Contacts of the helix formed by residues 522 - 546 (chain A) in PDB entry 5VOT
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 ALA 522 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU 4.7 6.3 + - - -
519A ASP 4.7 2.1 + - - -
521A LEU* 1.3 80.6 - - - +
523A TYR* 1.3 61.6 + - - +
524A GLU* 3.1 30.5 - - - +
525A ILE* 3.5 18.4 - - + +
526A TRP* 2.8 27.1 + - - -
788B SER 4.6 0.2 - - - +
789B LEU* 4.9 4.9 - - + -
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Residues in contact with TYR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 6.1 5.6 - - + -
522A ALA* 1.3 71.3 - - - +
524A GLU* 1.3 91.8 + - + +
525A ILE 3.1 1.6 - - - -
526A TRP* 2.8 28.0 + - - +
527A MET* 2.9 42.1 + - + +
174F TYR* 5.2 7.0 + + - -
175F SER* 5.3 3.6 - - - -
176F TYR* 3.3 28.3 + + - -
181F TYR* 4.1 11.4 + - - -
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Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ALA* 3.1 23.4 - - + +
523A TYR* 1.3 96.4 + - + +
525A ILE* 1.3 67.7 - - + +
527A MET* 3.1 24.6 + - + +
528A CYS* 2.9 28.2 + - - -
789B LEU* 5.3 6.2 - - - +
157F ILE* 4.5 18.6 - - + -
174F TYR* 5.3 7.3 + - - -
176F TYR* 3.7 30.4 + - + +
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Residues in contact with ILE 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 3.7 23.1 - - + -
522A ALA* 3.5 25.3 + - + +
523A TYR 3.1 0.4 - - - -
524A GLU* 1.3 81.0 - - + +
526A TRP* 1.3 63.6 + - + +
528A CYS* 3.0 10.8 + - + +
529A ILE* 2.9 42.3 + - + +
612A ILE* 4.8 6.3 - - + -
788B SER 3.1 28.9 - - - +
789B LEU* 3.2 24.0 - - - +
792B VAL* 5.5 12.1 - - + -
796B PHE* 5.9 4.5 - - + -
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Residues in contact with TRP 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 5.4 2.7 - + - -
518A LEU* 3.3 48.5 + - + +
520A PRO* 6.1 0.4 - - - +
521A LEU* 4.8 15.8 - - + +
522A ALA 2.8 28.7 + - - -
523A TYR* 2.8 15.0 + - - +
525A ILE* 1.3 73.9 - - + +
527A MET* 1.3 59.6 + - + +
529A ILE* 2.9 30.1 + - + +
530A VAL* 2.9 34.3 + - + +
584A PHE* 4.5 22.2 - + - -
613A ILE* 5.9 4.0 - - + -
616A TYR* 4.4 27.4 - + + -
607D PHE* 5.1 16.6 - + - -
610D LEU* 6.2 3.6 - - + -
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Residues in contact with MET 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A TYR* 2.9 47.4 + - + +
524A GLU* 3.1 18.3 + - + +
526A TRP* 1.3 75.6 - - + +
528A CYS* 1.3 58.8 + - - +
530A VAL* 3.2 10.7 + - - +
531A PHE* 2.9 50.2 + - + -
157F ILE* 6.4 0.2 - - + -
176F TYR* 5.3 1.8 - - + -
180F PHE* 5.1 7.9 - - + -
181F TYR* 4.3 27.6 - - + +
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Residues in contact with CYS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A GLU* 2.9 19.1 + - - -
525A ILE* 3.4 9.4 - - - +
527A MET* 1.3 75.9 - - - +
529A ILE* 1.3 58.0 + - - +
531A PHE* 3.0 21.2 + - + +
532A ALA* 2.9 30.5 + - - +
796B PHE* 3.9 25.3 - - + -
150F ILE* 5.4 0.5 - - - +
153F ILE* 5.3 1.1 - - - -
154F ILE* 4.7 20.5 - - + +
157F ILE* 4.2 24.0 - - - -
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Residues in contact with ILE 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU* 5.2 2.0 - - + -
525A ILE* 2.9 36.0 + - + +
526A TRP* 2.9 38.8 + - + +
528A CYS* 1.3 75.0 - - - +
530A VAL* 1.3 58.9 + - + +
532A ALA* 3.6 5.2 + - - +
533A TYR* 2.9 32.1 + - + +
584A PHE* 4.0 29.2 - - + -
605A TRP* 5.0 1.8 - - + -
608A PHE* 4.5 20.4 - - + -
612A ILE* 4.2 19.5 - - + -
796B PHE* 4.8 6.3 - - + -
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A TRP* 2.9 22.5 + - + +
527A MET* 3.4 10.8 - - + +
529A ILE* 1.3 77.1 - - + +
531A PHE* 1.3 70.4 + - + +
533A TYR* 3.1 11.4 + - + +
534A ILE* 2.9 38.5 + - + +
188F ILE* 6.1 3.6 - - + -
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Residues in contact with PHE 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A MET* 2.9 41.2 + - + -
528A CYS* 3.0 24.4 + - - +
530A VAL* 1.3 82.7 - - + +
532A ALA* 1.3 64.1 + - - +
534A ILE* 3.2 10.8 - - + +
535A GLY* 2.9 21.0 + - - -
150F ILE* 3.6 42.8 - - + +
153F ILE* 4.7 17.5 - - + -
154F ILE* 6.1 0.2 - - + -
157F ILE* 6.0 0.7 - - + -
180F PHE* 5.8 3.6 - + - -
184F ALA* 3.5 31.9 - - + -
187F PHE* 6.5 0.4 - - + -
188F ILE* 4.2 25.1 - - + -
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Residues in contact with ALA 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A CYS 2.9 16.2 + - - +
529A ILE* 4.2 4.9 - - - +
531A PHE* 1.3 73.8 - - - +
533A TYR* 1.3 56.9 + - - +
535A GLY* 4.5 1.3 - - - +
536A VAL* 2.9 40.6 + - + +
605A TRP* 4.5 14.6 - - + -
608A PHE* 5.5 2.2 - - + -
796B PHE* 5.1 10.8 - - + -
800B VAL* 4.9 23.1 - - + -
803B LEU* 5.7 0.2 - - + -
150F ILE* 4.8 4.6 - - + +
154F ILE* 6.4 1.6 - - + -
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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
----------------------------------------------------------
529A ILE* 2.9 22.4 + - + +
530A VAL* 3.1 13.5 - - + +
531A PHE 3.0 0.4 - - - -
532A ALA* 1.3 77.4 - - - +
534A ILE* 1.3 76.8 + - + +
536A VAL* 3.9 1.4 - - - +
537A SER* 3.0 26.0 + - - -
577A LEU* 3.4 33.9 + - + +
580A SER* 3.1 26.8 + - - -
581A LEU* 3.2 47.1 + - + +
584A PHE* 5.0 7.6 - + + -
605A TRP* 4.3 18.3 - + + -
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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
----------------------------------------------------------
530A VAL* 2.9 24.2 + - + +
531A PHE* 3.2 18.4 - - + +
533A TYR* 1.3 87.6 - - + +
535A GLY* 1.3 77.5 + - - +
537A SER* 3.4 7.0 + - - -
538A VAL* 2.9 32.5 + - + +
577A LEU* 5.3 4.0 - - + -
150F ILE* 4.2 9.9 - - + -
188F ILE* 5.1 18.4 - - + -
191F GLU* 3.9 29.4 - - + -
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Residues in contact with GLY 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE 2.9 16.5 + - - -
532A ALA* 3.9 1.8 - - - -
534A ILE* 1.3 82.4 - - - +
536A VAL* 1.3 63.9 + - - +
538A VAL* 3.1 7.1 + - - +
539A VAL* 2.9 29.7 + - - +
147F LEU* 4.5 17.9 - - - -
150F ILE* 5.4 1.3 - - - -
191F GLU* 4.8 7.4 - - - -
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ALA* 2.9 26.5 + - + +
533A TYR* 3.9 2.2 - - - +
535A GLY* 1.3 70.2 - - - +
537A SER* 1.3 65.9 + - - +
539A VAL* 3.3 6.6 + - - +
540A LEU* 2.9 41.3 + - + +
580A SER* 5.1 4.0 - - - +
601A VAL* 4.2 13.9 - - + -
605A TRP* 4.0 39.5 - - + -
803B LEU* 3.6 33.4 - - + -
147F LEU* 5.4 0.4 - - - +
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Residues in contact with SER 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A TYR 3.0 19.0 + - - -
534A ILE* 3.6 5.4 - - - -
536A VAL* 1.3 80.0 - - - +
538A VAL* 1.3 65.0 + - - +
540A LEU* 3.2 9.7 + - - +
541A PHE* 3.0 20.8 + - - +
573A ILE* 4.9 5.2 - - - -
576A SER* 4.6 5.6 - - - -
577A LEU* 3.3 35.0 - - - +
580A SER* 3.2 24.4 + - - -
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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
----------------------------------------------------------
534A ILE* 2.9 25.9 + - + +
535A GLY 3.6 3.6 - - - +
537A SER* 1.3 75.0 - - - +
539A VAL* 1.3 65.6 + - - +
541A PHE* 2.8 22.8 + - + +
542A LEU* 2.9 13.2 + - + +
573A ILE* 4.5 6.7 - - + -
143F VAL* 3.9 30.3 - - + -
191F GLU* 4.3 19.3 - - + +
192F MET* 6.2 1.6 - - - -
195F VAL* 3.9 32.5 - - + +
198F VAL* 6.2 2.7 - - + -
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLY* 2.9 19.6 + - - +
536A VAL* 3.8 6.1 - - - +
538A VAL* 1.3 74.6 - - - +
540A LEU* 1.3 62.8 + - + +
542A LEU* 2.9 15.7 + - + +
543A VAL* 2.9 24.7 + - + +
601A VAL* 5.2 11.7 - - + -
803B LEU* 5.2 10.3 - - + +
804B GLY* 5.5 2.5 - - - -
807B MET* 4.2 24.5 - - + -
143F VAL* 4.4 15.3 - - + -
147F LEU* 4.0 28.3 - - + -
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL* 2.9 34.0 + - + +
537A SER* 3.4 11.0 - - - +
539A VAL* 1.3 76.1 - - - +
541A PHE* 1.3 64.7 + - - +
543A VAL* 2.9 20.1 + - + +
544A SER* 2.9 11.3 + - - -
570A GLU* 5.6 2.6 - - + +
576A SER* 5.0 12.6 - - - +
579A PHE* 4.6 24.2 - - + -
580A SER* 5.6 3.6 - - - -
593A PRO* 5.8 4.9 - - + -
598A GLY* 4.0 23.1 - - - +
601A VAL* 3.6 34.5 - - + -
602A GLY* 4.3 5.4 - - - +
605A TRP* 6.1 1.8 - - + -
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Residues in contact with PHE 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A SER 3.0 7.4 + - - +
538A VAL* 2.8 15.0 + - + +
540A LEU* 1.3 71.6 - - - +
542A LEU* 1.3 59.7 + - - +
544A SER* 2.8 19.0 + - - +
545A ARG* 2.9 32.5 + - + +
570A GLU 3.8 8.1 - - - -
571A PHE 3.4 19.1 - - - -
572A GLY* 3.3 9.9 - - - -
573A ILE* 3.1 63.5 - - + -
576A SER* 4.3 7.1 + - - +
195F VAL* 5.1 9.6 - - + -
198F VAL* 4.3 23.8 - - + -
199F HIS* 5.0 21.3 - + + -
202F ILE* 5.9 0.9 - - + -
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Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 2.9 12.2 + - + +
539A VAL* 3.2 17.7 - - + +
541A PHE* 1.3 78.9 - - - +
543A VAL* 1.3 63.7 + - + +
544A SER 3.3 0.7 + - - -
545A ARG* 4.6 2.7 - - + +
546A PHE* 3.3 40.8 + - + +
807B MET* 5.8 2.5 - - + -
811B LEU* 4.4 22.9 - - + +
136F LEU* 5.5 4.0 - - + -
140F ILE* 4.1 32.1 - - + -
143F VAL* 5.9 7.9 - - + -
198F VAL* 3.8 34.1 - - + -
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A VAL* 2.9 23.8 + - + +
540A LEU* 2.9 21.4 + - + +
542A LEU* 1.3 76.8 - - + +
544A SER* 1.3 63.8 + - - +
546A PHE* 4.6 3.8 - - - +
547A SER* 5.0 1.7 + - - -
595A SER* 3.2 21.0 + - - +
597A SER* 3.0 36.6 - - - +
598A GLY* 3.6 11.4 - - - +
601A VAL* 5.0 4.5 - - + -
807B MET* 5.3 9.0 - - + -
811B LEU* 6.2 2.5 - - + -
814B PHE* 4.7 17.2 - - + -
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Residues in contact with SER 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LEU 2.9 7.8 + - - -
541A PHE* 2.8 13.3 + - - -
543A VAL* 1.3 81.4 - - - +
545A ARG* 1.3 63.7 + - - -
546A PHE 3.3 6.8 - - - +
547A SER* 4.9 0.3 + - - -
568A THR* 3.8 13.3 + - - +
570A GLU* 2.8 48.1 + - - +
571A PHE* 3.3 12.5 + - - -
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Residues in contact with ARG 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PHE* 2.9 41.0 + - + +
542A LEU* 4.9 3.1 - - + +
544A SER* 1.3 71.0 - - - +
546A PHE* 1.3 68.5 + - - +
547A SER 4.7 1.6 - - - -
548A PRO* 4.8 4.0 - - - +
571A PHE* 5.3 15.7 - - + +
198F VAL* 5.5 4.3 - - + +
202F ILE* 3.4 36.6 - - + +
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Residues in contact with PHE 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 3.3 31.0 + - + +
543A VAL* 4.6 2.4 + - - +
544A SER 3.3 8.7 - - - +
545A ARG* 1.3 85.1 - - - +
547A SER* 1.3 98.3 + - - +
548A PRO* 4.2 2.2 - - + -
811B LEU* 4.4 17.0 - - + -
814B PHE* 3.4 41.1 - + + -
815B CYS* 4.7 11.7 - - + -
136F LEU* 3.5 46.4 - - + -
140F ILE* 5.6 7.6 - - + -
202F ILE* 4.5 4.9 - - - +
205F HIS* 5.3 4.0 - + - -
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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