Contacts of the helix formed by residues 521 - 547 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D SER 5.1 2.5 - - - +
519D CYS 3.1 11.2 - - - +
520D ILE* 1.3 85.6 - - - +
522D LYS* 1.3 66.8 + - - +
523D THR* 3.1 16.5 + - - +
524D TYR* 3.3 36.3 + - + -
525D TRP* 3.1 12.9 + - - -
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Residues in contact with LYS 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D ILE 3.9 0.4 + - - -
521D PRO* 1.3 72.3 - - - +
523D THR* 1.3 59.8 + - - +
525D TRP* 3.1 15.4 + - - +
526D ASN* 2.6 40.5 + - - +
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Residues in contact with THR 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D PRO* 4.0 12.7 - - - +
522D LYS* 1.3 75.5 + - - +
524D TYR* 1.3 70.5 + - + +
526D ASN* 3.5 7.1 + - - +
527D LEU* 2.8 46.9 + - + +
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Residues in contact with TYR 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509D MET* 3.6 13.3 - - - +
520D ILE* 3.9 17.0 - - + -
521D PRO* 3.3 36.0 + - + +
523D THR* 1.3 88.1 - - + +
525D TRP* 1.3 67.8 + - - +
527D LEU* 3.2 19.8 + - + +
528D GLY 2.9 18.9 + - - -
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Residues in contact with TRP 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D THR* 6.2 2.7 - - + -
506D TYR* 4.0 27.6 - + + -
509D MET* 3.5 24.6 - - + +
510D VAL* 4.1 26.0 - - + -
513D ASN* 3.3 46.5 - - + +
520D ILE* 3.2 28.8 + - + +
521D PRO 3.1 28.7 - - - -
522D LYS* 3.1 12.3 + - - +
524D TYR* 1.3 76.9 - - - +
526D ASN* 1.3 66.8 + - - +
528D GLY* 2.9 14.2 + - - -
529D TYR* 2.9 12.6 + - - +
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Residues in contact with ASN 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D TYR* 4.9 11.1 - - - -
128D ILE* 4.4 31.6 - - + +
522D LYS* 2.6 37.2 + - - +
523D THR* 3.8 7.4 - - - +
525D TRP* 1.3 80.5 - - - +
527D LEU* 1.3 65.9 + - + +
529D TYR* 2.9 14.5 + - - +
530D TRP* 2.9 26.6 + - + -
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Residues in contact with LEU 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D THR* 2.8 39.6 + - + +
524D TYR* 3.3 26.7 - - + +
525D TRP 3.1 0.2 - - - -
526D ASN* 1.3 78.0 - - + +
528D GLY* 1.3 64.1 + - - +
530D TRP* 2.9 24.0 + - + +
531D LEU* 2.9 20.1 + - + +
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Residues in contact with GLY 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D PRO* 5.8 0.7 - - - -
506D TYR* 3.6 20.8 - - - +
509D MET* 4.2 5.6 - - - -
524D TYR 2.9 9.4 + - - -
525D TRP 2.9 9.0 + - - -
527D LEU* 1.3 75.1 - - - +
529D TYR* 1.3 61.9 + - - +
531D LEU* 3.2 18.5 + - - +
532D CYS* 2.9 26.0 + - - -
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Residues in contact with TYR 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PHE* 5.6 2.7 - - + -
143D TRP* 4.8 10.4 - + - -
144D LEU* 4.8 7.4 - - - +
147D ASP* 4.0 6.6 + - - -
148D TYR* 3.5 23.2 + - - -
506D TYR* 3.6 28.5 - + - -
525D TRP* 2.9 6.6 + - + +
526D ASN* 2.9 22.1 + - - +
528D GLY* 1.3 76.3 - - - +
530D TRP* 1.3 55.1 + - + +
532D CYS* 3.0 12.0 + - - +
533D TYR* 3.0 63.5 + + + -
2000D 0HK 3.3 45.0 - - + -
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Residues in contact with TRP 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D THR* 3.9 29.3 - - + +
77D LEU* 4.0 15.3 - - + -
121D MET* 3.1 50.0 - - + -
124D PHE* 4.8 3.1 - - + -
125D THR* 2.9 28.5 - - - -
128D ILE* 3.7 25.6 - - + +
526D ASN* 2.9 20.1 + - + -
527D LEU* 2.9 15.2 + - + +
529D TYR* 1.3 73.1 - - + +
531D LEU* 1.3 61.8 + - + +
533D TYR* 3.1 37.7 + + + +
534D ILE* 2.9 36.6 + - + +
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Residues in contact with LEU 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D THR* 3.3 22.3 - - + +
505D PRO* 3.9 31.2 - - + -
527D LEU* 2.9 18.5 + - + +
528D GLY* 3.2 17.3 - - - +
530D TRP* 1.3 77.3 - - + +
532D CYS* 1.3 64.0 + - - +
533D TYR 2.9 1.4 + - - -
534D ILE* 2.9 41.3 + - + +
535D ASN 3.0 5.0 + - - -
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Residues in contact with CYS 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 4.7 1.6 - - - +
502D THR 3.5 12.6 - - - -
503D TRP* 3.2 32.3 + - - +
506D TYR* 3.7 25.8 - - - -
528D GLY 2.9 28.2 + - - -
529D TYR 3.0 3.1 + - - +
531D LEU* 1.3 76.1 - - - +
533D TYR* 1.3 61.1 + - - +
535D ASN* 3.6 5.0 - - - +
536D SER* 4.2 5.4 + - - -
2000D 0HK 3.1 49.1 - - + -
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Residues in contact with TYR 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 3.7 30.5 - - + +
120D SER* 3.0 19.0 + - - -
121D MET* 3.5 33.1 - - + +
124D PHE* 4.1 10.8 - - + -
143D TRP* 3.7 4.3 - - - -
147D ASP* 2.7 25.1 + - - -
529D TYR* 3.0 29.3 + + + -
530D TRP* 3.3 43.3 - + + +
531D LEU 2.9 1.2 + - - -
532D CYS* 1.3 76.5 - - - +
534D ILE* 1.3 56.3 + - - +
535D ASN 2.9 4.9 - - - -
536D SER* 2.8 24.8 + - - -
537D THR* 3.0 10.4 + - - -
2000D 0HK 3.9 18.8 - - - -
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Residues in contact with ILE 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 3.6 30.7 - - + -
502D THR* 4.1 15.3 - - + -
530D TRP* 2.9 24.6 + - + +
531D LEU* 2.9 44.3 + - + +
533D TYR* 1.3 70.5 - - - +
535D ASN* 1.3 57.4 + - - +
537D THR* 3.2 14.2 - - + +
538D VAL* 2.9 41.1 + - + +
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Residues in contact with ASN 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D SER* 4.9 4.3 + - - -
498D ALA* 3.8 8.3 - - - +
499D PHE* 3.1 42.6 - - - +
502D THR* 2.8 24.1 + - - +
503D TRP* 3.6 27.3 + - - +
531D LEU 3.0 5.4 + - - +
532D CYS 3.6 3.4 - - - +
533D TYR 2.9 0.6 - - - -
534D ILE* 1.3 75.3 - - - +
536D SER* 1.3 66.4 + - - +
537D THR 2.9 3.8 - - - -
538D VAL* 2.8 20.8 + - - +
539D ASN* 3.0 29.2 + - - +
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Residues in contact with SER 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D THR* 3.7 9.7 - - - +
85D ASN* 3.9 0.7 + - - -
112D ALA 5.3 0.2 - - - -
113D ASP* 2.8 51.8 + - - +
116D ILE* 3.4 37.7 - - - +
154D SER* 5.2 3.1 + - - -
503D TRP* 5.7 2.3 - - - -
532D CYS 4.4 2.3 + - - -
533D TYR 2.8 12.4 + - - -
535D ASN* 1.3 82.2 + - - +
537D THR* 1.3 60.4 + - - +
539D ASN 4.2 0.2 - - - -
540D PRO* 3.8 5.4 - - - +
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Residues in contact with THR 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 3.8 24.6 - - + +
80D VAL* 4.5 13.8 - - + +
81D THR* 2.6 36.1 + - - +
121D MET* 4.0 4.0 - - - +
533D TYR 3.0 6.0 + - - -
534D ILE* 3.2 26.3 + - + +
535D ASN 2.9 0.2 - - - -
536D SER* 1.3 80.4 - - - +
538D VAL* 1.3 64.4 + - + +
539D ASN 3.5 0.7 + - - -
540D PRO* 3.6 9.2 - - - +
541D VAL* 3.7 12.6 - - + +
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Residues in contact with VAL 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D ALA* 4.7 11.2 - - + -
502D THR* 5.8 4.0 - - + -
534D ILE* 2.9 30.4 + - + +
535D ASN* 2.8 7.6 + - - +
537D THR* 1.3 83.1 - - + +
539D ASN* 1.3 66.3 + - - +
540D PRO 3.5 0.2 - - - -
541D VAL* 3.2 15.6 + - + +
542D CYS* 2.9 36.8 + - - -
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Residues in contact with ASN 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 4.3 19.0 - - + +
113D ASP* 2.7 29.3 + - - +
154D SER* 5.0 4.0 + - - -
158D LEU* 5.8 1.9 - - - +
495D ILE* 3.2 33.9 - - + +
498D ALA* 5.1 1.7 - - - +
535D ASN* 3.0 34.7 + - - +
538D VAL* 1.3 75.1 - - - +
540D PRO* 1.3 69.7 - - + +
542D CYS* 2.8 21.5 + - - +
543D TYR* 2.9 24.5 + - - +
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Residues in contact with PRO 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D THR 5.3 0.4 - - - +
84D GLY* 4.3 11.4 - - - -
85D ASN* 2.9 33.9 - - - +
88D VAL* 3.4 25.8 - - + -
110D ALA* 5.5 0.9 - - - -
113D ASP* 4.0 0.2 - - - +
536D SER 3.8 3.8 - - - +
537D THR 3.6 13.9 - - - +
539D ASN* 1.3 96.3 - - + +
541D VAL* 1.3 57.3 + - + +
543D TYR* 3.0 21.8 - - + +
544D ALA* 3.0 25.5 + - - +
554D PHE* 5.1 4.5 - - + -
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Residues in contact with VAL 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D VAL* 5.8 6.7 - - + -
537D THR* 3.7 21.5 - - + +
538D VAL* 3.5 16.8 - - + +
539D ASN 3.1 0.6 - - - -
540D PRO* 1.3 77.0 - - + +
542D CYS* 1.3 62.8 + - - +
544D ALA* 3.1 11.9 + - + +
545D LEU* 3.1 20.6 + - - +
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Residues in contact with CYS 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D THR* 4.0 2.8 + - - -
494D ALA* 4.2 25.9 - - + +
495D ILE* 3.2 24.2 - - + -
498D ALA* 4.4 8.5 - - - -
538D VAL* 2.9 36.2 + - - -
539D ASN 2.8 11.5 + - - +
541D VAL* 1.3 75.3 - - - +
543D TYR* 1.3 63.6 + - - +
545D LEU* 3.0 17.4 + - - +
546D CYS* 3.1 17.7 + - - +
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Residues in contact with TYR 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 4.1 23.3 - - + -
106D LEU* 3.3 56.0 + - + +
109D LEU* 3.2 34.3 - - - +
110D ALA* 4.9 2.7 - - + -
491D THR* 4.3 9.6 - - - -
495D ILE* 3.5 25.8 - - + -
539D ASN* 2.9 19.6 + - + +
540D PRO* 3.0 26.0 - - + +
542D CYS* 1.3 76.0 - - - +
544D ALA* 1.3 60.3 + - - +
547D ASN* 3.3 27.9 + - - +
550D PHE* 4.0 27.2 - + + +
554D PHE* 5.2 1.6 - - + -
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Residues in contact with ALA 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D PRO 3.0 11.6 + - - +
541D VAL* 3.3 15.3 - - + +
542D CYS 3.1 0.2 - - - -
543D TYR* 1.3 78.9 - - - +
545D LEU* 1.3 57.7 + - - +
546D CYS 3.5 0.3 + - - -
547D ASN 3.8 2.0 - - - +
550D PHE* 4.7 4.9 - - - -
551D ARG* 2.8 41.9 + - + +
554D PHE* 4.8 13.5 - - + -
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Residues in contact with LEU 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D ALA* 5.9 4.3 - - + -
541D VAL* 3.1 10.7 + - + +
542D CYS* 3.0 11.1 + - - +
544D ALA* 1.3 77.4 - - - +
546D CYS* 1.3 66.3 + - - +
551D ARG* 3.0 24.2 + - - +
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Residues in contact with CYS 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D THR* 3.2 51.8 - - - +
494D ALA* 4.1 17.9 - - - -
542D CYS 3.1 7.3 + - - +
543D TYR 4.2 0.9 - - - +
545D LEU* 1.3 87.6 - - - +
547D ASN* 1.3 68.8 + - - +
548D LYS* 3.5 2.8 + - - +
551D ARG* 4.6 4.7 + - - -
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Residues in contact with ASN 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 4.0 8.9 + - - +
106D LEU* 5.1 1.4 - - - +
490D GLN* 5.2 14.1 + - - +
491D THR* 4.8 15.7 - - - +
543D TYR* 3.3 7.4 + - - +
546D CYS* 1.3 82.7 - - - +
548D LYS* 1.3 63.5 + - - +
549D THR* 3.3 10.2 + - - +
550D PHE* 3.3 43.1 + - + +
551D ARG* 3.4 20.2 + - - +
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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