Contacts of the helix formed by residues 421 - 452 (chain C) in PDB entry 3A0B
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 SER 421 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C GLY* 5.0 3.1 - - - -
304C PRO* 5.2 0.7 - - - -
399C ALA 5.0 1.2 + - - -
400C PRO* 3.7 27.1 - - - +
401C LEU 5.2 0.8 + - - -
419C PHE* 3.2 24.4 - - - -
420C VAL* 1.3 72.6 - - - +
422C PRO* 1.3 69.3 - - - +
423C ARG* 2.8 24.4 + - - +
424C SER* 2.9 12.9 + - - -
425C TRP* 2.8 31.5 + - - -
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Residues in contact with PRO 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.6 40.6 - - + +
84C GLN 5.3 1.3 - - - +
86C LEU 4.2 18.8 - - - +
87C ILE* 4.3 11.0 - - + -
302C TYR* 4.0 22.2 - - + -
303C GLY* 3.8 8.7 - - - +
419C PHE* 4.3 0.7 - - + -
420C VAL 4.2 2.0 - - - +
421C SER* 1.3 85.6 - - - +
423C ARG* 1.3 52.5 + - - +
424C SER 3.0 4.7 - - - -
425C TRP* 2.7 13.9 + - + +
426C LEU* 2.7 40.2 + - + +
1056C DGD 6.6 0.2 - - - -
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Residues in contact with ARG 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C VAL* 3.0 44.4 + - + +
291C TRP* 3.4 13.0 + - + -
292C PHE 4.3 0.4 + - - -
293C ASN 2.6 30.9 + - - -
294C ASN* 4.7 0.6 - - - +
297C TYR* 2.8 30.3 + - - +
299C SER* 3.7 5.4 + - - +
302C TYR* 3.6 12.4 - - + +
303C GLY 2.6 59.9 + - - +
304C PRO 3.5 4.7 - - - -
305C THR* 3.4 29.3 - - - +
400C PRO* 4.8 1.6 - - + -
421C SER* 3.4 7.6 - - - +
422C PRO* 1.3 77.1 - - - +
424C SER* 1.3 58.3 + - - +
427C ALA* 3.2 26.5 + - - +
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Residues in contact with SER 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PHE* 3.2 16.4 + - - +
296A ASN 3.7 11.6 + - - -
297A LEU* 4.4 5.2 + - - +
291C TRP* 3.7 10.5 - - - -
400C PRO 3.6 20.3 + - - -
420C VAL* 4.3 9.6 - - - +
421C SER* 2.9 25.1 + - - -
423C ARG* 1.3 79.1 - - - +
425C TRP* 1.3 58.4 + - - +
427C ALA* 3.5 1.9 + - - +
428C THR* 2.8 29.7 + - - +
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Residues in contact with TRP 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.4 32.8 - - + -
87C ILE* 5.4 2.5 - - + -
403C SER 4.6 1.1 - - - -
404C LEU* 3.9 15.5 - - + -
406C SER* 3.7 13.9 - - - -
420C VAL* 3.1 32.0 - - + +
421C SER 2.8 27.3 + - - -
422C PRO* 2.7 12.4 + - + +
424C SER* 1.3 77.9 - - - +
426C LEU* 1.3 50.4 + - + +
428C THR* 2.8 18.0 - - + +
429C SER* 2.6 26.2 + - - -
1028C CLA 2.7 76.0 - - + +
1056C DGD 2.7 42.2 + - + -
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ILE* 4.4 18.2 - - + -
91C HIS* 4.7 4.9 - - + -
287C THR* 4.0 0.3 + - - -
290C VAL* 3.6 27.1 - - + +
297C TYR* 5.0 0.9 - - + -
302C TYR* 4.4 25.8 - - + -
422C PRO 2.7 20.1 + - - +
425C TRP* 1.3 71.0 - - - +
427C ALA* 1.3 64.4 + - - +
429C SER* 2.8 12.8 + - - -
430C HIS* 3.4 23.2 + - + +
1026C CLA 4.0 44.0 - - + -
1028C CLA 3.6 23.1 - - + -
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Residues in contact with ALA 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PHE* 3.7 23.1 - - + -
287C THR* 2.7 51.5 + - + +
290C VAL* 3.7 5.1 - - + +
291C TRP* 3.8 7.4 - - + -
423C ARG 3.2 20.7 + - - +
424C SER 3.7 4.0 - - - +
425C TRP 3.3 0.4 - - - -
426C LEU* 1.3 76.1 - - - +
428C THR* 1.3 67.0 + - - +
431C PHE* 3.4 3.6 + - - +
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Residues in contact with THR 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A THR* 2.9 34.0 + - - +
295A PHE* 4.4 11.8 - - - -
297A LEU* 3.7 21.0 - - + +
424C SER 2.8 19.4 + - - +
425C TRP* 2.8 17.0 - - - +
427C ALA* 1.3 74.3 - - - +
429C SER* 1.3 76.3 + - - +
431C PHE* 2.8 19.5 + - - +
432C VAL* 3.2 6.6 + - - +
1056C DGD 3.3 19.3 - - + +
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Residues in contact with SER 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425C TRP 2.6 21.7 + - - -
426C LEU* 2.8 15.1 + - - -
428C THR* 1.3 82.2 + - - +
430C HIS* 1.3 77.5 + - - -
432C VAL* 3.0 14.9 + - - +
433C LEU* 3.3 16.0 + - - +
1028C CLA 3.5 19.8 - - - +
1056C DGD 3.2 32.1 - - - -
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Residues in contact with HIS 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLY* 4.2 6.7 - - - +
286C ALA* 4.0 10.8 - - + -
287C THR* 3.0 20.0 - - - +
426C LEU* 3.4 15.9 + - + +
428C THR 3.4 0.2 - - - -
429C SER* 1.3 90.7 + - - +
431C PHE* 1.3 53.1 + - - +
433C LEU* 2.9 11.0 + - - +
434C ALA* 2.6 37.8 + - - +
1026C CLA 3.0 104.5 + + + +
1028C CLA 5.0 3.9 - - + +
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Residues in contact with PHE 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 3.1 46.7 - - + -
288A LEU* 5.5 4.5 - - + -
291A SER* 3.8 20.0 - - - +
292A THR* 6.2 0.9 - - - -
295A PHE* 3.5 24.9 - + + -
284C PHE* 3.5 33.7 - + - -
287C THR* 3.1 13.5 + - + +
427C ALA 3.5 8.5 - - - +
428C THR* 2.8 18.6 + - - +
430C HIS* 1.3 69.6 - - - +
432C VAL* 1.3 57.8 + - + +
434C ALA* 4.5 4.7 - - - +
435C PHE* 2.5 51.6 + + + +
1055C DGD 4.7 4.7 - - + -
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Residues in contact with VAL 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.5 13.9 - - + -
285A PHE* 5.8 0.2 - - + -
288A LEU* 3.2 36.5 - - + +
292A THR* 4.7 12.6 - - - +
428C THR* 4.0 11.4 - - - +
429C SER* 3.0 9.4 + - - +
431C PHE* 1.3 79.1 - - + +
433C LEU* 1.3 64.1 + - + +
435C PHE* 3.5 1.7 - - - +
436C PHE* 3.2 31.1 + - + +
1028C CLA 4.0 32.5 - - + -
1056C DGD 5.0 8.5 - - + -
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Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C SER* 3.4 21.1 - - - +
430C HIS* 2.9 10.3 + - - +
432C VAL* 1.3 76.1 - - + +
434C ALA* 1.3 63.5 + - - +
435C PHE 2.8 5.4 + - - -
436C PHE* 3.2 6.1 + - + +
437C PHE* 3.0 31.8 + - + -
1026C CLA 3.4 61.5 - - + -
1028C CLA 3.5 48.7 - - + -
1034C CLA 5.8 6.7 - - + -
1056C DGD 5.9 1.6 - - + -
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Residues in contact with ALA 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C SER* 2.3 47.7 + - - +
283C GLY* 3.2 39.9 - - - -
284C PHE* 3.3 10.6 - - + +
430C HIS 2.6 16.5 + - - +
431C PHE* 4.0 1.8 - - - +
433C LEU* 1.3 73.3 - - - +
435C PHE* 1.3 58.5 + - - +
437C PHE* 4.0 1.3 - - - -
438C LEU 3.4 0.5 + - - -
1026C CLA 3.5 11.3 - - + +
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Residues in contact with PHE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 5.2 2.5 - - - -
152A ALA* 3.7 31.6 - - + -
284A TRP* 4.0 22.7 - + - -
288A LEU* 3.2 35.9 - - + -
284C PHE* 3.5 11.6 - + - -
431C PHE* 2.5 41.1 + + + +
432C VAL* 3.5 3.6 - - - +
433C LEU 2.8 0.6 + - - -
434C ALA* 1.3 70.9 - - - +
436C PHE* 1.3 77.1 + + - +
437C PHE 2.5 0.3 + - - -
438C LEU* 2.4 43.5 + - + +
439C VAL* 3.6 16.8 + - + -
1055C DGD 4.1 20.9 - - + -
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Residues in contact with PHE 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL 5.7 0.2 - - - -
284A TRP* 4.2 18.2 - + + -
285A PHE* 4.0 17.5 - + - -
288A LEU* 4.3 9.2 - - + -
1063A LHG 3.2 45.1 - - + -
432C VAL* 3.2 22.0 + - + +
433C LEU* 3.7 5.4 - - + +
435C PHE* 1.3 103.0 - + - +
437C PHE* 1.3 52.9 + - + +
439C VAL* 2.5 33.1 + - + +
440C GLY 2.6 18.9 + - - -
1028C CLA 4.1 23.6 - - + -
1032C CLA 3.2 18.3 - - + +
1034C CLA 6.4 1.6 - - + -
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Residues in contact with PHE 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C LEU* 3.2 18.2 - - + +
279C LEU* 4.0 37.5 - - + -
280C SER* 3.7 10.3 - - - -
433C LEU* 3.0 25.2 + - + +
434C ALA* 3.6 7.4 - - - +
435C PHE 2.5 4.2 + - - -
436C PHE* 1.3 77.7 - - + +
438C LEU* 1.3 51.7 + - - +
440C GLY* 2.5 19.9 + - - -
441C HIS 2.6 15.9 + - - -
1026C CLA 3.3 37.9 - - + -
1032C CLA 3.2 44.6 - - + -
1034C CLA 4.3 21.3 - + + -
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Residues in contact with LEU 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C GLY 4.9 2.7 - - - +
280C SER* 2.8 27.9 + - - +
281C MET 5.6 0.4 - - - +
284C PHE* 4.5 13.9 - - + -
434C ALA 4.0 0.7 - - - +
435C PHE* 2.4 28.8 + - + +
437C PHE* 1.3 68.3 - - - +
439C VAL* 1.3 59.9 + - - +
441C HIS* 3.5 8.1 + - + +
442C LEU* 3.2 28.3 + - + +
1029C CLA 4.2 46.4 - - + -
1055C DGD 3.7 37.9 - - + -
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL* 4.4 13.2 - - + +
148A SER* 3.9 18.2 - - - +
284A TRP* 3.3 32.3 - - + -
435C PHE* 4.2 14.9 - - + +
436C PHE* 2.5 54.0 + - + +
438C LEU* 1.3 79.1 - - - +
440C GLY* 1.3 58.2 + - - +
442C LEU* 3.6 8.6 - - + +
443C TRP* 3.2 21.1 + - - +
1032C CLA 3.1 19.7 - - + +
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Residues in contact with GLY 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C LEU* 3.9 6.3 - - - -
436C PHE 2.6 4.9 + - - -
437C PHE 2.5 10.2 + - - -
439C VAL* 1.3 79.4 - - - +
441C HIS* 1.3 58.5 + - - -
442C LEU 3.3 0.2 - - - -
443C TRP* 3.1 18.8 - - - +
444C HIS* 3.4 18.4 + - - -
1032C CLA 3.4 33.7 - - - -
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Residues in contact with HIS 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C SER* 4.3 10.8 + - - +
274C TYR* 5.8 1.3 + - - -
276C LEU* 3.5 25.3 - - + +
277C GLY* 3.4 24.4 + - - +
437C PHE 2.6 11.1 + - - +
438C LEU* 3.8 7.4 - - + +
440C GLY* 1.3 69.9 - - - +
442C LEU* 1.3 91.5 + - + +
445C ALA* 3.0 27.9 + - + +
1029C CLA 2.7 74.8 + + + +
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 3.4 39.9 - - + -
142A TRP* 5.0 0.6 - - - -
144A CYS* 3.7 13.5 - - - +
145A VAL* 3.6 16.8 - - + -
148A SER* 5.3 1.8 - - - -
438C LEU* 3.2 15.2 + - + +
439C VAL* 3.6 11.7 - - - +
441C HIS* 1.3 100.5 - - + +
443C TRP* 1.3 70.4 + - - +
445C ALA* 5.0 0.4 - - - -
446C GLY* 2.9 19.3 + - - +
1029C CLA 3.3 44.9 - - + -
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Residues in contact with TRP 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TRP* 2.7 87.2 + + + +
145A VAL* 3.8 18.4 - - + +
1063A LHG 3.0 29.8 - - - -
439C VAL 3.2 11.5 + - - +
440C GLY* 3.1 15.5 - - - +
442C LEU* 1.3 81.2 - - - +
444C HIS* 1.3 94.7 + + - +
447C ARG* 3.3 6.7 + - - +
1032C CLA 3.3 59.8 + + + -
219D GLU* 4.2 4.5 - - - -
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Residues in contact with HIS 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C GLU* 3.5 31.9 + - + +
272C LEU* 3.6 27.2 - - + +
273C SER* 3.9 12.3 - - - -
276C LEU* 4.0 9.2 - - + -
440C GLY 3.4 17.5 + - - -
442C LEU 3.0 1.0 + - - -
443C TRP* 1.3 105.4 + + - +
445C ALA* 1.3 54.4 - - - +
446C GLY 2.7 11.4 + - - -
447C ARG* 2.8 1.0 + - - -
448C ALA* 2.6 35.1 + - - +
1032C CLA 3.3 54.7 + + + -
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ALA* 5.3 1.1 - - - +
273C SER* 3.4 24.0 - - - +
274C TYR* 5.6 0.4 - - + -
441C HIS* 3.0 40.1 + - + +
442C LEU* 4.2 0.7 - - - +
444C HIS* 1.3 72.6 - - - +
446C GLY* 1.3 56.4 + - - +
448C ALA* 4.4 5.0 - - - +
449C ARG* 3.7 3.7 + - - +
1029C CLA 3.0 53.3 - - + +
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Residues in contact with GLY 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TRP* 3.9 19.8 + - - -
141A PRO* 2.9 26.5 - - - +
142A TRP* 5.4 0.4 - - - -
442C LEU 2.9 13.8 + - - -
443C TRP 4.1 0.9 - - - -
444C HIS 2.7 2.2 + - - -
445C ALA* 1.3 79.4 - - - +
447C ARG* 1.3 60.4 + - - +
449C ARG* 3.5 13.4 - - - +
450C ALA* 3.9 2.6 + - - +
1029C CLA 5.4 3.1 - - - -
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Residues in contact with ARG 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO* 3.3 10.9 - - + +
142A TRP* 3.2 36.6 - - + +
1063A LHG 2.4 34.4 + - - -
33C PHE* 5.6 7.4 - - - -
269C GLU* 2.6 40.5 + - - +
443C TRP* 3.3 4.9 + - - +
444C HIS* 2.8 8.5 + - - +
446C GLY* 1.3 72.3 - - - +
448C ALA* 1.3 57.9 + - - +
449C ARG 2.8 4.9 - - - -
450C ALA* 2.5 33.8 + - + +
451C ALA* 3.3 3.2 + - - -
456C GLU* 3.4 31.7 + - + +
1032C CLA 2.8 29.1 + - - -
229D ALA* 4.7 11.7 + - - +
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Residues in contact with ALA 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ILE* 4.3 13.3 - - - +
267C SER* 4.4 5.3 - - - -
269C GLU* 3.6 17.9 - - + +
270C ALA* 3.5 41.5 - - + +
444C HIS 2.6 20.6 + - - +
445C ALA* 4.7 3.1 - - - -
447C ARG* 1.3 74.1 - - - +
449C ARG* 1.3 56.0 + - - +
450C ALA 3.1 1.8 - - - -
451C ALA* 3.6 14.1 + - - +
452C ALA* 3.8 8.3 + - - +
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Residues in contact with ARG 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TRP* 4.1 13.4 - - + +
135A TYR* 2.8 100.6 - - + -
136A ARG* 3.9 4.2 - - - +
263C ALA* 5.1 1.2 - - - +
264C PHE 5.1 4.8 - - - +
265C ILE* 3.3 31.6 - - - +
445C ALA 3.7 4.3 + - - +
446C GLY* 3.5 15.8 + - - +
447C ARG 2.8 0.4 + - - -
448C ALA* 1.3 78.9 - - - +
450C ALA* 1.3 57.3 + - - +
451C ALA 3.5 0.2 - - - -
452C ALA 4.4 2.0 - - - -
453C ALA* 3.0 7.8 + - - +
1029C CLA 2.8 52.7 + - - +
27I ASP* 3.2 27.0 + - - -
28I PRO* 4.4 7.4 - - - +
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Residues in contact with ALA 450 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO* 4.4 11.9 - - + -
446C GLY 3.9 1.7 + - - +
447C ARG* 2.5 26.9 + - - +
449C ARG* 1.3 71.8 - - - +
451C ALA* 1.3 52.2 + - - -
453C ALA* 3.5 6.5 - - - -
454C GLY* 2.2 31.9 + - - -
455C PHE* 2.8 26.8 + - + -
456C GLU* 3.1 26.8 - - + +
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Residues in contact with ALA 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C SER* 4.6 12.3 - - - +
269C GLU* 5.1 4.9 - - - +
447C ARG 3.3 3.6 + - - +
448C ALA* 3.9 15.7 - - - +
449C ARG 3.5 0.8 - - - -
450C ALA* 1.3 74.2 - - - +
452C ALA* 1.3 56.0 + - - +
453C ALA 2.4 15.3 + - - -
454C GLY* 2.7 12.5 + - - -
456C GLU* 3.3 25.8 - - + +
35I LYS 3.6 8.3 - - - +
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Residues in contact with ALA 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 5.2 0.7 - - - -
265C ILE* 3.4 43.3 - - + -
267C SER* 5.8 1.8 - - - -
448C ALA 3.8 4.0 + - - +
449C ARG 4.8 1.6 - - - +
450C ALA 3.6 0.2 - - - -
451C ALA* 1.3 76.9 - - - +
453C ALA* 1.3 57.0 + - - +
28I PRO 4.7 3.8 - - - +
34I ARG* 3.2 27.1 - - - +
35I LYS 5.2 1.3 - - - -
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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) + - + + + + + -
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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