Contacts of the helix formed by residues 407 - 437 (chain J) in PDB entry 2FRV
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 407 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J TRP* 4.7 9.4 - - + -
271J TRP* 4.1 20.4 - - + -
274J ILE 2.6 24.0 + - - -
275J GLY* 3.5 9.2 - - - -
406J SER* 1.3 68.3 - - - +
408J LEU* 1.3 65.1 + - - +
410J ARG* 3.2 21.9 + - - +
411J THR* 2.8 30.4 + - - +
522J ARG 3.6 29.6 - - - +
523J THR* 3.5 10.1 + - - -
526J SER* 3.7 9.8 + - - +
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Residues in contact with LEU 408 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J TRP* 5.1 10.5 - - + -
265J ALA* 4.0 39.3 - - + +
268J TYR* 3.7 27.8 - - + +
269J LYS* 4.1 7.0 - - + -
271J TRP* 3.1 26.5 + - + +
272J ALA* 3.6 22.2 - - + +
397J LEU* 4.9 12.1 - - + -
399J VAL* 6.5 0.7 - - + -
403J ALA 5.1 0.7 - - - +
406J SER 3.1 0.2 - - - -
407J THR* 1.3 79.5 - - - +
409J GLY* 1.3 56.3 + - - +
411J THR* 3.0 15.6 + - + +
412J ALA* 2.9 26.4 + - + +
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Residues in contact with GLY 409 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J LEU* 3.7 3.0 - - - +
403J ALA 3.8 6.4 + - - -
404J LEU* 3.5 35.3 - - - +
406J SER* 2.9 12.1 + - - -
408J LEU* 1.3 74.5 - - - +
410J ARG* 1.3 59.4 + - - +
412J ALA* 4.2 3.7 - - - +
413J ALA* 2.9 33.4 + - - +
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Residues in contact with ARG 410 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J GLY 2.7 23.6 + - - -
276J LYS* 4.6 0.2 - - - +
277J THR* 3.2 22.0 + - - -
368J GLU* 3.1 21.7 + - - +
371J PRO* 4.9 1.2 - - + +
372J LEU* 4.2 20.4 + - + +
404J LEU 4.2 0.4 + - - -
406J SER* 3.0 16.0 + - - +
407J THR* 3.2 34.7 + - - +
408J LEU 3.2 0.2 - - - -
409J GLY* 1.3 77.7 - - - +
411J THR* 1.3 59.8 + - - +
413J ALA* 4.1 2.4 - - - +
414J ARG* 3.7 26.6 + - - +
505J ALA* 4.4 1.6 - - - +
523J THR* 4.7 0.6 + - - +
526J SER* 3.3 39.8 + - - +
527J TYR* 3.3 37.6 + - - -
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Residues in contact with THR 411 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J PHE* 5.0 8.3 - - + -
116J HIS* 3.5 37.1 - - + +
120J TRP* 5.1 3.7 - - + +
257J TYR* 4.8 1.2 + - - -
261J LEU* 3.6 24.6 - - + +
407J THR* 2.8 19.2 + - - +
408J LEU* 3.0 15.8 + - + -
410J ARG* 1.3 77.9 - - - +
412J ALA* 1.3 65.3 + - - +
413J ALA 3.3 0.2 - - - -
414J ARG* 3.6 17.5 + - - +
415J GLY 3.7 4.2 + - - -
526J SER* 3.7 5.7 - - - -
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Residues in contact with ALA 412 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J LEU* 4.2 16.0 - - + +
262J LEU* 5.4 2.0 - - + -
393J VAL* 4.1 27.3 - - + +
397J LEU* 5.2 8.5 - - + -
404J LEU* 5.4 4.7 - - + -
408J LEU* 2.9 15.1 + - + +
409J GLY* 3.4 6.3 + - - +
411J THR* 1.3 75.6 - - - +
413J ALA* 1.3 53.5 + - - +
415J GLY* 2.7 24.3 + - - -
416J ILE* 3.0 16.1 + - + +
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Residues in contact with ALA 413 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371J PRO* 3.6 5.7 - - - +
372J LEU* 3.6 37.5 - - + +
375J VAL* 3.7 11.5 - - + +
404J LEU* 5.5 2.8 - - + +
409J GLY 2.9 19.1 + - - +
410J ARG 4.1 2.5 - - - +
411J THR 3.3 0.2 - - - -
412J ALA* 1.3 77.2 - - - +
414J ARG* 1.3 55.0 + - - +
416J ILE* 3.6 13.3 - - + +
417J GLN* 2.8 31.4 + - - +
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Residues in contact with ARG 414 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J HIS* 3.5 25.6 + - + -
111J HIS* 3.5 33.7 - - - -
112J PHE* 6.0 0.4 - - - -
116J HIS* 5.2 0.8 + - - -
257J TYR* 3.8 14.7 + - - +
371J PRO* 3.6 35.9 - - + +
410J ARG* 3.7 19.6 + - - +
411J THR* 3.6 15.2 + - - +
412J ALA 3.2 0.6 - - - -
413J ALA* 1.3 77.7 - - - +
415J GLY* 1.3 57.5 + - - +
417J GLN* 3.9 0.9 - - - -
418J CYS* 3.0 29.8 + - - +
462J PRO 5.3 0.8 + - - -
463J ARG* 5.7 1.2 - - - +
526J SER* 2.6 35.5 + - - +
527J TYR* 3.8 5.1 + - - +
528J ASP* 3.4 30.8 + - - +
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Residues in contact with GLY 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J TYR* 3.7 10.3 + - - -
258J ILE* 3.2 25.2 - - - +
261J LEU* 3.6 23.3 - - - -
411J THR 3.7 2.2 + - - -
412J ALA 2.7 10.5 + - - -
414J ARG* 1.3 81.7 - - - +
416J ILE* 1.3 59.5 - - - +
418J CYS* 3.5 2.9 + - - +
419J LEU* 3.3 15.8 + - - +
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Residues in contact with ILE 416 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258J ILE* 6.3 0.4 - - + -
375J VAL* 4.0 21.8 - - + -
386J THR* 4.7 9.6 - - + +
389J ALA* 3.8 25.4 - - + +
390J VAL* 3.9 29.6 - - + -
393J VAL* 4.1 28.5 - - + -
404J LEU* 5.3 6.1 - - + -
412J ALA* 3.0 19.1 + - + +
413J ALA* 3.7 13.7 - - + +
415J GLY* 1.3 75.6 - - - +
417J GLN* 1.3 66.2 + - - +
419J LEU* 3.0 17.8 + - + +
420J THR* 3.2 20.7 + - + +
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Residues in contact with GLN 417 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J TYR* 3.7 25.5 + - + -
108J HIS* 2.8 31.0 + - + -
370J GLY 4.5 0.2 - - - -
371J PRO* 3.5 25.2 - - + +
374J SER* 3.7 17.7 + - - -
375J VAL* 4.1 11.0 - - + +
413J ALA 2.8 20.5 + - - +
416J ILE* 1.3 74.1 - - - +
418J CYS* 1.3 60.9 + - - +
419J LEU 3.4 0.2 + - - -
420J THR* 3.9 7.9 + - - -
421J ALA* 3.4 23.0 + - - +
460J ASN* 4.2 5.4 - - - +
461J ALA 4.5 1.0 + - - +
462J PRO* 3.1 23.8 + - - +
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Residues in contact with CYS 418 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J TYR* 4.1 4.7 - - - -
105J MET* 4.0 13.3 - - - +
108J HIS* 3.1 39.0 - - + +
109J LEU 4.8 0.4 - - - -
253J ILE* 4.0 27.8 - - - +
257J TYR* 4.0 15.5 - - + -
414J ARG 3.0 13.6 + - - +
415J GLY 3.7 5.4 - - - +
416J ILE 3.1 0.4 - - - -
417J GLN* 1.3 79.8 - - - +
419J LEU* 1.3 56.1 + - - +
421J ALA* 4.0 4.4 - - - +
422J ALA* 3.4 21.3 + - - +
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Residues in contact with LEU 419 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253J ILE* 4.5 13.9 - - + -
254J GLU* 3.5 41.3 - - + +
258J ILE* 4.6 17.0 - - + -
389J ALA* 4.7 19.1 - - + -
392J LEU* 5.6 8.1 - - + -
415J GLY 3.3 14.1 + - - +
416J ILE* 3.0 7.6 + - + +
418J CYS* 1.3 76.4 - - - +
420J THR* 1.3 56.1 + - + +
421J ALA 3.3 1.6 - - - -
422J ALA* 3.3 8.5 + - + +
423J GLN* 2.8 57.1 + - + +
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Residues in contact with THR 420 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297J TYR* 3.2 25.9 + - - -
298J THR* 4.7 10.4 - - - +
375J VAL* 6.1 0.2 - - - +
383J HIS* 4.9 0.9 - - - -
385J PRO* 3.9 33.9 - - + +
386J THR* 4.0 15.4 + - - +
389J ALA* 4.5 5.4 - - + -
416J ILE* 3.2 23.3 + - + +
417J GLN* 3.9 8.8 + - - -
419J LEU* 1.3 75.3 - - + +
421J ALA* 1.3 66.9 + - - +
423J GLN* 3.2 11.4 + - - +
424J GLU* 3.0 19.8 + - - +
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Residues in contact with ALA 421 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J GLY* 4.7 5.2 - - - +
104J TYR* 3.7 33.9 - - + -
105J MET* 5.3 0.7 - - + -
286J PHE* 4.6 15.3 - - + -
297J TYR* 4.8 4.5 - - - -
417J GLN 3.4 16.8 + - - +
418J CYS 4.0 2.5 - - - +
420J THR* 1.3 80.0 + - - +
422J ALA* 1.3 63.0 + - - +
424J GLU* 3.0 16.4 + - - +
425J VAL* 3.2 18.3 + - - +
428J TRP* 4.6 1.2 - - - -
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Residues in contact with ALA 422 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J MET* 4.1 28.7 - - + +
246J TYR* 2.6 33.4 + - - -
250J ARG* 4.0 22.9 - - + +
253J ILE* 4.7 4.9 - - + -
418J CYS 3.4 13.7 + - - +
419J LEU* 3.3 16.1 + - + +
421J ALA* 1.3 79.5 - - - +
423J GLN* 1.3 56.0 + - - +
425J VAL* 3.6 2.5 + - - -
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Residues in contact with GLN 423 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G LYS 5.3 0.7 - - - +
167G MET 5.8 0.2 - - - +
246J TYR* 4.0 0.5 + - - -
250J ARG* 3.5 31.2 + - - +
254J GLU* 4.6 1.4 - - - +
297J TYR* 4.9 2.0 - - - +
385J PRO* 3.9 28.1 + - - +
388J LYS* 5.6 3.0 - - - +
389J ALA* 6.0 0.3 - - - +
419J LEU* 2.8 53.4 + - + +
420J THR* 3.6 12.2 - - - +
421J ALA 3.1 0.4 - - - -
422J ALA* 1.3 76.3 - - - +
424J GLU* 1.3 65.2 + - - +
425J VAL 3.4 0.5 + - - -
426J GLU* 3.7 17.3 + - - +
427J VAL* 4.5 1.9 + - - +
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Residues in contact with GLU 424 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G MET 5.4 1.0 - - - +
169G GLU* 5.4 1.4 - - - +
297J TYR* 3.5 37.2 + - + -
420J THR 3.0 11.2 + - - +
421J ALA 3.0 9.0 + - - +
423J GLN* 1.3 75.7 - - - +
425J VAL* 1.3 63.9 + - - +
426J GLU 3.1 3.1 - - - -
427J VAL* 3.1 49.0 + - - +
428J TRP* 3.2 43.2 + - + +
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Residues in contact with VAL 425 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J LEU* 3.6 20.2 - - + +
101J GLY* 3.8 31.6 - - - -
102J ALA* 4.4 2.2 - - - +
105J MET* 4.5 6.1 - - - -
242J PHE* 3.9 17.0 - - + -
246J TYR* 3.7 34.8 - - + -
421J ALA 3.2 16.0 + - - +
422J ALA 4.0 1.1 - - - +
423J GLN 3.3 1.8 - - - -
424J GLU* 1.3 75.0 - - - +
426J GLU* 1.3 62.0 + - - +
428J TRP* 3.5 13.7 + - + -
429J LEU* 3.1 22.7 + - + +
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Residues in contact with GLU 426 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G HIS* 4.9 4.5 - - + +
165G LYS* 3.8 41.5 - - + +
243J ARG* 3.4 22.7 + - - +
246J TYR* 2.9 41.6 + - - +
247J LYS* 3.9 19.9 - - - -
250J ARG* 4.0 7.1 + - - -
423J GLN 3.7 9.9 - - - +
424J GLU 3.1 0.2 - - - -
425J VAL* 1.3 78.6 - - - +
427J VAL* 1.3 60.8 + - + +
429J LEU* 3.6 4.8 - - - +
430J ASP* 3.2 38.5 + - - +
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Residues in contact with VAL 427 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G HIS* 6.4 0.2 - - + -
167G MET 4.3 11.4 - - - +
168G PRO* 4.7 0.7 - - + -
169G GLU* 3.9 50.3 - - + +
423J GLN 5.3 1.8 - - - +
424J GLU* 3.1 42.4 + - - +
426J GLU* 1.3 81.1 - - + +
428J TRP* 1.3 73.8 + - + +
430J ASP* 3.5 5.1 + - - +
431J LYS* 3.2 24.8 + - + +
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Residues in contact with TRP 428 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J LEU* 4.0 29.5 - - + +
97J ASN* 3.3 44.6 - - + +
98J LEU* 3.8 19.7 - - + +
101J GLY* 4.4 1.3 - - - -
286J PHE* 3.1 53.4 + + + +
297J TYR* 4.6 3.4 - + + +
421J ALA* 4.6 2.5 - - - -
424J GLU* 3.2 39.0 + - + +
425J VAL* 3.7 32.8 - - + +
427J VAL* 1.3 83.3 - - + +
429J LEU* 1.3 62.3 + - - +
431J LYS* 3.7 2.6 - - + +
432J LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 429 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J LEU* 4.0 21.5 - - + +
213J PHE* 4.3 7.4 - - + -
239J ILE* 4.1 18.4 - - + +
242J PHE* 3.9 30.1 - - + -
243J ARG* 3.4 54.1 - - + +
246J TYR* 4.9 6.5 - - + -
425J VAL 3.1 18.8 + - - +
426J GLU* 3.6 6.7 - - - +
428J TRP* 1.3 78.3 - - - +
430J ASP* 1.3 55.9 + - - +
432J LEU* 3.2 3.1 + - + +
433J GLU* 2.7 37.9 + - - +
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Residues in contact with ASP 430 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G HIS* 4.3 12.6 + - - -
165G LYS* 4.7 6.4 + - - +
178G MET* 5.7 3.8 - - - +
243J ARG* 2.9 33.2 + - - -
426J GLU* 3.2 26.7 + - - +
427J VAL* 3.5 6.9 - - - +
429J LEU* 1.3 80.7 - - - +
431J LYS* 1.3 55.7 + - - +
433J GLU* 3.3 7.9 + - - +
434J ALA* 3.0 27.7 + - - +
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Residues in contact with LYS 431 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G GLU* 2.5 45.0 + - - +
177G VAL* 3.9 15.7 - - + +
90J GLU* 5.2 13.0 - - - +
94J LEU* 3.9 28.0 - - + -
288J THR* 6.1 5.6 - - - -
427J VAL* 3.2 17.7 + - + +
428J TRP* 3.7 7.0 - - + +
430J ASP* 1.3 70.1 - - - +
432J LEU* 1.3 70.9 + - - +
433J GLU 3.0 1.6 - - - -
434J ALA* 3.1 6.2 + - + -
435J ASN* 2.9 31.9 + - - +
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Residues in contact with LEU 432 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ASN* 3.7 45.5 - - + +
94J LEU* 3.8 15.0 - - + +
95J MET* 4.4 6.7 - - + +
98J LEU* 4.5 9.6 - - + -
213J PHE* 4.4 18.2 - - + -
234J LEU* 3.9 24.2 - - + -
239J ILE* 3.6 26.7 - - + -
428J TRP 2.8 22.8 + - - +
429J LEU* 3.6 6.7 - - + +
431J LYS* 1.3 77.8 - - - +
433J GLU* 1.3 57.4 + - - +
435J ASN* 3.3 4.7 + - - +
436J VAL* 3.0 25.0 + - + +
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Residues in contact with GLU 433 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236J PRO* 5.1 8.8 - - + +
239J ILE* 3.7 30.8 - - + +
243J ARG* 3.0 24.8 + - - -
429J LEU 2.7 17.9 + - - +
430J ASP* 3.3 8.2 - - - +
431J LYS 3.0 0.2 - - - -
432J LEU* 1.3 78.4 - - - +
434J ALA* 1.3 56.5 + - - +
436J VAL* 3.4 4.5 + - + +
437J LYS* 3.0 63.6 + - - +
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Residues in contact with ALA 434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430J ASP 3.0 15.8 + - - +
431J LYS* 3.8 7.9 - - + +
433J GLU* 1.3 72.2 - - - +
435J ASN* 1.3 68.9 + - - +
437J LYS* 3.7 10.3 - - - +
438J ALA* 3.0 25.5 + - - +
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Residues in contact with ASN 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J GLU* 2.9 29.8 + - - +
91J ASN* 2.8 26.5 + - - +
94J LEU* 3.9 8.7 - - - +
431J LYS* 2.9 20.0 + - - +
432J LEU 3.4 8.1 - - - +
434J ALA* 1.3 78.5 - - - +
436J VAL* 1.3 64.7 + - - +
438J ALA* 3.4 7.9 + - - -
440J LYS* 2.8 51.7 + - + +
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Residues in contact with VAL 436 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ASN* 4.1 4.9 - - - +
234J LEU* 3.3 55.6 - - + +
236J PRO* 5.6 6.3 - - + -
239J ILE* 5.3 2.2 - - + -
432J LEU* 3.0 19.3 + - + +
433J GLU* 3.4 6.7 + - - +
434J ALA 3.2 0.2 - - - -
435J ASN* 1.3 81.0 - - - +
437J LYS* 1.3 58.9 + - + +
439J GLY* 3.0 19.6 + - - -
440J LYS 3.9 14.1 - - - +
441J ASP* 4.9 7.1 - - + +
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Residues in contact with LYS 437 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236J PRO* 4.8 18.2 - - - +
433J GLU* 3.0 53.0 + - - +
434J ALA* 3.7 9.0 - - - +
435J ASN 3.2 0.4 - - - -
436J VAL* 1.3 73.3 - - + +
438J ALA* 1.3 57.3 + - - +
439J GLY* 3.0 9.4 + - - -
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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