Contacts of the helix formed by residues 409 - 435 (chain A) in PDB entry 3DYQ
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 PRO 409 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PRO 3.7 14.6 - - - +
200A THR* 3.7 37.7 - - + +
407A VAL 4.6 0.9 - - - +
408A ARG* 1.3 88.4 - - + +
410A MET* 1.3 61.1 - - - +
411A GLU* 3.2 10.8 - - - +
412A VAL* 2.9 20.2 + - + +
413A ALA 2.8 24.3 + - - -
482A PRO* 6.1 1.3 - - + -
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Residues in contact with MET 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ARG 3.4 3.2 + - - -
409A PRO* 1.3 71.3 - - - +
411A GLU* 1.3 86.8 + - + +
413A ALA* 4.4 5.2 - - - +
414A GLU* 3.0 37.6 + - + +
486A SER* 5.9 4.5 - - - +
489A ARG* 3.8 54.5 - - - +
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TRP* 4.8 1.7 - - - -
409A PRO* 3.1 9.9 + - - +
410A MET* 1.3 104.2 + - + +
412A VAL* 1.3 60.4 + - + +
414A GLU* 5.0 1.3 - - - -
415A PRO* 3.3 21.2 - - - +
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR 4.6 2.0 - - - +
201A PHE 4.2 8.1 - - - +
202A ASP* 3.8 28.5 - - + +
203A VAL* 4.1 20.2 - - + -
204A TRP* 3.0 30.6 + - + -
408A ARG* 3.8 28.7 - - + -
409A PRO* 2.9 27.7 + - + +
411A GLU* 1.3 80.4 - - + +
413A ALA* 1.3 63.0 + - - +
414A GLU 3.4 0.2 - - - -
415A PRO* 3.6 1.3 - - - +
416A TRP* 3.4 7.2 - - - +
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ASN* 3.4 28.3 - - - +
406A GLU* 4.0 23.9 - - - +
408A ARG* 3.9 7.9 - - - +
409A PRO 2.8 18.4 + - - +
410A MET* 3.2 5.8 + - - +
412A VAL* 1.3 73.6 - - - +
414A GLU* 1.3 67.0 + - - +
416A TRP* 3.0 26.6 + - - +
417A VAL* 3.9 5.2 + - - +
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Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A MET* 3.0 22.7 + - + +
411A GLU* 4.9 1.1 - - - +
413A ALA* 1.3 77.8 - - - +
415A PRO* 1.3 72.9 - - + +
416A TRP 3.1 0.7 + - - -
417A VAL* 3.2 11.7 + - - +
418A ASP* 4.5 3.6 - - - +
449A LYS* 3.0 51.4 + - - -
489A ARG* 3.8 30.4 + - - +
490A TYR* 3.6 24.8 + - - +
493A LEU* 5.5 2.3 - - - +
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Residues in contact with PRO 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TRP* 3.6 30.1 - - + +
411A GLU 3.3 24.0 - - - +
412A VAL 3.6 2.9 - - - +
413A ALA 3.6 3.4 - - - -
414A GLU* 1.3 97.2 - - + +
416A TRP* 1.3 60.6 + - - +
417A VAL 3.2 0.6 + - - -
418A ASP* 3.4 19.8 + - - +
419A CYS* 3.4 15.6 + - - -
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Residues in contact with TRP 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 3.7 11.1 - - + +
204A TRP* 3.3 28.5 - + - +
250A PRO 4.8 1.6 - - - -
251A PHE* 3.7 45.9 - + + -
253A ASN* 4.0 7.9 - - - -
255A ARG* 3.8 27.4 - - + -
256A HIS* 3.5 28.0 - - + -
259A CYS* 3.4 26.3 - - - -
405A ASN* 3.4 33.4 + - + +
408A ARG* 5.5 1.9 - - - +
412A VAL* 3.4 23.3 - - + +
413A ALA* 3.0 13.1 + - - +
415A PRO* 1.3 77.9 - - - +
417A VAL* 1.3 64.3 + - + +
419A CYS* 3.0 10.3 + - + +
420A LEU* 2.9 22.0 + - - +
900A PCG 6.1 0.2 - - - +
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Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU* 3.5 12.8 - - - +
413A ALA 4.3 4.5 - - - +
414A GLU 3.2 11.1 + - - +
416A TRP* 1.3 77.4 - - + +
418A ASP* 1.3 62.9 + - - +
420A LEU* 3.1 10.2 + - + +
421A LEU* 3.0 30.4 + - + +
449A LYS* 3.9 31.6 - - + +
452A ALA* 4.9 2.2 - - + -
453A GLN* 3.4 42.8 - - + +
490A TYR* 3.6 14.1 - - - +
900A PCG 5.0 2.2 - - - +
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Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLU* 3.9 9.0 - - - +
415A PRO* 3.4 11.3 + - + +
416A TRP 3.3 0.4 - - - -
417A VAL* 1.3 76.4 - - - +
419A CYS* 1.3 57.4 + - - +
421A LEU* 3.6 6.0 + - - +
422A GLU* 3.0 31.3 + - - +
449A LYS* 3.0 42.0 + - - +
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Residues in contact with CYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TRP* 4.4 16.8 - - - -
250A PRO* 3.1 34.1 - - - +
251A PHE* 3.8 9.8 - - + +
415A PRO 3.4 13.9 + - - -
416A TRP* 3.0 16.4 + - + +
418A ASP* 1.3 76.5 - - - +
420A LEU* 1.3 66.5 + - - +
422A GLU* 3.3 15.5 + - - +
423A GLU* 3.2 18.4 + - - +
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 3.6 31.4 - - + -
252A HIS* 5.0 4.3 - - + -
416A TRP 2.9 13.1 + - - +
417A VAL* 3.5 12.3 - - + +
419A CYS* 1.3 75.9 - - - +
421A LEU* 1.3 63.8 + - + +
423A GLU* 3.1 7.2 + - + +
424A TYR* 2.9 65.1 + - + +
453A GLN* 4.9 1.3 - - - +
900A PCG 3.3 65.1 - - + +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A VAL* 3.0 21.0 + - + +
418A ASP* 4.1 4.9 - - - +
420A LEU* 1.3 76.2 - - + +
422A GLU* 1.3 60.7 + - - +
424A TYR* 3.9 26.5 - - + -
425A PHE* 2.8 58.6 + - + -
447A VAL* 3.9 22.0 - - + +
448A THR* 4.0 7.9 - - - +
449A LYS* 3.8 37.5 - - + +
452A ALA* 4.3 13.2 - - + -
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO* 3.8 23.7 - - + +
418A ASP* 3.0 18.0 + - - +
419A CYS* 3.3 17.5 - - - +
421A LEU* 1.3 75.7 - - - +
423A GLU* 1.3 57.3 + - - +
425A PHE* 4.0 4.9 - - - +
426A MET* 3.1 40.9 + - + +
444A ARG* 6.3 0.2 - - - +
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASN* 3.3 9.0 - - - +
250A PRO* 3.5 11.0 - - + +
251A PHE* 2.8 33.1 + - + -
252A HIS* 2.3 43.8 + - - +
296A HIS* 3.9 1.2 - - - -
298A GLY* 3.5 36.6 - - - +
419A CYS 3.2 6.3 + - - +
420A LEU* 3.1 9.7 + - + +
422A GLU* 1.3 78.2 - - - +
424A TYR* 1.3 69.4 + - + +
426A MET* 3.3 9.6 + - + +
427A GLN* 3.1 23.3 + - - +
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Residues in contact with TYR 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS* 5.9 2.9 - + - -
300A ASN* 6.0 0.2 - - - -
420A LEU* 2.9 47.2 + - + +
421A LEU* 3.7 22.9 - - + +
423A GLU* 1.3 82.3 - - + +
425A PHE* 1.3 61.1 + - + +
427A GLN* 3.5 4.2 + - - +
428A SER* 3.0 29.1 + - - -
441A PHE* 3.8 43.2 - + - -
442A MET* 3.6 34.9 - - + +
452A ALA* 6.1 1.6 - - + -
900A PCG 2.5 42.0 + - - -
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Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 2.8 44.4 + - + +
422A GLU* 4.1 4.7 - - - +
424A TYR* 1.3 74.8 - - + +
426A MET* 1.3 67.1 + - - +
428A SER* 3.7 2.9 - - - -
429A ASP* 3.0 32.8 + - - -
442A MET 3.3 16.8 - - - -
443A ASP 4.0 2.5 - - - -
444A ARG* 3.5 71.8 - - + +
447A VAL* 4.0 34.8 - - + -
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Residues in contact with MET 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO* 3.9 27.8 - - + -
298A GLY 5.5 2.9 - - - +
299A TYR* 3.7 27.5 - - + +
422A GLU* 3.1 27.3 + - + +
423A GLU* 3.5 11.4 - - - +
425A PHE* 1.3 79.2 - - - +
427A GLN* 1.3 62.2 + - - +
429A ASP* 3.8 5.2 - - - +
430A ARG* 3.3 21.1 + - - +
444A ARG* 5.6 0.2 - - - +
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Residues in contact with GLN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLY 4.5 0.9 - - - +
299A TYR* 3.4 27.8 - - + -
300A ASN* 2.8 58.9 + - - +
302A THR* 4.8 0.6 - - - -
303A TYR* 3.7 8.9 - - + +
423A GLU 3.1 12.0 + - - +
424A TYR* 3.7 5.9 - - - +
426A MET* 1.3 81.2 - - - +
428A SER* 1.3 58.4 + - - +
430A ARG* 3.2 4.2 + - - +
431A GLU* 2.8 55.1 + - + +
442A MET* 3.6 17.7 - - - +
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR 3.0 12.3 + - - -
425A PHE* 3.4 7.4 + - - -
427A GLN* 1.3 73.4 - - - +
429A ASP* 1.3 68.0 + - - +
431A GLU* 3.2 15.5 - - - +
432A LYS* 3.0 36.6 + - - +
438A VAL* 3.7 14.7 - - - +
442A MET* 2.9 36.7 + - - -
443A ASP* 4.4 1.3 - - - -
444A ARG* 4.2 6.9 + - - +
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Residues in contact with ASP 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PHE 3.0 21.1 + - - +
426A MET* 3.8 5.9 - - - +
428A SER* 1.3 80.9 + - - +
430A ARG* 1.3 54.0 + - - +
432A LYS* 3.1 13.6 + - - +
433A SER* 2.8 34.0 + - - -
444A ARG* 2.5 42.9 + - - +
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Residues in contact with ARG 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TYR* 3.2 50.4 + - + -
303A TYR* 3.0 30.6 + - + +
426A MET 3.3 10.4 + - - +
427A GLN 3.2 8.7 + - - +
429A ASP* 1.3 77.0 - - - +
431A GLU* 1.3 67.0 + - - +
433A SER* 3.1 8.0 + - - -
434A GLU* 2.8 55.9 + - + +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 4.8 6.6 - - - +
303A TYR* 3.9 26.2 + - + +
306A ASN* 5.3 1.8 + - + +
427A GLN* 2.8 46.2 + - - +
428A SER* 3.2 25.9 + - - +
430A ARG* 1.3 73.6 - - - +
432A LYS* 1.3 61.6 + - - +
434A GLU 3.6 0.2 - - - -
435A GLY 3.0 4.0 + - - -
436A LEU* 2.8 45.6 + - + +
437A PRO 3.4 27.9 - - - +
438A VAL* 3.9 10.0 - - + -
439A ALA* 4.5 3.8 + - - +
442A MET* 5.3 2.6 - - - +
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Residues in contact with LYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A SER* 3.0 21.7 + - - +
429A ASP* 3.1 14.0 + - - +
431A GLU* 1.3 74.7 - - - +
433A SER* 1.3 65.1 + - - +
435A GLY* 3.2 12.4 + - - -
436A LEU 4.7 1.6 - - - -
438A VAL* 3.7 24.0 - - + +
443A ASP* 2.7 40.8 + - - +
444A ARG* 4.7 8.3 - - - +
445A ASP* 3.8 13.7 + - - -
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Residues in contact with SER 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ASP 2.8 15.9 + - - -
430A ARG* 3.5 11.6 + - - +
432A LYS* 1.3 74.5 - - - +
434A GLU* 1.3 66.4 + - - +
435A GLY 3.3 0.9 + - - -
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 2.8 23.9 + - - -
307A ALA* 4.7 1.0 - - - +
430A ARG* 2.8 52.9 + - + +
431A GLU 4.2 1.3 - - - +
433A SER* 1.3 80.2 - - - +
435A GLY* 1.3 61.8 + - - +
436A LEU* 3.2 26.7 + - + +
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Residues in contact with GLY 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLU 3.0 3.9 + - - -
432A LYS* 3.2 9.9 + - - -
433A SER 3.3 1.6 + - - -
434A GLU* 1.3 78.9 - - - +
436A LEU* 1.3 64.0 + - - +
437A PRO* 4.1 1.4 - - - +
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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