Contacts of the helix formed by residues 548 - 570 (chain A) in PDB entry 2DDH
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 ASP 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PHE* 5.2 0.2 - - - +
15A ASN 5.4 0.7 + - - -
18A LEU* 3.3 34.0 - - + +
546A ILE* 3.4 9.1 - - - +
547A GLN* 1.3 76.2 - - - +
549A LYS* 1.3 60.3 + - - +
550A ALA* 3.1 15.6 + - - +
551A VAL* 3.0 35.2 + - + +
552A GLN* 3.0 23.7 + - - +
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Residues in contact with LYS 549 (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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546A ILE 3.7 4.8 + - - -
547A GLN* 3.2 21.7 + - - +
548A ASP* 1.3 71.8 + - - +
550A ALA* 1.3 60.7 + - - +
552A GLN* 3.2 27.4 + - - +
553A ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 550 (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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13A THR* 3.2 27.5 + - - +
14A PHE* 3.8 10.3 - - + +
15A ASN 5.3 0.2 - - - +
548A ASP* 3.1 10.1 + - - +
549A LYS* 1.3 78.6 - - - +
551A VAL* 1.3 62.8 + - - +
553A ALA* 3.6 6.0 + - - +
554A VAL* 3.2 28.4 + - - +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.4 8.3 - - + -
15A ASN 4.4 7.2 - - - +
18A LEU* 3.9 22.9 - - + -
19A ILE* 3.7 26.7 - - + -
22A ILE* 4.1 9.9 - - + -
546A ILE* 3.7 15.7 - - + -
548A ASP* 3.0 31.5 + - + +
549A LYS 3.1 0.2 - - - -
550A ALA* 1.3 75.2 - - - +
552A GLN* 1.3 66.7 + - - +
554A VAL* 2.9 23.1 - - - +
555A LEU* 3.1 17.9 + - + +
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Residues in contact with GLN 552 (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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543A LEU* 3.2 37.8 + - + +
544A PRO* 4.2 10.4 - - - +
546A ILE* 3.2 31.7 - - + +
548A ASP 3.0 13.6 + - - +
549A LYS* 3.2 21.4 + - - +
551A VAL* 1.3 77.7 - - - +
553A ALA* 1.3 57.2 + - - +
555A LEU* 3.4 2.5 + - - +
556A ARG* 2.8 40.0 + - + +
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Residues in contact with ALA 553 (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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549A LYS 2.9 18.0 + - - +
550A ALA* 3.8 7.6 - - - +
552A GLN* 1.3 76.5 - - - +
554A VAL* 1.3 63.1 + - + +
556A ARG* 3.2 11.8 + - - +
557A ASN* 3.2 25.2 + - - -
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.7 7.2 - - - +
14A PHE* 3.7 28.9 - - + -
19A ILE* 4.7 0.9 - - + -
550A ALA 3.2 14.1 + - - +
551A VAL* 2.9 24.2 - - - +
553A ALA* 1.3 75.8 - - + +
555A LEU* 1.3 70.0 + - + +
557A ASN* 3.1 21.6 + - - +
558A LEU* 3.2 15.5 + - - +
599A ILE* 5.6 0.3 - - - +
602A ASN* 3.3 32.1 - - + +
606A LEU* 4.5 13.1 - - + +
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Residues in contact with LEU 555 (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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19A ILE* 4.4 14.4 - - + -
22A ILE* 5.0 2.2 - - + -
339A TYR* 3.8 33.0 - - + -
343A PHE* 4.1 25.8 - - + -
539A PHE* 3.8 6.9 - - + -
543A LEU* 3.7 16.9 - - + +
546A ILE* 4.4 14.4 - - + -
551A VAL* 3.1 33.3 + - + +
552A GLN* 4.5 0.4 - - - -
554A VAL* 1.3 82.4 - - + +
556A ARG* 1.3 60.3 + - - +
558A LEU* 3.4 18.9 + - + +
559A CYS* 3.0 27.0 + - - +
606A LEU* 4.6 2.5 - - + -
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Residues in contact with ARG 556 (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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478A ASN 5.4 1.2 + - - -
479A SER* 4.9 5.1 - - - +
480A LEU* 3.4 45.0 - - + +
481A GLU* 4.7 9.1 + - - -
543A LEU* 3.8 19.8 - - + +
552A GLN* 2.8 26.4 + - + +
553A ALA* 3.4 10.3 - - - +
554A VAL 3.1 0.2 - - - -
555A LEU* 1.3 77.1 - - - +
557A ASN* 1.3 61.5 + - - +
559A CYS* 3.2 3.2 + - - +
560A LEU* 2.8 45.2 + - + +
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Residues in contact with ASN 557 (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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553A ALA 3.2 13.5 + - - +
554A VAL* 3.1 14.8 + - - +
556A ARG* 1.3 83.5 - - - +
558A LEU* 1.3 56.2 + - - +
560A LEU* 3.6 14.7 - - - +
561A LEU* 2.9 28.9 + - - +
591A ARG* 5.1 3.2 - - - +
595A LEU* 3.8 23.0 - - + +
598A LEU* 4.3 22.4 - - - +
599A ILE* 3.9 21.4 - - + +
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Residues in contact with LEU 558 (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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332A PHE 4.7 2.5 - - - +
335A LEU* 4.6 5.6 - - + +
336A ALA* 3.3 35.5 - - + +
339A TYR* 3.5 36.8 - - + -
539A PHE* 4.0 7.6 - - + -
554A VAL 3.2 10.9 + - - +
555A LEU* 3.7 24.5 - - + +
556A ARG 3.2 0.2 - - - -
557A ASN* 1.3 73.1 - - - +
559A CYS* 1.3 61.6 + - - +
561A LEU* 3.2 1.3 + - - -
562A TYR* 2.8 27.5 + - - +
599A ILE* 3.9 24.0 - - + -
606A LEU* 4.1 25.6 - - + -
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Residues in contact with CYS 559 (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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480A LEU* 3.8 12.3 - - + -
536A VAL* 4.5 0.9 - - - -
539A PHE* 3.5 39.9 - - + -
540A SER* 3.5 34.8 - - - -
543A LEU* 3.9 9.9 - - + -
555A LEU 3.0 18.1 + - - +
556A ARG 3.5 5.2 - - - +
558A LEU* 1.3 77.3 - - - +
560A LEU* 1.3 59.1 + - - +
562A TYR* 3.7 1.6 - - - +
563A SER* 2.8 33.9 + - - -
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Residues in contact with LEU 560 (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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477A ILE 5.7 0.4 - - - +
478A ASN 4.7 10.5 - - - +
480A LEU* 3.8 32.8 - - + +
483A LEU* 3.8 18.4 - - + -
556A ARG* 2.8 39.6 + - - +
557A ASN* 3.6 21.5 - - - +
559A CYS* 1.3 77.0 - - - +
561A LEU* 1.3 55.8 + - - +
563A SER* 3.4 1.7 + - - -
564A LEU* 2.9 40.4 + - + +
591A ARG* 5.1 8.5 - - - +
595A LEU* 3.9 17.3 - - + -
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Residues in contact with LEU 561 (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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332A PHE* 3.6 39.3 - - + +
333A PRO* 3.7 15.5 - - + -
336A ALA* 4.4 3.4 - - + -
557A ASN 2.9 18.9 + - - +
558A LEU 3.6 4.5 - - - +
560A LEU* 1.3 76.8 - - - +
562A TYR* 1.3 58.0 + - - +
564A LEU* 4.7 0.9 - - - -
565A TYR* 2.8 36.3 + - + +
592A ILE* 3.8 40.2 - - + +
595A LEU* 3.8 10.7 - - + +
596A LEU* 4.2 7.4 - - + -
599A ILE* 3.6 24.9 - - + -
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Residues in contact with TYR 562 (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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333A PRO 4.8 2.9 - - - -
336A ALA* 4.0 11.6 - - + +
337A THR* 3.4 47.6 - - + -
340A ALA* 4.3 11.2 - - + -
341A PHE* 3.7 3.7 - + - -
380A PHE* 3.5 19.9 - - - -
384A THR* 5.9 0.2 - - - +
487A TYR* 3.9 2.4 + - - -
532A HIS* 3.5 27.6 + + - -
535A VAL* 3.5 27.4 - - + +
536A VAL* 3.9 25.1 - - + -
539A PHE* 4.7 6.5 - + + -
558A LEU 2.8 20.3 + - - +
559A CYS* 3.7 6.1 - - - +
561A LEU* 1.3 71.8 - - - +
563A SER* 1.3 61.3 + - - +
565A TYR* 3.7 9.3 - + - +
566A GLY* 3.0 23.2 + - - -
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Residues in contact with SER 563 (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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480A LEU* 3.9 6.6 - - - +
483A LEU* 3.9 26.9 - - - -
487A TYR* 2.6 38.6 + - - -
536A VAL* 3.6 20.2 - - - +
559A CYS* 2.8 25.0 + - - -
560A LEU* 3.7 3.6 - - - -
562A TYR* 1.3 77.9 - - - +
564A LEU* 1.3 66.8 + - - +
566A GLY 3.2 0.2 + - - -
567A ILE* 3.2 8.2 + - - +
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Residues in contact with LEU 564 (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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477A ILE* 4.0 24.0 - - + +
483A LEU* 3.7 28.9 - - + -
560A LEU* 2.9 31.0 + - + +
561A LEU 4.1 0.7 - - - +
563A SER* 1.3 72.5 - - - +
565A TYR* 1.3 63.6 + - - +
567A ILE* 3.0 6.2 + - - +
568A SER 2.9 19.2 + - - -
588A VAL* 3.4 22.3 - - + +
591A ARG* 3.5 25.1 - - + -
592A ILE* 3.6 16.8 - - + +
595A LEU* 3.4 27.1 - - + -
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Residues in contact with TYR 565 (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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329A TYR* 3.7 41.0 + + - -
333A PRO* 3.8 39.1 - - + +
334A LEU* 5.6 7.5 - - + +
337A THR* 5.5 5.2 - - - -
561A LEU* 2.8 28.9 + - + +
562A TYR* 3.7 8.5 - + - +
564A LEU* 1.3 73.5 - - - +
566A GLY* 1.3 59.8 + - - +
568A SER* 3.2 1.9 + - - -
569A GLN* 2.9 61.5 + - + +
592A ILE* 3.5 14.7 - - + +
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Residues in contact with GLY 566 (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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487A TYR* 3.0 18.4 - - - -
490A ARG* 5.0 0.5 + - - -
532A HIS* 3.9 18.6 - - - -
562A TYR 3.0 13.6 + - - -
563A SER 3.2 0.6 + - - -
565A TYR* 1.3 80.2 - - - +
567A ILE* 1.3 60.9 + - - +
569A GLN* 3.6 6.2 + - - +
570A LYS* 3.2 26.0 + - - +
574A PHE* 4.3 2.0 - - - -
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Residues in contact with ILE 567 (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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477A ILE* 4.2 10.5 - - + -
483A LEU* 3.6 30.5 - - + -
486A ALA* 4.6 10.3 - - + -
487A TYR* 3.6 20.4 - - + -
563A SER 3.2 12.3 + - - +
564A LEU* 3.0 11.0 + - - +
566A GLY* 1.3 75.0 - - - +
568A SER* 1.3 60.3 - - - +
570A LYS 3.3 1.0 - - - -
571A GLY* 2.8 29.3 + - - -
574A PHE* 3.7 24.5 - - + -
580A ILE* 4.0 26.9 - - + -
585A LEU* 4.1 7.6 - - + +
588A VAL* 4.2 10.8 - - + -
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Residues in contact with SER 568 (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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329A TYR* 4.7 5.0 + - - -
564A LEU 2.9 6.2 + - - -
565A TYR* 3.6 7.6 - - - -
567A ILE* 1.3 78.4 - - - +
569A GLN* 1.3 71.7 + - - +
570A LYS 3.3 0.7 + - - -
571A GLY* 3.4 7.4 + - - -
585A LEU* 4.1 11.2 - - - +
588A VAL* 4.2 1.5 - - - +
589A ASN* 2.5 30.8 + - - -
592A ILE* 3.7 20.7 - - - +
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Residues in contact with GLN 569 (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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329A TYR* 3.1 26.7 + - - -
565A TYR* 2.9 54.2 + - + +
566A GLY* 3.9 6.5 - - - +
567A ILE 3.3 0.4 - - - -
568A SER* 1.3 82.6 + - - +
570A LYS* 1.3 67.5 + - + +
571A GLY 3.6 0.4 - - - -
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Residues in contact with LYS 570 (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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490A ARG* 3.6 15.9 - - - +
525A ARG* 3.1 28.3 - - - +
528A GLU* 4.0 21.3 + - - -
532A HIS* 5.8 4.5 - - + +
566A GLY 3.2 13.8 + - - +
567A ILE 3.3 3.6 - - - -
568A SER 3.2 0.4 - - - -
569A GLN* 1.3 84.1 - - + +
571A GLY* 1.3 66.0 + - - +
572A GLY* 3.1 3.6 - - - -
573A ASP* 2.9 41.1 + - - +
574A PHE* 3.4 5.4 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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