Contacts of the helix formed by residues 537 - 570 (chain B) in PDB entry 3TNF
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 THR 537 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 4.0 3.6 - - - +
440B ASN* 4.9 0.3 + - - -
443B ASP* 5.3 0.7 + - - -
454B PHE* 5.2 0.3 - - - -
465B LEU* 3.6 26.3 - - - +
468B ALA* 3.7 20.0 + - - +
469B HIS* 3.0 21.9 + - - +
470B TYR* 4.2 4.5 - - - -
471B VAL* 4.2 8.4 - - - +
535B PRO 3.7 0.4 + - - -
536B MET* 1.3 77.9 - - - +
538B VAL* 1.3 55.9 + - - +
539B LYS* 4.0 8.7 + - + +
540B LYS* 3.1 32.8 + - + +
541B LEU* 2.8 32.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.8 12.5 - - - +
70A PHE* 4.1 7.2 - - + -
247B LEU* 3.9 14.8 - - + -
436B LEU* 3.6 37.5 - - + +
439B ALA* 3.4 29.4 - - + -
440B ASN* 3.6 19.4 + - - +
443B ASP* 3.9 14.7 + - - +
537B THR* 1.3 73.4 + - - +
539B LYS* 1.3 65.8 + - - +
541B LEU* 3.2 8.5 + - - +
542B VAL* 2.9 22.7 + - + +
----------------------------------------------------------
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Residues in contact with LYS 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 3.9 43.2 + - + +
248B GLU* 5.4 11.0 - - - +
440B ASN* 4.8 3.6 + - - +
537B THR* 3.3 8.6 + - + +
538B VAL* 1.3 78.9 - - - +
540B LYS* 1.3 62.8 + - - +
542B VAL* 3.2 5.9 + - - +
543B HIS* 3.1 21.4 + - + +
----------------------------------------------------------
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Residues in contact with LYS 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLU* 4.7 8.3 - - - +
469B HIS* 3.1 41.8 + - + +
470B TYR* 3.7 28.0 + - - -
536B MET* 3.5 24.9 - - + -
537B THR* 3.1 25.2 + - + +
539B LYS* 1.3 79.5 - - - +
541B LEU* 1.3 63.6 + - - +
543B HIS* 3.0 15.7 + - + +
544B HIS* 2.9 23.7 + - + +
----------------------------------------------------------
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Residues in contact with LEU 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 4.4 11.9 - - - +
41A ILE* 4.2 11.4 - - + -
67A GLN* 3.5 24.9 - - - +
69A ARG* 4.1 8.3 - - - +
70A PHE* 3.9 22.7 - - + -
534B THR* 4.7 8.7 - - + -
536B MET* 4.1 27.5 - - + +
537B THR 2.8 17.6 + - - +
538B VAL* 3.5 7.9 - - - +
540B LYS* 1.3 72.6 - - - +
542B VAL* 1.3 58.8 + - + +
544B HIS* 3.3 9.0 + - + +
545B ASN* 2.8 53.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.4 11.0 - - + -
240B TYR* 3.3 24.3 - - + -
243B TYR* 4.2 15.5 - - + -
244B GLU* 5.0 9.6 - - + +
247B LEU* 4.0 21.3 - - + -
436B LEU* 3.6 31.4 - - + -
538B VAL 2.9 16.7 + - - +
539B LYS 3.5 8.1 - - - +
540B LYS 3.2 0.2 - - - -
541B LEU* 1.3 77.0 - - + +
543B HIS* 1.3 58.3 + - - +
545B ASN* 4.0 4.9 - - - +
546B LYS* 3.1 25.5 + - - +
----------------------------------------------------------
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Residues in contact with HIS 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLU* 5.9 1.3 - - - -
539B LYS* 3.1 11.7 + - + +
540B LYS* 3.0 18.7 + - + +
542B VAL* 1.3 77.4 - - + +
544B HIS* 1.3 69.4 + - + +
546B LYS* 3.3 15.0 + - - +
547B GLY* 3.1 19.1 + - - -
----------------------------------------------------------
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Residues in contact with HIS 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE 4.7 4.1 + - - -
536B MET* 3.8 34.2 - - + +
540B LYS* 2.9 12.9 + - + +
541B LEU* 3.4 10.8 - - + +
543B HIS* 1.3 79.2 - - + +
545B ASN* 1.3 78.1 + - - +
547B GLY* 3.2 4.2 + - - -
548B LEU* 3.1 50.7 + - + +
----------------------------------------------------------
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Residues in contact with ASN 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE 4.7 0.7 - - - +
38A ILE* 3.9 18.0 - - + +
39A SER 2.9 36.2 + - - +
41A ILE* 3.3 21.2 - - + +
240B TYR* 3.3 14.4 - - + +
541B LEU* 2.8 35.9 + - - +
542B VAL* 4.0 3.8 - - - +
544B HIS* 1.3 80.4 - - - +
546B LYS* 1.3 56.9 + - - +
548B LEU* 3.2 7.2 + - - +
549B GLU* 2.9 34.3 + - - +
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Residues in contact with LYS 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MPD 5.1 14.4 - - + +
240B TYR* 3.3 43.8 + - + -
244B GLU* 3.0 34.2 + - - +
542B VAL 3.1 19.0 + - - +
543B HIS* 3.4 14.8 - - - +
544B HIS 3.2 0.4 - - - -
545B ASN* 1.3 77.5 - - - +
547B GLY* 1.3 57.8 + - - +
549B GLU* 3.5 0.9 + - - +
550B THR* 2.9 42.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B HIS 3.1 12.7 + - - -
544B HIS 3.2 3.3 + - - -
546B LYS* 1.3 76.0 - - - +
548B LEU* 1.3 59.9 + - - +
550B THR* 3.8 5.5 - - - +
551B THR* 2.9 36.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 3.6 21.8 - - + -
37A PHE 3.6 21.1 - - - +
38A ILE* 3.8 14.8 - - + -
544B HIS* 3.1 49.9 + - + +
545B ASN* 3.2 10.3 + - - +
547B GLY* 1.3 76.9 - - - +
549B GLU* 1.3 56.9 + - - +
551B THR* 3.5 6.8 + - - +
552B ILE* 3.0 33.1 + - - +
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Residues in contact with GLU 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.7 33.0 - - + +
236B LEU* 3.7 22.7 - - + +
239B LYS* 3.1 24.5 + - - -
240B TYR* 2.9 29.3 + - + +
545B ASN 2.9 21.2 + - - +
546B LYS 4.1 1.8 - - - +
548B LEU* 1.3 70.0 - - - +
550B THR* 1.3 60.4 + - - +
552B ILE* 3.9 4.4 - - - +
553B HIS* 2.9 31.5 + - - +
----------------------------------------------------------
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Residues in contact with THR 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MPD 2.7 45.6 + - + +
236B LEU* 5.1 1.6 - - - +
240B TYR* 5.9 0.5 - - - -
546B LYS* 2.9 27.9 + - - +
547B GLY* 3.8 5.2 - - - -
549B GLU* 1.3 72.7 - - - +
551B THR* 1.3 67.4 + - - +
553B HIS* 3.6 6.1 + - - +
554B LYS* 3.2 41.7 + - - +
----------------------------------------------------------
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Residues in contact with THR 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B GLY 2.9 22.1 + - - -
548B LEU* 3.6 8.7 - - - +
550B THR* 1.3 81.0 - - - +
552B ILE* 1.3 66.9 + - + +
554B LYS* 3.2 8.3 + - - +
555B GLU* 3.2 45.2 + - - +
----------------------------------------------------------
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Residues in contact with ILE 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.2 33.0 - - - +
36A THR* 4.0 21.8 - - + +
38A ILE* 4.1 15.0 - - + -
548B LEU 3.0 17.0 + - - +
549B GLU* 4.0 4.7 - - - +
551B THR* 1.3 81.4 - - + +
553B HIS* 1.3 67.9 + - - +
555B GLU* 3.2 11.6 + - + +
556B ARG* 3.1 47.1 + - + +
----------------------------------------------------------
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Residues in contact with HIS 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MPD 3.5 22.6 + - + +
229B LEU* 3.1 44.8 + - + +
230B GLU* 5.4 1.1 - - - -
232B GLN* 4.3 6.0 - - + +
233B GLY* 3.6 18.2 + - - -
236B LEU* 4.1 18.4 - - + -
549B GLU 2.9 18.9 + - - +
550B THR 3.8 6.5 - - - +
552B ILE* 1.3 78.9 - - - +
554B LYS* 1.3 60.0 + - - +
556B ARG* 3.0 11.0 + - + +
557B VAL* 2.8 40.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MPD 5.0 12.6 - - + -
550B THR* 3.2 38.5 - - - +
551B THR* 3.2 8.1 + - - +
553B HIS* 1.3 73.4 - - + +
555B GLU* 1.3 62.8 + - - +
556B ARG 2.9 5.6 + - - -
557B VAL* 2.9 28.8 + - + +
558B GLU* 3.1 20.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B THR* 3.2 33.4 + - + +
552B ILE* 3.2 17.7 + - + +
554B LYS* 1.3 79.8 - - - +
556B ARG* 1.3 59.8 + - + +
558B GLU* 4.5 4.0 - - - -
559B GLU* 3.7 21.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.7 21.2 - - - -
30A GLU* 4.9 10.3 + - - +
32A ALA* 4.8 18.0 - - - +
34A ASN* 4.9 14.8 + - - +
229B LEU* 3.7 18.4 - - + +
552B ILE* 3.1 33.5 - - + +
553B HIS* 3.0 10.7 + - + +
554B LYS 2.9 0.4 - - - -
555B GLU* 1.3 82.2 - - - +
557B VAL* 1.3 61.1 + - - +
558B GLU 3.4 1.1 - - - -
559B GLU* 4.3 5.8 - - - -
560B THR* 2.6 31.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 4.1 4.9 - - + +
229B LEU* 5.0 9.6 - - + -
553B HIS* 2.8 36.3 + - + +
554B LYS* 2.9 19.2 + - + +
556B ARG* 1.3 79.2 - - - +
558B GLU* 1.3 75.0 + - - +
561B LYS* 3.0 44.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B LYS* 3.1 13.5 + - - +
555B GLU* 5.4 2.7 - - - -
557B VAL* 1.3 96.2 - - - +
559B GLU* 1.3 57.3 + - - +
561B LYS* 3.0 19.8 + - + +
562B GLN* 2.8 37.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B GLU 3.7 21.2 + - - +
556B ARG* 4.2 3.5 + - - -
558B GLU* 1.3 78.3 - - - +
560B THR* 1.3 59.3 + - - +
562B GLN* 3.6 7.0 + - - +
563B GLN* 2.9 42.8 + - + +
----------------------------------------------------------
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Residues in contact with THR 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 4.0 6.0 - - + +
225B LYS* 3.7 40.3 - - + +
226B LEU* 3.5 33.9 - - + +
229B LEU* 4.0 8.1 - - - +
556B ARG* 2.6 27.8 + - - +
558B GLU 3.2 0.6 - - - -
559B GLU* 1.3 75.9 - - - +
561B LYS* 1.3 60.2 + - - +
563B GLN* 3.2 14.7 + - - +
564B LEU 2.9 24.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.4 21.3 - - + -
557B VAL* 3.0 42.8 + - + +
558B GLU* 3.0 20.3 + - + +
560B THR* 1.3 73.6 - - - +
562B GLN* 1.3 60.1 + - - +
564B LEU* 3.5 4.3 + - - +
565B GLU* 3.0 31.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B GLU* 2.8 19.9 + - + +
559B GLU* 3.7 7.6 - - - +
561B LYS* 1.3 71.8 - - - +
563B GLN* 1.3 54.4 + - - +
564B LEU 3.0 0.7 - - - -
565B GLU* 2.8 19.1 + - + +
566B ASP* 2.7 63.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 3.0 47.1 - - + +
225B LYS* 4.2 8.5 - - - +
559B GLU* 2.9 34.2 + - + +
560B THR* 3.2 23.2 + - - +
562B GLN* 1.3 74.2 - - - +
564B LEU* 1.3 57.9 + - - +
566B ASP* 4.2 7.3 - - - +
567B ASN* 3.4 13.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LYS 4.6 2.0 - - - +
219B GLY* 4.3 7.4 - - - +
222B LEU* 3.5 15.0 - - + -
223B GLU* 3.5 58.3 - - + +
226B LEU* 3.7 25.1 - - + -
560B THR 2.9 6.7 + - - +
561B LYS* 3.8 5.2 - - - +
563B GLN* 1.3 77.0 - - - +
565B GLU* 1.3 66.0 + - - +
566B ASP 3.2 0.2 - - - -
567B ASN* 3.0 14.1 + - + +
568B GLY* 3.1 11.6 + - - -
----------------------------------------------------------
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Residues in contact with GLU 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LYS* 3.0 17.3 + - - +
562B GLN* 2.8 24.1 + - - +
564B LEU* 1.3 75.8 - - - +
566B ASP* 1.3 57.9 + - - +
568B GLY* 3.5 1.4 + - - -
569B LYS* 3.0 27.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 566 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B GLN* 2.7 41.4 + - - +
563B GLN* 4.3 7.8 - - - +
565B GLU* 1.3 73.7 - - - +
567B ASN* 1.3 52.3 + - - +
568B GLY 3.1 0.4 - - - -
569B LYS* 3.3 26.6 + - - +
570B GLU* 2.6 38.7 + - - +
----------------------------------------------------------
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Residues in contact with ASN 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASN* 2.7 56.6 + - - -
218B LYS* 3.2 36.0 + - - +
219B GLY* 3.1 21.4 - - - +
222B LEU* 4.3 1.4 - - + +
563B GLN 3.4 17.6 + - - +
564B LEU* 3.0 7.4 + - + +
566B ASP* 1.3 77.3 - - - +
568B GLY* 1.3 57.1 + - - +
570B GLU* 3.8 12.8 - - - +
571B LYS* 3.6 10.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 568 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B LEU 3.1 10.5 + - - -
565B GLU* 4.0 2.5 - - - -
567B ASN* 1.3 77.1 - - - +
569B LYS* 1.3 65.3 + - - +
570B GLU 3.2 0.9 - - - -
571B LYS* 3.2 27.0 - - - +
572B ILE* 3.4 12.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B GLU 3.0 13.7 + - - +
566B ASP* 3.4 29.9 + - - +
568B GLY* 1.3 75.9 - - - +
570B GLU* 1.3 64.8 + - - +
572B ILE* 3.0 41.6 + - + +
573B GLU* 3.2 14.1 - - - +
----------------------------------------------------------
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Residues in contact with GLU 570 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG 5.3 2.1 - - - +
214B GLU* 5.7 3.6 - - - +
215B ASN* 3.1 35.4 + - + +
218B LYS* 5.0 10.2 + - - +
566B ASP* 2.6 23.3 + - - +
567B ASN* 3.8 11.9 - - - +
569B LYS* 1.3 75.7 - - - +
571B LYS* 1.3 58.1 + - - +
573B GLU* 3.3 19.2 + - + +
574B ILE* 3.4 24.5 - - + +
----------------------------------------------------------
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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).
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