Contacts of the helix formed by residues 512 - 543 (chain A) in PDB entry 5JAJ
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 512 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ALA 3.5 4.2 - - - +
511A MET* 1.3 89.0 - - + +
513A GLU* 1.3 65.6 + - - +
514A ARG* 3.2 4.9 - - + +
515A LYS* 3.1 27.4 + - + +
516A TYR* 2.9 19.4 + - - +
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Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A MET 3.3 4.6 + - - -
512A PRO* 1.3 71.0 - - - +
514A ARG* 1.3 59.2 + - - +
516A TYR* 3.3 7.9 + - + +
517A ARG* 2.7 78.3 + - + +
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Residues in contact with ARG 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A PRO* 3.2 3.9 - - + +
513A GLU* 1.3 78.9 + - - +
515A LYS* 1.3 63.6 + - - +
517A ARG* 4.0 5.3 - - - +
518A LEU* 3.1 42.3 + - + +
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Residues in contact with LYS 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A MET* 3.7 21.6 - - + +
512A PRO* 3.1 31.2 + - + +
514A ARG* 1.3 79.6 - - - +
516A TYR* 1.3 62.4 + - - +
518A LEU* 3.5 6.9 + - - +
519A LYS* 3.1 23.7 + - + +
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Residues in contact with TYR 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.9 16.8 - - + -
189A CYS* 3.3 23.0 - - - +
194A THR* 2.7 33.4 + - - +
195A GLU* 3.7 16.2 - - - -
508A VAL* 3.9 15.0 - - + -
511A MET* 3.7 23.3 - - + +
512A PRO 2.9 16.7 + - - +
513A GLU* 3.7 8.7 - - + +
515A LYS* 1.3 77.1 - - - +
517A ARG* 1.3 73.8 + - + +
519A LYS* 3.2 4.0 + - - +
520A ILE* 2.9 50.0 + - + +
707A EDO 3.8 28.5 - - - +
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Residues in contact with ARG 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 5.4 5.5 + - - -
513A GLU* 2.7 64.8 + - + +
514A ARG* 4.0 6.1 - - - +
516A TYR* 1.3 81.2 - - + +
518A LEU* 1.3 58.3 + - + +
520A ILE* 3.3 7.4 + - - +
521A VAL* 3.0 36.2 + - + +
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ARG* 3.1 34.7 + - + +
515A LYS* 3.9 5.6 - - - +
517A ARG* 1.3 77.3 - - + +
519A LYS* 1.3 63.1 + - - +
521A VAL* 3.4 13.7 + - + +
522A GLU* 3.0 25.0 + - - +
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Residues in contact with LYS 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 2.9 40.8 + - - -
186A LEU* 3.7 28.3 - - + -
511A MET* 5.0 3.4 - - + -
515A LYS* 3.1 18.8 + - + +
516A TYR* 3.5 6.7 - - - +
518A LEU* 1.3 76.6 - - - +
520A ILE* 1.3 63.3 + - - +
522A GLU* 3.2 30.3 + - - +
523A LEU* 2.9 39.1 + - + +
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Residues in contact with ILE 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 5.3 1.6 - - - +
186A LEU* 3.7 15.7 - - + +
189A CYS* 3.7 14.8 - - + +
190A ALA* 3.7 27.1 - - + +
193A ASP* 4.8 3.4 - - - +
194A THR 4.7 5.2 - - - +
516A TYR* 2.9 49.5 + - + +
517A ARG* 3.7 6.3 - - - +
519A LYS* 1.3 74.7 - - - +
521A VAL* 1.3 59.1 + - + +
523A LEU* 3.2 4.8 + - + +
524A GLN* 2.8 57.9 + - + +
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Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 6.2 1.8 - - - +
517A ARG* 3.0 24.1 + - + +
518A LEU* 3.6 16.4 - - + +
520A ILE* 1.3 76.2 - - + +
522A GLU* 1.3 63.0 + - - +
524A GLN* 3.2 9.1 + - - +
525A ARG* 2.9 67.5 + - + +
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Residues in contact with GLU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU 3.0 13.3 + - - +
519A LYS* 3.5 37.7 + - - +
521A VAL* 1.3 80.0 - - - +
523A LEU* 1.3 59.5 + - + +
525A ARG* 3.7 7.6 - - - +
526A ASN* 3.0 49.3 + - - +
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 3.4 25.4 - - - +
186A LEU* 3.6 40.2 - - + +
187A GLN* 3.7 24.2 + - - +
190A ALA* 3.6 16.2 - - + -
519A LYS* 2.9 36.8 + - + +
520A ILE* 3.7 1.3 - - - +
522A GLU* 1.3 75.3 - - + +
524A GLN* 1.3 61.8 + - - +
526A ASN* 3.4 14.5 + - + +
527A ALA* 2.9 28.2 + - - +
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Residues in contact with GLN 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.4 23.6 - - + +
153A LYS* 3.1 20.1 + - - -
154A LEU* 4.0 21.0 - - + +
190A ALA* 3.0 33.3 + - + +
193A ASP* 3.0 25.0 + - - +
520A ILE* 2.8 39.0 + - - +
521A VAL* 3.8 7.2 - - - +
523A LEU* 1.3 69.8 - - - +
525A ARG* 1.3 66.4 + - - +
527A ALA* 3.2 7.0 + - - +
528A VAL* 3.1 28.2 + - - +
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Residues in contact with ARG 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.9 19.4 - - + +
521A VAL* 2.9 46.6 + - + +
522A GLU* 3.7 6.7 - - - +
524A GLN* 1.3 77.4 - - - +
526A ASN* 1.3 64.5 + - - +
528A VAL* 3.3 5.1 + - + +
529A LEU* 3.0 35.7 + - + +
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Residues in contact with ASN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A GLU* 3.0 39.0 + - - +
523A LEU* 3.7 15.6 - - + +
525A ARG* 1.3 78.1 - - - +
527A ALA* 1.3 56.9 + - - +
529A LEU* 3.9 11.1 - - - +
530A SER* 2.8 39.1 + - - +
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Residues in contact with ALA 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 4.0 19.6 - - + +
150A LEU* 4.6 7.0 - - + -
187A GLN* 5.0 11.0 - - - +
191A ASN* 5.1 3.8 - - - +
523A LEU 2.9 16.8 + - - +
524A GLN* 3.2 9.1 + - - +
526A ASN* 1.3 77.9 - - - +
528A VAL* 1.3 56.9 + - - +
530A SER* 3.4 5.1 + - - -
531A TRP* 3.0 28.6 + - - +
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Residues in contact with VAL 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 4.0 19.3 - - + -
150A LEU* 4.0 20.6 - - + -
151A GLN* 4.0 26.1 + - + +
154A LEU* 3.9 19.5 - - + -
524A GLN 3.1 15.9 + - - +
525A ARG* 3.4 13.7 - - + +
527A ALA* 1.3 76.2 - - + +
529A LEU* 1.3 67.2 + - + +
531A TRP* 3.6 6.2 + - - +
532A GLN* 3.3 26.6 + - - +
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ARG* 3.0 29.0 + - + +
526A ASN* 3.9 11.0 - - - +
528A VAL* 1.3 80.6 - - + +
530A SER* 1.3 64.7 + - - +
532A GLN* 3.2 12.1 + - + +
533A VAL* 3.1 27.9 + - + +
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Residues in contact with SER 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASN* 2.8 29.9 + - - +
527A ALA* 3.8 5.8 - - - -
529A LEU* 1.3 73.0 - - - +
531A TRP* 1.3 56.9 + - - +
533A VAL* 3.3 8.6 + - - +
534A LYS* 2.9 29.3 + - - +
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Residues in contact with TRP 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 6.0 0.4 - - - -
147A LEU* 3.2 32.3 - - + +
151A GLN* 3.2 31.6 - - - +
527A ALA 3.0 17.6 + - - +
528A VAL* 3.7 5.8 - - - +
530A SER* 1.3 77.6 - - - +
532A GLN* 1.3 89.4 + - + +
534A LYS* 3.3 9.3 + - + +
535A GLU* 2.9 63.3 + - + +
706A EDO 3.6 19.0 + - - -
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Residues in contact with GLN 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLN* 4.1 6.7 - - - +
528A VAL 3.3 13.8 + - - +
529A LEU* 3.2 14.2 + - + +
531A TRP* 1.3 107.8 - - - +
533A VAL* 1.3 58.2 + - + +
535A GLU* 3.3 5.3 + - - +
536A ALA* 3.0 28.2 + - - +
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Residues in contact with VAL 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 3.1 15.3 + - + +
530A SER* 3.7 9.9 - - - +
531A TRP 3.3 0.2 - - - -
532A GLN* 1.3 74.1 - - + +
534A LYS* 1.3 67.8 + - - +
536A ALA* 3.3 8.2 + - - +
537A ARG* 3.0 25.5 + - + +
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Residues in contact with LYS 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 2.6 37.6 + - - +
530A SER 2.9 17.8 + - - +
531A TRP* 3.7 10.1 - - + +
533A VAL* 1.3 78.2 - - - +
535A GLU* 1.3 62.7 + - - +
537A ARG* 3.2 10.4 + - + +
538A SER* 3.0 40.1 + - - +
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Residues in contact with GLU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A TRP* 2.9 67.4 + - + +
532A GLN* 3.7 7.4 - - - +
534A LYS* 1.3 83.8 - - - +
536A ALA* 1.3 57.8 + - - +
538A SER* 3.4 9.8 + - - -
539A SER* 2.9 30.0 + - - -
542A ARG* 5.0 4.5 + - - -
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLN 3.0 17.4 + - - +
533A VAL* 3.6 7.6 - - - +
535A GLU* 1.3 77.0 - - - +
537A ARG* 1.3 56.3 + - - +
539A SER* 3.3 6.6 + - - -
540A GLU* 3.0 28.8 + - - +
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Residues in contact with ARG 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A VAL* 3.0 19.7 + - + +
534A LYS* 3.7 9.2 - - - +
536A ALA* 1.3 72.7 - - - +
538A SER* 1.3 65.8 + - - +
540A GLU* 3.3 11.3 + - - +
541A ARG* 3.1 23.0 + - + +
1Y G 3.9 21.1 + - - -
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Residues in contact with SER 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LYS* 3.0 26.2 + - - +
535A GLU* 3.7 12.8 + - - -
537A ARG* 1.3 78.8 - - - +
539A SER* 1.3 61.4 + - - +
541A ARG* 3.4 7.5 + - - +
542A ARG* 3.1 42.7 + - - +
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Residues in contact with SER 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU 2.9 19.5 + - - -
536A ALA* 3.6 7.0 - - - -
538A SER* 1.3 73.9 - - - +
540A GLU* 1.3 65.3 + - - +
542A ARG* 3.2 21.8 + - - +
543A GLN* 3.1 36.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ALA 3.0 17.1 + - - +
537A ARG* 3.3 10.1 + - - +
539A SER* 1.3 76.9 - - - +
541A ARG* 1.3 63.1 + - - +
543A GLN* 3.3 12.0 + - - +
544A LEU* 3.6 23.1 + - + +
----------------------------------------------------------
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Residues in contact with ARG 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ARG* 3.1 13.2 + - + +
538A SER* 3.7 10.8 - - - +
540A GLU* 1.3 77.9 - - - +
542A ARG* 1.3 61.9 + - - +
543A GLN 3.3 0.9 + - - -
544A LEU* 3.3 23.2 + - + +
643A GLU* 5.6 2.8 + - - -
645A LYS* 3.6 23.4 - - - +
647A TYR* 3.4 19.2 + - - -
652A THR* 3.0 36.8 + - - +
653A VAL 4.5 1.8 - - - +
654A THR* 3.2 34.9 - - + +
1Y G 5.2 12.9 + - - -
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Residues in contact with ARG 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU* 5.0 4.6 + - - -
538A SER* 3.1 36.5 + - - +
539A SER* 3.2 32.7 + - - +
541A ARG* 1.3 76.8 - - - +
543A GLN* 1.3 69.1 - - - +
544A LEU 3.4 0.4 - - - -
651A SER 5.0 11.3 + - - -
653A VAL* 3.9 15.0 - - + +
654A THR 4.0 0.2 - - - -
655A PHE* 2.9 44.1 - - - +
656A PRO* 3.1 14.2 - - + +
657A ILE 5.4 1.1 - - - +
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Residues in contact with GLN 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A SER* 3.1 26.8 + - - +
540A GLU* 3.3 6.5 + - - +
541A ARG 3.2 0.6 - - - -
542A ARG* 1.3 91.2 - - - +
544A LEU* 1.3 62.2 + - - +
545A HIS* 3.3 6.6 + - - +
656A PRO* 3.8 32.5 - - - +
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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