Contacts of the helix formed by residues 538 - 565 (chain B) in PDB entry 1OH7
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 HIS 538 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B PHE* 4.7 11.0 - + + -
403B LEU* 3.5 46.0 - - + +
534B LEU 4.0 11.3 + - - -
535B LEU 3.1 6.3 + - - +
537B PRO* 1.3 92.0 + - + +
539B LEU* 1.3 64.9 + - - +
540B GLU* 3.3 3.1 - - - -
541B ALA* 3.2 9.3 + - + +
542B LEU* 2.9 26.4 + - + +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 4.0 12.3 - - + -
254B HIS* 4.0 18.6 - - + +
256B ARG* 3.3 23.6 - - - +
352B LEU* 3.9 28.0 - - + +
355B LEU* 4.6 15.0 - - + -
356B ALA* 4.1 15.7 - - + +
535B LEU 3.9 1.2 + - - -
536B LEU* 3.0 26.7 + - + +
537B PRO 3.3 1.0 - - - -
538B HIS* 1.3 76.0 - - - +
540B GLU* 1.3 64.5 + - - +
542B LEU* 3.1 10.2 + - - +
543B GLN* 2.9 35.0 + - + +
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Residues in contact with GLU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ARG* 3.7 44.9 + - - +
537B PRO 4.9 3.4 + - - +
538B HIS 3.3 1.2 + - - -
539B LEU* 1.3 75.7 - - - +
541B ALA* 1.3 63.8 + - - +
543B GLN* 3.1 6.5 + - - +
544B GLN* 3.0 40.9 + - + +
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Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LYS 4.7 1.9 - - - +
400B PHE* 3.5 30.1 - - + -
538B HIS* 3.2 10.5 + - + +
540B GLU* 1.3 78.8 - - - +
542B LEU* 1.3 56.8 + - - +
544B GLN* 3.4 15.9 + - - +
545B SER* 3.0 22.9 + - - -
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.5 2.7 - - + +
352B LEU* 3.3 28.5 - - + +
355B LEU* 4.0 27.4 - - + -
368B MET* 5.0 4.9 - - - -
372B PHE* 3.7 33.9 - - + -
400B PHE* 4.0 24.0 - - + -
403B LEU* 4.5 8.3 - - + -
535B LEU* 4.2 8.7 - - + +
538B HIS* 2.9 26.7 + - + +
539B LEU* 3.1 9.6 + - - +
541B ALA* 1.3 76.6 - - - +
543B GLN* 1.3 56.7 + - - +
545B SER* 3.1 5.9 + - - -
546B ALA 3.0 24.1 + - - -
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Residues in contact with GLN 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B SER 5.6 0.4 + - - -
152B SER 3.7 15.5 + - - +
254B HIS* 3.0 43.2 + - - +
256B ARG* 2.8 39.6 + - - -
352B LEU* 4.0 16.5 - - + +
539B LEU* 2.9 24.8 + - + +
540B GLU* 3.5 5.7 - - - +
542B LEU* 1.3 74.3 - - - +
544B GLN* 1.3 64.6 + - - +
546B ALA* 3.6 2.6 + - - +
547B SER* 3.1 26.6 + - - -
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Residues in contact with GLN 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LYS* 3.3 40.9 - - + +
540B GLU* 3.0 38.3 + - + +
541B ALA* 3.6 12.7 - - - +
543B GLN* 1.3 75.8 - - - +
545B SER* 1.3 57.2 + - - +
547B SER* 4.3 1.3 - - - -
548B ALA* 3.0 29.5 + - - +
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Residues in contact with SER 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.1 6.3 - - - +
372B PHE* 5.9 0.9 - - - -
375B LEU* 4.4 4.7 - - - +
396B LYS 3.8 3.8 + - - -
397B MET* 2.6 30.5 + - - +
400B PHE* 3.8 14.1 - - - -
541B ALA 3.0 14.4 + - - -
542B LEU* 3.1 11.0 + - - -
544B GLN* 1.3 73.3 - - - +
546B ALA* 1.3 55.6 + - - +
548B ALA* 2.9 3.5 + - - +
549B LEU* 2.8 51.5 + - - +
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Residues in contact with ALA 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 3.3 16.9 - - - +
348B LEU* 3.8 16.7 - - + +
349B GLU* 3.9 27.3 - - + +
352B LEU* 3.7 27.4 - - + -
542B LEU 3.0 9.4 + - - +
543B GLN* 3.9 4.5 - - - +
545B SER* 1.3 72.8 + - - +
547B SER* 1.3 56.1 + - - +
549B LEU* 4.3 3.6 - - - -
550B ALA* 3.0 21.8 + - - +
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Residues in contact with SER 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET* 4.0 11.6 - - - +
349B GLU* 5.5 6.1 - - - -
396B LYS* 3.7 15.8 + - - -
543B GLN 3.1 20.0 + - - -
544B GLN* 3.7 7.0 - - - -
546B ALA* 1.3 75.0 - - - +
548B ALA* 1.3 65.4 + - - +
549B LEU 3.2 0.2 - - - -
550B ALA* 3.1 7.8 + - - +
551B GLU* 3.1 22.9 + - - +
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Residues in contact with ALA 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 3.8 26.0 - - + +
396B LYS* 3.6 30.7 - - + +
397B MET* 3.9 11.9 - - - +
544B GLN 3.0 17.9 + - - +
545B SER 2.9 4.1 + - - +
547B SER* 1.3 76.9 - - - +
549B LEU* 1.3 58.9 + - - +
551B GLU* 3.4 1.3 + - - -
552B LEU* 3.0 29.0 + - - +
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Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 3.8 12.7 - - + +
342B LEU* 4.0 17.0 - - + +
345B VAL* 3.9 18.4 - - + -
348B LEU* 3.8 19.7 - - + -
371B ALA* 5.8 0.9 - - + -
375B LEU* 4.1 11.2 - - + -
378B LEU* 3.8 18.4 - - + -
397B MET* 3.5 32.8 - - + -
545B SER* 2.8 35.6 + - - +
546B ALA 3.7 5.4 - - - +
548B ALA* 1.3 78.1 - - - +
550B ALA* 1.3 62.2 + - - +
552B LEU* 3.6 6.2 + - + +
553B ASP* 3.0 22.7 + - - +
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Residues in contact with ALA 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 3.7 31.2 - - + +
303B GLY* 3.8 1.7 - - - -
306B MET* 3.7 20.0 - - + -
349B GLU* 5.5 4.3 - - - +
546B ALA 3.0 16.3 + - - +
547B SER* 3.1 11.8 + - - +
549B LEU* 1.3 74.2 - - - +
551B GLU* 1.3 64.1 + - - +
553B ASP* 3.0 21.6 + - - +
554B VAL* 3.1 12.0 + - - +
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Residues in contact with GLU 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET* 3.4 16.6 - - + +
310B TRP* 3.9 26.7 - - + -
324B ARG* 4.9 5.5 + - - +
393B LEU* 3.7 21.4 - - + +
396B LYS* 5.5 4.3 + - - -
547B SER 3.1 9.7 + - - +
548B ALA* 3.9 7.0 - - - +
550B ALA* 1.3 77.9 - - - +
552B LEU* 1.3 64.3 + - - +
554B VAL* 2.9 14.4 + - - +
555B LEU* 2.9 33.1 + - + +
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Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 5.5 3.8 - - + -
338B LEU* 4.9 3.6 - - + -
342B LEU* 3.8 32.3 - - + -
378B LEU* 4.9 5.4 - - + -
382B LEU* 4.1 37.9 - - + -
390B VAL* 5.0 6.5 - - + +
393B LEU* 3.7 37.0 - - + +
397B MET* 5.3 4.3 - - + -
548B ALA 3.0 17.3 + - - +
549B LEU* 3.7 11.4 - - + +
551B GLU* 1.3 76.6 - - - +
553B ASP* 1.3 63.4 + - - +
555B LEU* 4.5 3.4 - - - +
556B VAL* 3.0 39.9 + - + +
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Residues in contact with ASP 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 3.3 9.7 - - - +
299B VAL* 3.1 33.2 + - - +
300B THR* 2.7 44.5 + - - +
303B GLY* 3.4 3.9 - - - -
339B GLN* 5.2 1.6 + - - -
342B LEU* 4.5 12.4 - - + +
549B LEU 3.0 13.9 + - - +
550B ALA 3.0 14.5 + - - +
552B LEU* 1.3 77.4 - - - +
554B VAL* 1.3 55.6 + - - +
556B VAL* 4.0 1.7 - - - +
557B ASN* 3.1 27.0 + - - +
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Residues in contact with VAL 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 4.2 5.8 - - - -
303B GLY 3.1 25.8 - - - +
306B MET* 3.8 12.3 - - + -
307B LEU* 3.8 27.6 - - + +
310B TRP* 3.6 38.8 - - + -
550B ALA 3.1 12.1 + - - +
551B GLU* 2.9 10.5 + - - +
553B ASP* 1.3 76.3 - - - +
555B LEU* 1.3 53.2 + - - +
557B ASN* 3.3 3.3 + - - +
558B LEU* 2.8 41.4 + - + +
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TRP* 3.8 27.8 - - + -
324B ARG* 4.3 21.8 - - + +
327B THR* 3.6 32.8 - - + +
328B ILE* 3.6 13.0 - - + +
331B LEU* 4.3 4.7 - - + +
389B PRO* 6.4 0.2 - - + -
393B LEU* 4.0 12.1 - - + -
551B GLU* 2.9 41.7 + - + +
552B LEU* 4.2 2.7 - - - +
554B VAL* 1.3 73.2 - - - +
556B VAL* 1.3 67.1 + - - +
557B ASN 3.1 0.4 - - - -
558B LEU* 3.3 9.8 + - + +
559B ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 4.2 18.4 - - + +
335B THR* 3.4 17.4 + - - +
338B LEU* 4.0 34.3 - - + -
339B GLN* 3.5 30.7 - - + +
342B LEU* 4.4 6.7 - - + -
552B LEU* 3.0 31.6 + - + +
553B ASP* 4.1 3.4 - - - +
555B LEU* 1.3 77.5 - - - +
557B ASN* 1.3 58.8 + - - +
559B ALA* 3.4 4.3 + - - +
560B GLU* 3.1 19.2 + - - +
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Residues in contact with ASN 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU 3.1 20.4 + - - +
297B CYS* 2.8 39.9 + - - +
298B THR* 3.7 17.2 - - + +
307B LEU* 4.0 14.8 - - - +
339B GLN* 4.0 9.6 - - - +
553B ASP 3.1 20.3 + - - +
554B VAL 3.4 6.5 + - - +
555B LEU 3.1 0.2 - - - -
556B VAL* 1.3 74.0 - - - +
558B LEU* 1.3 73.7 + - - +
559B ALA 2.9 4.9 + - - -
560B GLU* 3.2 3.1 + - - +
561B ARG* 2.9 25.8 + - - +
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Residues in contact with LEU 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 5.0 16.4 - - + +
307B LEU* 4.1 19.1 - - + -
310B TRP* 4.3 17.5 - - + -
324B ARG* 5.9 0.4 - - + -
328B ILE* 3.4 32.8 - - + +
554B VAL* 2.8 37.8 + - + +
555B LEU* 3.3 3.1 + - + +
557B ASN* 1.3 81.1 - - - +
559B ALA* 1.3 56.3 + - - +
561B ARG* 3.9 5.4 - - + +
562B ALA* 3.1 26.5 + - - +
567B TYR* 5.7 0.3 - - - -
636B ILE* 4.7 9.4 - - + -
637B GLY 5.2 0.9 - - - -
638B SER* 4.1 31.2 + - - +
639B TYR 5.4 0.3 + - - -
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Residues in contact with ALA 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE* 3.3 38.1 - - + +
331B LEU* 4.5 3.4 - - + -
332B GLN* 3.5 22.3 - - - +
335B THR* 4.3 5.4 - - - +
555B LEU 3.0 17.6 + - - +
556B VAL* 3.6 7.4 - - - +
557B ASN 2.9 0.6 - - - -
558B LEU* 1.3 76.4 - - - +
560B GLU* 1.3 64.1 + - - +
561B ARG 3.3 0.2 - - - -
562B ALA* 3.9 0.5 - - - +
563B TYR* 3.2 18.4 + - - +
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Residues in contact with GLU 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B CYS* 4.3 8.7 - - - +
332B GLN* 6.0 0.4 - - - +
335B THR* 3.7 32.4 + - + -
339B GLN* 4.2 13.1 + - - +
556B VAL 3.1 10.9 + - - +
557B ASN* 3.7 6.8 - - - +
559B ALA* 1.3 75.8 - - - +
561B ARG* 1.3 98.0 + - - +
563B TYR* 3.7 3.6 - - - +
564B THR* 2.5 63.5 + - - +
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Residues in contact with ARG 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B VAL* 3.2 29.7 + - - +
295B LEU* 3.8 27.4 - - + +
297B CYS* 3.7 22.5 - - - -
557B ASN* 2.9 30.8 + - - +
558B LEU* 3.9 7.0 - - + +
560B GLU* 1.3 108.4 + - - +
562B ALA* 1.3 66.1 + - - +
564B THR* 3.9 14.3 - - - +
565B LEU* 3.1 54.1 + - + +
567B TYR* 4.5 3.7 - - + -
590B GLN* 6.1 0.4 - - - -
----------------------------------------------------------
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Residues in contact with ALA 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE* 4.3 4.5 - - + -
332B GLN* 5.1 1.6 - - - +
558B LEU 3.1 19.2 + - - +
559B ALA 3.9 4.5 - - - +
560B GLU 3.4 0.4 - - - -
561B ARG* 1.3 77.6 - - - +
563B TYR* 1.3 62.5 + - - +
566B ASN* 3.1 4.2 + - - -
567B TYR* 3.0 37.6 + - + +
639B TYR* 3.4 45.1 - - + -
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Residues in contact with TYR 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLN* 3.0 49.0 - - + +
333B ASP* 5.5 6.5 + - - -
559B ALA 3.2 15.3 + - - +
560B GLU* 3.7 5.4 - - - +
562B ALA* 1.3 80.1 - - - +
564B THR* 1.3 66.9 + - - +
565B LEU 3.2 0.7 + - - -
566B ASN* 3.5 10.4 + - - +
----------------------------------------------------------
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Residues in contact with THR 564 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B GLU* 2.5 47.8 + - - +
561B ARG* 3.9 11.0 - - - +
563B TYR* 1.3 80.0 - - - +
565B LEU* 1.3 75.7 + - + +
566B ASN* 3.7 10.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B VAL* 4.3 9.9 - - + -
295B LEU* 5.6 0.2 - - + -
561B ARG* 3.1 50.8 + - + +
564B THR* 1.3 96.5 - - + +
566B ASN* 1.3 76.9 + - - +
567B TYR* 3.4 28.3 - - + +
584B ARG* 3.0 17.7 + - - -
589B GLU* 4.6 0.2 - - - +
590B GLN* 3.5 36.9 + - - +
----------------------------------------------------------
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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