Contacts of the helix formed by residues 37 - 66 (chain 1) in PDB entry 3J9X
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 VAL 37 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 ILE 3.0 21.3 + - - +
341 LEU* 3.5 15.3 - - + +
361 ASN* 1.3 76.5 - - - +
381 SER* 1.3 69.5 + - - +
391 PRO* 3.5 1.3 - - - -
401 VAL* 3.3 9.4 + - + +
411 ALA* 2.9 20.2 + - + +
212 PHE* 4.5 9.0 - - + -
287 T 3.9 21.8 - - - +
297 A 3.9 4.7 - - - +
16z LYS* 4.7 10.5 - - + -
19z ALA* 3.7 18.6 - - + -
20z LYS* 3.6 30.5 - - + -
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Residues in contact with SER 38 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341 LEU 2.6 22.6 + - - -
351 SER* 3.3 15.0 - - - -
371 VAL* 1.3 81.2 - - - +
391 PRO* 1.4 72.1 - - - +
411 ALA* 2.9 11.1 + - - +
421 GLN* 2.9 27.4 + - - +
212 PHE* 3.5 21.7 - - - -
222 ASN* 5.5 1.8 + - - -
252 SER* 4.7 4.9 + - - -
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Residues in contact with PRO 39 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351 SER 4.0 4.3 - - - +
361 ASN 3.6 11.7 - - - +
371 VAL 3.5 1.8 - - - -
381 SER* 1.4 98.1 - - - +
401 VAL* 1.3 68.2 + - + +
421 GLN* 3.5 18.9 - - - +
431 GLN* 3.1 21.7 + - - +
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Residues in contact with VAL 40 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361 ASN 4.3 13.5 - - - +
371 VAL* 3.5 13.0 - - + +
381 SER 3.0 0.6 + - - -
391 PRO* 1.3 79.5 - - + +
411 ALA* 1.3 67.2 + - - +
431 GLN* 3.1 9.6 + - - +
441 ASN* 3.1 32.1 + - - +
287 T 4.8 1.6 - - - +
12z GLN* 5.0 2.2 - - - +
15z ALA* 4.1 29.8 - - + +
16z LYS* 3.9 32.5 - - + +
19z ALA* 4.5 3.8 - - + -
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Residues in contact with ALA 41 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 VAL 2.9 18.8 + - - +
381 SER 3.4 3.6 - - - +
401 VAL* 1.3 76.4 - - - +
421 GLN* 1.3 57.7 + - - +
441 ASN* 3.1 2.6 + - - +
451 PHE* 2.8 30.7 + - - +
172 TRP* 4.1 15.7 - - + -
212 PHE* 4.5 9.0 - - + -
277 A 3.9 4.4 - - - +
287 T 3.5 39.0 + - - +
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Residues in contact with GLN 42 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 SER* 2.9 21.3 + - - +
391 PRO* 3.5 30.5 - - + +
401 VAL 3.1 0.2 - - - -
411 ALA* 1.3 77.1 - - - +
431 GLN* 1.3 61.8 + - - +
451 PHE* 3.3 0.9 + - - +
461 GLN* 2.9 34.4 + - - +
142 TYR* 3.9 9.1 + - - +
172 TRP* 4.2 12.1 - - + -
182 GLN* 3.2 41.2 - - - +
212 PHE* 5.8 0.9 - - + -
222 ASN* 4.6 2.2 + - - -
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Residues in contact with GLN 43 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 PRO 3.1 10.2 + - - +
401 VAL* 3.1 11.6 + - - +
421 GLN* 1.3 80.7 - - - +
441 ASN* 1.3 60.8 + - - +
461 GLN* 3.4 13.2 + - - +
471 THR* 2.6 61.2 + - - +
12z GLN* 5.3 7.6 - - + +
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Residues in contact with ASN 44 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401 VAL* 3.1 21.0 + - - +
411 ALA 3.1 7.9 + - - +
431 GLN* 1.3 76.4 - - - +
451 PHE* 1.3 65.0 + - - +
471 THR* 3.4 4.6 + - - -
481 ASN* 3.1 24.6 + - - +
277 A 3.6 23.1 - - - +
287 T 2.9 19.6 + - - -
8z ARG* 3.7 25.5 - - - +
12z GLN* 2.9 35.3 + - - +
16z LYS* 5.5 3.8 - - - +
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Residues in contact with PHE 45 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411 ALA 2.8 16.1 + - - +
421 GLN 3.7 3.8 - - - +
441 ASN* 1.3 77.1 - - - +
461 GLN* 1.3 58.5 + - - +
491 VAL* 2.9 69.3 + - + +
102 TYR* 5.1 1.1 - + - -
132 ARG* 4.4 5.8 - - + -
142 TYR* 3.5 43.1 - + + -
172 TRP* 3.5 56.8 - + + -
267 T 4.5 10.5 - - - -
277 A 3.5 27.9 - - - -
3248 T 5.3 6.1 - - - -
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Residues in contact with GLN 46 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421 GLN* 2.9 27.5 + - - +
431 GLN* 3.8 13.7 + - - +
451 PHE* 1.3 80.3 - - - +
471 THR* 1.3 63.8 + - - +
501 PRO* 3.1 25.4 - - - +
102 TYR* 5.2 11.6 + - - +
142 TYR* 3.4 47.2 + - + -
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Residues in contact with THR 47 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431 GLN* 2.6 47.3 + - - +
441 ASN* 3.7 6.5 - - - -
451 PHE 3.2 0.2 - - - -
461 GLN* 1.3 80.6 - - - +
481 ASN* 1.3 71.6 + - - +
501 PRO* 4.3 2.3 - - - +
511 LYS* 3.4 23.7 - - - +
12z GLN* 4.9 12.9 + - - +
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Residues in contact with ASN 48 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441 ASN* 3.1 10.0 + - - +
471 THR* 1.3 87.0 - - - +
491 VAL* 1.3 67.5 + - - +
501 PRO* 3.4 1.8 - - - -
511 LYS* 2.9 49.1 + - + +
521 PHE* 3.4 12.3 - - + -
881 ASN* 4.9 5.9 + - - -
267 T 3.8 18.6 + - - +
277 A 3.0 21.0 + - - -
7z SER* 4.5 7.5 + - - -
8z ARG* 3.8 13.1 - - - +
12z GLN* 5.5 4.2 - - - +
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Residues in contact with VAL 49 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 PHE* 2.9 57.5 + - + +
481 ASN* 1.3 74.2 - - - +
501 PRO* 1.3 64.4 - - + +
511 LYS 3.0 0.2 - - - -
521 PHE* 2.9 26.1 + - - +
531 THR* 3.0 12.5 + - - +
102 TYR* 4.6 6.5 - - + -
132 ARG* 3.8 30.2 + - + +
267 T 3.6 33.7 - - + +
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Residues in contact with PRO 50 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451 PHE 3.8 0.7 - - - +
461 GLN 3.1 26.5 - - - +
471 THR 4.2 2.2 - - - +
481 ASN 3.4 3.1 - - - +
491 VAL* 1.3 97.2 - - + +
511 LYS* 1.3 60.4 + - + +
521 PHE 3.2 0.2 - - - -
531 THR* 3.8 1.1 - - - +
541 SER* 3.2 23.6 + - - -
102 TYR* 3.7 47.8 - - + -
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Residues in contact with LYS 51 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471 THR* 3.4 23.4 + - - +
481 ASN* 2.9 36.9 + - - +
491 VAL 3.0 0.4 - - - -
501 PRO* 1.3 78.6 - - + +
521 PHE* 1.3 64.2 + - + +
541 SER* 2.9 18.7 + - - -
551 VAL* 3.3 13.2 - - - +
841 ALA* 5.5 1.0 - - - +
881 ASN* 3.9 26.4 + - - +
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Residues in contact with PHE 52 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481 ASN* 3.4 20.0 - - + -
491 VAL* 2.9 8.0 + - + +
511 LYS* 1.3 76.4 - - + +
531 THR* 1.3 66.1 + - - +
541 SER 3.2 1.8 - - - -
551 VAL* 3.1 6.7 + - - +
561 ASN* 2.9 27.7 + - - +
811 LEU* 3.7 28.7 - - + +
841 ALA* 3.6 26.2 - - + -
851 ARG* 3.6 14.6 - - - -
881 ASN* 3.3 30.5 - - - -
132 ARG* 4.5 6.5 - - - +
257 A 3.7 17.5 - - + +
267 T 3.4 40.8 - - - +
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Residues in contact with THR 53 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491 VAL* 3.0 7.5 + - - +
501 PRO 3.4 5.8 + - - -
521 PHE* 1.3 77.0 - - - +
541 SER* 1.3 62.4 + - - +
561 ASN* 3.1 8.2 + - + +
571 GLU* 3.0 23.8 + - + +
82 ARG 4.7 4.5 - - - +
92 SER* 4.2 6.7 - - - -
102 TYR* 3.1 46.9 - - + +
132 ARG* 2.7 29.3 + - - +
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Residues in contact with SER 54 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501 PRO 3.2 11.0 + - - -
511 LYS* 2.9 22.0 + - - -
531 THR* 1.3 78.2 - - - +
551 VAL* 1.3 56.8 + - - +
571 GLU* 3.4 6.6 + - - +
581 ASN* 3.0 40.6 + - - -
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Residues in contact with VAL 55 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511 LYS 3.3 18.2 - - - +
521 PHE* 3.1 11.0 + - - +
531 THR 3.1 0.2 - - - -
541 SER* 1.3 76.0 + - - +
561 ASN* 1.3 61.6 + - - +
581 ASN* 4.9 3.4 - - - +
591 VAL* 2.8 52.2 + - + +
771 GLN* 5.2 0.7 - - - +
801 GLY 4.1 13.2 - - - +
811 LEU* 4.3 9.9 - - + +
841 ALA* 4.0 19.7 - - + -
1251 ILE* 3.9 26.5 - - + -
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Residues in contact with ASN 56 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521 PHE* 2.9 17.8 + - - +
531 THR* 3.4 9.1 - - + +
551 VAL* 1.3 75.5 - - - +
571 GLU* 1.3 57.3 + - - +
601 SER* 2.9 31.2 + - - -
771 GLN* 3.1 20.5 + - - +
811 LEU* 3.3 29.8 - - - +
132 ARG* 4.0 22.2 - - - +
3258 A 4.8 4.6 + - - +
3268 T 4.1 35.8 + - - +
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Residues in contact with GLU 57 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531 THR* 3.0 14.8 + - + +
541 SER* 3.5 11.7 - - - +
561 ASN* 1.3 74.1 - - - +
581 ASN* 1.3 73.9 + - - +
601 SER* 3.2 8.4 + - - -
611 ALA* 3.0 23.1 + - + +
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Residues in contact with ASN 58 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541 SER* 3.0 23.0 + - - +
551 VAL* 4.1 3.3 - - - +
571 GLU* 1.3 88.8 - - - +
591 VAL* 1.3 63.5 + - + +
611 ALA* 3.2 10.2 + - - +
621 VAL* 3.2 25.3 + - - +
1241 ILE* 3.7 27.0 - - + +
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Residues in contact with VAL 59 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551 VAL* 2.8 37.1 + - + +
581 ASN* 1.3 74.3 - - + +
601 SER* 1.3 66.4 + - - +
621 VAL* 3.1 9.0 + - - +
631 LEU* 2.9 33.1 + - + +
761 TYR 4.3 1.1 - - - +
771 GLN* 3.3 32.8 - - - +
801 GLY* 4.7 2.0 - - - -
1211 VAL* 4.0 38.6 - - + +
1241 ILE* 5.5 3.4 - - + -
1251 ILE* 4.4 7.2 - - + -
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Residues in contact with SER 60 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561 ASN 2.9 22.3 + - - -
571 GLU* 3.4 10.8 - - - -
591 VAL* 1.3 76.7 - - - +
611 ALA* 1.3 63.2 + - - +
631 LEU* 3.1 3.0 + - - -
641 THR* 3.0 12.7 + - - -
731 ARG* 2.7 41.0 + - - +
771 GLN* 3.4 12.5 - - - +
893 ARG 4.7 2.9 + - - -
903 ILE 4.7 4.0 + - - -
3268 T 4.9 0.4 - - - -
3278 A 3.4 9.8 + - - -
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Residues in contact with ALA 61 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571 GLU* 3.0 16.2 + - + +
581 ASN* 3.4 13.0 - - - +
591 VAL 3.2 0.2 - - - -
601 SER* 1.3 76.4 - - - +
621 VAL* 1.3 63.0 + - + +
641 THR* 3.2 8.0 + - - -
651 GLN* 3.1 30.9 + - - +
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Residues in contact with VAL 62 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581 ASN 3.2 13.4 + - - +
591 VAL* 3.1 12.2 + - + +
611 ALA* 1.3 78.2 - - + +
631 LEU* 1.3 68.8 + - + +
651 GLN* 2.9 23.2 + - - +
661 TYR* 3.0 39.0 + - + -
1171 VAL* 5.3 0.7 - - + +
1201 ALA* 4.0 17.5 - - + +
1211 VAL* 4.8 6.1 - - + +
1241 ILE* 3.6 32.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591 VAL* 2.9 34.6 + - + +
601 SER* 3.1 6.9 + - - +
621 VAL* 1.3 79.1 - - + +
641 THR* 1.3 61.2 + - - +
661 TYR* 3.2 2.9 + - - +
671 GLY 3.0 4.2 + - - -
681 ILE* 2.9 43.0 + - + -
731 ARG* 3.5 48.7 - - + +
761 TYR* 3.6 34.3 - - + -
771 GLN* 4.0 9.6 - - + +
1171 VAL* 4.1 11.4 - - + -
1211 VAL* 5.1 0.9 - - + -
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Residues in contact with THR 64 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601 SER 3.0 5.3 + - - -
611 ALA* 3.6 11.1 - - - -
631 LEU* 1.3 76.8 - - - +
651 GLN* 1.3 62.9 + - + +
671 GLY 3.1 9.9 + - - -
731 ARG* 3.0 21.6 + - - +
903 ILE* 2.6 34.2 + - + +
913 GLY 3.8 6.7 - - - +
923 SER 3.3 28.7 - - - +
933 GLY* 4.6 1.1 - - - -
943 PRO* 3.3 4.6 - - + +
953 ALA* 3.3 18.7 + - + +
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Residues in contact with GLN 65 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611 ALA* 3.1 18.8 + - - +
621 VAL* 2.9 17.8 + - - +
641 THR* 1.3 78.2 - - + +
661 TYR* 1.3 65.5 + - + +
671 GLY 3.3 0.2 - - - -
943 PRO* 3.4 23.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621 VAL* 3.0 35.9 + - + +
631 LEU* 3.2 6.7 + - - +
651 GLN* 1.3 84.6 - - + +
671 GLY* 1.3 62.0 + - - +
681 ILE* 3.2 22.1 + - + +
1161 GLN* 2.9 43.0 + - - -
1171 VAL* 4.1 16.4 - - + -
1201 ALA* 3.5 27.8 - - + +
943 PRO* 4.6 0.9 - - - -
----------------------------------------------------------
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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