Contacts of the helix formed by residues 29 - 55 (chain 3) in PDB entry 3EXG
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 29 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13 PHE* 3.1 29.8 - - - -
23 ALA 4.3 10.1 + - - +
33 ASN* 2.8 31.3 + - - +
283 THR* 1.3 72.4 - - - +
303 GLU* 1.3 70.8 + - - +
323 GLY* 3.6 0.9 + - - -
333 LEU* 3.3 39.6 + - - +
2953 MET* 5.0 1.6 - - - +
3003 LEU* 2.4 68.5 + - + +
3013 ALA* 3.5 14.8 - - - +
3053 GLU* 3.0 21.4 + - - -
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Residues in contact with GLU 30 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33 ASN 4.6 0.4 + - - -
283 THR* 3.2 6.6 + - - +
293 ARG* 1.3 89.9 - - - +
313 ASP* 1.3 61.1 + - - +
333 LEU* 3.6 16.6 - - + +
343 LYS* 3.7 7.8 + - - +
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Residues in contact with ASP 31 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273 LEU* 3.8 11.0 - - + -
283 THR* 3.0 40.2 + - - +
303 GLU* 1.3 71.4 - - - +
323 GLY* 1.3 54.8 + - - +
333 LEU 3.0 4.0 - - - -
343 LYS* 2.6 37.2 + - - +
353 TYR* 3.0 37.1 + - + -
2343 ARG* 4.4 6.0 + - - -
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Residues in contact with GLY 32 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273 LEU* 3.3 20.6 - - - +
283 THR 3.1 7.8 + - - -
313 ASP* 1.3 78.6 - - - +
333 LEU* 1.3 56.7 + - - +
343 LYS 3.2 0.4 - - - -
353 TYR* 3.6 13.0 - - - -
363 TYR* 3.2 19.6 + - - +
2913 LEU* 3.8 3.8 - - - +
2953 MET* 2.8 29.2 - - - +
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Residues in contact with LEU 33 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293 ARG* 3.3 45.1 + - - +
303 GLU* 3.6 11.9 - - + +
313 ASP 2.9 0.6 + - - -
323 GLY* 1.3 76.4 - - - +
343 LYS* 1.3 60.0 + - - +
363 TYR* 4.1 1.5 - - - +
373 ARG* 3.6 19.9 + - - +
2953 MET* 3.5 20.4 - - + +
3003 LEU 5.1 0.2 - - - +
3013 ALA* 3.9 21.3 - - + -
3053 GLU* 4.2 9.6 - - + +
3063 LEU* 4.6 8.3 - - + -
3093 ILE* 4.2 17.6 - - + +
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Residues in contact with LYS 34 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303 GLU 3.7 6.9 + - - +
313 ASP* 2.6 19.5 + - - +
333 LEU* 1.3 80.8 - - - +
353 TYR* 1.3 74.4 + - - +
363 TYR 3.2 0.2 - - - -
373 ARG* 3.5 8.6 + - + +
383 MET* 2.9 49.5 + - + +
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Residues in contact with TYR 35 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273 LEU* 4.0 15.9 - - + -
313 ASP* 3.0 25.5 + - + -
323 GLY* 3.6 15.5 - - - +
343 LYS* 1.3 84.7 - - - +
363 TYR* 1.3 51.6 + - - +
383 MET* 3.1 21.3 + - + +
393 MET* 2.7 40.2 + - - +
733 VAL* 4.1 9.1 - - - +
773 ALA* 3.8 21.8 - - + +
2303 ILE* 4.6 24.5 - - + -
2313 LEU* 5.0 4.5 - - + -
2343 ARG* 3.2 42.0 + - - -
2383 ARG* 4.8 2.6 + - - -
2913 LEU* 3.9 15.3 - - + -
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Residues in contact with TYR 36 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323 GLY 3.2 17.1 + - - +
333 LEU 4.3 3.1 - - - +
353 TYR* 1.3 78.4 - - - +
373 ARG* 1.3 70.0 + - - +
393 MET* 2.9 8.8 + - + +
403 GLN* 2.8 34.3 + - + +
2883 ILE* 3.8 34.4 - - + +
2913 LEU* 3.7 16.3 - - + +
2923 LYS* 4.2 19.6 - - + +
2953 MET* 4.4 1.6 - - + -
3063 LEU* 3.6 51.6 + - + +
3093 ILE* 4.2 13.5 - - + -
3103 ASP* 2.9 33.7 + - - -
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Residues in contact with ARG 37 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333 LEU 3.6 13.9 + - - +
343 LYS* 3.5 9.5 + - - +
353 TYR 3.5 0.2 - - - -
363 TYR* 1.3 80.0 - - - +
383 MET* 1.3 63.5 + - + +
403 GLN* 4.0 3.8 - - - +
413 THR* 2.9 37.0 + - - +
3093 ILE* 3.3 45.6 - - + +
3123 GLU* 3.2 45.4 + - - +
3133 VAL* 4.2 9.3 - - + +
3163 GLU* 6.0 0.2 + - - -
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Residues in contact with MET 38 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343 LYS* 2.9 73.5 + - + +
353 TYR* 3.4 14.4 - - + +
363 TYR 2.9 0.8 + - - -
373 ARG* 1.3 76.4 - - + +
393 MET* 1.3 68.7 + - - +
413 THR* 3.1 14.9 + - - -
423 VAL* 3.1 15.3 + - - +
733 VAL* 3.3 27.8 - - + +
763 GLU* 5.7 6.5 - - - -
963 PHE* 4.3 18.3 - - + -
973 THR* 5.2 12.3 - - - +
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Residues in contact with MET 39 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353 TYR 2.7 23.3 + - - +
363 TYR* 2.9 6.3 + - + +
383 MET* 1.3 70.5 - - - +
403 GLN* 1.3 56.3 + - - +
423 VAL* 3.0 5.9 + - - +
433 ARG* 2.8 27.9 + - - +
693 GLU* 3.8 24.5 - - + +
703 ALA* 4.1 5.8 - - - -
733 VAL* 3.4 28.5 - - + +
2303 ILE* 4.3 15.9 - - + -
2873 PRO 3.3 26.9 - - - +
2883 ILE* 3.6 29.2 - - + +
2913 LEU* 3.7 30.3 - - + -
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Residues in contact with GLN 40 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363 TYR* 2.8 37.2 + - + +
373 ARG* 4.0 4.5 - - - +
393 MET* 1.3 72.2 - - - +
413 THR* 1.3 57.0 + - - +
433 ARG* 4.2 11.3 - - - +
443 ARG* 2.9 62.3 + - - +
2883 ILE* 3.7 33.2 - - + +
3093 ILE* 5.7 0.4 - - + -
3103 ASP* 3.3 34.3 + - - +
3133 VAL* 3.9 16.2 - - + +
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Residues in contact with THR 41 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373 ARG* 2.9 25.5 + - - +
383 MET* 3.1 4.9 + - - -
403 GLN* 1.3 75.4 - - - +
423 VAL* 1.3 63.0 + - - +
453 MET* 3.1 25.6 + - + +
963 PHE* 3.3 33.2 - - + -
1023 VAL* 3.6 21.3 - - + -
3133 VAL* 3.4 23.1 - - + +
3163 GLU* 5.6 6.3 - - + +
3173 ILE* 4.0 10.1 - - + +
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Residues in contact with VAL 42 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383 MET 3.1 8.1 + - - +
393 MET* 3.0 8.6 + - - +
413 THR* 1.3 79.1 - - - +
433 ARG* 1.3 62.3 + - - +
453 MET* 3.5 7.7 + - - +
463 GLU* 3.0 25.2 + - + +
653 CYS* 4.1 14.4 - - - -
693 GLU* 3.7 20.0 - - + -
723 CYS* 4.3 9.9 - - - -
733 VAL* 5.9 0.7 - - + -
923 HIS 5.4 0.4 - - - -
933 GLY* 3.8 32.8 - - - +
963 PHE* 3.6 29.2 - - + -
973 THR* 4.7 4.0 - - + -
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Residues in contact with ARG 43 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393 MET 2.8 15.2 + - - +
403 GLN* 3.7 15.6 - - - +
423 VAL* 1.3 75.3 - - - +
443 ARG* 1.3 69.0 + - - +
463 GLU* 3.2 4.6 + - - +
473 LEU* 3.1 44.2 + - + +
663 ASP* 3.6 14.2 + - - +
673 GLY* 3.5 10.7 - - - +
693 GLU* 2.8 42.7 + - - +
2603 TYR* 3.7 11.2 - - - -
2823 ARG* 5.1 4.9 - - - +
2863 ASP* 3.1 32.3 + - - -
2873 PRO* 4.3 1.6 - - - +
2883 ILE* 3.7 20.6 - - + +
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Residues in contact with ARG 44 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403 GLN* 2.9 38.4 + - - +
433 ARG* 1.3 83.1 - - - +
453 MET* 1.3 58.5 + - - +
473 LEU* 3.3 34.0 + - - +
483 LYS* 2.9 30.0 + - - +
3103 ASP 5.5 0.4 - - - +
3133 VAL* 3.4 17.5 - - + +
3143 ARG* 3.0 55.5 - - - +
3173 ILE* 3.5 24.9 - - + +
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Residues in contact with MET 45 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413 THR 3.1 20.2 + - - +
423 VAL* 3.6 7.9 - - - +
433 ARG 3.1 0.2 - - - -
443 ARG* 1.3 77.7 - - - +
463 GLU* 1.3 68.2 + - - +
483 LYS* 3.3 1.8 + - - +
493 ALA* 2.8 31.7 + - - +
923 HIS* 4.5 10.1 - - - +
963 PHE* 4.3 11.9 - - + -
1023 VAL* 3.3 47.8 - - + -
1053 ILE* 3.4 45.5 - - + -
1063 LEU* 4.3 13.3 - - + +
1093 LEU* 6.1 0.7 - - - -
3173 ILE* 4.2 12.5 - - + +
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Residues in contact with GLU 46 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423 VAL* 3.0 23.7 + - + +
433 ARG 3.2 3.8 + - - +
453 MET* 1.3 84.5 - - - +
473 LEU* 1.3 51.5 + - - +
493 ALA* 3.5 3.7 + - - +
503 ASP* 2.7 34.3 + - - +
633 HIS 4.1 0.2 - - - +
643 LEU* 3.4 19.2 - - + +
653 CYS* 2.9 45.7 + - - +
663 ASP* 3.9 26.2 - - + +
903 ARG 6.0 0.2 - - - -
923 HIS* 3.0 40.7 + - - +
933 GLY 4.9 0.2 - - - -
1093 LEU* 5.6 0.2 - - - +
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Residues in contact with LEU 47 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433 ARG* 3.1 37.6 + - + +
443 ARG* 3.3 42.6 - - - +
453 MET 3.3 0.2 - - - -
463 GLU* 1.3 72.8 - - - +
483 LYS* 1.3 59.7 + - - +
503 ASP* 3.1 14.3 + - + +
513 GLN* 2.9 30.0 + - - +
663 ASP* 5.0 11.9 - - - +
2823 ARG* 6.3 1.6 - - - +
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Residues in contact with LYS 48 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443 ARG 2.9 18.4 + - - +
453 MET* 3.8 3.4 - - - +
473 LEU* 1.3 72.7 - - - +
493 ALA* 1.3 67.2 + - - +
513 GLN* 3.2 33.8 + - - +
523 LEU* 2.9 33.7 + - + +
1063 LEU* 3.9 13.9 - - + -
3173 ILE* 3.6 13.7 - - + -
3183 GLU* 2.8 32.8 + - - -
3213 ALA* 3.4 31.3 - - + +
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Residues in contact with ALA 49 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 MET* 2.8 18.0 + - + +
463 GLU* 3.8 7.2 - - - +
483 LYS* 1.3 77.9 - - - +
503 ASP* 1.3 63.6 + - - +
523 LEU* 3.2 2.7 + - - -
533 TYR* 3.1 24.3 + - - +
583 ILE* 3.6 13.6 - - + +
623 CYS* 4.6 4.0 - - - -
643 LEU* 4.4 11.9 - - + -
1063 LEU* 4.0 17.2 - - + +
1093 LEU* 4.1 17.7 - - + -
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Residues in contact with ASP 50 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463 GLU 2.7 22.1 + - - +
473 LEU* 3.1 17.1 + - + +
493 ALA* 1.3 74.9 - - - +
513 GLN* 1.3 61.9 + - - +
533 TYR* 3.4 10.2 + - - +
543 LYS* 2.9 52.9 + - - +
623 CYS* 5.4 0.4 - - - -
643 LEU* 3.6 24.0 - - + +
663 ASP* 5.8 0.4 - - - +
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Residues in contact with GLN 51 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473 LEU 2.9 15.8 + - - +
483 LYS* 3.3 35.0 + - - +
503 ASP* 1.3 74.9 - - - +
523 LEU* 1.3 62.5 + - - +
533 TYR 2.8 10.4 + - - -
543 LYS* 3.4 8.2 + - - +
553 GLN* 3.0 45.5 + - + +
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Residues in contact with LEU 52 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483 LYS* 2.9 42.4 + - + +
493 ALA* 3.6 9.0 - - - +
513 GLN* 1.3 76.7 - - - +
533 TYR* 1.3 58.0 + - - +
553 GLN* 3.7 13.5 - - - +
563 LYS 3.4 2.6 + - - -
573 ILE* 3.1 43.8 + - + +
583 ILE* 3.6 14.5 + - + -
1063 LEU* 4.6 11.9 - - + -
1093 LEU* 6.5 0.2 - - + -
1103 THR* 4.3 15.9 - - + -
3213 ALA* 4.5 10.5 - - + -
3243 ALA* 5.4 0.4 - - + -
3253 THR* 3.7 27.8 - - + -
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Residues in contact with TYR 53 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493 ALA 3.1 15.2 + - - +
503 ASP* 3.8 11.0 - - - +
513 GLN 2.9 1.0 - - - -
523 LEU* 1.3 79.2 - - - +
543 LYS* 1.3 72.7 + - + +
553 GLN 3.0 0.7 - - - -
563 LYS* 3.1 14.3 + - - +
583 ILE* 3.3 39.5 - - + +
593 ARG 4.8 0.7 - - - -
603 GLY 3.5 23.4 + - - -
613 PHE* 4.4 1.1 - - - -
623 CYS* 3.4 41.4 + - + -
643 LEU* 6.2 1.1 - - + -
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Residues in contact with LYS 54 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503 ASP* 2.9 51.5 + - - +
513 GLN* 3.4 7.6 + - - +
533 TYR* 1.3 81.0 - - + +
553 GLN* 1.3 59.2 + - + +
563 LYS* 3.5 10.7 + - - +
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Residues in contact with GLN 55 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513 GLN* 3.0 50.8 + - + +
523 LEU* 3.7 13.6 - - - +
533 TYR 3.0 1.2 - - - -
543 LYS* 1.3 77.9 - - + +
563 LYS* 1.3 70.9 + - - +
573 ILE* 3.3 22.4 + - + +
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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