Contacts of the helix formed by residues 546 - 575 (chain E) in PDB entry 2CEA
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 546 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D ARG* 4.4 0.2 - - - +
547D GLU* 2.9 23.3 - - - -
550D ALA* 3.8 6.0 - - - +
551D SER* 3.6 23.9 - - - -
554D ASP* 2.8 25.4 + - - -
543E ARG* 3.8 1.8 - - - -
545E TYR* 1.3 77.3 - - - +
547E GLU* 1.3 56.0 + - - +
548E GLU* 3.4 7.7 + - - +
549E VAL* 3.1 18.2 + - - +
550E ALA* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D GLU* 2.7 27.2 + - + +
543E ARG* 3.3 23.5 + - - +
546E SER* 1.3 72.2 - - - +
548E GLU* 1.3 62.8 + - - +
550E ALA* 3.4 1.6 - - - +
551E SER* 2.9 24.8 + - - -
543F ARG* 5.1 3.1 + - - -
546F SER* 2.9 19.3 - - - -
547F GLU* 2.5 45.8 + - + +
548F GLU* 4.0 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D GLU* 3.6 4.2 + - - +
551D SER* 3.2 25.7 + - - +
555D GLU* 4.1 15.0 - - - +
546E SER* 3.1 10.3 - - - +
547E GLU* 1.3 78.4 - - - +
549E VAL* 1.3 63.7 + - + +
551E SER* 3.2 19.6 + - - -
552E LYS* 3.3 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 549 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D ASP* 3.7 25.4 - - + +
521E LEU* 4.1 12.3 - - + -
526E TRP* 3.7 36.6 - - + -
545E TYR* 4.4 4.7 - - + -
546E SER* 3.1 18.4 + - - +
548E GLU* 1.3 75.3 - - + +
550E ALA* 1.3 67.1 + - - +
551E SER 3.1 2.2 - - - -
552E LYS* 3.1 16.4 + - - +
553E ILE* 2.8 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E ARG* 5.6 0.2 + - - -
543E ARG* 3.8 20.4 - - - +
545E TYR* 3.7 23.5 - - + +
546E SER 2.8 13.8 + - - +
547E GLU* 3.0 10.5 + - - +
549E VAL* 1.3 77.3 - - - +
551E SER* 1.3 57.7 + - - +
553E ILE* 3.4 6.1 - - - +
554E ASP* 3.1 30.3 + - - +
545F TYR 5.1 1.1 - - - -
546F SER* 3.8 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 551 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547E GLU* 2.9 12.1 + - - -
548E GLU* 3.2 11.4 + - - -
550E ALA* 1.3 77.7 - - - +
552E LYS* 1.3 66.8 + - - +
554E ASP* 3.2 2.3 + - - +
555E GLU* 3.0 28.3 + - - +
546F SER* 3.5 22.9 - - - -
548F GLU* 3.1 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 552 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A GLU* 5.1 9.9 - - - +
520E GLU* 3.9 32.5 - - + +
521E LEU* 3.8 20.5 - - + +
548E GLU* 3.3 42.4 + - - +
549E VAL* 3.1 16.8 + - - +
551E SER* 1.3 75.3 + - - +
553E ILE* 1.3 66.3 + - - +
555E GLU* 3.4 16.2 + - - +
556E GLU* 3.1 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 553 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E ARG* 3.8 19.7 - - - +
512E VAL* 4.4 2.9 - - + -
513E CYS* 3.7 32.3 - - - -
521E LEU* 3.7 22.4 - - + +
526E TRP* 3.9 14.6 - - + -
545E TYR* 3.6 34.3 - - + +
549E VAL* 2.8 24.1 + - + +
550E ALA* 3.4 7.6 - - - +
552E LYS* 1.3 76.5 - - - +
554E ASP* 1.3 63.2 + - - +
556E GLU* 3.2 3.0 + - - +
557E VAL* 3.0 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 554 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E ARG* 3.3 29.3 + - - -
550E ALA 3.1 9.5 + - - +
551E SER 3.2 5.1 + - - +
553E ILE* 1.3 75.8 - - - +
555E GLU* 1.3 56.7 + - - +
557E VAL* 3.7 5.4 - - - +
558E LYS* 3.0 30.8 + - - +
526F TRP* 3.8 13.0 - - + -
545F TYR* 3.8 10.4 - - - +
546F SER* 2.6 45.0 + - - +
549F VAL* 3.5 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 555 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLU* 5.3 1.3 - - + +
552A LYS* 5.3 11.4 + - - +
555A GLU* 4.5 19.8 - - - +
551E SER* 3.0 14.1 + - - +
552E LYS* 3.6 22.9 - - - +
553E ILE 3.3 0.2 - - - -
554E ASP* 1.3 73.1 - - - +
556E GLU* 1.3 64.7 + - + +
558E LYS* 3.4 8.7 + - + +
559E LYS* 2.8 38.0 + - - +
548F GLU* 4.9 8.0 - - - +
552F LYS* 6.0 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 556 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A LYS* 5.7 2.6 + - - -
512E VAL* 4.2 15.7 - - + -
518E SER* 3.5 20.5 - - - +
519E GLU* 4.1 13.9 + - - +
520E GLU* 4.4 17.5 - - + +
521E LEU* 4.3 16.4 - - + -
552E LYS* 3.1 16.8 + - + +
553E ILE 3.6 3.8 - - - +
555E GLU* 1.3 78.2 - - + +
557E VAL* 1.3 61.6 + - - +
559E LYS* 3.1 27.2 + - - +
560E ILE* 2.9 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 557 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E THR* 4.6 4.5 - - + -
508E ALA* 4.0 22.9 - - + +
509E ARG* 3.9 43.3 - - + +
512E VAL* 4.4 4.9 - - + -
553E ILE* 3.0 26.9 + - + +
554E ASP* 3.7 6.1 - - - +
556E GLU* 1.3 73.7 - - - +
558E LYS* 1.3 67.1 + - - +
560E ILE* 3.0 5.9 + - - +
561E VAL* 3.0 23.6 + - + +
524F LEU* 3.5 21.8 - - + -
526F TRP* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 558 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLU* 5.9 4.5 - - - +
554E ASP 3.0 18.7 + - - +
555E GLU* 3.6 8.7 - - + +
557E VAL* 1.3 77.1 - - - +
559E LYS* 1.3 57.0 + - - +
561E VAL* 4.3 0.3 - - - +
562E THR* 2.9 45.8 + - - +
520F GLU* 3.4 32.0 + - - +
521F LEU* 4.3 14.5 - - + +
522F GLY* 5.5 0.7 - - - -
524F LEU* 4.1 23.8 - - + +
526F TRP* 4.7 11.2 - - + -
552F LYS* 5.0 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 559 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A GLU* 3.1 24.4 + - - +
520A GLU* 3.0 50.4 + - - +
556A GLU* 5.1 1.8 + - - -
559A LYS* 5.3 9.6 - - - +
519E GLU* 5.7 4.9 - - - +
555E GLU* 2.8 23.9 + - - +
556E GLU* 3.1 30.5 + - - +
558E LYS* 1.3 74.3 - - - +
560E ILE* 1.3 66.8 + - + +
562E THR* 3.9 2.9 - - - -
563E ASN* 3.0 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 560 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469E ARG* 4.7 16.4 - - - +
473E LEU* 4.0 16.6 - - + -
476E LEU* 3.9 27.8 - - + -
508E ALA* 4.3 13.5 - - + +
511E MET* 4.6 15.3 - - + -
512E VAL* 3.5 32.3 - - + -
518E SER* 5.6 0.9 - - - -
556E GLU* 2.9 24.5 + - - +
557E VAL* 3.7 4.9 - - - +
559E LYS* 1.3 78.4 - - + +
561E VAL* 1.3 66.1 + - - +
563E ASN* 3.2 6.3 + - - +
564E CYS* 3.0 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 561 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476E LEU* 4.3 10.1 - - + -
480E LEU* 3.7 21.3 - - + -
504E ALA* 4.4 7.9 - - + +
505E THR* 4.5 5.2 - - - -
508E ALA* 3.8 22.7 - - + -
557E VAL 3.0 13.9 + - - +
560E ILE* 1.3 77.3 - - - +
562E THR* 1.3 63.8 + - - +
564E CYS* 3.1 8.0 + - - +
565E TYR* 2.9 19.8 + - - +
523F PRO* 3.6 31.2 - - + +
524F LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 562 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLU* 5.8 3.4 - - - +
558E LYS* 2.9 36.4 + - - +
559E LYS* 3.9 3.6 - - - -
560E ILE 3.1 0.2 - - - -
561E VAL* 1.3 77.5 - - - +
563E ASN* 1.3 72.0 + - - +
565E TYR* 2.9 18.5 + - + +
566E GLU* 3.0 21.3 + - + +
522F GLY* 5.0 2.8 - - - -
523F PRO* 4.7 13.2 - - - +
524F LEU* 4.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 563 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559E LYS* 3.0 38.4 + - - +
560E ILE* 3.7 5.6 - - - +
562E THR* 1.3 81.0 - - - +
564E CYS* 1.3 64.5 + - - +
566E GLU* 3.2 7.3 + - - +
567E ARG* 2.9 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 564 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473E LEU* 3.8 26.0 - - - -
476E LEU* 3.8 23.8 - - + -
477E THR* 3.7 24.9 - - - +
480E LEU* 3.8 14.8 - - + -
560E ILE 3.0 16.1 + - - +
561E VAL* 3.4 9.4 - - - +
563E ASN* 1.3 78.9 - - - +
565E TYR* 1.3 61.4 + - - +
567E ARG* 3.3 8.4 + - - +
568E ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 565 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480E LEU* 3.7 23.0 - - + +
483E ARG* 3.5 39.4 + - + +
484E ALA* 3.8 15.3 - - + -
487E GLU* 2.4 32.4 + - - +
561E VAL 2.9 12.0 + - - +
562E THR* 2.9 11.6 + - + +
564E CYS* 1.3 76.7 - - - +
566E GLU* 1.3 67.3 + - + +
568E ALA* 3.1 5.7 + - - +
569E LYS* 2.9 52.3 + - + +
523F PRO* 4.0 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 566 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLU* 5.1 10.6 - - - +
569B LYS* 5.4 4.4 + - - -
562E THR* 3.0 19.4 + - + +
563E ASN* 3.8 8.5 - - - +
565E TYR* 1.3 83.1 - - + +
567E ARG* 1.3 61.8 + - - +
569E LYS* 2.6 38.5 + - - +
570E GLU* 3.0 35.2 + - - +
573E ARG* 4.4 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 567 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E VAL* 3.6 20.2 - - - +
435E PRO* 3.9 14.6 - - - +
473E LEU* 4.1 7.5 + - - +
474E ASP* 2.7 33.9 + - - +
477E THR* 3.5 25.8 + - + -
563E ASN 2.9 16.9 + - - +
564E CYS* 3.5 8.5 - - - +
565E TYR 3.1 0.2 - - - -
566E GLU* 1.3 72.5 - - - +
568E ALA* 1.3 66.9 + - - +
570E GLU* 3.4 15.9 + - - +
571E ILE* 3.2 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 568 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E VAL* 4.3 8.7 - - + +
477E THR* 3.7 29.5 - - + +
480E LEU* 4.2 6.7 - - + +
484E ALA* 3.8 18.6 - - + -
564E CYS 3.0 12.7 + - - +
565E TYR* 3.1 10.3 + - - +
567E ARG* 1.3 76.9 - - - +
569E LYS* 1.3 62.5 + - - +
571E ILE* 3.0 8.6 + - - +
572E ILE* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 569 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484E ALA* 3.9 22.7 - - + -
487E GLU* 4.0 20.7 + - + +
488E VAL* 4.2 19.5 - - + +
565E TYR* 2.9 46.3 + - + +
566E GLU* 2.6 44.5 + - - +
568E ALA* 1.3 75.6 - - - +
570E GLU* 1.3 63.8 + - - +
572E ILE* 3.1 4.4 + - - +
573E ARG* 2.9 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 570 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B GLU* 5.6 1.9 - - - +
566E GLU* 3.0 25.0 + - - +
567E ARG* 3.6 17.1 - - - +
569E LYS* 1.3 74.9 - - - +
571E ILE* 1.3 58.1 + - + +
573E ARG* 3.3 20.6 + - - +
574E LYS* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 571 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E VAL* 4.1 13.2 - - + -
430E VAL* 4.0 22.4 - - + -
433E VAL* 4.1 24.7 - - + -
434E VAL* 4.6 12.1 - - + -
477E THR* 4.5 11.4 - - + -
567E ARG* 3.2 28.0 + - + +
568E ALA* 3.0 11.1 + - - +
570E GLU* 1.3 77.8 - - + +
572E ILE* 1.3 57.7 + - - +
574E LYS* 3.1 6.3 + - - -
575E TYR* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 572 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E GLY* 4.0 18.4 - - - +
429E VAL* 4.7 6.3 - - + -
430E VAL* 4.4 13.2 - - + -
481E GLY 4.5 0.4 - - - +
484E ALA* 4.0 17.0 - - + -
485E ALA* 3.9 23.8 - - + +
488E VAL* 4.0 26.0 - - + -
489E VAL* 5.2 0.4 - - + -
568E ALA 3.0 12.5 + - - +
569E LYS* 3.5 8.1 - - - +
571E ILE* 1.3 78.0 - - - +
573E ARG* 1.3 58.2 + - - +
575E TYR* 3.1 3.9 + - - -
576E ARG* 2.8 32.8 + - - +
579E LEU* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 573 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ARG* 3.6 57.8 - - - +
488E VAL* 3.6 36.1 - - + +
566E GLU* 4.4 9.9 + - - -
569E LYS* 2.9 31.5 + - - +
570E GLU* 3.7 31.9 - - - +
572E ILE* 1.3 79.7 - - - +
574E LYS* 1.3 61.4 + - - +
575E TYR 3.4 0.3 + - - -
576E ARG* 3.5 17.5 + - - +
577E LYS* 6.1 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 574 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570E GLU 2.8 17.2 + - - +
571E ILE* 3.1 8.0 + - - +
573E ARG* 1.3 76.2 - - - +
575E TYR* 1.3 86.2 + - + +
576E ARG 3.5 1.0 + - - -
577E LYS* 5.1 7.1 + - - -
578E GLN* 4.2 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 575 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E VAL* 4.0 16.3 - - + +
433E VAL* 3.5 44.3 - - + +
571E ILE* 2.8 30.4 + - + +
572E ILE* 3.2 3.6 - - - -
574E LYS* 1.3 104.6 - - + +
576E ARG* 1.3 64.1 + - - +
577E LYS 3.1 3.3 + - - -
578E GLN* 3.2 34.5 + - + +
579E LEU* 3.0 19.6 + - - +
601E LEU* 4.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
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