Contacts of the helix formed by residues 407 - 437 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TRP* 4.7 9.8 - - + -
271B TRP* 4.1 20.0 - - + -
274B ILE 2.6 23.6 + - - -
275B GLY* 3.5 8.5 - - - -
406B SER* 1.3 68.4 - - - +
408B LEU* 1.3 65.4 + - - +
410B ARG* 3.2 23.1 + - - +
411B THR* 2.8 30.7 + - - +
522B ARG 3.6 28.9 - - - +
523B THR* 3.5 10.8 + - - -
526B SER* 3.7 10.0 + - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TRP* 5.1 9.0 - - + -
265B ALA* 4.0 38.6 - - + +
268B TYR* 3.7 28.3 - - + +
269B LYS* 4.1 7.4 - - + -
271B TRP* 3.1 27.6 + - + +
272B ALA* 3.6 21.3 - - + +
397B LEU* 4.9 12.6 - - + -
399B VAL* 6.5 0.4 - - + -
403B ALA 5.1 0.2 - - - +
406B SER 3.1 0.2 - - - -
407B THR* 1.3 79.9 - - - +
409B GLY* 1.3 55.9 - - - +
411B THR* 3.0 15.1 + - + +
412B ALA* 2.9 27.7 + - + +
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Residues in contact with GLY 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.7 2.6 - - - +
403B ALA 3.8 7.7 + - - -
404B LEU* 3.5 33.5 - - - +
406B SER* 2.9 11.5 + - - -
408B LEU* 1.3 74.3 - - - +
410B ARG* 1.3 58.4 + - - +
412B ALA* 4.2 3.9 - - - +
413B ALA* 2.9 34.0 + - - +
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLY 2.7 24.0 + - - -
276B LYS* 4.6 0.4 - - - +
277B THR* 3.2 22.2 + - - +
368B GLU* 3.1 22.7 + - - +
371B PRO* 4.9 1.8 - - + +
372B LEU* 4.2 20.0 + - + +
404B LEU 4.2 0.6 + - - -
406B SER 3.0 16.2 + - - +
407B THR* 3.2 34.6 + - - +
408B LEU 3.2 0.2 - - - -
409B GLY* 1.3 77.1 - - - +
411B THR* 1.3 60.3 - - - +
413B ALA* 4.1 2.6 - - - +
414B ARG* 3.7 26.4 + - - +
505B ALA* 4.4 1.6 - - - +
523B THR* 4.7 0.8 + - - +
526B SER* 3.3 38.7 + - - +
527B TYR* 3.3 37.9 + - - -
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Residues in contact with THR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 5.0 8.3 - - + -
116B HIS* 3.5 35.5 - - + +
120B TRP* 5.1 4.3 - - + +
257B TYR* 4.8 1.7 + - - -
261B LEU* 3.6 24.5 - - + +
265B ALA* 6.4 0.9 - - + -
407B THR* 2.8 19.0 + - - +
408B LEU* 3.0 18.0 + - + -
410B ARG* 1.3 78.3 - - - +
412B ALA* 1.3 64.8 + - - +
414B ARG* 3.6 18.5 + - - +
415B GLY 3.7 4.2 + - - -
526B SER* 3.7 6.1 - - - -
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.2 17.2 - - + +
262B LEU* 5.4 2.2 - - + -
265B ALA* 6.1 3.8 - - + -
393B VAL* 4.1 27.9 - - + +
397B LEU* 5.2 8.5 - - + -
404B LEU* 5.4 4.0 - - + -
408B LEU* 2.9 14.8 + - + +
409B GLY* 3.4 6.3 + - - +
411B THR* 1.3 77.0 - - - +
413B ALA* 1.3 53.6 + - - +
415B GLY* 2.7 24.4 + - - -
416B ILE* 3.0 16.7 + - + +
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Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PRO* 3.6 5.7 - - - +
372B LEU* 3.6 37.7 - - + +
375B VAL* 3.7 10.8 - - + +
404B LEU* 5.5 2.6 - - + +
409B GLY 2.9 19.3 + - - +
410B ARG 4.1 2.2 - - - +
412B ALA* 1.3 75.6 - - - +
414B ARG* 1.3 55.4 + - - +
416B ILE* 3.7 13.1 - - - +
417B GLN* 2.8 31.7 + - - +
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B HIS* 3.5 25.9 + - + -
111B HIS* 3.5 33.5 - - - -
112B PHE* 5.5 0.4 - - - +
116B HIS* 5.2 0.6 + - - -
257B TYR* 3.8 13.0 + - - +
371B PRO* 3.6 37.6 - - + +
410B ARG* 3.7 19.0 + - - +
411B THR* 3.6 15.0 + - - +
412B ALA 3.2 0.6 - - - -
413B ALA* 1.3 79.0 - - - +
415B GLY* 1.3 56.8 + - - +
417B GLN* 4.5 0.4 - - - -
418B CYS* 3.0 29.8 + - - +
462B PRO 5.3 0.4 + - - -
463B ARG* 5.7 1.0 - - - +
526B SER* 2.6 36.1 + - - +
527B TYR* 3.8 5.9 + - - +
528B ASP* 3.4 30.6 + - - +
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Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B TYR* 3.7 10.3 + - - -
258B ILE* 3.2 25.4 - - - +
261B LEU* 3.6 22.9 - - - -
411B THR 3.7 2.2 + - - -
412B ALA 2.7 10.7 + - - -
414B ARG* 1.3 81.3 - - - +
416B ILE* 1.3 59.7 + - - +
418B CYS* 3.5 2.8 + - - +
419B LEU* 3.3 15.9 + - - +
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B VAL* 4.0 21.8 - - + -
386B THR* 4.7 9.6 - - + +
389B ALA* 3.8 26.0 - - + +
390B VAL* 3.9 29.4 - - + -
393B VAL* 4.1 27.8 - - + -
404B LEU* 5.3 6.3 - - + -
412B ALA* 3.0 18.9 + - + +
413B ALA* 3.3 15.0 + - - +
415B GLY* 1.3 75.1 - - - +
417B GLN* 1.3 65.6 + - - +
419B LEU* 3.0 17.1 + - + +
420B THR* 3.2 20.9 + - + +
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Residues in contact with GLN 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR* 3.7 25.5 + - + -
108B HIS* 2.8 30.3 + - + -
370B GLY 4.5 0.2 - - - -
371B PRO* 3.5 25.0 - - + +
374B SER* 3.7 17.5 + - - -
375B VAL* 4.1 11.0 - - + +
413B ALA 2.8 20.6 + - - +
416B ILE* 1.3 74.3 - - - +
418B CYS* 1.3 61.8 + - - +
419B LEU 3.4 0.3 + - - -
420B THR* 3.9 7.4 + - - -
421B ALA* 3.4 22.3 + - - +
460B ASN* 4.2 5.4 - - - +
461B ALA 4.5 1.2 + - - +
462B PRO* 3.1 24.2 + - - +
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Residues in contact with CYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR* 4.1 5.4 - - - -
105B MET* 4.0 13.2 + - - +
108B HIS* 3.1 38.8 - - + +
109B LEU 4.8 0.4 - - - -
253B ILE* 4.0 27.6 - - - -
257B TYR* 4.0 15.7 - - + -
414B ARG 3.0 14.7 + - - +
415B GLY 3.7 5.4 - - - +
416B ILE 3.1 0.2 - - - -
417B GLN* 1.3 80.8 - - - +
419B LEU* 1.3 56.2 + - - +
421B ALA* 4.0 4.0 - - - +
422B ALA* 3.4 21.7 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ILE* 4.5 14.6 - - + -
254B GLU* 3.5 40.8 - - + +
258B ILE* 4.6 16.6 - - + -
389B ALA* 4.7 18.4 - - + -
392B LEU* 5.6 8.3 - - + -
415B GLY 3.3 13.9 + - - +
416B ILE* 3.0 6.5 + - + +
418B CYS* 1.3 77.1 - - - +
420B THR* 1.3 55.9 + - + +
421B ALA 3.3 1.6 - - - -
422B ALA* 3.3 9.6 + - + +
423B GLN* 2.8 57.5 + - + +
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Residues in contact with THR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TYR* 3.2 26.6 + - - -
298B THR* 4.7 10.6 - - - +
375B VAL* 6.1 0.3 - - - +
383B HIS* 4.9 0.7 - - - -
385B PRO* 3.9 33.9 - - + +
386B THR* 4.0 15.4 + - - +
389B ALA* 4.5 4.9 - - + -
416B ILE* 3.2 22.5 + - + +
417B GLN* 3.9 8.8 + - - -
419B LEU* 1.3 73.6 - - + +
421B ALA* 1.3 67.6 + - - +
423B GLN* 3.2 11.4 + - - +
424B GLU* 3.0 19.2 + - - +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY* 4.7 5.4 - - - +
104B TYR* 3.7 34.1 - - + -
105B MET* 5.3 0.2 - - + -
286B PHE* 4.6 16.2 - - + -
297B TYR* 4.8 4.2 - - - -
417B GLN 3.4 16.4 + - - +
418B CYS 4.0 2.5 - - - +
420B THR* 1.3 80.8 + - - +
422B ALA* 1.3 62.6 + - - +
424B GLU* 3.0 17.3 + - - +
425B VAL* 3.2 18.3 + - - +
428B TRP* 4.6 1.2 - - - -
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 4.1 27.1 - - + +
246B TYR* 2.6 33.4 + - - -
250B ARG* 4.0 22.6 - - + +
253B ILE* 4.7 5.6 - - + -
418B CYS 3.4 14.1 + - - +
419B LEU* 3.3 15.4 + - + +
421B ALA* 1.3 79.7 - - - +
423B GLN* 1.3 57.1 + - - +
425B VAL* 3.6 2.6 + - - -
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Residues in contact with GLN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TYR* 4.0 0.5 + - - -
250B ARG* 3.5 32.0 + - - +
254B GLU* 4.6 1.4 - - - +
297B TYR* 4.7 2.0 + - - +
385B PRO* 3.9 28.5 + - - +
388B LYS* 5.6 3.4 - - - +
389B ALA* 6.0 0.3 - - - +
419B LEU* 2.8 52.6 + - + +
420B THR* 3.6 12.6 - - - +
421B ALA 3.1 0.6 - - - -
422B ALA* 1.3 76.6 - - - +
424B GLU* 1.3 64.1 - - - +
425B VAL 3.4 0.3 + - - -
426B GLU* 3.7 17.0 + - - +
427B VAL* 4.5 2.1 + - - +
165E LYS 5.2 0.9 - - - +
167E MET 5.7 0.7 - - - +
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B TYR* 3.5 37.0 + - + -
420B THR 3.0 10.9 + - - +
421B ALA 3.0 8.3 + - - +
423B GLN* 1.3 76.6 - - - +
425B VAL* 1.3 64.0 + - - +
426B GLU 3.1 2.9 - - - -
427B VAL* 3.1 49.5 + - - +
428B TRP* 3.2 41.4 + - + +
167E MET 5.3 1.6 - - - +
169E GLU* 5.3 1.6 - - - +
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.6 20.0 - - + +
101B GLY* 3.8 32.3 - - - -
102B ALA* 4.4 1.6 - - - +
105B MET* 4.5 5.6 - - - -
242B PHE* 3.9 17.3 - - + -
246B TYR* 3.7 33.7 - - + -
421B ALA 3.2 15.8 + - - +
422B ALA 4.0 1.6 - - - +
423B GLN 3.3 1.2 - - - -
424B GLU* 1.3 76.0 - - - +
426B GLU* 1.3 61.9 + - - +
428B TRP* 3.5 13.9 + - + -
429B LEU* 3.1 22.2 + - + +
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Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ARG* 3.4 22.6 + - - -
246B TYR* 2.9 41.0 + - - +
247B LYS* 3.9 20.0 - - - -
250B ARG* 4.0 6.8 + - - -
423B GLN 3.7 10.3 - - - +
425B VAL* 1.3 79.1 - - - +
427B VAL* 1.3 60.9 + - + +
429B LEU* 3.5 4.4 + - - +
430B ASP* 3.2 38.4 + - - +
161E HIS* 4.8 4.0 - - + +
165E LYS* 3.8 42.3 - - + +
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLN 5.3 1.3 - - - +
424B GLU* 3.1 44.6 + - - +
426B GLU* 1.3 79.7 - - + +
428B TRP* 1.3 73.4 + - + +
430B ASP* 3.5 5.6 + - - +
431B LYS* 3.2 23.8 + - + +
161E HIS* 6.3 0.4 - - + -
167E MET 4.2 11.0 - - - +
168E PRO* 5.1 0.4 - - + -
169E GLU* 3.8 52.5 - - + +
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.0 29.2 - - + +
97B ASN* 3.3 44.2 - - + +
98B LEU* 3.8 19.8 - - + +
101B GLY* 4.4 1.1 - - - -
286B PHE* 3.1 53.6 + + + +
297B TYR* 4.6 3.4 - + + +
421B ALA 4.6 2.2 - - - -
424B GLU* 3.2 39.6 + - + +
425B VAL* 3.7 31.6 - - + +
427B VAL* 1.3 83.5 - - + +
429B LEU* 1.3 61.4 + - - +
431B LYS* 3.7 2.6 - - + +
432B LEU* 2.8 31.0 + - - +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.0 21.1 - - + +
213B PHE* 4.3 8.3 - - + -
239B ILE* 4.1 19.0 - - + +
242B PHE* 3.9 29.8 - - + -
243B ARG* 3.4 53.8 - - + +
246B TYR* 4.9 6.3 - - + -
425B VAL 3.1 18.2 + - - +
426B GLU* 3.6 6.1 - - - +
428B TRP* 1.3 78.7 - - - +
430B ASP* 1.3 55.2 + - - +
432B LEU* 3.2 3.3 + - + +
433B GLU* 2.7 37.5 + - - +
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Residues in contact with ASP 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ARG* 2.9 32.6 + - - -
426B GLU* 3.2 28.0 + - - +
427B VAL* 3.5 6.9 - - - +
429B LEU* 1.3 81.6 - - - +
431B LYS* 1.3 55.8 + - - +
433B GLU* 3.3 8.1 + - - +
434B ALA* 3.0 27.6 + - - +
161E HIS* 4.4 12.6 + - - -
165E LYS* 4.7 6.1 + - - +
178E MET* 5.7 4.3 - - - +
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Residues in contact with LYS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU* 5.2 13.5 - - - +
94B LEU* 3.9 28.9 - - + -
288B THR* 6.1 5.2 - - - -
427B VAL* 3.2 17.0 + - + +
428B TRP* 3.7 7.2 - - + +
430B ASP* 1.3 69.8 - - - +
432B LEU* 1.4 70.8 + - - +
433B GLU 3.0 1.6 - - - -
434B ALA* 4.4 5.8 - - - -
435B ASN* 2.9 31.9 + - - +
169E GLU* 2.4 48.9 + - - +
177E VAL* 3.8 16.7 - - + +
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 3.7 45.8 - - + +
94B LEU* 3.8 15.7 - - + +
95B MET* 4.4 6.3 - - + +
98B LEU* 4.5 9.9 - - + -
213B PHE* 4.4 17.7 - - + -
234B LEU* 3.9 24.2 - - + -
239B ILE* 3.6 26.5 - - + -
428B TRP 2.8 23.2 + - - +
429B LEU* 3.6 7.2 - - + +
431B LYS* 1.4 76.1 - - - +
433B GLU* 1.3 57.7 + - - +
435B ASN* 3.3 4.3 + - - +
436B VAL* 3.0 25.5 + - + +
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Residues in contact with GLU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PRO* 5.1 9.0 - - + +
239B ILE* 3.7 30.4 - - + +
243B ARG* 3.0 25.0 + - - -
429B LEU 2.7 16.8 + - - +
430B ASP* 3.3 8.1 - - - +
432B LEU* 1.3 79.9 - - - +
434B ALA* 1.3 54.9 + - - +
436B VAL* 3.4 4.5 + - + +
437B LYS* 3.0 62.7 + - - +
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B ASP 3.0 15.1 + - - +
431B LYS* 3.1 8.3 + - + +
433B GLU* 1.3 73.9 - - - +
435B ASN* 1.3 70.5 + - - +
437B LYS* 3.7 9.6 - - - +
438B ALA* 3.0 25.5 + - - +
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Residues in contact with ASN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU* 2.9 29.8 + - - +
91B ASN* 2.8 26.5 + - - +
94B LEU* 3.9 8.7 - - - +
431B LYS* 2.9 18.7 + - - +
432B LEU 3.4 8.5 - - - +
434B ALA* 1.3 78.3 - - - +
436B VAL* 1.3 64.8 + - - +
438B ALA* 3.4 4.8 + - - -
439B GLY 3.4 2.8 + - - -
440B LYS* 2.8 50.0 + - + +
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Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN* 4.1 5.2 - - - +
234B LEU* 3.3 55.2 - - + +
236B PRO* 5.6 6.1 - - + -
239B ILE* 5.3 2.5 - - + -
432B LEU* 3.0 19.1 + - + +
433B GLU* 3.4 6.3 + - - +
434B ALA 3.2 0.2 - - - -
435B ASN* 1.3 81.4 - - - +
437B LYS* 1.3 58.2 + - - +
439B GLY* 3.0 20.0 + - - -
440B LYS 3.9 13.5 - - - +
441B ASP* 4.9 5.8 - - + +
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Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PRO* 4.8 17.6 - - - +
433B GLU* 3.0 54.3 + - - +
434B ALA* 3.7 9.2 - - - +
436B VAL* 1.3 74.0 - - + +
438B ALA* 1.3 55.6 + - - +
439B GLY* 3.0 9.6 + - - -
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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