Contacts of the helix formed by residues 405 - 436 (chain A) in PDB entry 2BG9
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 VAL 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 5.8 0.9 - - + -
301A ARG* 3.3 33.9 - - - +
402A VAL* 5.0 6.2 - - + -
404A MET* 1.3 93.3 - - + +
406A ILE* 1.3 60.4 + - + +
407A ASP 2.8 5.8 - - - -
408A HIS* 2.7 40.5 + - + +
409A ILE* 2.8 22.8 + - + +
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Residues in contact with ILE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 4.3 2.3 - - - +
236A PRO* 3.9 18.8 - - + +
237A THR* 3.4 40.9 - - - +
298A THR* 5.0 0.2 - - + -
299A HIS* 6.0 2.5 - - - -
301A ARG* 3.0 47.3 - - - +
402A VAL 3.3 23.1 - - - +
403A ALA* 4.2 2.8 + - - +
404A MET 3.5 0.8 - - - -
405A VAL* 1.3 78.0 - - - +
407A ASP* 1.3 62.5 + - - +
409A ILE* 3.1 24.7 - - + +
410A LEU* 3.2 20.4 + - - +
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Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR* 2.2 36.6 + - - +
403A ALA 3.2 13.5 - - - +
404A MET* 3.4 11.7 - - - +
406A ILE* 1.3 77.4 - - - +
408A HIS* 1.3 64.6 + - - +
410A LEU* 2.9 22.5 - - - +
411A LEU* 3.0 13.0 + - - +
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Residues in contact with HIS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A MET* 2.8 38.0 + - + +
405A VAL* 2.7 28.3 + - + +
407A ASP* 1.3 76.7 - - - +
409A ILE* 1.3 50.6 + - - +
410A LEU 3.1 0.3 + - - -
411A LEU* 3.1 3.1 + - - +
412A CYS* 2.3 54.3 + - - -
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Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.8 9.8 - - + -
236A PRO* 5.8 0.9 - - + -
294A VAL* 6.0 4.3 - - + -
295A VAL* 5.4 20.9 - - + +
298A THR* 4.2 23.3 - - + +
299A HIS* 6.1 1.8 - - - -
405A VAL* 2.8 20.7 + - + +
406A ILE* 3.1 50.0 - - + +
408A HIS* 1.3 73.0 - - - +
410A LEU* 1.3 57.4 + - - +
412A CYS* 3.3 11.7 - - + -
413A VAL* 2.9 43.8 + - + +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.3 33.2 - - + +
234A TYR* 3.2 62.8 - - + +
237A THR* 4.3 3.8 - - + -
406A ILE 3.2 13.3 + - - +
407A ASP* 2.9 20.4 - - - +
409A ILE* 1.3 77.6 - - - +
411A LEU* 1.3 66.3 + - + +
414A PHE* 2.8 51.3 + - + +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 5.0 4.7 - - - +
407A ASP 3.0 10.4 + - - +
408A HIS* 4.2 2.5 - - - +
410A LEU* 1.3 91.8 - - + +
412A CYS* 1.3 69.9 + - - +
413A VAL 3.3 0.2 - - - -
414A PHE* 3.9 6.7 - - + -
415A MET* 3.2 39.3 + - + +
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Residues in contact with CYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A HIS* 2.3 61.4 + - - +
409A ILE* 3.3 17.3 - - + +
411A LEU* 1.3 71.1 - - - +
413A VAL* 1.3 63.1 + - + +
415A MET* 3.9 3.1 - - - +
416A LEU* 3.4 16.1 + - - +
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Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.3 31.2 - - + -
291A VAL* 3.9 19.5 - - + -
294A VAL* 5.9 2.7 - - + -
295A VAL* 4.9 3.4 - - + -
409A ILE* 2.9 22.2 + - + +
412A CYS* 1.3 80.4 - - + +
414A PHE* 1.3 53.9 + - - +
415A MET 3.0 2.0 - - - -
416A LEU* 2.6 30.9 + - + +
417A ILE* 2.3 50.8 + - + +
420A ILE* 6.0 0.2 - - + -
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Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 3.0 53.2 - - + -
233A PHE* 4.7 4.0 - + - -
234A TYR* 3.3 30.7 - + - -
410A LEU* 2.8 41.2 + - + +
411A LEU* 3.6 7.4 + - + -
413A VAL* 1.3 75.6 - - - +
415A MET* 1.3 60.0 + - + +
417A ILE* 3.4 21.5 - - + +
418A CYS* 2.6 44.4 + - - +
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Residues in contact with MET 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 3.2 36.1 + - + +
412A CYS 3.9 3.8 - - - +
413A VAL 3.0 0.2 - - - -
414A PHE* 1.3 84.8 - - + +
416A LEU* 1.3 54.7 + - - +
418A CYS* 3.3 17.1 - - + +
419A ILE* 2.5 36.3 + - - +
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER* 5.1 1.1 - - - +
291A VAL* 4.4 14.8 - - + -
412A CYS 3.4 6.3 + - - +
413A VAL* 2.6 47.4 + - + +
415A MET* 1.3 77.4 - - - +
417A ILE* 1.3 52.8 + - - -
419A ILE* 2.6 16.9 - - + +
420A ILE* 2.4 52.3 + - + +
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 6.5 0.7 - - + -
226A SER* 5.3 14.1 - - - +
230A VAL* 5.3 2.0 - - + -
233A PHE* 3.1 36.8 - - + -
291A VAL* 6.2 0.2 - - + -
413A VAL* 2.3 48.1 + - + +
414A PHE* 3.4 34.8 - - + +
416A LEU* 1.3 65.0 - - - +
418A CYS* 1.3 61.2 + - - +
419A ILE 3.0 1.6 - - - -
420A ILE* 3.2 20.2 - - + -
421A GLY* 2.5 33.4 + - - +
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Residues in contact with CYS 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 2.6 32.9 + - - +
415A MET* 3.3 20.4 - - + +
417A ILE* 1.3 75.1 - - - +
419A ILE* 1.3 51.8 + - - +
422A THR* 2.5 41.5 + - - +
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A MET 2.5 17.0 + - - +
416A LEU* 2.6 40.6 - - + +
418A CYS* 1.3 71.3 - - - +
420A ILE* 1.4 66.7 + - + +
421A GLY 3.1 0.2 - - - -
422A THR* 2.8 4.2 + - - -
423A VAL* 2.4 72.3 + - + +
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 6.4 2.5 - - + -
284A PHE* 5.5 7.2 - - + +
287A SER* 4.0 28.3 - - - +
291A VAL* 5.6 1.6 - - + -
416A LEU* 2.4 56.1 + - + +
417A ILE* 3.2 28.3 - - + +
419A ILE* 1.4 75.8 - - + +
421A GLY* 1.3 64.0 + - - +
423A VAL* 2.8 9.9 + - - +
424A SER* 2.4 48.0 + - - +
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Residues in contact with GLY 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ILE* 2.5 27.7 + - - -
418A CYS* 4.8 0.2 - - - -
420A ILE* 1.3 75.6 - - - +
422A THR* 1.3 50.5 + - - -
424A SER* 3.0 9.9 + - - -
425A VAL* 2.7 33.7 + - - +
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Residues in contact with THR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A CYS* 2.5 29.9 + - - +
419A ILE* 2.8 7.0 + - - -
421A GLY* 1.3 71.0 - - - +
423A VAL* 1.3 58.3 + - + +
425A VAL* 2.7 33.3 - - + +
426A PHE* 2.8 11.3 + - - +
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 5.4 0.4 - - - -
419A ILE* 2.4 71.6 + - + +
420A ILE* 3.2 8.7 - - - +
422A THR* 1.3 68.4 - - + +
424A SER* 1.3 62.6 + - - +
425A VAL 3.1 1.3 - - - -
426A PHE* 2.8 35.1 + - + +
427A ALA* 3.6 5.9 + - - +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.0 60.4 - - - -
420A ILE* 2.4 37.7 + - - +
421A GLY* 3.4 8.1 - - - -
423A VAL* 1.3 71.1 - - - +
425A VAL* 1.4 64.2 + - - +
426A PHE 3.2 0.2 - - - -
427A ALA* 4.2 1.6 + - - +
428A GLY* 3.4 16.3 + - - -
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLY 2.7 11.0 + - - +
422A THR* 2.7 42.6 - - + +
424A SER* 1.4 76.6 - - - +
426A PHE* 1.3 56.1 + - - +
428A GLY* 4.4 1.3 - - - +
429A ARG* 2.5 62.6 + - + +
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A THR 2.8 14.2 + - - +
423A VAL* 2.8 32.1 - - + +
425A VAL* 1.3 78.4 - - - +
427A ALA* 1.3 77.7 + - + +
429A ARG* 3.3 3.8 - - - +
430A LEU* 2.6 63.2 + - + +
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Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A PHE* 5.8 10.3 - - + -
423A VAL 3.6 5.5 + - - +
424A SER* 5.1 1.3 - - - +
426A PHE* 1.3 95.7 - - + +
428A GLY* 1.3 65.3 + - - +
430A LEU* 3.8 6.5 - - + -
431A ILE* 3.2 27.1 + - + +
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Residues in contact with GLY 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 5.5 4.6 - - - -
280A PHE* 6.5 1.8 - - - -
424A SER 3.4 13.5 + - - -
425A VAL* 3.1 6.1 + - - -
426A PHE 2.9 1.2 - - - -
427A ALA* 1.3 83.7 - - - +
429A ARG* 1.3 61.4 + - - +
431A ILE 4.1 0.3 - - - -
432A GLU* 3.1 21.3 + - - +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 2.5 52.8 + - + +
426A PHE* 3.3 3.6 - - - +
428A GLY* 1.3 69.9 - - - +
430A LEU* 1.3 58.7 + - - +
432A GLU* 2.9 10.6 + - - +
433A LEU* 2.8 28.8 + - - +
436A GLU* 3.6 22.8 + - - -
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 2.6 48.4 + - + +
427A ALA* 3.9 4.7 - - + -
428A GLY 3.4 0.2 - - - -
429A ARG* 1.3 70.3 - - - +
431A ILE* 1.3 76.7 + - + +
433A LEU* 2.5 47.7 + - + +
434A SER* 3.2 5.4 + - - +
----------------------------------------------------------
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Residues in contact with ILE 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 4.6 18.3 - - + +
138A ASP* 4.7 17.9 - - + +
427A ALA* 3.2 19.6 + - + +
428A GLY 4.1 0.9 - - - +
430A LEU* 1.3 104.3 - - + +
432A GLU* 1.3 56.8 + - - +
433A LEU 3.0 1.6 - - - -
434A SER* 3.4 20.0 - - - -
435A GLN* 2.8 22.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 3.1 19.5 - - + -
428A GLY 3.1 20.6 + - - +
429A ARG* 3.2 16.4 - - - +
430A LEU 2.8 1.2 - - - -
431A ILE* 1.3 77.6 - - - +
433A LEU* 1.3 57.9 + - - +
434A SER 3.1 2.7 - - - -
435A GLN* 2.3 35.3 + - - +
436A GLU* 2.6 79.4 + - - +
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 2.8 9.1 + - - +
430A LEU* 2.5 26.1 + - + +
432A GLU 1.3 80.8 - - - +
434A SER* 1.3 55.5 + - - +
436A GLU* 4.7 2.2 - - - +
437A GLY* 4.5 6.8 + - - -
----------------------------------------------------------
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 6.3 1.3 - - - -
179A LYS* 5.3 0.2 + - - -
430A LEU* 3.2 5.3 + - - +
431A ILE* 3.4 26.7 + - - -
433A LEU* 1.3 79.7 - - - +
435A GLN* 1.3 64.0 + - - +
436A GLU 3.5 0.2 - - - -
437A GLY* 3.3 17.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 2.4 75.2 - - + +
138A ASP* 5.5 2.2 - - - +
179A LYS* 2.8 28.1 + - - +
208A GLN* 2.6 27.8 + - - +
209A ARG 4.8 2.1 - - - +
431A ILE* 2.8 16.1 + - + +
432A GLU* 2.3 40.5 + - - +
434A SER* 1.3 73.9 - - - +
436A GLU* 1.3 54.6 + - - +
437A GLY 2.7 16.1 + - - -
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Residues in contact with GLU 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 4.9 0.4 - - - -
208A GLN* 5.7 1.8 - - - +
429A ARG* 3.6 18.6 + - - -
432A GLU* 2.6 64.5 + - - +
433A LEU* 4.9 1.1 - - - -
435A GLN* 1.3 79.5 - - - +
437A GLY* 1.3 62.2 + - - +
----------------------------------------------------------
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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