Contacts of the helix formed by residues 397 - 423 (chain A) in PDB entry 5DSG
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 LYS 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ARG* 1.3 76.2 - - - +
398A VAL* 1.3 59.5 + - - +
399A THR 3.3 0.2 - - - -
400A ARG* 3.2 14.8 + - - +
401A THR* 3.0 31.6 + - - -
456A CYS 4.0 15.5 - - - +
457A ASN* 4.6 16.2 - - - +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 4.5 21.3 - - + +
71A LEU* 6.3 3.1 - - + -
130A ARG* 5.1 6.7 - - - +
396A ARG 3.1 6.4 - - - +
397A LYS* 1.3 76.9 - - - +
399A THR* 1.3 60.9 + - - +
401A THR* 3.3 7.5 + - - -
402A ILE* 2.9 43.1 + - + +
457A ASN* 5.2 5.5 - - - +
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Residues in contact with THR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 4.0 24.7 + - + +
215A TYR* 5.9 6.7 - - + -
218A ILE* 4.1 26.9 - - + +
396A ARG* 3.6 12.5 + - - -
397A LYS 3.3 0.4 - - - -
398A VAL* 1.3 77.6 - - - +
400A ARG* 1.3 59.7 + - + +
402A ILE* 3.5 10.2 + - - +
403A PHE* 2.9 30.1 + - + +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ARG 4.5 7.2 - - - +
397A LYS* 3.2 15.1 + - - +
398A VAL 3.2 0.4 - - - -
399A THR* 1.3 76.9 - - + +
401A THR* 1.3 64.4 + - - +
403A PHE* 3.3 11.5 + - + +
404A ALA* 2.9 23.0 + - - +
456A CYS* 3.5 42.5 + - - +
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Residues in contact with THR 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 5.1 5.4 - - + -
397A LYS 3.0 15.5 + - - -
398A VAL* 3.6 10.4 - - - -
400A ARG* 1.3 76.3 - - - +
402A ILE* 1.3 59.0 + - + +
404A ALA* 3.0 6.3 + - - +
405A ILE* 2.9 33.9 + - + +
452A CYS 4.3 11.9 - - - +
453A TYR* 3.6 38.1 - - + -
456A CYS* 3.6 25.7 + - - +
457A ASN* 4.0 11.8 + - + +
460A PHE* 6.2 0.7 - - + -
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 5.4 6.7 - - + +
71A LEU* 4.9 16.2 - - + -
123A LEU* 5.9 4.2 - - + +
126A ILE* 3.6 36.8 - - + -
127A SER* 5.1 9.6 - - - +
130A ARG* 3.6 31.4 - - + -
398A VAL* 2.9 30.9 + - + +
399A THR* 3.8 4.9 - - - +
401A THR* 1.3 75.9 - - + +
403A PHE* 1.3 58.6 + - - +
405A ILE* 3.2 10.7 + - + +
406A LEU* 2.9 30.2 + - + +
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Residues in contact with PHE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 3.4 55.6 - + + -
399A THR* 2.9 19.8 + - + +
400A ARG* 3.5 9.9 - - + +
401A THR 3.3 0.2 - - - -
402A ILE* 1.3 76.4 - - - +
404A ALA* 1.3 60.5 + - - +
406A LEU* 3.4 14.0 + - + +
407A LEU* 2.9 52.7 + - + +
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ARG 2.9 12.9 + - - +
401A THR 3.0 9.8 + - - +
403A PHE* 1.3 81.5 - - + +
405A ILE* 1.3 57.2 + - - +
407A LEU* 3.2 10.2 + - - +
408A ALA* 2.9 29.6 + - - +
452A CYS* 4.0 19.0 - - + -
456A CYS* 3.6 24.5 - - - -
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Residues in contact with ILE 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 5.4 3.4 - - + -
74A LEU* 3.8 12.8 - - + -
123A LEU* 3.8 26.5 - - + -
126A ILE* 6.3 0.2 - - + -
401A THR* 2.9 26.4 + - + +
402A ILE* 3.5 10.3 - - + +
404A ALA* 1.3 77.0 - - - +
406A LEU* 1.3 55.9 + - - +
408A ALA* 3.3 5.2 + - - +
409A PHE* 2.9 26.9 + - - +
445A ASN* 3.9 1.8 + - - +
449A ASN* 3.3 41.3 - - + +
452A CYS* 3.6 23.8 - - + -
453A TYR* 4.3 17.5 - - + +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 5.0 7.2 - - + +
127A SER* 5.3 4.0 - - - +
208A VAL 5.8 0.7 - - - +
211A MET* 3.7 59.9 - - + +
212A THR* 5.2 2.5 - - - +
215A TYR* 4.6 14.4 - - + -
402A ILE* 2.9 20.0 + - + +
403A PHE* 3.7 17.0 - - + +
405A ILE* 1.3 76.4 - - - +
407A LEU* 1.3 58.7 + - - +
409A PHE* 3.2 9.2 + - + +
410A ILE* 2.9 56.6 + - + +
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A PHE* 2.9 42.6 + - + +
404A ALA* 3.2 8.0 + - - +
406A LEU* 1.3 78.5 - - - +
408A ALA* 1.3 56.3 + - - +
410A ILE* 3.4 10.3 + - + +
411A LEU* 2.9 63.0 + - + +
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA 2.9 13.6 + - - +
405A ILE* 3.3 7.2 + - - +
407A LEU* 1.3 75.7 - - - +
409A PHE* 1.3 52.9 + - - +
411A LEU* 4.7 5.6 - - - -
412A THR* 2.5 42.1 + - - +
445A ASN* 3.4 16.4 - - - +
448A ILE* 3.7 34.5 - - + -
449A ASN* 4.4 3.4 - - - +
452A CYS* 4.6 1.1 - - - -
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 5.9 2.0 - - - -
120A VAL* 3.7 28.3 - - + -
123A LEU* 3.6 28.7 - - + -
204A PHE* 3.9 12.8 - + - -
207A PRO* 6.0 0.2 - - + -
208A VAL* 3.8 23.8 - - + -
211A MET* 4.1 16.6 - - + -
405A ILE 2.9 13.6 + - - +
406A LEU* 3.4 10.5 - - + +
408A ALA* 1.3 75.3 - - - +
410A ILE* 1.3 72.6 + - + +
412A THR* 3.1 3.3 + - - -
413A TRP* 2.9 74.6 + + - +
445A ASN* 3.1 17.6 - - - +
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Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 5.0 4.5 - - + -
208A VAL* 4.4 26.9 - - + -
212A THR* 4.8 7.2 - - - +
406A LEU* 2.9 43.3 + - + +
407A LEU* 3.8 11.4 - - + +
409A PHE* 1.3 86.3 - - + +
411A LEU* 1.3 63.4 + - + +
414A THR* 2.3 50.1 + - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A LEU* 2.9 48.6 + - + +
408A ALA* 4.0 5.4 - - - +
410A ILE* 1.3 81.7 - - + +
412A THR* 1.3 63.9 + - + +
414A THR* 4.4 2.5 - - - -
415A PRO* 3.4 19.6 - - - +
441A LEU* 4.8 2.3 - - - +
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA 2.5 24.3 + - - +
409A PHE 3.1 6.6 + - - -
411A LEU* 1.3 79.9 - - + +
413A TRP* 1.3 71.1 + - - +
415A PRO* 3.8 4.6 - - - +
416A TYR 5.3 0.3 + - - -
438A GLY 4.8 0.2 - - - +
441A LEU* 3.5 53.5 - - + +
442A CYS* 3.8 3.6 + - - -
444A VAL* 4.4 4.5 - - + -
445A ASN* 3.3 17.2 - - - +
448A ILE* 3.7 27.1 - - + -
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Residues in contact with TRP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 5.6 6.3 - - + -
116A SER* 3.6 41.5 - - - -
119A SER* 5.4 4.9 - - - -
120A VAL* 3.7 7.0 - - + -
204A PHE* 3.5 18.6 - + + -
409A PHE* 2.9 44.7 + + - +
412A THR* 1.3 94.9 - - - +
414A THR* 1.3 62.3 + - - +
415A PRO* 3.4 2.1 - - - -
416A TYR* 3.5 5.3 + - - +
417A ASN* 2.7 29.6 + - - +
442A CYS* 2.9 35.4 + - + -
445A ASN* 3.9 11.7 - - - +
1201A 0HK 3.7 53.4 - - + -
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Residues in contact with THR 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 3.9 18.8 - - + -
205A TYR* 6.6 0.2 - - + -
410A ILE* 2.3 40.7 + - - +
411A LEU* 4.4 2.5 - - - -
413A TRP* 1.3 76.9 - - - +
415A PRO* 1.4 71.0 - - + +
417A ASN* 3.2 4.0 + - - +
418A VAL* 2.9 40.5 + - + +
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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
----------------------------------------------------------
411A LEU 3.4 17.9 - - - +
412A THR 3.8 5.4 - - - +
413A TRP 3.5 4.0 - - - -
414A THR* 1.4 92.3 - - + +
416A TYR* 1.3 54.7 + - - +
418A VAL* 3.2 10.0 + - + +
419A MET* 2.9 46.5 + - + +
438A GLY* 5.3 1.6 - - - -
441A LEU* 3.8 23.3 - - + -
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Residues in contact with TYR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 4.0 11.1 + - - -
196A THR* 6.0 0.5 - - - +
412A THR 5.3 0.2 + - - -
413A TRP 3.5 2.1 + - - +
414A THR 3.3 0.6 - - - -
415A PRO* 1.3 79.4 - - - +
417A ASN* 1.3 58.1 + - - +
419A MET* 3.1 14.6 + - - +
420A VAL* 2.9 38.1 + - + +
435A TRP* 3.7 35.0 - + - -
438A GLY* 4.0 7.5 - - - +
439A TYR* 3.6 47.9 - + + -
442A CYS* 3.7 23.1 - - - -
1201A 0HK 3.5 54.4 - - + +
1205A P6G 4.7 18.5 + - - -
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Residues in contact with ASN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ALA* 4.0 10.2 - - - +
204A PHE* 3.4 41.4 - - + +
205A TYR* 2.8 26.2 + - + +
413A TRP* 2.7 26.9 + - - +
414A THR 3.2 5.9 + - - +
416A TYR* 1.3 74.4 - - - +
418A VAL* 1.3 58.9 + - - +
420A VAL* 3.2 11.0 + - + +
421A LEU 2.9 19.2 + - - -
1201A 0HK 2.7 44.8 + - - +
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 3.9 9.4 - - + +
414A THR* 2.9 35.8 + - + +
415A PRO* 3.4 10.8 - - + +
417A ASN* 1.3 75.7 - - + +
419A MET* 1.3 59.8 + - + +
421A LEU* 3.1 13.3 + - + +
422A VAL* 2.9 38.0 + - + +
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Residues in contact with MET 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PRO* 2.9 33.4 + - + +
416A TYR* 3.1 12.8 + - - +
418A VAL* 1.3 78.6 - - + +
420A VAL* 1.3 55.9 + - - +
422A VAL* 3.3 8.2 + - - +
423A ASN* 2.9 30.5 + - - +
430A ILE* 4.1 19.7 - - + +
434A VAL* 3.5 48.0 - - + +
435A TRP* 3.4 27.9 - - + -
437A ILE* 6.1 1.1 - - + -
438A GLY* 3.9 19.1 - - - +
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Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PRO 5.0 1.0 - - - +
196A THR* 3.8 23.3 - - + +
197A PHE* 3.8 28.5 - - + +
200A ALA* 3.9 9.2 - - + -
416A TYR* 2.9 42.0 + - + +
417A ASN* 3.3 15.3 - - - +
419A MET* 1.3 77.9 - - - +
421A LEU* 1.3 61.2 + - - +
423A ASN* 3.4 13.5 + - + +
424A THR* 3.5 12.3 - - - +
435A TRP* 4.1 13.0 - - + -
1201A 0HK 4.2 10.8 - - + -
1205A P6G 5.9 0.4 - - - +
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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
----------------------------------------------------------
197A PHE* 3.6 35.0 - - + -
205A TYR* 3.9 14.6 - - + +
417A ASN 2.9 13.3 + - - +
418A VAL* 3.1 17.5 + - + +
420A VAL* 1.3 77.3 - - - +
422A VAL* 1.3 60.7 + - + +
424A THR* 2.6 34.7 + - - +
425A PHE* 3.8 8.8 - - + -
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 2.9 32.2 + - + +
419A MET* 3.3 6.5 + - - +
421A LEU* 1.3 79.5 - - + +
423A ASN* 1.3 56.2 + - - +
424A THR 3.0 2.8 + - - -
425A PHE* 3.2 28.7 + - + -
426A CYS 2.9 36.4 + - - +
429A CYS* 4.1 12.1 - - + -
430A ILE* 4.0 24.0 - - + -
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Residues in contact with ASN 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PRO* 3.3 33.7 - - + +
196A THR* 5.8 0.9 - - - +
419A MET 2.9 18.0 + - - +
420A VAL* 3.6 9.0 - - - +
421A LEU 3.2 0.6 - - - -
422A VAL* 1.3 75.0 - - - +
424A THR* 1.3 60.7 + - - +
425A PHE 3.3 0.6 + - - -
426A CYS 3.7 7.8 + - - -
427A GLN* 3.5 41.6 + - - +
430A ILE* 5.1 1.1 - - - +
435A TRP* 3.5 28.8 - - + +
1205A P6G 4.3 14.8 + - - -
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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