Contacts of the helix formed by residues 486 - 509 (chain A) in PDB entry 4WMJ
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 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 2.7 28.5 + - + +
175A LEU* 3.8 4.9 - - - -
178A TYR* 3.4 15.7 - - - +
484A LYS* 3.7 25.1 - - + +
485A PHE* 1.3 77.5 - - - +
487A PRO* 1.4 77.7 - - - +
488A PHE 3.1 2.5 + - - -
489A THR* 3.0 19.4 + - + +
490A LEU* 2.9 23.0 + - - +
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Residues in contact with PRO 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.9 26.9 - - + -
178A TYR* 3.5 27.1 - - + -
291A ILE* 4.7 0.2 - - + -
295A ASN* 3.4 48.0 - - + +
298A LYS* 3.8 9.6 - - + -
299A LEU* 3.3 20.5 - - - +
486A THR* 1.4 86.6 - - - +
488A PHE* 1.3 60.8 + - - +
491A GLY 3.0 18.7 + - - -
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Residues in contact with PHE 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.7 27.4 - - + -
50A PRO* 4.2 15.7 - - + -
51A ASN 6.2 0.2 - - - -
52A ASP* 3.5 34.5 - - + +
298A LYS* 3.4 21.5 + - + +
301A ASP* 3.7 24.9 - - + -
302A GLY* 3.3 19.3 - - - -
305A PHE* 3.5 35.0 - + + -
486A THR* 3.1 1.4 + - - -
487A PRO* 1.3 80.2 - - - +
489A THR* 1.3 67.2 + - - +
491A GLY 3.3 0.3 + - - -
492A ALA* 3.0 20.6 + - + +
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Residues in contact with THR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 5.3 0.9 - - + -
52A ASP* 3.8 33.2 - - + +
55A ILE* 4.8 12.3 - - + +
482A VAL* 4.3 21.5 - - + -
484A LYS 2.8 28.1 + - - +
485A PHE* 3.4 6.6 - - - -
486A THR* 3.0 16.7 + - + +
488A PHE* 1.3 79.1 - - + +
490A LEU* 1.3 63.3 + - - +
492A ALA* 3.4 6.4 + - - +
493A LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET* 4.7 1.6 - - - -
171A VAL* 4.2 15.3 - - + -
174A ALA* 3.7 25.4 - - + -
175A LEU* 3.9 24.0 - - + -
299A LEU* 4.3 2.5 - - + -
348A LEU* 3.9 27.6 - - + -
351A PHE* 4.4 9.4 - - + -
485A PHE* 5.3 9.4 - - + -
486A THR 2.9 17.8 + - - +
487A PRO 3.9 2.0 - - - +
489A THR* 1.3 80.7 + - - +
491A GLY* 1.3 57.7 + - - +
493A LEU* 3.1 7.7 + - + -
494A ILE* 2.9 54.4 + - + +
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Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TRP* 3.7 10.2 - - - -
299A LEU* 3.6 34.0 - - - +
303A ALA* 3.5 9.4 - - - -
487A PRO 3.0 12.2 + - - -
488A PHE 3.8 0.2 - - - -
490A LEU* 1.3 74.7 - - - +
492A ALA* 1.3 62.1 + - - +
495A ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 4.0 24.5 - - + -
302A GLY* 3.3 23.5 - - - +
305A PHE* 4.4 6.7 - - + -
306A MET* 3.3 24.1 - - + +
488A PHE* 3.0 16.8 + - + +
489A THR* 3.6 6.1 - - - +
491A GLY* 1.3 75.8 - - - +
493A LEU* 1.3 57.4 + - - +
496A MET* 2.9 25.6 + - - +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 4.4 18.6 - - + -
306A MET* 5.8 0.4 - - + -
348A LEU* 6.1 0.4 - - + -
351A PHE* 4.9 13.9 - - + -
410A LEU* 4.3 14.6 - - + -
480A ILE* 4.0 17.5 - - + -
482A VAL* 4.1 12.3 - - + -
485A PHE* 3.7 31.2 - - + -
489A THR 3.0 21.4 + - - +
490A LEU* 3.7 7.2 - - + +
492A ALA* 1.3 77.1 - - + +
494A ILE* 1.3 67.3 + - - +
496A MET* 3.2 27.9 + - + +
497A TYR* 3.2 30.7 + - + -
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Residues in contact with ILE 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET* 3.9 24.0 - - + -
171A VAL* 4.1 14.1 - - + -
279A LEU* 4.5 3.4 - - + -
280A TRP* 3.4 32.3 - - + -
299A LEU* 4.6 3.1 - - + -
351A PHE* 4.4 5.8 - - + -
354A TYR* 4.1 14.1 - - + +
355A PHE* 3.6 22.7 - - + -
490A LEU* 2.9 45.5 + - + +
491A GLY 3.9 0.7 - - - +
493A LEU* 1.3 76.4 - - - +
495A ALA* 1.3 62.8 + - - +
497A TYR 3.2 3.1 + - - -
498A GLU* 2.9 26.5 + - - +
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Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.8 20.2 - - - +
280A TRP* 4.3 0.6 - - - -
303A ALA* 3.8 19.5 - - + +
306A MET* 3.9 11.9 - - + -
307A ASP* 4.1 2.2 - - - +
491A GLY 3.0 17.9 + - - +
492A ALA 3.8 3.4 - - - +
494A ILE* 1.3 77.0 - - - +
496A MET* 1.3 63.4 + - - +
498A GLU* 3.2 13.6 + - - +
499A HIS* 3.0 26.9 + - - -
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Residues in contact with MET 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 6.0 0.4 - - - -
55A ILE* 5.8 3.4 - - - -
57A LEU* 5.4 4.9 - - - -
306A MET* 3.4 25.5 - - + +
319A ALA* 4.2 14.1 - - + -
320A PRO* 3.6 23.7 - - + +
323A LEU* 3.7 27.1 - - + -
480A ILE* 3.9 15.3 - - + -
492A ALA 2.9 16.1 + - - +
493A LEU* 3.2 30.2 + - + +
495A ALA* 1.3 74.6 - - - +
497A TYR* 1.3 88.0 + - + +
499A HIS 3.2 1.6 + - - -
500A LYS* 2.9 25.6 + - - +
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Residues in contact with TYR 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.5 7.2 - - + -
341A LEU* 3.5 18.1 - - + +
351A PHE* 3.8 28.9 - + - -
355A PHE* 3.3 31.6 - + + -
408A ASP* 2.7 40.8 + - - +
410A LEU* 4.4 9.2 - - + +
480A ILE* 3.7 9.4 - - - +
493A LEU* 3.2 19.0 + - + -
494A ILE 3.2 1.8 + - - +
496A MET* 1.3 94.0 - - + +
498A GLU* 1.3 68.5 + - - +
500A LYS* 3.2 27.9 + - + +
501A ILE* 3.0 32.8 + - + +
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Residues in contact with GLU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A HIS* 3.6 6.8 + - - +
108A ARG* 2.9 34.0 + - - -
276A ARG 5.8 0.2 - - - +
277A TYR* 3.6 44.8 + - + -
280A TRP* 2.8 30.6 + - - -
354A TYR* 4.2 5.7 + - - +
355A PHE* 4.2 7.2 - - + -
494A ILE* 2.9 24.8 + - + +
495A ALA* 3.2 8.7 + - - +
497A TYR* 1.3 77.7 - - - +
499A HIS* 1.3 60.5 + - - +
501A ILE* 3.3 8.9 + - - +
502A PHE* 3.0 25.6 + - - +
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Residues in contact with HIS 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.0 14.1 - - + +
89A PHE* 4.2 1.1 - + - -
104A HIS* 4.7 6.4 + - - -
105A VAL* 3.9 19.7 - - + -
108A ARG* 3.8 7.3 + - - -
306A MET* 4.4 4.9 - - + -
307A ASP* 2.7 35.3 + - - -
310A PHE* 3.3 44.7 - + + -
320A PRO* 3.6 19.5 - - + -
495A ALA* 3.0 21.6 + - + +
498A GLU* 1.3 75.9 - - + +
500A LYS* 1.3 65.6 + - - +
502A PHE* 3.6 5.3 - - - +
503A THR* 2.8 30.3 + - - -
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Residues in contact with LYS 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 3.6 17.5 - - - +
323A LEU* 3.8 31.8 - - + +
324A ALA* 3.5 16.9 - - - +
327A GLY* 5.2 3.3 - - - -
339A HIS* 3.6 38.6 + - - -
359A ASP* 4.5 9.3 + - - -
408A ASP* 4.6 3.6 + - - -
496A MET 2.9 14.5 + - - +
497A TYR* 3.5 28.0 - - + +
499A HIS* 1.3 78.0 - - - +
501A ILE* 1.3 66.2 + - + +
503A THR 3.2 1.0 + - - -
504A GLN* 3.0 47.8 + - - +
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Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 3.6 12.6 - - + +
355A PHE* 3.9 20.9 - - + -
358A GLY* 3.6 7.6 - - - +
359A ASP* 3.6 44.9 - - + +
362A SER* 3.5 30.7 - - - -
363A ASN* 2.9 32.3 + - - +
497A TYR* 3.0 22.7 + - + +
498A GLU* 3.5 5.6 - - - +
500A LYS* 1.3 79.7 - - + +
502A PHE* 1.3 63.7 + - - +
504A GLN* 3.4 5.4 + - - +
505A GLY 3.1 8.5 + - - -
512A SER* 3.8 3.1 + - - +
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Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.4 4.3 - - + -
84A ALA* 3.5 27.6 - - + -
85A ARG* 3.6 25.6 - - + -
88A MET* 3.9 21.5 - - + -
94A ILE* 4.0 16.8 - - + -
277A TYR* 5.2 0.2 + - - -
310A PHE* 3.8 21.8 - + - -
498A GLU 3.0 13.9 + - - +
499A HIS* 3.6 11.7 - - - +
501A ILE* 1.3 76.5 - - - +
503A THR* 1.3 66.7 + - - +
505A GLY* 3.1 4.0 + - - -
506A VAL* 3.0 43.6 + - + +
512A SER* 4.4 6.6 + - - -
513A PHE* 3.8 29.6 - + + -
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Residues in contact with THR 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.0 27.1 - - + +
310A PHE* 3.5 23.0 - - - -
320A PRO 4.7 0.7 - - - -
321A VAL* 4.2 16.2 - - + +
324A ALA* 3.4 21.3 - - + -
325A LEU* 5.7 0.2 - - + -
499A HIS 2.8 21.5 + - - -
500A LYS* 3.6 4.5 - - - -
502A PHE* 1.3 82.6 - - - +
504A GLN* 1.3 60.2 + - - +
506A VAL* 3.3 7.7 + - - +
507A ILE* 3.1 29.5 + - + +
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Residues in contact with GLN 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 3.1 30.8 + - + +
327A GLY* 3.6 22.8 - - - -
328A VAL* 3.9 4.6 - - + +
359A ASP* 4.4 10.6 - - - +
363A ASN* 3.8 7.6 + - - +
380A PRO* 5.0 3.5 - - - +
500A LYS* 3.0 44.7 + - - +
501A ILE* 3.8 6.3 - - - +
503A THR* 1.3 70.8 - - - +
505A GLY* 1.3 65.9 + - - +
507A ILE* 3.2 8.8 + - - +
508A TRP* 3.0 59.9 + - + -
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Residues in contact with GLY 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASN* 3.8 3.3 - - - +
501A ILE 3.1 7.4 + - - -
502A PHE 3.1 4.5 + - - -
504A GLN* 1.3 76.2 - - - +
506A VAL* 1.3 57.3 + - - +
508A TRP 3.5 0.3 + - - -
509A ASP* 3.0 22.2 + - - -
510A ILE* 3.2 31.8 + - - +
512A SER* 3.3 23.6 - - - -
----------------------------------------------------------
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Residues in contact with VAL 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 3.7 20.2 + - - +
79A ARG 3.4 23.3 - - - +
81A VAL* 4.2 14.6 - - + -
84A ALA* 3.7 31.6 - - + -
502A PHE* 3.0 39.4 + - + +
503A THR* 3.6 8.7 - - - +
504A GLN 3.2 0.2 - - - -
505A GLY* 1.3 74.3 - - - +
507A ILE* 1.3 65.5 + - - +
509A ASP* 3.0 13.8 + - - +
510A ILE 5.5 0.4 - - - -
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Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.7 12.6 - - + +
75A LEU* 4.0 26.2 - - + +
76A ALA* 4.9 0.9 - - - -
79A ARG* 3.0 51.9 + - + -
81A VAL* 4.2 10.5 - - + -
324A ALA* 5.1 1.8 - - + -
325A LEU* 3.8 29.4 - - + -
328A VAL* 4.3 20.2 - - + -
503A THR* 3.1 28.1 + - + +
504A GLN* 3.2 7.6 + - - +
506A VAL* 1.3 77.4 - - - +
508A TRP* 1.3 67.5 + - + +
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Residues in contact with TRP 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.8 19.9 - - + +
79A ARG* 4.4 0.2 - - - -
327A GLY 5.2 2.0 - - - -
328A VAL* 4.1 20.2 - - + +
331A GLY* 6.2 0.7 - - - -
332A ASN* 2.9 31.5 - - - +
363A ASN* 3.8 13.5 - - + -
368A THR* 4.2 0.3 - - - +
376A TYR* 2.5 36.2 + + + -
377A SER 3.5 12.0 + - - -
378A THR* 3.5 35.9 - - + -
379A GLY* 3.6 18.6 - - - -
380A PRO* 4.4 4.5 - - + -
504A GLN* 3.0 51.0 + - + +
507A ILE* 1.3 78.1 - - + +
509A ASP* 1.3 66.1 + - - +
510A ILE* 3.3 27.4 + - + +
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Residues in contact with ASP 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 3.7 41.8 + - + +
5A VAL 5.5 0.2 - - - +
79A ARG* 3.8 16.2 - - - +
96A PHE* 5.8 0.3 - - - -
368A THR* 3.1 14.5 + - + -
369A ARG* 3.0 49.6 + - - +
370A SER* 4.6 2.9 + - - -
376A TYR* 4.6 1.6 - - - +
505A GLY 3.0 8.0 + - - -
506A VAL* 3.0 10.2 + - - +
507A ILE 3.2 0.2 - - - -
508A TRP* 1.3 78.9 - - - +
510A ILE* 1.3 60.3 + - - +
----------------------------------------------------------
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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