Contacts of the helix formed by residues 531 - 559 (chain D) in PDB entry 2W3S
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 SER 531 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D ILE* 5.4 3.6 - - - -
458D SER* 5.5 3.4 - - - -
459D PHE* 3.1 26.4 - - - -
465D ASN* 5.2 1.8 - - - -
526D ALA 4.4 2.4 + - - -
528D ALA 2.7 22.7 + - - -
529D ALA* 3.9 7.6 - - - -
530D SER* 1.3 78.6 - - - +
532D GLY* 1.3 66.3 + - - +
533D ALA 3.4 0.7 - - - -
534D ASP* 3.1 8.7 + - - +
535D MET* 3.0 47.4 + - - +
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Residues in contact with GLY 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D LEU* 3.8 9.1 - - - +
527D THR* 4.1 12.1 - - - -
528D ALA 4.2 0.2 + - - -
530D SER 3.3 0.4 - - - -
531D SER* 1.3 73.9 + - - +
533D ALA* 1.3 60.1 + - - +
536D ASN* 3.0 40.3 + - - +
1778D MTE 2.6 29.4 + - - -
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Residues in contact with ALA 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D LEU* 3.7 16.2 - - + -
495D LYS* 4.4 16.2 - - + +
496D MET* 4.0 3.5 - - + +
530D SER 4.8 1.7 + - - +
531D SER 3.4 0.4 - - - -
532D GLY* 1.3 73.0 - - - +
534D ASP* 1.3 65.4 + - - +
537D GLY* 2.7 32.2 + - - -
655D LEU* 4.3 20.6 - - + -
722D ILE* 3.9 5.1 - - + +
727D ALA* 6.4 1.6 - - - -
1778D MTE 3.5 11.6 + - - +
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Residues in contact with ASP 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D ILE* 3.7 7.2 - - + +
530D SER 4.3 2.4 - - - +
531D SER* 3.1 12.7 + - - +
533D ALA* 1.3 85.4 - - - +
535D MET* 1.3 65.4 + - + +
538D MET* 3.4 26.0 + - - +
602D TYR* 4.6 3.4 - - + -
620D LEU* 5.6 0.3 - - - +
621D TYR* 2.5 41.4 + - - -
721D THR* 4.5 11.3 - - - +
722D ILE* 3.7 13.1 + - - +
725D SER* 4.8 5.7 + - - +
726D LYS* 4.1 3.1 - - - -
727D ALA* 3.5 21.3 + - - +
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Residues in contact with MET 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D PHE* 4.0 5.4 - - + -
464D LEU 3.8 12.1 - - - +
465D ASN* 3.5 31.4 - - - +
466D GLN 3.7 19.7 - - - +
467D ALA* 3.4 19.1 - - + +
525D SER* 5.0 3.8 - - - -
526D ALA 5.8 0.7 - - - +
531D SER* 3.0 40.4 + - - +
534D ASP* 1.3 80.0 - - + +
536D ASN* 1.3 69.4 + - - +
537D GLY 3.3 1.1 - - - -
538D MET* 3.2 3.8 + - - +
539D ALA* 2.9 19.4 + - - +
602D TYR* 3.7 17.8 - - + +
604D THR* 3.7 16.6 - - - +
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Residues in contact with ASN 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D ALA* 3.8 17.0 - - - +
468D GLY 3.7 4.7 - - - +
483D HIS* 3.6 12.6 + - + +
484D GLY* 3.1 15.5 + - - -
485D GLY* 3.0 36.0 + - - +
496D MET* 3.8 15.0 - - - -
532D GLY* 3.0 31.7 + - - +
535D MET* 1.3 79.6 - - - +
537D GLY* 1.3 63.7 + - - +
539D ALA* 3.0 4.9 + - - +
540D VAL* 2.8 26.2 + - - +
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Residues in contact with GLY 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D MET* 3.4 21.8 - - - -
499D VAL* 3.5 6.9 - - - +
533D ALA 2.7 26.0 + - - -
536D ASN* 1.3 72.1 - - - +
538D MET* 1.3 54.8 + - - +
540D VAL* 3.5 1.5 + - - +
541D LYS* 3.1 22.7 + - - +
722D ILE* 3.5 23.2 - - - +
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Residues in contact with MET 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D ASP 3.4 16.8 + - - +
535D MET 3.2 3.0 + - - +
536D ASN 3.2 0.6 - - - -
537D GLY* 1.3 71.1 - - - +
539D ALA* 1.3 56.6 + - - +
540D VAL 3.2 0.2 - - - -
541D LYS* 3.3 21.8 + - - +
542D ASP* 2.8 33.6 + - - +
602D TYR* 3.4 55.2 - - + +
720D GLU 3.7 18.8 - - - +
721D THR* 4.3 0.9 - - - -
722D ILE* 3.7 36.1 - - + +
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Residues in contact with ALA 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D ALA 3.6 24.5 - - - +
468D GLY* 3.7 21.5 - - - +
469D ALA* 3.8 3.6 - - + +
535D MET 2.9 12.6 + - - +
536D ASN* 3.5 7.9 - - - +
538D MET* 1.3 75.7 - - - +
540D VAL* 1.3 57.4 + - - +
542D ASP* 3.2 4.9 - - - +
543D ALA 3.0 22.2 + - - -
600D GLY* 3.3 9.3 - - - +
601D PHE* 3.7 16.4 - - - +
602D TYR* 3.8 1.0 - - - +
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Residues in contact with VAL 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ALA* 3.6 20.9 - - + -
471D VAL* 5.1 0.2 - - + -
481D LEU* 3.7 23.1 - - + -
483D HIS* 4.1 12.3 - - + -
496D MET* 4.0 16.8 - - - +
499D VAL* 4.0 4.5 - - + -
500D ALA* 4.0 34.5 - - + +
536D ASN 2.8 20.2 + - - +
537D GLY* 3.6 5.4 - - - +
539D ALA* 1.3 72.7 - - - +
541D LYS* 1.3 60.3 + - - +
542D ASP 3.1 0.9 - - - -
543D ALA* 3.1 4.6 + - - +
544D CYS* 2.8 30.8 + - - +
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Residues in contact with LYS 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D VAL* 3.9 6.7 - - + -
503D VAL* 3.9 23.8 - - + -
537D GLY 3.1 17.0 + - - +
538D MET* 3.6 23.1 + - - +
540D VAL* 1.3 75.9 - - - +
542D ASP* 1.3 54.1 + - - +
544D CYS* 3.7 1.1 - - - +
545D GLU* 2.8 68.6 + - - +
722D ILE* 3.6 23.3 - - + -
723D PHE* 4.5 13.2 - - + +
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Residues in contact with ASP 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D MET 2.8 15.0 + - - +
539D ALA* 3.2 12.3 - - - +
541D LYS* 1.3 74.9 - - - +
543D ALA* 1.3 66.2 + - - +
545D GLU* 3.5 11.9 + - - +
546D THR* 3.2 28.7 + - - -
599D THR 4.7 0.4 - - - +
600D GLY* 3.3 4.9 - - - -
601D PHE* 2.9 34.1 + - - +
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Residues in contact with ALA 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ALA* 4.5 3.1 - - + +
471D VAL* 3.6 25.6 - - + -
539D ALA 3.0 11.1 + - - +
540D VAL* 3.6 4.5 - - - +
542D ASP* 1.3 73.3 - - - +
544D CYS* 1.3 59.2 + - - +
546D THR* 2.9 20.5 + - - -
547D LEU* 3.0 12.2 + - - +
598D ALA* 3.7 13.5 - - - +
599D THR 3.4 31.4 - - - +
600D GLY* 3.8 3.3 - - - +
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Residues in contact with CYS 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D VAL* 4.3 14.6 - - - -
500D ALA* 3.7 37.9 - - - -
503D VAL* 3.4 24.2 - - + -
504D LEU* 3.8 18.5 - - + +
540D VAL* 2.8 25.4 + - - +
541D LYS* 3.7 1.1 - - - +
543D ALA* 1.3 74.8 - - - +
545D GLU* 1.3 56.0 + - - +
547D LEU* 3.2 8.7 + - - +
548D ARG* 2.8 30.0 + - - +
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Residues in contact with GLU 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D VAL* 3.7 17.4 - - + +
541D LYS* 2.8 64.7 + - - +
542D ASP* 3.9 10.9 - - - +
544D CYS* 1.3 70.3 - - - +
546D THR* 1.3 66.1 + - - +
548D ARG* 3.8 21.5 + - - +
549D GLY* 2.9 20.4 + - - -
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Residues in contact with THR 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D ASP* 3.2 17.5 + - - -
543D ALA* 2.9 12.5 + - - -
545D GLU* 1.3 76.4 - - - +
547D LEU* 1.3 63.6 + - - +
549D GLY* 3.1 3.5 + - - -
550D ARG* 3.1 52.9 + - + +
598D ALA* 3.8 10.5 - - + -
599D THR 4.8 3.5 + - - +
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Residues in contact with LEU 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D VAL* 3.7 42.6 - - + +
473D ILE* 3.9 30.5 - - + -
504D LEU* 4.5 3.6 - - + -
543D ALA 3.0 7.9 + - - +
544D CYS* 3.2 8.9 + - - +
546D THR* 1.3 76.4 - - - +
548D ARG* 1.3 64.0 + - - +
550D ARG* 2.9 44.2 + - - +
551D LEU* 3.0 17.7 + - + +
595D SER 4.2 1.8 - - - +
596D LEU* 3.5 26.7 - - + +
597D SER 3.6 1.8 - - - +
598D ALA* 3.7 15.5 - - + -
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Residues in contact with ARG 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D ALA 5.1 0.8 + - - -
503D VAL* 2.9 42.9 + - - +
504D LEU* 4.2 15.4 - - + +
544D CYS 2.8 19.7 + - - +
545D GLU* 3.9 27.7 + - - +
547D LEU* 1.3 71.7 - - - +
549D GLY* 1.3 58.2 + - - +
551D LEU* 3.6 9.1 + - - +
552D ALA* 2.9 30.2 + - - +
566D VAL 5.8 0.4 - - - -
568D PHE* 3.6 36.7 - - + +
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Residues in contact with GLY 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D GLU 2.9 15.7 + - - -
546D THR 3.5 5.4 - - - -
547D LEU 3.0 0.6 + - - -
548D ARG* 1.3 76.0 - - - +
550D ARG* 1.3 66.4 + - - +
552D ALA* 3.4 4.9 + - - +
553D GLY* 3.0 21.1 + - - -
563D ALA* 5.6 0.7 - - - +
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Residues in contact with ARG 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B THR* 4.3 7.3 + - - -
546D THR* 3.1 37.6 + - + +
547D LEU* 2.9 19.7 + - - +
549D GLY* 1.3 75.5 - - - +
551D LEU* 1.3 65.4 + - + +
552D ALA 3.1 0.3 + - - -
553D GLY* 3.2 1.1 + - - -
554D PHE* 2.9 23.9 + - - +
594D ILE* 3.7 21.7 - - + +
595D SER* 2.9 44.9 + - - +
596D LEU* 6.3 0.4 - - + -
597D SER 2.9 28.9 + - - -
598D ALA* 3.9 4.8 - - - +
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Residues in contact with LEU 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D ILE* 4.3 12.6 - - + -
504D LEU* 5.1 1.1 - - + -
547D LEU 3.0 17.9 + - - +
548D ARG* 3.8 7.2 - - - +
550D ARG* 1.3 78.2 - - + +
552D ALA* 1.3 56.2 + - - +
554D PHE* 3.4 7.6 - - - +
555D VAL* 3.1 31.4 + - - +
568D PHE* 3.7 19.1 - - + -
582D PHE* 4.0 32.8 - - + -
585D ILE* 3.7 25.4 - - + -
586D VAL* 4.2 16.4 - - + -
589D ALA* 3.8 24.9 - - + -
594D ILE* 5.5 0.7 - - + -
596D LEU* 4.5 9.4 - - + -
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Residues in contact with ALA 552 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ARG* 2.9 21.4 + - + +
549D GLY* 3.9 5.6 - - - +
550D ARG 3.2 0.2 - - - -
551D LEU* 1.3 72.5 - - - +
553D GLY* 1.3 56.8 + - - +
554D PHE 3.1 1.3 - - - -
555D VAL 3.1 1.4 + - - -
556D ALA* 2.7 36.4 + - - +
563D ALA* 3.7 27.8 - - + +
566D VAL* 3.6 10.7 - - + +
568D PHE* 3.9 18.1 - - + -
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Residues in contact with GLY 553 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D GLY 3.0 14.6 + - - -
550D ARG 3.7 2.9 - - - -
552D ALA* 1.3 75.7 - - - +
554D PHE* 1.3 63.7 + - - +
556D ALA* 3.6 6.5 - - - +
557D ALA* 2.9 26.5 + - - +
563D ALA* 4.2 9.5 - - - +
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Residues in contact with PHE 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D ARG 2.9 11.5 + - - +
551D LEU* 3.4 14.1 - - - +
553D GLY* 1.3 79.0 - - - +
555D VAL* 1.3 73.6 + - + +
557D ALA* 3.2 5.1 + - + +
558D ARG* 3.0 44.8 + - + +
585D ILE* 3.9 15.0 - - + -
588D ALA* 3.5 32.3 - - + -
589D ALA* 3.6 23.8 - - + -
592D ALA* 3.4 19.7 - - + -
594D ILE* 3.4 33.4 - - + +
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Residues in contact with VAL 555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D LEU 3.1 14.1 + - - +
552D ALA 3.1 5.8 + - - +
554D PHE* 1.3 82.2 - - + +
556D ALA* 1.3 56.0 + - - +
558D ARG* 4.6 6.7 - - - +
559D GLU* 2.7 46.5 + - + +
566D VAL* 3.7 31.2 - - + -
568D PHE* 5.4 0.2 - - + -
573D VAL* 4.6 1.6 - - + -
575D ALA* 3.9 17.0 - - + -
580D TRP* 4.3 6.5 - - + -
585D ILE* 3.7 38.1 - - + -
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Residues in contact with ALA 556 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ALA 2.7 20.5 + - - +
553D GLY* 3.6 4.7 - - - +
555D VAL* 1.3 74.2 - - - +
557D ALA* 1.3 51.8 + - - +
559D GLU* 5.1 0.2 - - - -
560D GLY* 2.6 29.6 + - - -
561D CYS* 2.8 41.3 + - - +
562D ALA 3.6 18.2 - - - +
563D ALA* 3.7 8.5 - - + +
566D VAL* 4.1 0.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D GLY 2.9 17.1 + - - +
554D PHE* 3.5 5.4 - - + +
556D ALA* 1.3 75.5 - - - +
558D ARG* 1.3 64.5 + - - +
560D GLY* 3.3 11.1 + - - -
----------------------------------------------------------
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Residues in contact with ARG 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D PHE* 3.0 39.9 + - + +
555D VAL* 3.9 4.9 - - - +
557D ALA* 1.3 77.7 - - + +
559D GLU* 1.3 90.6 + - - +
560D GLY 3.2 1.1 + - - -
578D LYS* 5.1 0.4 - - - +
580D TRP* 3.3 33.5 - - - +
584D GLU 5.2 0.6 + - - -
585D ILE* 4.3 14.2 - - - +
588D ALA* 3.6 26.9 - - - +
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Residues in contact with GLU 559 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D VAL* 2.7 29.2 + - + +
556D ALA* 3.4 1.6 - - - +
558D ARG* 1.3 101.2 + - - +
560D GLY* 1.3 68.9 + - - +
561D CYS* 5.4 1.1 - - - -
575D ALA* 5.0 3.6 - - + -
576D SER* 3.7 24.7 + - - +
578D LYS* 2.6 45.9 + - - +
580D TRP* 3.5 22.6 - - + -
----------------------------------------------------------
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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