Contacts of the helix formed by residues 498 - 533 (chain F) in PDB entry 1GO4
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 ALA 498 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494E SER* 4.1 10.5 - - - +
497E GLU* 3.5 36.6 - - + +
498E ALA* 4.6 3.4 - - + -
501E LEU* 3.3 14.2 - - + +
494F SER 4.6 1.8 - - - +
495F ARG 4.1 11.0 - - - +
496F GLU 2.7 0.4 - - - -
497F GLU* 1.3 81.1 - - - +
499F ASP* 1.3 59.4 + - - +
500F THR 3.3 1.8 - - - -
501F LEU* 3.7 3.1 - - - -
502F ARG* 3.0 31.7 + - - +
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Residues in contact with ASP 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495F ARG* 3.7 22.3 + - - +
496F GLU* 2.9 26.4 + - - +
498F ALA* 1.3 78.4 - - - +
500F THR* 1.3 63.2 + - - +
501F LEU 3.1 1.6 - - - -
502F ARG* 2.6 55.9 + - - +
503F LEU* 3.1 11.5 - - - +
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Residues in contact with THR 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496F GLU* 3.3 27.9 + - + +
497F GLU* 3.9 12.8 + - - +
499F ASP* 1.3 77.0 - - - +
501F LEU* 1.3 67.2 + - - +
503F LEU* 3.3 16.1 + - + +
504F LYS* 3.0 26.0 + - - +
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Residues in contact with LEU 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498E ALA* 3.9 17.9 - - + +
501E LEU* 3.4 41.7 - - + -
502E ARG* 3.9 17.9 - - + +
505E VAL* 4.8 11.7 - - + -
497F GLU* 3.2 26.7 - - + +
498F ALA 3.5 1.5 + - - +
499F ASP 3.1 0.2 - - - -
500F THR* 1.3 85.7 + - - +
502F ARG* 1.3 53.0 - - - +
503F LEU 2.9 4.9 - - - -
504F LYS* 4.1 14.1 - - + +
505F VAL* 2.7 41.6 + - + +
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Residues in contact with ARG 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497E GLU* 5.4 8.3 - - - +
501E LEU* 4.2 14.1 - - + -
498F ALA* 3.0 25.4 + - - +
499F ASP* 2.6 61.7 + - - +
501F LEU* 1.3 76.0 - - - +
503F LEU* 1.3 76.5 + - - +
505F VAL* 4.1 5.7 - - - +
506F GLU* 3.3 28.5 + - - +
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Residues in contact with LEU 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499F ASP* 3.1 17.5 - - - +
500F THR* 3.3 15.3 - - + +
501F LEU 2.9 0.2 - - - -
502F ARG* 1.3 95.6 - - - +
504F LYS* 1.3 63.4 + - - +
505F VAL 3.2 1.3 - - - -
506F GLU* 2.8 41.9 - - - +
507F GLU* 3.1 18.7 + - - +
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Residues in contact with LYS 504 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E VAL* 3.4 31.0 - - + +
509E GLU* 3.4 18.3 + - - -
500F THR 3.0 16.0 + - - +
501F LEU* 3.1 16.4 + - + +
503F LEU* 1.3 76.8 - - - +
505F VAL* 1.3 60.1 + - - +
507F GLU* 3.2 23.9 + - - +
508F LEU* 2.8 34.2 - - + +
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Residues in contact with VAL 505 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501E LEU* 4.2 19.5 - - + +
504E LYS* 3.7 32.1 - - + +
505E VAL* 2.8 35.4 - - + +
508E LEU* 3.4 18.5 - - + +
501F LEU 2.7 29.2 + - - +
502F ARG* 4.4 4.9 - - - +
504F LYS* 1.3 68.4 - - - +
506F GLU* 1.3 63.6 + - - +
507F GLU 3.1 2.1 + - - -
508F LEU* 3.5 0.9 + - - -
509F GLU* 3.0 35.2 + - - +
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Residues in contact with GLU 506 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502F ARG* 3.3 19.4 + - - +
503F LEU* 2.8 44.4 - - - +
505F VAL* 1.3 75.3 - - - +
507F GLU* 1.3 62.6 + - + +
509F GLU* 3.9 13.2 - - - +
510F GLY* 2.9 24.8 + - - -
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Residues in contact with GLU 507 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503F LEU* 3.1 21.1 + - - +
504F LYS* 3.2 31.1 + - - +
506F GLU* 1.3 76.1 - - + +
508F LEU* 1.3 72.2 + - + +
510F GLY* 2.9 5.0 + - - -
511F GLU* 2.8 37.2 + - - +
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Residues in contact with LEU 508 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E VAL* 4.4 4.5 - - + +
508E LEU* 3.4 37.5 - - + +
509E GLU* 2.9 31.4 - - - +
512E ARG* 3.5 31.8 - - + +
504F LYS* 2.8 41.9 + - + +
505F VAL* 4.8 0.7 - - - -
507F GLU* 1.3 83.2 - - + +
509F GLU* 1.3 52.2 + - - +
511F GLU* 2.9 10.6 + - - +
512F ARG* 2.5 40.5 + - + +
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Residues in contact with GLU 509 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E LYS* 3.5 25.8 + - - -
508E LEU* 3.4 20.2 - - + +
505F VAL* 3.0 27.3 + - - +
506F GLU* 3.9 12.0 - - - +
508F LEU* 1.3 76.0 - - - +
510F GLY* 1.3 58.3 + - - +
512F ARG* 3.9 10.6 - - - +
513F SER* 2.9 30.1 + - - -
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Residues in contact with GLY 510 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506F GLU 2.9 12.3 + - - -
507F GLU* 2.9 8.2 + - - -
509F GLU* 1.3 76.7 - - - +
511F GLU* 1.3 61.2 + - - +
513F SER* 3.4 8.1 - - - -
514F ARG* 3.3 27.5 + - - +
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Residues in contact with GLU 511 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512E ARG* 2.8 43.0 + - + +
507F GLU* 2.8 30.2 + - - +
508F LEU* 3.4 12.6 - - + +
510F GLY* 1.3 72.4 - - - +
512F ARG* 1.3 66.7 + - - +
513F SER 3.0 1.8 - - - -
514F ARG* 2.9 9.6 + - - +
515F LEU* 2.8 38.7 + - + +
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Residues in contact with ARG 512 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E LEU* 4.0 20.9 - - + +
511E GLU* 2.8 46.5 + - + -
512E ARG* 5.6 7.1 - - + +
515E LEU* 3.9 20.4 - - + +
508F LEU 2.5 22.1 + - - +
509F GLU* 3.9 7.6 - - - +
511F GLU* 1.3 72.4 - - - +
513F SER* 1.3 57.3 + - - +
515F LEU* 3.3 5.7 + - - +
516F GLU* 2.9 59.8 + - - +
512H ARG* 4.5 16.8 - - - +
516H GLU* 5.6 7.3 + - - -
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Residues in contact with SER 513 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F GLU 2.9 19.9 + - - -
510F GLY* 3.4 9.6 - - - -
512F ARG* 1.3 77.6 - - - +
514F ARG* 1.3 57.9 + - - +
516F GLU* 3.2 14.3 + - - +
517F GLU* 3.0 27.9 + - - +
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Residues in contact with ARG 514 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510F GLY 3.3 15.9 + - - +
511F GLU* 2.9 9.9 + - - +
513F SER* 1.3 73.9 - - - +
515F LEU* 1.3 63.5 + - + +
517F GLU* 3.8 5.8 - - - +
518F GLU* 2.9 51.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 515 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512E ARG* 3.7 49.1 - - + +
515E LEU* 3.5 31.8 - - + +
516E GLU* 4.1 11.0 - - + +
519E LYS* 4.8 15.4 - - - +
511F GLU* 2.8 39.0 + - + +
512F ARG* 3.7 2.5 - - - +
514F ARG* 1.3 79.2 - - + +
516F GLU* 1.3 55.5 + - - +
518F GLU* 3.7 15.6 - - - +
519F LYS* 3.0 28.1 + - - +
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Residues in contact with GLU 516 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515E LEU* 4.1 17.8 - - + +
512F ARG* 2.9 60.0 + - - +
513F SER* 3.5 11.4 - - - +
514F ARG 3.1 0.2 - - - -
515F LEU* 1.3 76.4 - - - +
517F GLU* 1.3 60.1 + - - +
519F LYS* 3.3 8.2 + - + +
520F ARG* 2.8 59.2 + - - +
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Residues in contact with GLU 517 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513F SER 3.0 15.4 + - - +
514F ARG* 4.0 6.3 - - - +
516F GLU* 1.3 73.8 - - - +
518F GLU* 1.3 65.4 + - + +
520F ARG* 3.3 18.8 + - - +
521F MET* 3.1 45.7 + - + +
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Residues in contact with GLU 518 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519E LYS* 3.2 36.4 + - + +
514F ARG* 2.9 49.8 + - - +
515F LEU* 3.7 12.2 + - - +
517F GLU* 1.3 75.3 - - + +
519F LYS* 1.3 65.9 + - - +
521F MET* 3.1 22.9 + - + +
522F LEU* 3.0 31.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 519 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515E LEU* 4.2 17.4 - - + +
518E GLU* 2.6 38.2 + - + +
519E LYS* 5.0 7.4 - - + +
522E LEU* 4.1 19.1 - - + -
515F LEU 3.0 18.8 + - - +
516F GLU* 3.5 7.4 - - + +
518F GLU* 1.3 75.3 - - - +
520F ARG* 1.3 70.4 + - - +
522F LEU* 3.3 6.6 + - - +
523F GLU* 2.9 54.2 + - - +
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Residues in contact with ARG 520 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516F GLU* 2.8 54.1 + - - +
517F GLU* 3.3 26.7 + - - +
519F LYS* 1.3 82.6 - - - +
521F MET* 1.3 63.2 + - + +
523F GLU* 3.1 17.9 + - - +
524F ALA* 2.9 23.8 + - - +
504G LYS* 5.3 8.5 - - - +
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Residues in contact with MET 521 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517F GLU* 3.2 29.8 - - + +
518F GLU* 3.1 31.5 + - + +
520F ARG* 1.3 76.4 - - + +
522F LEU* 1.3 68.0 + - + +
524F ALA* 3.3 8.0 + - - +
525F GLN* 3.1 32.7 + - - +
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Residues in contact with LEU 522 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519E LYS* 3.7 42.8 - - + +
522E LEU* 3.6 23.3 - - + -
523E GLU* 4.2 10.5 - - + +
526E LEU* 4.3 16.0 - - + +
518F GLU* 3.0 20.3 + - + +
519F LYS* 3.5 7.6 - - - +
521F MET* 1.3 83.6 - - + +
523F GLU* 1.3 56.9 + - - +
525F GLN* 3.2 20.4 + - - +
526F LEU* 3.0 33.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 523 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522E LEU* 4.1 20.3 - - + +
519F LYS* 2.9 52.1 + - - +
520F ARG* 3.1 16.8 + - - +
522F LEU* 1.3 73.8 - - - +
524F ALA* 1.3 61.6 + - - +
526F LEU* 3.7 7.0 - - + +
527F GLU* 2.8 33.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 524 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520F ARG 2.9 15.4 + - - +
521F MET* 3.6 9.0 - - - +
522F LEU 3.3 0.2 - - - -
523F GLU* 1.3 76.8 - - - +
525F GLN* 1.3 57.6 + - + +
527F GLU* 3.9 4.8 - - - +
528F ARG* 2.9 30.3 + - - +
----------------------------------------------------------
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Residues in contact with GLN 525 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526E LEU* 4.1 22.5 - - + +
521F MET* 3.1 24.2 + - - +
522F LEU* 3.4 20.2 - - - +
523F GLU 3.2 0.2 - - - -
524F ALA* 1.3 74.1 - - + +
526F LEU* 1.3 64.8 + - - +
528F ARG* 3.4 4.3 + - - +
529F ARG* 3.0 38.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 526 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522E LEU* 3.3 47.6 - - + +
525E GLN* 3.8 19.3 - - + +
526E LEU* 3.1 45.8 - - + +
529E ARG* 4.4 23.8 + - - +
522F LEU 3.0 17.9 + - - +
523F GLU* 3.8 5.2 - - - +
525F GLN* 1.3 75.7 - - - +
527F GLU* 1.3 58.3 + - - +
529F ARG* 3.5 5.9 + - + +
530F ALA* 2.9 29.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 527 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ARG* 2.9 47.0 + - - +
523F GLU 2.8 19.0 + - - +
524F ALA* 3.9 4.9 - - - +
526F LEU* 1.3 74.3 - - - +
528F ARG* 1.3 67.4 + - - +
530F ALA* 3.2 7.3 + - - +
531F LEU* 3.0 36.8 + - + +
496G GLU* 5.1 1.4 - - - +
----------------------------------------------------------
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Residues in contact with ARG 528 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B THR 3.1 24.4 + - - -
177B ASN* 4.8 0.4 - - - +
178B SER 3.1 21.4 + - - +
180B GLU* 3.0 27.7 + - - +
201B ILE* 5.0 2.4 - - - +
534E ASP* 3.4 22.3 + - - +
535E TYR 3.0 24.9 + - - -
536E ASP* 4.8 3.6 - - - +
537E GLN 5.7 0.6 - - - +
524F ALA 2.9 18.5 + - - +
525F GLN* 4.0 4.5 - - - +
527F GLU* 1.3 76.5 - - - +
529F ARG* 1.3 64.9 + - + +
531F LEU* 3.2 13.0 + - - +
532F GLN* 3.0 37.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 529 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526E LEU* 3.0 55.8 + - - +
529E ARG* 3.5 11.1 - - - +
531E LEU* 3.2 30.1 + - + -
532E GLN* 3.5 11.5 + - - +
534E ASP* 3.4 24.9 - - - +
525F GLN* 3.0 27.3 + - - +
526F LEU* 3.8 5.1 - - - +
528F ARG* 1.3 77.3 - - + +
530F ALA* 1.3 61.7 + - - +
532F GLN* 3.0 17.6 + - - +
533F GLY 3.1 0.7 + - - -
534F ASP* 2.9 52.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 530 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 4.7 3.0 + - - +
101B GLN* 3.0 15.2 + - - -
103B ASP* 5.4 2.6 - - - +
182B ARG* 5.1 4.0 - - - +
196B MET* 5.1 1.1 - - - -
529E ARG* 4.7 12.1 - - - +
526F LEU 2.9 18.4 + - - +
527F GLU* 3.5 15.9 - - - +
528F ARG 3.2 0.2 - - - -
529F ARG* 1.3 77.0 - - - +
531F LEU* 1.3 63.3 + - - +
533F GLY* 3.0 12.3 + - - -
534F ASP* 4.0 10.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 531 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 4.9 1.6 + - - -
101B GLN* 4.1 9.9 + - - +
180B GLU* 3.7 30.7 - - + +
182B ARG* 3.5 40.4 - - + +
196B MET* 3.8 37.0 - - + +
197B VAL 5.2 0.3 - - - -
198B ALA* 4.1 13.7 + - - +
527F GLU* 3.0 31.8 + - + +
528F ARG* 3.5 11.7 - - - +
530F ALA* 1.3 77.0 - - - +
532F GLN* 1.3 60.3 + - - +
533F GLY 3.5 0.7 + - - -
496G GLU* 4.2 16.8 - - - +
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Residues in contact with GLN 532 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 3.4 19.1 + - - -
174B PHE* 3.6 15.8 - - - -
175B ILE 3.4 11.0 + - - +
176B THR* 3.1 18.4 + - - +
178B SER* 3.1 21.6 + - - +
180B GLU* 4.0 7.9 - - + +
198B ALA* 4.6 6.1 - - - -
531E LEU* 3.6 14.1 - - + +
534E ASP* 2.4 43.5 + - - +
528F ARG* 3.0 32.1 + - - +
529F ARG* 3.0 20.4 + - - +
531F LEU* 1.3 77.3 - - - +
533F GLY* 1.3 57.8 + - - +
534F ASP 3.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with GLY 533 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 4.9 0.9 - - - -
99B ARG* 3.6 6.1 - - - -
101B GLN* 3.1 23.8 - - - -
156B TYR* 2.6 24.0 + - - -
174B PHE* 3.4 7.3 - - - -
530F ALA 3.0 8.6 + - - -
531F LEU 3.3 1.4 + - - -
532F GLN* 1.3 79.6 - - - +
534F ASP* 1.3 68.5 + - - +
535F TYR* 3.3 8.0 - - - -
----------------------------------------------------------
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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