Contacts of the helix formed by residues 483 - 506 (chain A) in PDB entry 2CVP
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 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS 4.8 1.3 + - - +
171A LEU* 4.0 2.5 - - - -
174A TYR* 3.6 13.2 - - - +
481A LYS* 3.0 16.6 + - + +
482A LEU* 1.3 75.8 - - - +
484A PRO* 1.3 76.3 - - - +
485A PHE* 3.5 7.6 + - - +
486A ILE* 3.1 27.1 + - - +
487A LEU* 2.9 22.5 + - - +
557B LEU* 4.0 30.3 - - + -
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Residues in contact with PRO 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.8 28.5 - - + -
174A TYR* 3.6 26.9 - - + -
292A HIS* 3.4 40.8 - - + +
295A GLN* 3.8 20.4 - - + +
296A LEU* 3.4 16.6 - - - +
483A THR* 1.3 86.9 - - - +
485A PHE* 1.3 61.6 + - - +
487A LEU* 3.8 0.4 - - + +
488A GLY 3.0 18.5 + - - -
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Residues in contact with PHE 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.5 31.9 - - + -
48A HIS* 3.7 43.7 - + + -
295A GLN* 3.4 26.4 + - + +
298A SER* 3.5 15.7 - - - -
299A GLY* 3.2 39.5 - - - -
302A TRP* 3.7 26.9 - + + -
483A THR* 3.2 7.9 + - - +
484A PRO* 1.3 78.9 - - - +
486A ILE* 1.3 70.5 + - + +
488A GLY 3.3 1.2 + - - -
489A ALA* 3.1 20.5 + - + +
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Residues in contact with ILE 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 4.1 13.7 - - - +
48A HIS 3.7 23.8 - - - +
49A GLY* 4.2 10.3 - - - -
50A HIS 4.7 2.5 - - - +
51A ILE* 4.2 21.5 - - + -
479A PHE* 3.7 31.0 - - + -
480A THR 5.5 0.4 - - - +
481A LYS 3.4 25.8 - - - +
482A LEU* 4.7 1.1 - - + -
483A THR* 3.1 18.1 + - + +
485A PHE* 1.3 76.4 - - + +
487A LEU* 1.3 67.1 + - - +
489A ALA* 3.2 4.6 + - - +
490A LEU* 2.9 29.8 + - + +
557B LEU* 5.1 1.8 - - + -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 4.5 8.5 - - - -
167A VAL* 4.0 19.7 - - + -
170A ALA* 3.8 20.6 - - + -
171A LEU* 3.7 29.2 - - + -
296A LEU* 4.0 4.7 - - + -
345A MET* 5.2 2.2 - - + -
348A PHE* 4.5 12.8 - - + -
482A LEU* 3.8 24.1 - - + +
483A THR 2.9 18.0 + - - +
484A PRO 3.8 3.1 - - - +
486A ILE* 1.3 77.6 - - - +
488A GLY* 1.3 62.4 + - - +
490A LEU* 3.1 6.2 + - + +
491A ILE* 2.9 48.4 + - + +
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TRP* 3.6 11.0 - - - -
296A LEU* 3.4 33.7 - - - +
300A ALA* 3.5 16.7 - - - -
484A PRO 3.0 11.1 + - - -
485A PHE 3.7 2.0 - - - -
487A LEU* 1.3 75.7 - - - +
489A ALA* 1.3 59.6 + - - +
491A ILE 3.5 0.2 + - - -
492A ALA* 3.1 18.4 + - - +
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Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 5.4 0.2 - - + -
51A ILE* 3.9 20.6 - - + -
299A GLY* 3.3 22.5 - - - +
302A TRP* 4.9 6.1 - - + -
303A MET* 3.5 19.7 - - + +
485A PHE* 3.1 17.6 + - + +
486A ILE* 3.2 9.4 + - - +
488A GLY* 1.3 75.5 - - - +
490A LEU* 1.3 58.2 + - - +
492A ALA 3.5 0.5 + - - -
493A MET* 2.9 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
----------------------------------------------------------
51A ILE* 4.2 18.6 - - + -
345A MET* 4.8 8.5 - - + -
348A PHE* 4.9 11.9 - - + -
407A LEU* 4.9 5.4 - - + -
477A ILE* 4.0 27.1 - - + -
479A PHE* 3.6 39.3 - - + -
482A LEU* 4.1 13.5 - - + -
486A ILE* 2.9 22.8 + - + +
487A LEU* 3.1 6.9 + - + +
489A ALA* 1.3 73.4 - - - +
491A ILE* 1.3 66.3 + - - +
493A MET* 3.3 17.8 + - + +
494A TYR* 3.3 28.5 + - + -
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Residues in contact with ILE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 3.9 21.8 - - + -
167A VAL* 4.1 13.5 - - + -
276A LEU* 4.5 3.6 - - + -
277A TRP* 3.5 31.2 - - + -
296A LEU* 4.4 3.1 - - + -
348A PHE* 4.4 5.4 - - + -
351A TYR* 3.9 17.0 - - + +
352A PHE* 3.6 21.8 - - + -
487A LEU* 2.9 48.3 + - + +
490A LEU* 1.3 74.8 - - - +
492A ALA* 1.3 59.1 + - - +
494A TYR 3.2 2.6 + - - -
495A GLU* 2.9 32.8 + - - +
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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
----------------------------------------------------------
104A ARG* 3.7 20.4 - - - +
277A TRP* 4.4 0.6 - - - -
300A ALA* 3.8 21.1 - - + +
303A MET* 3.9 16.2 - - + -
304A ASP* 4.1 2.2 - - - +
488A GLY 3.1 17.5 + - - +
491A ILE* 1.3 75.9 - - - +
493A MET* 1.3 63.7 + - - +
495A GLU* 3.2 12.3 + - - +
496A HIS* 2.9 28.9 + - - -
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Residues in contact with MET 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 5.0 2.5 - - - -
53A VAL* 4.1 10.8 - - + -
303A MET* 3.4 29.1 - - - +
316A ALA* 4.1 15.5 - - - -
317A PRO* 3.4 19.1 - - + +
320A LEU* 3.8 31.6 - - + -
477A ILE* 4.1 17.5 - - + -
489A ALA 2.9 18.6 + - - +
490A LEU* 3.4 23.1 - - + +
491A ILE 3.3 0.2 - - - -
492A ALA* 1.3 76.6 - - - +
494A TYR* 1.3 77.5 + - + +
496A HIS* 3.4 0.7 + - - -
497A LYS* 3.0 23.9 + - - +
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.8 7.0 - - + -
338A LEU* 3.9 16.7 - - + +
348A PHE* 3.9 30.1 - + - -
352A PHE* 3.3 29.2 - + + -
405A ASP* 2.7 36.7 + - - +
407A LEU* 3.9 12.2 - - + +
477A ILE* 3.3 20.7 - - + +
490A LEU* 3.3 18.5 + - + -
491A ILE 3.2 1.8 + - - +
493A MET* 1.3 87.7 - - + +
495A GLU* 1.3 67.8 + - - +
496A HIS 3.2 0.2 - - - -
497A LYS* 3.2 28.0 + - + +
498A ILE* 2.9 31.7 + - + +
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A HIS* 3.8 5.9 + - - +
104A ARG* 2.8 33.9 + - - -
273A ARG 5.6 0.4 - - - +
274A TYR* 3.6 42.2 + - + -
277A TRP* 2.8 30.9 + - - -
351A TYR* 4.0 11.3 + - - +
352A PHE* 4.2 7.1 - - + -
491A ILE* 2.9 22.2 + - + +
492A ALA* 3.4 8.4 - - - +
494A TYR* 1.3 75.9 - - - +
496A HIS* 1.3 62.9 + - - +
498A ILE* 3.3 8.9 + - - +
499A PHE* 3.0 24.8 + - - +
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Residues in contact with HIS 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 4.0 13.0 - - + +
85A PHE* 4.5 0.7 - + - -
100A HIS* 4.8 5.9 + - - -
101A VAL* 3.8 19.3 - - + -
104A ARG* 3.7 8.6 + - - -
303A MET* 4.3 9.0 - - + -
304A ASP* 2.7 33.6 + - - -
307A PHE* 3.4 44.9 - + + -
317A PRO* 3.6 20.0 - - + -
492A ALA 2.9 24.5 + - - +
495A GLU* 1.3 75.1 - - + +
497A LYS* 1.3 59.1 + - - +
499A PHE* 3.3 5.5 + - - +
500A VAL* 3.0 35.2 + - - +
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Residues in contact with LYS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO* 3.7 15.0 - - + +
320A LEU* 3.7 25.3 + - + +
321A ALA* 3.5 20.5 - - - +
324A GLY* 5.1 2.6 - - - -
336A HIS* 3.4 39.0 + - - -
356A ASP* 4.7 8.3 + - - +
405A ASP* 4.6 4.0 + - - -
493A MET 3.0 14.0 + - - +
494A TYR* 3.4 30.1 - - + +
496A HIS* 1.3 74.4 - - - +
498A ILE* 1.3 67.5 + - + +
500A VAL 3.3 1.6 + - - -
501A GLN* 3.0 54.7 + - - +
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Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 3.6 13.5 - - + +
352A PHE* 3.9 22.0 - - + -
355A GLY* 3.7 6.1 - - - +
356A ASP* 3.6 43.5 - - + +
359A SER* 3.5 31.2 - - - -
360A ASN* 3.1 32.6 + - - +
494A TYR* 2.9 21.5 + - + +
495A GLU* 3.5 9.6 - - - +
497A LYS* 1.3 80.2 - - + +
499A PHE* 1.3 63.2 + - - +
501A GLN* 4.7 3.1 - - - +
502A GLY 3.1 8.7 + - - -
509A SER* 3.8 3.5 + - - +
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Residues in contact with PHE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.7 3.1 - - + -
80A ALA* 3.6 23.6 - - + -
81A ARG* 3.6 26.5 - - + -
84A MET* 3.9 16.6 - - + -
90A ILE* 3.7 24.9 - - + -
100A HIS* 6.3 0.4 - - - +
274A TYR* 5.2 0.8 + - - -
307A PHE* 3.7 22.0 - + - -
495A GLU 3.0 14.0 + - - +
496A HIS* 3.4 11.2 - - - +
498A ILE* 1.3 76.7 - - - +
500A VAL* 1.3 66.5 + - + +
502A GLY* 3.2 3.5 + - - -
503A ILE* 3.0 50.0 + - + +
509A SER* 4.4 5.3 + - - -
510A PHE* 3.5 28.7 - + + -
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Residues in contact with VAL 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.0 27.1 - - + -
307A PHE* 3.6 30.5 - - + -
318A VAL* 4.0 24.5 - - + +
321A ALA* 3.6 24.0 - - + -
322A LEU 5.4 0.2 - - - +
496A HIS 3.0 20.3 + - - +
497A LYS 3.3 0.2 + - - -
499A PHE* 1.3 77.7 - - + +
501A GLN* 1.3 64.5 + - - +
503A ILE* 3.4 6.2 + - - +
504A MET* 3.0 33.6 + - - +
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Residues in contact with GLN 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA* 3.1 31.0 + - + +
324A GLY* 3.4 23.4 - - - -
325A ILE* 3.9 11.4 - - + +
328A ILE* 4.4 5.3 - - - +
356A ASP* 4.5 10.7 - - - +
360A ASN* 3.9 5.3 + - - +
377A PRO* 4.8 4.2 - - - +
497A LYS* 3.0 44.3 + - - +
498A ILE* 3.8 5.6 - - - +
499A PHE 3.3 0.2 - - - -
500A VAL* 1.3 77.5 - - - +
502A GLY* 1.3 55.9 + - - +
504A MET* 3.2 4.7 + - - +
505A TRP* 2.9 61.6 + - + -
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Residues in contact with GLY 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ASN* 3.7 5.0 - - - +
498A ILE 3.1 10.5 + - - -
499A PHE 3.6 0.4 - - - -
501A GLN* 1.3 73.1 - - - +
503A ILE* 1.3 65.4 + - - +
505A TRP* 3.3 2.1 + - - -
506A ASP 3.0 17.8 + - - -
507A ILE* 3.1 31.6 + - - +
509A SER* 3.4 23.1 - - - -
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 2.9 43.7 + - - +
76A GLY 4.2 0.2 - - - +
77A VAL* 4.1 18.4 - - + -
80A ALA* 3.7 28.5 - - + -
90A ILE* 5.5 3.8 - - + -
499A PHE* 3.0 50.3 + - + +
500A VAL 3.7 7.0 - - - +
502A GLY* 1.3 74.9 - - - +
504A MET* 1.3 60.0 + - - +
506A ASP* 3.1 6.8 + - - +
507A ILE 5.0 5.4 - - - +
510A PHE* 5.9 1.6 - - + -
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Residues in contact with MET 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.7 18.1 - - + +
71A LEU* 3.5 35.2 - - + -
72A ALA* 4.0 13.7 - - - +
75A ARG* 2.9 32.6 + - + +
77A VAL* 3.7 15.0 - - + -
322A LEU* 3.5 34.3 - - + -
325A ILE* 4.4 22.2 - - + -
500A VAL* 3.0 30.6 + - - +
501A GLN* 3.2 6.3 + - - +
503A ILE* 1.3 77.7 - - - +
505A TRP* 1.3 59.7 + - + +
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Residues in contact with TRP 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.6 14.5 + - + +
325A ILE* 3.5 20.2 - - + +
328A ILE* 3.8 24.2 - - + -
329A ASN* 2.7 23.3 + - - -
360A ASN* 3.6 23.3 - - + -
365A THR* 3.7 12.5 - - - +
373A HIS* 3.5 35.9 + + + -
374A GLN 3.4 7.4 + - - -
375A THR* 3.6 30.7 - - + -
376A GLY* 3.7 15.3 - - - -
501A GLN* 2.9 38.7 + - + +
502A GLY 3.3 4.0 + - - +
504A MET* 1.3 74.6 - - - +
506A ASP* 1.3 69.0 + - - +
507A ILE* 3.4 26.8 + - + +
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Residues in contact with ASP 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.6 23.9 + - + +
75A ARG* 3.2 21.7 + - - +
92A TYR* 3.5 1.8 + - - -
365A THR* 3.1 18.8 - - + -
366A LYS* 2.8 49.8 + - - +
367A SER* 4.0 8.5 + - - -
502A GLY 3.0 4.0 + - - -
503A ILE* 3.1 11.7 + - - +
504A MET 3.2 0.6 - - - -
505A TRP* 1.3 80.3 - - - +
507A ILE* 1.3 59.8 + - - +
----------------------------------------------------------
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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