Contacts of the helix formed by residues 408 - 433 (chain A) in PDB entry 6EBT
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 PHE 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY* 4.5 1.1 - - - -
396A VAL* 5.5 4.0 - - + -
397A GLY* 3.8 36.8 - - - +
400A ASN* 3.5 46.0 - - + -
402A HIS* 4.6 10.8 - + - -
406A ASN* 2.9 13.5 + - - +
407A VAL* 1.3 90.1 - - + +
409A LYS* 1.3 64.3 + - - +
410A PRO* 3.5 4.3 - - - -
411A MET* 3.3 18.8 - - + +
412A MET* 3.2 21.8 + - + +
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY 2.9 17.8 + - - +
145A SER* 3.9 17.0 - - - +
188A ASN* 4.0 2.9 - - - +
191A PHE* 3.5 25.4 - - + -
192A PRO* 3.8 23.0 - - + +
195A MET* 3.4 11.0 - - - +
315A LEU 3.2 18.4 + - - -
318A HIS* 2.8 35.2 + - + +
405A LEU* 3.4 20.6 - - - +
406A ASN 2.8 26.8 + - - +
408A PHE* 1.3 76.6 - - - +
410A PRO* 1.3 64.8 - - + +
412A MET* 3.2 5.5 + - - +
413A ILE* 3.1 23.2 + - - +
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Residues in contact with PRO 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.0 13.0 - - + +
140A VAL* 3.2 30.4 - - + +
142A GLN* 4.3 3.6 - - + +
143A THR 3.4 18.6 - - - +
144A GLY* 3.2 18.4 - - - +
146A GLY* 4.0 7.6 - - - +
191A PHE* 3.8 20.6 - - + -
408A PHE* 3.6 3.1 - - - -
409A LYS* 1.3 90.2 - - + +
411A MET* 1.3 57.5 + - - +
413A ILE* 3.2 4.8 - - + +
414A LYS* 3.0 29.5 + - - +
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Residues in contact with MET 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 3.6 8.9 - - + +
141A TRP* 3.7 31.6 - - + -
393A ALA* 3.5 35.9 - - + +
397A GLY* 4.6 6.7 - - - -
408A PHE* 3.3 26.9 + - + +
410A PRO* 1.3 77.4 - - - +
412A MET* 1.3 79.2 + - - +
414A LYS* 3.7 1.3 - - - +
415A ASN* 2.7 51.5 + - - +
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Residues in contact with MET 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A HIS* 3.7 38.8 - - + +
321A LEU* 4.3 12.1 - - + -
322A VAL* 3.9 6.1 - - + -
394A VAL* 3.6 28.9 - - + +
397A GLY 3.7 5.2 - - - +
398A GLY* 3.4 37.2 - - - +
406A ASN* 4.1 11.7 - - - +
408A PHE* 3.2 18.6 - - + +
409A LYS* 3.2 5.3 + - - +
411A MET* 1.3 92.5 - - - +
413A ILE* 1.3 56.4 + - - +
415A ASN 3.4 1.6 + - - -
416A VAL* 3.0 33.3 + - - +
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 5.1 2.7 - - - -
89A PRO* 5.6 0.4 - - + -
92A VAL* 3.9 16.2 - - + -
191A PHE* 4.1 7.6 - - + -
195A MET* 3.4 55.0 - - + +
199A ALA* 4.3 9.0 - - + +
321A LEU* 4.3 11.9 - - + +
409A LYS 3.1 11.9 + - - +
410A PRO* 3.2 17.5 - - + +
412A MET* 1.3 74.7 - - - +
414A LYS* 1.3 64.1 + - + +
416A VAL* 4.3 4.0 - - + -
417A LEU* 2.9 58.3 + - + +
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Residues in contact with LYS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR 4.6 13.5 + - - -
86A GLU* 5.9 4.0 - - - +
87A ARG 5.3 3.4 + - - +
89A PRO* 3.8 28.7 - - + +
140A VAL* 3.9 28.0 - - + -
141A TRP* 5.5 6.3 - - + -
410A PRO 3.0 20.7 + - - +
411A MET 3.7 4.9 - - - +
413A ILE* 1.3 76.4 - - - +
415A ASN* 1.3 63.2 + - - +
417A LEU* 3.7 0.7 - - - +
418A HIS* 2.8 61.4 + - - +
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Residues in contact with ASN 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TRP* 5.4 4.2 - - - -
390A ASN* 3.2 34.1 + - + +
393A ALA* 3.8 12.9 - - - +
394A VAL* 3.5 22.7 - - + -
411A MET* 2.7 47.2 + - - +
414A LYS* 1.3 84.0 - - - +
416A VAL* 1.3 64.3 + - - +
418A HIS* 3.6 7.9 + - - +
419A SER* 3.0 29.6 + - - -
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA* 4.4 9.9 - - + -
321A LEU* 3.9 42.6 - - + +
324A LEU* 4.0 26.5 - - + -
325A SER* 4.3 6.1 - - - -
328A MET* 3.5 15.3 - - + +
394A VAL* 4.0 12.8 - - + -
412A MET 3.0 21.0 + - - +
413A ILE* 3.8 8.5 - - + +
414A LYS 3.3 0.2 - - - -
415A ASN* 1.3 78.2 - - - +
417A LEU* 1.3 65.5 + - + +
419A SER 3.3 0.2 + - - -
420A ALA* 3.0 22.2 + - + +
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 3.8 22.0 - - + -
91A PRO* 4.0 16.2 - - + -
92A VAL* 3.7 29.8 - - + -
198A ALA* 3.8 25.8 - - + +
199A ALA* 4.0 15.9 - - + +
202A GLU* 4.0 17.9 - - + +
413A ILE* 2.9 29.8 + - + +
414A LYS 3.9 2.2 - - - +
416A VAL* 1.3 74.2 - - + +
418A HIS* 1.3 66.1 + - - +
420A ALA* 3.9 3.9 - - + +
421A ARG* 2.9 27.5 + - - +
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Residues in contact with HIS 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLN* 4.1 15.5 - - + -
390A ASN* 3.2 21.9 + - - +
414A LYS* 2.8 48.1 + - - +
415A ASN* 3.6 7.0 + - - +
417A LEU* 1.3 72.9 - - - +
419A SER* 1.3 63.4 + - - +
421A ARG* 3.8 4.4 - - + +
422A LEU* 3.0 58.2 + - + +
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Residues in contact with SER 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A SER* 5.4 2.5 + - - -
328A MET* 3.8 18.8 - - - -
387A VAL* 3.8 29.2 + - - +
390A ASN* 3.2 25.4 + - - +
415A ASN 3.0 18.3 + - - -
416A VAL 3.8 3.6 - - - -
418A HIS* 1.3 75.2 - - - +
420A ALA* 1.3 59.6 + - - +
422A LEU* 3.8 2.9 - - - +
423A LEU* 2.9 35.2 + - - +
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 4.1 19.7 - - + -
203A VAL* 5.2 4.7 - - + -
206A VAL* 4.1 3.5 - - - +
207A LEU* 3.8 25.3 - - + +
324A LEU* 6.4 0.4 - - + -
328A MET* 3.5 17.6 - - + -
416A VAL* 3.0 20.3 + - + +
417A LEU* 3.9 4.9 - - + +
419A SER* 1.3 75.8 - - - +
421A ARG* 1.3 64.0 + - - +
424A GLY* 3.0 21.7 + - - -
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Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 3.8 21.2 - - - +
206A VAL* 4.2 13.0 - - - +
417A LEU 2.9 18.4 + - - +
418A HIS* 3.8 6.1 - - + +
420A ALA* 1.3 78.0 - - - +
422A LEU* 1.3 63.6 + - + +
424A GLY* 3.9 0.2 - - - -
425A ASP* 2.7 66.0 + - - +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A VAL* 3.6 31.6 - - + +
386A GLN* 4.1 20.0 - - + -
387A VAL* 5.2 1.3 - - + -
390A ASN* 4.9 0.4 - - - +
418A HIS* 3.0 57.4 + - + +
419A SER* 3.9 5.8 - - - +
421A ARG* 1.3 81.8 - - + +
423A LEU* 1.3 56.9 + - - +
425A ASP* 4.1 4.0 - - + +
426A ALA* 2.7 34.8 + - - +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.5 18.6 - - + -
211A LEU* 5.6 0.4 - - + -
328A MET* 3.7 44.0 - - + +
331A THR* 4.3 10.1 - - + -
332A ALA* 4.6 9.4 - - + -
335A LEU* 3.8 26.2 - - + -
380A MET* 4.8 1.9 - - - +
383A VAL* 4.0 11.4 - - + -
384A ALA* 5.1 2.5 - - - -
387A VAL* 3.8 22.2 - - + -
419A SER 2.9 20.3 + - - +
422A LEU* 1.3 75.7 - - - +
424A GLY* 1.3 54.3 + - - +
426A ALA* 4.1 1.9 - - - +
427A SER* 2.7 39.0 + - - +
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Residues in contact with GLY 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL* 3.6 26.2 - - - -
207A LEU* 3.9 10.2 - - - +
210A GLY* 3.9 0.7 - - - -
420A ALA 3.0 16.1 + - - -
421A ARG 3.9 0.4 - - - -
423A LEU* 1.3 76.9 - - - +
425A ASP* 1.3 62.6 + - - +
427A SER* 3.2 6.5 + - - -
428A VAL* 3.1 27.2 + - - +
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Residues in contact with ASP 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 3.8 12.3 - - - +
421A ARG* 2.7 60.6 + - - +
422A LEU* 4.1 4.4 - - + +
424A GLY* 1.3 71.4 - - - +
426A ALA* 1.3 57.2 + - - +
428A VAL* 3.2 8.4 + - - +
429A SER* 2.9 28.9 + - - -
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ALA* 5.4 2.2 - - + -
380A MET* 3.4 28.3 - - + +
383A VAL* 4.1 19.3 - - + -
422A LEU 2.7 25.9 + - - +
423A LEU 4.1 0.9 - - - +
425A ASP* 1.3 72.4 - - - +
427A SER* 1.3 52.6 + - - +
429A SER* 3.8 6.2 - - - -
430A PHE* 2.7 37.8 + - - +
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Residues in contact with SER 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLY 3.4 25.6 - - - -
211A LEU* 3.5 22.5 - - - +
214A LEU* 4.2 10.4 - - - +
335A LEU* 4.2 1.7 - - - +
380A MET* 3.6 13.9 - - - +
423A LEU 2.7 23.8 + - - -
424A GLY 3.2 4.7 + - - -
426A ALA* 1.3 77.9 - - - +
428A VAL* 1.3 60.5 + - - +
430A PHE* 3.8 2.1 - - - +
431A THR* 2.8 31.3 + - - -
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL 5.7 0.2 - - - +
210A GLY* 3.9 19.1 - - - -
213A LYS* 4.3 21.3 - - + -
424A GLY 3.1 16.0 + - - +
425A ASP* 3.2 8.9 + - - +
427A SER* 1.3 75.9 - - - +
429A SER* 1.3 63.2 + - - +
431A THR* 3.1 6.7 + - - -
432A GLU* 2.9 51.2 + - + +
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Residues in contact with SER 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLN* 2.6 29.1 + - - +
379A ALA* 6.5 0.2 - - - -
425A ASP 2.9 16.7 + - - -
426A ALA* 3.8 7.0 - - - -
428A VAL* 1.3 76.8 - - - +
430A PHE* 1.3 62.6 + - - +
432A GLU* 5.1 2.2 - - - -
433A ASN* 3.0 41.2 + - - +
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Residues in contact with PHE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.6 29.2 - - + -
335A LEU* 6.1 0.7 - - + -
338A ILE* 4.4 11.0 - - + -
339A ALA* 4.2 17.5 - - + -
342A ILE* 3.9 26.9 - - + -
376A GLN* 3.8 28.4 + - + +
377A CYS* 3.7 30.5 - - - -
380A MET* 3.9 19.5 - - + -
426A ALA 2.7 21.9 + - - +
427A SER 3.8 2.9 - - - +
429A SER* 1.3 72.4 - - - +
431A THR* 1.3 58.9 + - - +
434A CYS* 3.3 20.4 - - + +
435A VAL* 3.1 37.2 + - + +
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Residues in contact with THR 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 3.8 15.5 - - + +
214A LEU* 3.1 27.6 + - - +
217A ALA* 3.4 28.0 - - + -
427A SER 2.8 21.5 + - - -
428A VAL* 3.1 6.7 + - - -
430A PHE* 1.3 77.4 - - - +
432A GLU* 1.3 69.1 + - + +
435A VAL* 3.3 10.5 + - - -
436A VAL* 3.1 35.9 + - + +
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 4.4 13.3 - - - -
428A VAL* 2.9 41.6 + - + +
429A SER* 4.5 1.4 - - - +
431A THR* 1.3 80.2 - - + +
433A ASN* 1.3 71.7 + - - +
436A VAL* 3.4 21.5 - - + +
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Residues in contact with ASN 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PRO* 4.2 10.8 - - - +
361A ASN* 2.7 46.4 + - - +
376A GLN* 3.7 16.8 - - - +
429A SER* 3.0 36.1 + - - +
432A GLU* 1.3 87.6 + - - +
434A CYS* 1.3 61.4 + - - +
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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