALA* 3.7 31.0 - - + -
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLY* 2.9 8.9 + - - +
415A PHE* 1.3 78.1 - - - +
417A LYS* 1.3 72.8 + - - +
419A LEU* 3.8 0.6 - - - +
420A LEU* 3.0 26.6 + - - +
397B TYR* 3.7 32.1 - - + -
415B PHE* 4.1 11.4 - - + -
419B LEU* 4.0 24.9 - - + -
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Residues in contact with LYS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 6.5 0.2 - - + -
360A MET* 3.4 33.2 - - + -
413A GLY 2.6 15.5 + - - +
414A ARG* 3.4 8.5 - - - +
416A ALA* 1.3 82.5 - - - +
418A LEU* 1.3 63.9 - - - +
420A LEU* 2.9 13.4 + - - +
421A ARG* 3.4 9.5 + - - +
390B GLU* 3.4 36.2 + - - +
393B ARG* 6.2 1.6 - - - +
394B GLU* 2.5 33.8 + - - +
397B TYR* 3.5 24.6 + - - +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A MET* 4.0 16.8 - - + -
362A MET* 3.8 37.0 - - + -
366A GLU* 3.5 38.4 - - + +
370A LEU* 3.7 21.7 - - + +
400A LEU* 4.0 16.4 - - + -
404A CYS* 3.8 14.6 - - - -
414A ARG* 2.8 26.1 + - + +
415A PHE* 3.6 4.5 - - - +
417A LYS* 1.3 74.9 - - - +
419A LEU* 1.3 67.0 + - - +
421A ARG* 2.7 23.7 + - - +
422A LEU 4.1 0.5 + - - -
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 4.4 10.3 - - + -
373A ILE* 4.1 26.2 - - + -
397A TYR* 4.9 0.7 - - + -
400A LEU* 5.0 1.3 - - + -
415A PHE* 3.0 40.7 + - + +
416A ALA 3.9 4.0 - - - +
418A LEU* 1.3 76.3 - - - +
420A LEU* 1.3 59.0 - - - +
422A LEU* 3.0 30.3 + - + +
423A PRO* 4.0 2.3 - - - +
416B ALA* 3.6 41.1 - - + +
419B LEU* 4.0 27.6 - - + +
420B LEU* 4.1 19.9 - - + +
423B PRO* 5.5 0.3 - - - +
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 3.0 22.5 + - + +
417A LYS* 2.9 8.9 + - - +
418A LEU 2.7 4.0 + - - -
419A LEU* 1.3 73.5 - - - +
421A ARG* 1.3 76.3 + - - +
422A LEU 3.0 6.1 + - - -
423A PRO* 3.3 17.5 - - + +
424A ALA* 4.6 1.4 + - - +
373B ILE* 4.1 13.2 - - + -
393B ARG* 4.7 18.5 + - - +
397B TYR* 3.5 36.8 - - + -
419B LEU* 4.5 17.0 - - + +
422B LEU* 3.4 33.4 - - + -
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Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU 2.8 35.5 + - - -
353A LEU* 4.0 12.7 - - + +
356A LYS* 3.4 38.9 - - + +
357A MET* 5.3 4.5 - - + -
360A MET* 5.3 8.7 - - - -
362A MET* 4.7 21.1 - - + -
370A LEU* 5.1 4.7 - - + -
417A LYS 3.4 6.3 + - - +
418A LEU 2.7 17.9 + - - +
420A LEU* 1.3 89.9 + - - +
422A LEU* 1.3 60.4 + - + +
423A PRO 3.7 0.2 - - - -
424A ALA* 3.4 12.8 - - - +
425A LEU* 3.0 26.7 + - - +
379B ASP* 2.5 38.1 + - - -
393B ARG* 4.2 16.4 - - - +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 4.9 1.4 - - - +
370A LEU* 4.4 23.3 - - + +
373A ILE* 3.9 17.7 - - + -
374A VAL* 3.7 28.0 - - + -
419A LEU* 3.0 24.8 + - + +
420A LEU 3.0 4.4 - - - -
421A ARG* 1.3 78.6 - - + +
423A PRO* 1.3 67.2 - - + +
425A LEU* 3.0 17.7 + - + +
426A ARG* 2.8 23.2 + - - +
420B LEU* 3.6 28.9 - - + -
423B PRO* 3.9 14.3 - - + +
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Residues in contact with PRO 423 (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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419A LEU 4.0 3.1 - - - +
420A LEU* 3.3 22.4 - - + +
422A LEU* 1.3 89.5 - - + +
424A ALA* 1.3 63.5 + - - +
426A ARG* 2.9 13.7 + - + +
427A SER* 2.9 12.3 + - - -
419B LEU 5.9 0.4 - - - +
422B LEU* 3.6 33.9 - - + -
423B PRO* 3.8 17.9 - - + -
426B ARG* 3.4 38.6 + - + +
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Residues in contact with ALA 424 (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 GLU* 4.2 20.6 - - + +
353A LEU* 4.6 2.0 - - + -
420A LEU 4.6 0.2 + - - -
421A ARG* 3.4 39.3 - - - +
423A PRO* 1.3 79.7 - - - +
425A LEU* 1.3 61.5 + - - +
427A SER* 3.4 1.6 + - - -
428A ILE* 3.2 29.2 + - - +
379B ASP* 4.1 7.9 - - - +
426B ARG* 3.3 15.4 - - - +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 3.6 50.2 - - + +
310A ILE* 3.7 23.7 - - + +
311A ALA* 4.0 17.0 - - + +
353A LEU* 4.0 21.7 - - + +
357A MET* 6.0 0.4 - - + -
374A VAL* 3.9 11.2 - - + -
421A ARG 3.0 14.5 + - - +
422A LEU* 3.0 28.0 + - + +
424A ALA* 1.3 71.6 - - - +
426A ARG* 1.3 66.0 + - - +
428A ILE* 3.5 2.2 + - - +
429A GLY* 3.2 16.5 + - - -
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Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 2.9 39.3 + - - +
374A VAL* 6.3 0.2 - - - +
377A ASN* 3.7 26.4 + - - +
379A ASP* 5.6 6.3 + - - +
393A ARG* 5.2 6.3 - - - +
422A LEU 2.8 18.8 + - - +
423A PRO* 2.9 4.0 + - + +
425A LEU* 1.3 72.7 - - - +
427A SER* 1.3 63.4 + - - +
429A GLY* 3.4 2.9 + - - -
430A LEU* 3.4 25.4 + - - +
352B GLU* 4.7 5.5 + - - -
423B PRO* 3.8 31.0 - - + +
424B ALA* 3.8 18.4 - - - +
426B ARG* 4.9 0.9 - - + -
427B SER* 3.5 42.8 + - - +
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 5.9 1.0 - - - -
352A GLU* 5.0 2.8 + - - -
423A PRO 2.9 11.4 + - - -
424A ALA* 3.4 7.3 + - - -
426A ARG* 1.3 77.7 - - - +
428A ILE* 1.3 74.5 + - - +
430A LEU* 3.0 6.2 + - - +
431A LYS* 3.0 33.4 + - - +
426B ARG* 3.9 24.4 + - - -
430B LEU* 3.5 28.7 - - - +
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Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 4.0 20.6 - - + -
345A ILE* 4.1 20.2 - - + +
348A ARG* 3.7 42.2 - - + +
349A VAL* 4.1 10.5 - - + -
352A GLU* 4.0 13.5 - - + +
353A LEU* 3.6 29.2 - - + -
424A ALA 3.2 16.0 + - - +
425A LEU* 3.9 4.7 - - - +
426A ARG 3.4 0.2 - - - -
427A SER* 1.3 86.8 + - - +
429A GLY* 1.3 59.7 + - - +
431A LYS* 3.5 8.0 + - - +
432A CYS* 3.2 21.3 + - - -
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Residues in contact with GLY 429 (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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306A ASN* 2.8 36.6 + - - -
307A GLU* 5.0 3.8 - - - -
310A ILE* 3.6 12.9 - - - +
425A LEU 3.2 12.0 + - - -
426A ARG 3.4 4.9 + - - -
427A SER 3.1 0.8 - - - -
428A ILE* 1.3 76.7 - - - +
430A LEU* 1.3 64.6 + - - +
432A CYS* 3.1 10.2 + - - +
433A LEU* 3.3 4.5 + - - +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 3.4 17.7 + - + +
427A SER* 3.0 6.7 + - - +
429A GLY* 1.3 76.7 - - - +
431A LYS* 1.3 52.4 + - - +
433A LEU* 2.9 26.3 + - + +
434A GLU* 2.7 47.3 + - - +
427B SER* 3.8 41.3 - - - +
430B LEU* 4.7 15.0 - - + -
431B LYS* 4.3 19.5 - - + +
434B GLU* 5.0 5.4 - - - +
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Residues in contact with LYS 431 (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 ALA 5.8 0.7 - - - +
345A ILE* 3.7 15.5 - - + -
348A ARG* 3.6 43.9 - - - +
427A SER* 3.0 22.6 + - - +
428A ILE* 3.6 8.3 - - - +
430A LEU* 1.3 76.0 - - - +
432A CYS* 1.3 60.7 + - - +
434A GLU* 3.5 23.4 + - - +
435A HIS* 2.9 32.7 + - + +
430B LEU* 3.8 36.6 - - + +
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Residues in contact with CYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASN* 4.2 8.1 - - - +
310A ILE* 4.2 17.0 - - - -
313A PHE* 6.4 1.1 - - - -
345A ILE* 3.6 30.1 - - - -
428A ILE 3.2 15.4 + - - -
429A GLY 3.1 8.2 + - - +
431A LYS* 1.3 72.3 - - - +
433A LEU* 1.3 56.3 + - + +
435A HIS* 2.8 6.6 + - - +
436A LEU* 2.5 37.0 + - + +
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASN* 4.2 17.5 - - - +
429A GLY 3.3 7.4 + - - +
430A LEU* 2.9 30.9 + - + +
432A CYS* 1.3 75.2 - - - +
434A GLU* 1.3 55.0 + - + +
436A LEU* 3.8 25.1 - - + -
437A PHE* 2.7 57.7 + - + -
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 2.7 30.8 + - - +
431A LYS* 3.6 31.6 + - - +
433A LEU* 1.3 77.2 - - + +
435A HIS* 1.3 66.2 + - + +
437A PHE* 3.9 4.4 - - - +
438A PHE* 3.0 24.8 + - - +
430B LEU* 4.8 8.3 - - - +
434B GLU* 2.8 34.1 - - - +
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Residues in contact with HIS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY 3.0 28.8 + - - -
342A VAL* 4.0 8.1 - - + +
344A ALA* 4.1 15.8 - - + +
345A ILE* 3.4 26.9 - - + +
431A LYS* 2.9 31.2 + - + +
432A CYS* 2.8 14.5 + - - +
434A GLU* 1.3 72.6 - - + +
436A LEU* 1.3 68.3 + - - +
437A PHE 2.8 1.6 + - - -
438A PHE* 2.8 6.7 + + - -
439A PHE* 2.8 52.4 + + + -
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Residues in contact with LEU 436 (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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265A VAL* 6.5 0.9 - - + -
269A CYS* 5.4 11.2 - - - -
432A CYS* 2.5 20.0 + - + +
433A LEU* 3.5 27.1 - - + +
435A HIS* 1.3 73.5 - - - +
437A PHE* 1.3 68.8 + - + +
439A PHE* 3.5 10.0 + - + +
440A LYS* 3.3 43.7 + - + +
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Residues in contact with PHE 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU* 2.7 51.9 + - + +
434A GLU* 3.9 4.5 - - - +
435A HIS 2.8 2.6 + - - -
436A LEU* 1.3 80.0 - - + +
438A PHE* 1.3 62.9 + - - +
439A PHE 3.2 0.2 + - - -
440A LYS* 3.3 7.6 + - + +
441A LEU* 3.0 24.2 + - - +
450A PHE* 4.7 20.0 - + - -
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Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLU 3.0 16.7 + - - +
435A HIS* 2.8 5.9 + + - +
437A PHE* 1.3 76.4 - - - +
439A PHE* 1.3 74.6 + + - +
441A LEU* 4.2 18.8 - - + -
442A ILE* 2.7 72.5 + - + +
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 5.0 16.2 - - + -
340A ALA 3.7 22.0 - - - -
341A GLY* 4.7 5.4 - - - -
342A VAL* 4.4 10.8 - - + -
435A HIS* 2.8 55.8 + + + +
436A LEU* 3.8 9.0 - - + +
438A PHE* 1.3 94.6 - + - +
440A LYS* 1.3 72.8 + - - +
442A ILE* 4.1 7.1 - - + +
443A GLY* 2.8 24.4 + - - -
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Residues in contact with LYS 440 (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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269A CYS* 5.8 5.7 - - - -
436A LEU* 3.3 34.8 + - + +
437A PHE* 3.3 10.5 + - + +
439A PHE* 1.3 82.7 - - - +
441A LEU* 1.3 62.1 + - - +
444A ASP* 3.1 17.3 + - - +
446A PRO 4.9 6.6 - - - +
447A ILE* 3.7 20.6 - - + +
450A PHE* 6.3 4.5 - - + -
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE 3.0 17.4 + - - +
438A PHE* 3.5 23.6 - - + +
440A LYS* 1.3 75.9 - - - +
442A ILE* 1.3 61.8 + - + +
444A ASP* 1.5 41.4 + - - +
447A ILE* 4.1 12.3 - - + -
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE* 2.7 59.6 + - + +
439A PHE* 4.1 7.9 - - + +
441A LEU* 1.3 76.3 - - + +
443A GLY* 1.3 76.0 + - - +
444A ASP* 3.5 6.4 - - - +
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Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PHE 2.8 17.8 + - - -
440A LYS* 5.3 0.2 - - - -
442A ILE* 1.3 83.5 - - - +
444A ASP* 1.3 67.0 + - - +
445A THR* 2.3 28.3 + - - +
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Residues in contact with ASP 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A LYS 3.1 10.0 + - - +
441A LEU* 1.5 39.7 - - - +
442A ILE* 3.4 7.5 - - - +
443A GLY* 1.3 78.5 - - - +
445A THR* 1.3 78.4 + - - +
446A PRO* 2.4 13.7 - - - +
447A ILE* 2.8 35.0 - - + +
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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