Contacts of the helix formed by residues 491 - 516 (chain D) in PDB entry 3G4L
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 PRO 491 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D TRP* 5.1 4.7 - - + +
269D GLY* 3.8 30.3 - - - +
489D THR 4.7 0.9 - - - +
490D LYS* 1.3 84.9 - - + +
492D LEU* 1.3 68.1 - - - +
493D GLN* 3.2 5.4 - - + +
494D LEU* 2.8 27.1 + - + +
495D TYR 3.1 7.8 + - - -
564D THR* 4.4 7.8 - - + -
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Residues in contact with LEU 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490D LYS 3.3 3.7 + - - -
491D PRO* 1.3 68.7 - - - +
493D GLN* 1.3 64.0 + - - +
495D TYR* 3.1 18.6 + - + -
496D ARG* 2.9 49.8 + - + +
564D THR* 5.3 0.4 - - - +
568D ASN* 3.7 24.1 + - + +
571D TRP* 3.6 53.2 - - + +
572D TYR* 4.9 0.9 - - + -
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Residues in contact with GLN 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D SO4 5.6 1.8 - - - +
491D PRO* 3.0 5.8 + - + +
492D LEU* 1.3 77.9 - - - +
494D LEU* 1.3 62.6 + - + +
496D ARG* 3.8 7.8 + - - +
497D GLN* 3.2 31.6 + - - +
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Residues in contact with LEU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D SO4 2.9 30.7 - - - +
269D GLY* 4.0 24.7 - - - +
270D LEU 3.7 23.1 - - - +
271D HIS* 5.1 3.1 - - + -
272D VAL* 4.6 6.3 - - + +
273D PHE* 3.7 22.6 - - + -
490D LYS* 4.2 12.6 - - + -
491D PRO* 2.8 28.1 + - + +
493D GLN* 1.3 72.0 - - + +
495D TYR* 1.3 66.3 + - - +
497D GLN* 3.1 16.1 + - - +
498D TRP* 3.1 24.5 + - - +
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Residues in contact with TYR 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D ASN* 3.5 21.2 + - + +
488D PRO* 3.4 29.7 - - + +
490D LYS* 4.2 0.8 - - - +
491D PRO 3.1 7.2 + - - +
492D LEU* 3.1 11.8 + - + +
494D LEU* 1.3 78.4 - - - +
496D ARG* 1.3 56.8 + - - +
498D TRP* 3.2 6.5 + - - +
499D THR* 2.9 38.9 + - - -
535D GLN* 2.5 36.8 + - - +
539D ILE* 3.5 20.1 - - + +
568D ASN* 3.6 38.6 - - + +
572D TYR* 3.4 26.5 - + - -
904D ROF 3.5 12.1 - - - -
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Residues in contact with ARG 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D LEU* 2.9 33.6 + - + +
493D GLN* 4.1 7.4 - - - +
495D TYR* 1.3 74.8 - - - +
497D GLN* 1.3 58.6 + - + +
499D THR* 3.6 1.7 - - - -
500D ASP* 2.9 38.9 + - - +
571D TRP* 3.2 47.9 - - - -
572D TYR* 3.7 16.0 + - - +
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Residues in contact with GLN 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D SO4 3.6 25.7 + - - -
273D PHE* 3.4 37.9 - - + +
493D GLN* 3.2 24.1 + - - +
494D LEU* 3.1 6.3 + - - +
496D ARG* 1.3 74.8 - - + +
498D TRP* 1.3 65.4 + - - +
500D ASP* 3.4 10.4 + - - +
501D ARG* 3.0 33.1 + - - +
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Residues in contact with TRP 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D VAL* 3.8 8.7 - - + +
273D PHE* 3.6 34.7 - + - -
325D TYR* 3.6 24.4 - + + -
327D ASN* 5.4 0.4 - - - -
329D ILE* 3.9 11.2 - - + -
330D HIS* 3.9 37.9 - - + -
333D ASP* 3.3 27.0 + - + -
487D ASN* 3.3 35.6 - - + +
490D LYS* 5.2 4.3 - - + +
494D LEU* 3.1 35.4 + - + +
495D TYR* 3.5 6.5 - - - +
497D GLN* 1.3 76.3 - - - +
499D THR* 1.3 58.1 + - - +
501D ARG* 3.4 11.4 + - - +
502D ILE* 2.9 25.8 + - - +
904D ROF 3.2 21.1 - - - -
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Residues in contact with THR 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D TYR* 2.9 32.2 + - - -
496D ARG 3.6 4.7 - - - -
498D TRP* 1.3 74.3 - - - +
500D ASP* 1.3 68.0 + - - +
502D ILE* 3.4 2.1 + - - +
503D MET* 3.0 26.2 + - + +
531D VAL* 3.8 21.5 - - + -
535D GLN* 3.8 25.6 - - + +
572D TYR* 3.1 26.8 + - - +
904D ROF 3.5 8.5 - - - -
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Residues in contact with ASP 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D ARG* 2.9 28.8 + - - +
497D GLN* 3.7 10.2 - - - +
499D THR* 1.3 76.5 - - - +
501D ARG* 1.3 58.9 + - + +
503D MET* 3.9 5.1 - - - +
504D GLU* 3.0 31.9 + - - +
572D TYR* 5.5 0.3 + - - -
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Residues in contact with ARG 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D PHE* 3.4 31.6 - - - -
324D ALA* 2.8 53.7 + - + +
325D TYR* 3.8 7.5 - - + +
327D ASN* 3.6 13.0 - - - +
329D ILE* 3.9 21.0 - - - +
497D GLN* 3.0 21.8 + - - +
498D TRP* 3.7 18.2 - - - +
500D ASP* 1.3 77.3 - - + +
502D ILE* 1.3 64.4 + - - +
504D GLU* 3.4 5.2 + - - +
505D GLU* 3.1 19.2 + - - +
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Residues in contact with ILE 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D TYR* 3.4 40.5 - - + -
326D HIS* 4.0 11.4 - - + +
498D TRP 2.9 14.8 + - - +
499D THR* 3.4 11.0 - - - +
501D ARG* 1.3 77.0 - - - +
503D MET* 1.3 71.8 + - + +
505D GLU* 3.3 3.5 + - - +
506D PHE* 2.9 68.7 + - + -
535D GLN* 4.8 1.6 - - - +
904D ROF 3.7 42.0 - - + +
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Residues in contact with MET 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D THR* 3.0 19.6 + - + +
500D ASP* 3.9 4.5 - - - +
502D ILE* 1.3 83.7 - - + +
504D GLU* 1.3 61.5 + - - +
506D PHE* 3.6 5.5 - - + +
507D PHE* 2.8 78.5 + - + -
523D MET* 3.6 17.5 - - + +
529D ALA* 5.2 2.5 - - + -
530D SER 6.2 0.2 - - - +
531D VAL* 3.7 40.8 - - + -
534D SER* 5.6 1.6 - - - +
535D GLN* 5.1 1.8 - - - -
904D ROF 4.0 27.4 - - + -
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Residues in contact with GLU 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D ALA* 3.7 9.7 - - + +
500D ASP* 3.0 19.7 + - - +
501D ARG* 3.6 7.4 - - - +
502D ILE 3.3 0.2 - - - -
503D MET* 1.3 77.4 - - - +
505D GLU* 1.3 61.1 + - - +
507D PHE* 3.4 8.3 + - - +
508D ARG* 2.6 60.0 + - + +
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Residues in contact with GLU 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D VAL* 3.0 15.3 - - + +
324D ALA* 4.2 3.1 - - + +
325D TYR* 2.8 35.7 + - + +
326D HIS* 2.8 37.0 + - - -
370D HIS* 4.2 1.4 - - - -
372D GLY* 3.3 33.8 - - - +
501D ARG 3.1 12.9 + - - +
502D ILE* 3.6 9.6 - - - +
504D GLU* 1.3 76.9 - - - +
506D PHE* 1.3 69.1 - - + +
508D ARG* 3.3 17.1 + - + +
509D GLN* 3.1 20.4 + - - +
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Residues in contact with PHE 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D HIS* 5.5 1.6 - + - -
502D ILE* 2.9 49.4 + - + +
503D MET* 3.6 14.8 - - - +
505D GLU* 1.3 80.9 - - + +
507D PHE* 1.3 64.4 + - - +
509D GLN* 3.1 10.3 + - - +
510D GLY 3.0 17.2 + - - -
522D PRO 5.3 1.8 - - - -
523D MET* 3.9 31.6 - - + +
524D CYS* 3.2 26.7 - - - +
904D ROF 4.1 49.4 - + + -
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Residues in contact with PHE 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503D MET* 2.8 59.3 + - + +
504D GLU* 3.8 6.7 - - - +
506D PHE* 1.3 73.7 - - - +
508D ARG* 1.3 65.2 + - + +
510D GLY* 3.1 1.4 + - - -
511D ASP* 2.9 30.5 + - - +
523D MET 3.8 7.9 - - - -
524D CYS 3.7 10.3 - - - +
525D ASP 4.1 4.3 - - - -
526D LYS* 3.6 46.9 - - + +
529D ALA* 3.9 20.0 - - + -
531D VAL* 4.4 6.5 - - + -
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Residues in contact with ARG 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D ASP 3.4 26.0 + - - -
323D VAL* 4.2 2.8 - - - +
324D ALA* 3.4 26.0 - - - +
504D GLU* 2.6 52.0 + - + +
505D GLU* 3.6 19.9 - - + +
506D PHE 3.2 0.4 - - - -
507D PHE* 1.3 76.1 - - + +
509D GLN* 1.3 63.1 + - - +
511D ASP* 3.3 9.9 + - - +
512D ARG* 3.1 30.1 + - + +
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Residues in contact with GLN 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D GLY 4.2 2.5 - - - +
373D VAL* 3.1 22.1 - - + -
374D SER* 2.8 50.0 + - - +
377D PHE* 3.7 13.7 - - + +
505D GLU 3.1 11.2 + - - +
506D PHE* 3.1 15.9 + - - +
508D ARG* 1.3 77.7 - - - +
510D GLY* 1.3 56.6 + - - +
512D ARG* 3.2 8.8 + - - +
513D GLU* 2.9 56.5 + - + +
521D SER* 3.8 7.9 + - - -
524D CYS* 4.5 9.5 - - - -
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Residues in contact with GLY 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D PHE 3.0 10.9 + - - -
507D PHE 3.1 0.6 + - - -
509D GLN* 1.3 73.8 - - - +
511D ASP* 1.3 55.9 + - - +
513D GLU* 3.1 15.0 + - - +
514D ARG* 2.7 41.2 + - - +
520D ILE* 4.2 7.3 - - - +
524D CYS* 3.1 24.2 - - - -
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Residues in contact with ASP 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D PHE* 2.9 17.6 + - - +
508D ARG* 3.7 11.2 - - - +
510D GLY* 1.3 74.3 - - - +
512D ARG* 1.3 58.8 + - + +
514D ARG* 3.0 28.0 + - - +
515D GLU* 2.9 39.1 + - + +
524D CYS 5.4 0.3 - - - +
526D LYS* 2.9 39.1 + - - +
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Residues in contact with ARG 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 4.3 7.4 - - - +
317B ASP* 2.7 53.4 + - - +
624B EDO 4.4 6.3 - - - -
371D PRO* 4.8 8.5 + - - +
373D VAL* 3.4 34.3 - - - +
377D PHE* 4.1 20.5 - - + -
508D ARG* 3.1 18.5 + - + +
509D GLN* 3.5 7.8 - - - +
510D GLY 3.1 0.8 - - - -
511D ASP* 1.3 76.1 - - + +
513D GLU* 1.3 65.4 + - - +
515D GLU* 3.6 12.3 - - - +
516D ARG* 3.2 47.4 + - - +
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Residues in contact with GLU 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D PHE* 3.8 20.8 - - + +
509D GLN* 2.9 35.0 + - - +
510D GLY* 3.5 13.3 - - - +
512D ARG* 1.3 76.8 - - - +
514D ARG* 1.3 60.6 + - - +
516D ARG 3.4 1.0 + - - -
517D GLY 3.1 3.1 + - - -
518D MET* 2.8 45.8 + - + +
519D GLU 3.9 15.8 - - - +
520D ILE* 3.5 7.8 - - - +
521D SER* 2.5 49.2 + - - -
524D CYS* 4.1 1.0 - - - +
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Residues in contact with ARG 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510D GLY 2.7 16.5 + - - +
511D ASP* 3.0 35.6 + - - +
512D ARG 3.3 0.2 - - - -
513D GLU* 1.3 69.9 - - - +
515D GLU* 1.3 66.2 + - - +
517D GLY* 2.8 16.2 + - - -
518D MET 4.7 4.0 - - - -
520D ILE* 3.8 24.1 - - + +
525D ASP* 3.1 27.1 + - - +
526D LYS* 4.3 9.5 - - - +
527D HIS* 3.4 29.4 + - - -
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Residues in contact with GLU 515 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 2.7 49.7 + - - +
309B ILE* 5.6 1.7 - - - +
313B MET* 3.9 32.2 - - + +
317B ASP* 5.0 0.3 - - - +
511D ASP* 2.9 30.3 + - + +
512D ARG* 3.6 17.2 - - - +
514D ARG* 1.3 73.0 - - - +
516D ARG* 1.3 59.6 + - + +
517D GLY 3.4 2.3 + - - -
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Residues in contact with ARG 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B THR* 4.6 24.1 + - + +
313B MET* 4.6 14.7 - - + +
314B THR* 3.1 36.4 + - - +
317B ASP* 2.8 29.3 + - - -
409B GLU* 4.8 1.2 + - - -
412B CYS* 5.5 0.6 - - - -
624B EDO 4.0 15.1 + - - -
377D PHE* 3.9 16.5 - - - -
381D THR* 4.3 11.9 - - - +
512D ARG* 3.2 32.2 + - - +
514D ARG 3.1 1.0 - - - -
515D GLU* 1.3 83.3 + - + +
517D GLY* 1.3 64.5 + - - +
518D MET* 3.2 29.7 + - + +
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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