Contacts of the helix formed by residues 535 - 558 (chain A) in PDB entry 2O2C
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 THR 535 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP* 4.0 15.7 + - - +
97A ASN* 3.1 17.5 + - - -
219A LEU* 3.8 5.7 - - - +
222A PHE* 3.9 14.1 - - + -
348A GLU* 6.0 0.2 - - - -
466A GLN* 4.8 2.0 - - - +
533A SER* 3.1 24.5 + - - +
534A LEU* 1.3 76.3 - - - +
536A PRO* 1.4 76.2 - - + +
537A ARG* 3.7 8.1 + - - +
538A ALA* 3.0 19.6 + - - +
539A LEU* 3.0 9.5 + - - +
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Residues in contact with PRO 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 3.7 28.9 - - + -
222A PHE* 3.9 30.1 - - + -
341A ILE* 4.7 0.2 - - + -
345A ASN* 3.3 46.4 - - + +
348A GLU* 3.9 7.6 - - + -
349A LEU* 3.4 17.1 - - - +
535A THR* 1.4 85.3 - - - +
537A ARG* 1.3 61.4 + - - +
539A LEU 3.3 1.0 + - - -
540A GLY 3.1 18.4 + - - -
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Residues in contact with ARG 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 2.8 48.1 + - + -
92A GLY* 3.6 15.6 + - - -
93A SER* 3.7 27.1 - - - +
97A ASN* 5.6 0.4 - - - +
348A GLU* 2.9 60.2 + - - +
351A THR* 3.7 28.0 - - - +
352A GLY* 3.3 26.7 - - - +
355A VAL* 4.4 1.8 - - - +
535A THR* 3.1 8.4 + - - +
536A PRO* 1.3 78.2 - - - +
538A ALA* 1.3 62.1 + - - +
540A GLY 3.4 0.3 + - - -
541A ALA* 3.1 20.1 + - - +
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.8 14.1 - - + +
97A ASN* 3.7 7.9 - - - +
531A ILE* 4.0 17.8 - - + +
533A SER 3.3 26.7 - - - +
534A LEU* 4.1 0.7 - - - -
535A THR* 3.0 18.6 + - - +
537A ARG* 1.3 74.3 - - - +
539A LEU* 1.3 65.1 + - - +
541A ALA* 3.3 4.0 + - - +
542A ILE* 3.1 28.9 + - - +
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Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 3.9 16.2 - - + -
215A ALA* 4.0 17.0 - - + -
218A ALA* 3.9 17.0 - - + -
219A LEU* 3.8 29.6 - - + -
329A MET* 4.9 0.4 - - + -
349A LEU* 4.0 10.3 - - + -
398A LEU* 3.8 29.4 - - + -
401A LEU* 5.2 0.4 - - + -
534A LEU* 4.1 10.0 - - + +
535A THR 3.0 12.2 + - - +
536A PRO 3.7 7.6 - - - +
538A ALA* 1.3 76.0 - - - +
540A GLY* 1.3 63.8 + - - +
542A ILE* 3.2 9.2 + - + +
543A ILE* 3.0 40.3 + - + +
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Residues in contact with GLY 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TRP* 3.6 11.4 - - - -
349A LEU* 3.4 32.4 - - - +
353A ALA* 3.5 10.6 - - - -
536A PRO 3.1 11.5 + - - -
537A ARG 3.4 2.2 + - - -
538A ALA 3.3 0.2 - - - -
539A LEU* 1.3 75.0 - - - +
541A ALA* 1.3 61.6 + - - +
543A ILE 3.6 0.3 + - - -
544A ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.6 28.9 - - + -
99A LEU* 4.2 10.1 - - + -
352A GLY 3.5 12.0 - - - +
356A ILE* 3.6 18.4 - - + +
531A ILE* 6.5 0.2 - - + -
537A ARG 3.1 13.4 + - - +
538A ALA* 3.4 10.3 - - - +
539A LEU 3.2 0.2 - - - -
540A GLY* 1.3 77.7 - - - +
542A ILE* 1.3 56.7 + - + +
545A MET* 3.0 29.6 + - - +
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.1 20.2 - - + -
398A LEU* 5.0 4.3 - - + -
401A LEU* 4.5 17.5 - - + -
460A ILE* 4.2 22.9 - - + -
529A LEU* 6.2 0.7 - - + -
531A ILE* 4.0 27.6 - - + -
534A LEU* 4.2 12.6 - - + -
538A ALA 3.1 15.7 + - - +
539A LEU* 3.2 10.3 + - + +
541A ALA* 1.3 73.7 - - - +
543A ILE* 1.3 69.8 + - + +
545A MET* 3.3 11.9 + - + +
546A TYR* 3.2 44.1 + - + -
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Residues in contact with ILE 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A MET* 3.8 24.0 - - + -
329A MET* 4.1 5.4 - - + -
330A TRP* 3.6 25.6 - - + -
401A LEU* 3.5 32.3 - - + -
404A TYR* 3.6 31.4 - - + +
405A LEU* 4.9 3.1 - - + -
408A LEU* 5.0 1.8 - - + -
539A LEU* 3.0 26.2 + - + +
542A ILE* 1.3 75.7 - - + +
544A ALA* 1.3 61.3 + - - +
546A TYR* 3.2 7.5 + - + +
547A GLU* 2.9 38.0 + - + +
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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
----------------------------------------------------------
152A ARG* 3.8 13.7 - - - +
330A TRP* 4.4 0.8 - - - -
353A ALA* 3.8 28.0 - - + +
356A ILE* 4.1 7.0 - - + -
357A ASP* 4.0 3.1 - - - +
540A GLY 3.1 19.4 + - - +
541A ALA 3.9 3.1 - - - +
543A ILE* 1.3 76.0 - - - +
545A MET* 1.3 57.2 + - - +
547A GLU* 3.2 12.4 + - - +
548A HIS* 3.0 37.0 + - - -
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Residues in contact with MET 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.9 14.6 - - + -
356A ILE* 3.8 10.9 - - + +
369A VAL* 3.6 28.7 - - + -
370A PRO* 3.7 15.9 - - + +
373A LEU* 3.9 20.6 - - + -
529A LEU* 3.3 35.9 - - + -
541A ALA 3.0 14.7 + - - +
542A ILE* 3.4 14.6 - - + +
544A ALA* 1.3 75.2 - - - +
546A TYR* 1.3 90.3 + - + +
548A HIS 3.3 1.0 + - - -
549A LYS* 2.9 26.5 + - - +
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Residues in contact with TYR 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 4.2 10.5 - - + -
391A ILE* 3.7 12.1 - - + +
405A LEU* 3.8 45.1 - - + -
408A LEU* 4.0 4.7 - - + -
458A ASP* 2.7 41.3 + - - +
460A ILE* 3.6 19.2 - - + +
529A LEU* 3.5 8.9 - - + +
542A ILE* 3.2 27.0 + - + -
543A ILE* 3.2 8.3 + - - +
545A MET* 1.3 96.9 - - + +
547A GLU* 1.3 64.4 + - - +
549A LYS* 3.3 23.0 + - + +
550A VAL* 3.1 31.0 + - + +
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Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A HIS* 3.5 6.4 + - - +
152A ARG* 2.8 34.2 + - - -
326A ARG 4.6 0.2 - - - +
327A TYR* 3.7 44.0 + - + -
330A TRP* 2.9 31.4 + - - -
404A TYR* 4.4 2.9 + - - -
408A LEU* 3.9 17.9 - - + +
543A ILE* 2.9 23.5 + - + +
544A ALA* 3.5 7.3 - - - +
546A TYR* 1.3 75.3 - - - +
548A HIS* 1.3 63.7 + - - +
550A VAL* 3.5 4.9 + - - +
551A LEU* 3.1 23.7 + - - +
562A TYR* 5.0 0.3 + - - -
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Residues in contact with HIS 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 4.0 11.6 - + - -
148A HIS* 4.6 7.3 + - - -
149A ILE* 3.8 14.6 - - + -
152A ARG* 3.8 13.0 + - - -
356A ILE* 4.2 9.2 - - + -
357A ASP* 2.7 33.6 + - - -
360A PHE* 3.5 38.2 - + + -
370A PRO* 3.6 20.2 - - + -
544A ALA 3.0 21.8 + - - +
547A GLU* 1.3 78.7 - - - +
549A LYS* 1.3 62.4 + - - +
551A LEU* 3.3 13.5 + - + +
552A VAL* 3.1 28.4 + - - +
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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
----------------------------------------------------------
370A PRO* 3.8 15.5 - - - +
373A LEU* 3.9 32.2 + - + +
374A ALA* 3.5 22.5 - - - +
377A GLY* 5.1 2.4 - - - -
389A HIS* 3.6 36.8 + - - -
409A ASP* 4.5 13.4 + - - +
458A ASP* 4.5 4.2 + - - -
545A MET 2.9 17.9 + - - +
546A TYR* 3.3 21.4 + - + +
548A HIS* 1.3 75.1 - - - +
550A VAL* 1.3 59.1 + - + +
552A VAL 3.3 1.6 + - - -
553A GLN* 3.0 55.0 + - - +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 3.7 13.5 - - - +
408A LEU* 4.0 10.1 - - + +
409A ASP* 4.0 33.9 - - + +
412A SER* 3.5 26.9 - - - +
413A ASN* 3.1 25.1 + - - +
546A TYR* 3.1 18.9 + - + +
547A GLU* 3.6 6.1 - - - +
549A LYS* 1.3 77.7 - - + +
551A LEU* 1.3 63.4 + - - +
553A GLN* 4.7 3.1 - - - +
554A GLY* 3.0 20.1 + - - -
561A SER* 3.8 4.1 + - - -
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 5.4 1.1 - - + -
128A PHE* 3.7 29.8 - - + -
129A VAL* 3.9 20.9 - - + -
132A VAL* 4.1 25.1 - - + -
133A PHE* 5.1 2.7 - - + -
148A HIS* 5.6 3.8 - - - +
360A PHE* 4.1 19.7 - - + -
547A GLU 3.1 12.1 + - - +
548A HIS* 3.4 20.4 - - + +
549A LYS 3.3 0.4 - - - -
550A VAL* 1.3 77.5 - - - +
552A VAL* 1.3 62.6 + - + +
554A GLY* 3.8 0.7 - - - -
555A ALA* 3.0 29.3 + - + +
561A SER* 4.7 2.0 + - - -
562A TYR* 3.3 27.8 - - - +
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Residues in contact with VAL 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.1 18.6 - - + -
360A PHE* 3.5 28.0 - - + -
371A LEU* 3.8 28.5 - - + +
374A ALA* 3.6 22.9 - - + -
375A LEU* 5.3 0.7 - - + -
548A HIS 3.1 15.2 + - - +
549A LYS 3.3 0.4 + - - +
551A LEU* 1.3 79.1 - - + +
553A GLN* 1.3 56.5 + - - +
555A ALA* 3.2 6.1 + - - +
556A ILE* 2.9 45.3 + - + +
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Residues in contact with GLN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ALA* 3.1 31.4 + - + +
377A GLY* 3.5 23.6 - - - -
378A VAL* 4.1 6.5 - - + -
381A ILE* 4.2 8.1 - - - +
409A ASP* 4.4 11.3 - - - +
413A ASN* 3.9 9.5 + - - +
430A PRO* 4.9 1.4 - - - +
549A LYS* 3.0 44.7 + - - +
550A VAL* 5.0 1.4 - - - -
552A VAL* 1.3 74.1 - - - +
554A GLY* 1.3 62.9 + - - +
556A ILE* 3.3 8.8 + - - +
557A TRP* 3.1 58.6 + - + -
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Residues in contact with GLY 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASN* 3.7 9.1 - - - +
419A ARG* 4.8 0.2 - - - -
550A VAL 3.0 11.1 + - - -
551A LEU 3.8 0.2 - - - -
553A GLN* 1.3 76.4 - - - +
555A ALA* 1.3 57.3 + - - +
557A TRP 3.5 0.5 + - - -
558A GLY 2.9 22.2 + - - -
559A ILE* 3.0 27.9 + - - +
561A SER* 3.3 24.0 - - - -
----------------------------------------------------------
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Residues in contact with ALA 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 3.8 12.4 + - - +
125A ILE* 3.6 24.9 - - + +
128A PHE* 3.7 29.1 - - + -
419A ARG* 3.7 15.5 + - - +
551A LEU 3.0 17.8 + - - +
552A VAL* 3.6 1.6 - - - +
554A GLY* 1.3 75.0 - - - +
556A ILE* 1.3 65.2 + - - +
558A GLY* 3.3 10.9 + - - -
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Residues in contact with ILE 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.6 17.2 - - + +
56A TRP* 4.4 3.4 - - + -
119A LEU* 4.0 25.6 - - + -
120A ALA* 5.4 1.8 - - - -
123A ARG* 2.9 37.6 + - + +
125A ILE* 4.0 15.5 - - + -
374A ALA 5.3 0.9 - - - +
375A LEU* 3.7 30.1 - - + -
378A VAL* 3.9 25.4 - - + -
552A VAL* 2.9 33.4 + - + +
553A GLN* 3.3 5.6 + - - +
555A ALA* 1.3 76.0 - - - +
557A TRP* 1.3 63.6 + - + +
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Residues in contact with TRP 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 4.4 4.7 - - - +
50A LEU* 4.0 16.5 - - + +
56A TRP* 5.0 0.2 - + - -
123A ARG* 3.9 3.5 + - - -
378A VAL* 4.3 15.4 - - + +
381A ILE* 3.8 25.4 - - + -
382A ASN* 2.7 31.0 + - - -
413A ASN* 3.9 13.7 - - + -
418A THR* 4.1 12.6 - - - +
424A VAL* 4.6 3.6 - - - +
426A THR* 3.6 18.9 + - - +
427A LEU 3.5 7.8 + - - -
428A THR* 3.5 42.8 - - + -
429A GLY* 3.5 16.4 - - - -
430A PRO* 5.2 0.2 - - + -
553A GLN* 3.1 45.6 + - + +
554A GLY 4.0 3.1 - - - +
556A ILE* 1.3 80.7 - - + +
558A GLY* 1.3 61.6 + - - +
559A ILE* 3.3 17.8 + - + +
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Residues in contact with GLY 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 3.6 14.8 - - - -
418A THR* 3.4 9.3 - - - -
419A ARG* 3.0 41.3 + - - +
554A GLY 2.9 7.0 + - - -
555A ALA 3.3 5.3 + - - -
556A ILE 3.2 4.0 - - - -
557A TRP* 1.3 78.7 - - - +
559A ILE* 1.3 62.4 + - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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