Contacts of the helix formed by residues 521 - 547 (chain A) in PDB entry 4DAJ
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 521 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A SER 5.6 1.1 - - - +
519A CYS 3.5 9.4 - - - +
520A ILE* 1.3 88.2 - - - +
522A LYS* 1.3 66.3 + - - +
523A THR* 3.0 12.7 + - - +
524A TYR* 3.1 41.9 + - + +
525A TRP* 3.5 6.7 - - - -
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Residues in contact with LYS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR* 6.1 0.9 - - - +
219A GLU* 2.6 39.5 + - - +
520A ILE 4.0 0.8 + - - +
521A PRO* 1.3 71.3 - - - +
523A THR* 1.3 64.3 + - - +
525A TRP* 3.1 18.3 + - + +
526A ASN* 3.0 35.0 + - - +
1051B GLY 5.4 5.3 + - - -
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Residues in contact with THR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PRO* 3.1 9.2 - - - +
522A LYS* 1.3 76.0 - - - +
524A TYR* 1.3 80.7 + - + +
526A ASN* 2.9 24.0 + - - +
527A LEU* 2.9 36.0 + - + +
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Residues in contact with TYR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A MET* 3.3 26.1 - - - +
519A CYS 5.3 2.5 - - - -
520A ILE* 3.8 12.6 - - + -
521A PRO* 3.1 36.1 + - + +
523A THR* 1.3 93.6 - - + +
525A TRP* 1.3 56.7 + - - +
527A LEU* 3.3 16.5 + - + +
528A GLY 2.9 25.6 + - - -
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Residues in contact with TRP 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A TYR* 4.1 20.4 - + + -
509A MET* 3.7 28.7 - - + -
510A VAL* 3.8 26.9 - - + -
513A ASN* 3.7 42.5 - - + +
520A ILE* 3.4 29.6 + - + +
521A PRO 3.5 20.2 - - - -
522A LYS* 3.1 21.0 + - + +
524A TYR* 1.3 76.4 - - - +
526A ASN* 1.3 67.9 + - - +
528A GLY* 3.4 1.0 + - - -
529A TYR* 2.9 28.9 + - + +
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Residues in contact with ASN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 3.6 23.3 - - + -
127A TYR* 5.4 7.0 - - - -
128A ILE* 4.4 24.2 - - + +
522A LYS* 3.0 28.3 + - - +
523A THR* 2.9 11.1 + - - +
525A TRP* 1.3 77.8 - - - +
527A LEU* 1.3 60.9 + - + +
529A TYR* 3.1 5.5 - - - +
530A TRP* 2.9 33.8 + - + -
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A THR* 2.9 38.1 + - + +
524A TYR* 3.5 20.4 - - + +
525A TRP 3.2 0.2 - - - -
526A ASN* 1.3 78.1 - - + +
528A GLY* 1.3 66.0 + - - +
530A TRP* 3.0 15.1 + - + +
531A LEU* 2.9 27.3 + - + +
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Residues in contact with GLY 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A THR 4.2 0.2 - - - +
505A PRO* 5.3 1.8 - - - -
506A TYR* 3.9 19.0 - - - +
509A MET* 4.2 6.7 - - - -
524A TYR 2.9 13.8 + - - -
525A TRP 3.8 2.2 - - - -
527A LEU* 1.3 74.1 - - - +
529A TYR* 1.3 60.5 + - - +
531A LEU* 3.1 15.9 + - - +
532A CYS* 2.8 31.5 + - - -
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Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 3.5 26.2 - + + -
143A TRP* 4.4 9.2 - + - -
144A LEU* 4.8 7.3 - - - +
147A ASP* 4.2 5.4 + - - -
148A TYR* 3.3 31.8 + - - -
506A TYR* 3.5 29.3 - + - -
525A TRP* 2.9 13.8 + - + +
526A ASN 3.1 10.8 - - - +
528A GLY* 1.3 73.8 - - - +
530A TRP* 1.3 64.8 + - - +
532A CYS* 2.8 24.9 + - - +
533A TYR* 3.0 44.5 + + - -
2000A 0HK 3.5 31.0 - - + -
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Residues in contact with TRP 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 3.4 35.1 - - + +
77A LEU* 5.8 1.8 - - + -
121A MET* 3.1 46.7 - - + -
124A PHE* 3.3 25.1 - + - -
125A THR* 3.1 22.0 - - - -
128A ILE* 3.3 13.5 - - + +
526A ASN* 2.9 26.0 + - + -
527A LEU* 3.0 14.3 + - + +
529A TYR* 1.3 74.7 - - - +
531A LEU* 1.3 56.4 + - + +
533A TYR* 2.6 61.1 + + + +
534A ILE* 2.9 21.9 + - + +
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Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ILE 4.7 4.3 - - - +
502A THR* 3.2 24.5 - - + +
505A PRO* 3.8 33.4 - - + -
527A LEU 2.9 18.7 + - - +
528A GLY* 3.3 9.0 - - - +
530A TRP* 1.3 76.7 - - + +
532A CYS* 1.3 64.2 + - - +
534A ILE* 2.8 38.4 + - + +
535A ASN 3.0 10.4 + - - -
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Residues in contact with CYS 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.7 2.8 - - - +
502A THR 3.7 11.4 - - - -
503A TRP* 3.6 19.4 + - - +
506A TYR* 3.9 15.9 - - - -
528A GLY 2.8 35.9 + - - -
529A TYR* 2.8 8.0 + - - +
531A LEU* 1.3 73.7 - - - +
533A TYR* 1.3 60.7 + - - +
535A ASN* 3.5 14.1 - - - +
536A SER* 4.2 6.1 + - - -
2000A 0HK 2.9 55.0 - - + -
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Residues in contact with TYR 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.6 29.4 - - + -
120A SER* 3.5 16.9 + - - -
121A MET* 3.9 32.2 - - + +
124A PHE* 3.5 25.1 - + - -
143A TRP* 3.9 7.1 - - - -
147A ASP* 3.0 19.8 + - - -
529A TYR* 3.0 32.0 + + - -
530A TRP* 2.6 42.5 + + + +
532A CYS* 1.3 71.6 - - - +
534A ILE* 1.3 50.6 + - - +
535A ASN 2.9 5.2 - - - -
536A SER* 2.7 31.2 + - - -
537A THR* 3.0 10.4 + - - -
2000A 0HK 4.1 17.0 - - - -
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Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 5.8 6.3 - - + -
121A MET* 5.7 2.7 - - + -
502A THR* 3.6 17.7 - - + -
530A TRP* 3.1 25.1 - - + +
531A LEU* 2.8 32.5 + - + +
533A TYR* 1.3 67.8 - - + +
535A ASN* 1.3 60.6 + - - +
537A THR* 3.4 16.6 - - + +
538A VAL* 2.8 46.3 + - + +
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Residues in contact with ASN 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP* 4.3 1.4 - - - +
154A SER* 4.5 9.5 + - - -
158A LEU* 5.9 0.6 - - - +
498A ALA* 3.9 2.5 - - - +
499A PHE* 3.3 37.5 - - - +
502A THR* 3.0 23.6 - - - +
503A TRP* 3.7 15.6 + - - +
531A LEU 3.0 6.1 + - - -
532A CYS 3.5 12.7 - - - +
533A TYR 2.9 0.2 - - - -
534A ILE* 1.3 77.0 - - - +
536A SER* 1.3 60.8 + - - +
538A VAL* 2.8 25.5 + - - +
539A ASN* 2.8 49.6 + - - +
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Residues in contact with SER 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 3.7 10.1 - - - +
85A ASN* 3.7 0.2 + - - -
113A ASP* 2.8 53.6 + - - +
116A ILE* 3.3 34.5 - - - +
121A MET* 5.8 1.1 - - - -
154A SER* 5.6 0.3 + - - -
532A CYS 4.3 2.4 + - - -
533A TYR* 2.7 15.6 + - - -
535A ASN* 1.3 79.2 + - - +
537A THR* 1.3 57.7 + - - -
539A ASN* 3.5 0.2 - - - +
540A PRO* 3.4 9.9 - - - +
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Residues in contact with THR 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.9 11.5 + - + +
80A VAL* 4.1 25.5 - - + +
81A THR* 2.5 32.9 + - - +
121A MET* 4.0 6.4 - - - +
533A TYR 3.0 5.1 + - - -
534A ILE* 3.4 24.0 - - + +
535A ASN 3.0 0.6 - - - -
536A SER* 1.3 77.8 - - - +
538A VAL* 1.3 62.0 + - + +
540A PRO* 3.2 18.0 - - - +
541A VAL* 3.6 12.6 - - + +
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ALA* 4.2 14.6 - - + -
502A THR* 5.6 2.5 - - + -
534A ILE* 2.8 38.4 + - + +
535A ASN* 2.8 10.9 + - - +
537A THR* 1.3 78.1 - - + +
539A ASN* 1.3 57.3 + - - +
540A PRO 3.5 0.2 - - - -
541A VAL* 3.1 18.3 - - + +
542A CYS* 2.9 42.9 + - - -
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Residues in contact with ASN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 5.6 7.4 - - + +
110A ALA* 6.3 0.2 - - - -
113A ASP* 3.2 28.1 + - - +
154A SER* 5.5 1.0 + - - -
495A ILE* 3.8 35.7 - - + +
498A ALA* 4.5 3.3 - - - +
535A ASN* 2.8 57.1 + - - +
536A SER* 3.5 0.6 - - - +
538A VAL* 1.3 73.5 - - - +
540A PRO* 1.3 67.0 - - + +
542A CYS* 3.3 4.5 + - - +
543A TYR* 2.9 37.6 + - + +
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Residues in contact with PRO 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR 5.0 0.7 - - - +
84A GLY* 4.0 14.4 - - - +
85A ASN* 2.8 37.0 - - - +
88A VAL* 3.8 16.6 - - + -
110A ALA* 5.4 1.1 - - + -
113A ASP* 4.1 0.2 - - - +
536A SER 3.4 8.3 - - - +
537A THR 3.2 16.6 - - - +
539A ASN* 1.3 95.0 - - + +
541A VAL* 1.3 62.9 + - + +
543A TYR* 2.9 27.1 + - + +
544A ALA* 2.9 15.7 + - - +
554A PHE* 4.8 5.1 - - + -
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 5.8 5.6 - - + -
537A THR* 3.6 22.2 - - + +
538A VAL* 3.1 20.4 + - + +
540A PRO* 1.3 77.3 - - + +
542A CYS* 1.3 57.6 + - - +
544A ALA* 3.5 4.4 + - - +
545A LEU* 2.9 57.3 + - + +
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Residues in contact with CYS 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A THR* 4.7 0.9 - - - -
494A ALA* 3.7 25.8 - - + -
495A ILE* 3.6 15.3 - - + -
498A ALA* 4.3 14.1 - - - -
538A VAL* 2.9 44.1 + - - -
539A ASN* 3.6 7.4 - - - +
541A VAL* 1.3 74.0 - - - +
543A TYR* 1.3 67.9 + - - +
545A LEU* 4.5 6.3 - - - -
546A CYS* 2.9 30.5 + - - +
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Residues in contact with TYR 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.9 31.0 - - + -
106A LEU* 2.7 78.1 + - + +
109A LEU* 3.1 20.4 - - + +
110A ALA* 4.3 6.3 - - + -
491A THR* 4.3 7.0 - - + -
495A ILE* 3.6 23.1 - - + -
539A ASN* 2.9 25.0 + - + -
540A PRO* 2.9 12.7 + - + +
542A CYS* 1.3 79.2 - - - +
544A ALA* 1.3 65.1 + - - +
546A CYS* 3.8 1.2 - - - +
547A ASN* 3.0 24.8 + - - +
550A PHE* 4.1 21.4 - + + -
554A PHE* 5.4 1.1 - - + -
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A PRO 2.9 9.7 + - - +
541A VAL* 4.0 4.3 - - - +
543A TYR* 1.3 76.7 - - - +
545A LEU* 1.3 66.2 + - + +
547A ASN 2.6 22.3 - - - +
550A PHE* 3.7 13.2 - - + -
551A ARG* 3.1 19.1 - - + +
554A PHE* 3.6 31.0 - - + -
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Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A VAL* 2.9 47.1 + - + +
542A CYS* 4.1 5.4 - - - +
544A ALA* 1.3 80.7 - - + +
546A CYS* 1.3 61.8 + - - +
551A ARG* 2.8 34.6 + - + +
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Residues in contact with CYS 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A THR* 3.1 35.7 - - - +
494A ALA* 3.7 26.2 - - - -
542A CYS* 2.9 24.7 + - - +
543A TYR 3.8 1.3 - - - +
545A LEU* 1.3 82.3 - - - +
547A ASN* 1.3 62.7 + - - +
548A LYS* 3.8 3.6 + - - +
551A ARG* 4.9 1.6 + - - -
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Residues in contact with ASN 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 4.7 8.1 + - - +
106A LEU* 5.7 3.0 - - - +
490A GLN* 3.3 20.8 + - - +
491A THR* 3.2 20.7 + - - -
543A TYR 3.0 6.3 + - - -
544A ALA 2.6 20.8 - - - +
546A CYS* 1.3 76.6 - - - +
548A LYS* 1.3 64.8 + - - +
549A THR* 3.1 12.9 + - - +
550A PHE* 3.2 47.1 + - + +
551A ARG* 3.3 3.0 + - - -
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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