Contacts of the helix formed by residues 482 - 505 (chain A) in PDB entry 1JLH
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 482 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS 4.6 5.2 + - - -
170A LEU* 3.9 2.6 - - - +
173A TYR* 3.5 15.5 - - + +
480A LYS* 3.0 30.8 + - + +
481A LEU* 1.3 76.6 - - - +
483A PRO* 1.3 72.3 - - - +
484A PHE* 3.6 8.2 + - - +
485A MET* 3.1 21.4 + - - +
486A LEU* 2.9 28.1 + - - +
556B VAL* 4.6 18.8 - - + +
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Residues in contact with PRO 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.8 30.7 - - + -
173A TYR* 3.7 27.1 - - + -
291A ASN* 3.5 47.1 - - + +
294A GLN* 3.9 6.7 - - + -
295A LEU* 3.3 15.3 - - - +
482A THR* 1.3 89.2 - - - +
484A PHE* 1.3 63.3 + - - +
486A LEU* 3.4 0.5 + - - +
487A GLY 3.1 18.2 + - - -
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.6 30.7 - - + -
47A HIS* 3.5 45.1 - + + -
294A GLN* 3.3 39.9 + - + +
297A SER* 3.5 22.4 - - - -
298A GLY* 3.1 24.9 - - - -
301A TRP* 3.8 27.1 - + + -
482A THR* 3.2 7.7 + - - +
483A PRO* 1.3 80.3 - - - +
485A MET* 1.3 66.8 + - + +
487A GLY 3.2 1.6 + - - -
488A ALA* 3.1 19.0 + - + +
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Residues in contact with MET 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 4.3 4.7 - - + +
47A HIS 4.3 5.6 - - - +
48A GLY* 3.8 25.6 - - - +
49A HIS 3.7 13.2 - - - +
50A ILE* 3.5 42.8 - - + -
478A PHE* 3.8 24.9 - - + -
479A THR 4.7 2.2 - - - +
480A LYS 3.2 27.1 - - - +
481A LEU* 4.4 1.6 - - - -
482A THR* 3.1 13.6 + - - +
484A PHE* 1.3 83.9 - - + +
486A LEU* 1.3 63.0 + - - +
488A ALA* 3.2 4.3 + - - -
489A LEU* 3.0 28.2 + - + +
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 4.5 4.0 - - - -
166A VAL* 3.8 35.4 - - + -
169A ALA* 3.9 13.2 - - + -
170A LEU* 3.8 17.9 - - + -
295A LEU* 4.4 3.4 - - + -
344A LEU* 4.2 16.4 - - + -
347A PHE* 4.5 10.1 - - + -
481A LEU* 4.0 23.7 - - + +
482A THR 2.9 16.7 + - - +
483A PRO 3.8 3.8 - - - +
485A MET* 1.3 75.8 - - - +
487A GLY* 1.3 64.2 + - - +
489A LEU* 3.2 5.8 + - + +
490A VAL* 3.0 45.3 + - + +
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Residues in contact with GLY 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP* 3.6 9.6 - - - -
295A LEU* 3.4 34.5 - - - +
299A ALA* 3.4 10.0 - - - -
483A PRO 3.1 11.1 + - - -
484A PHE 3.2 1.5 + - - -
485A MET 3.2 0.2 - - - -
486A LEU* 1.3 78.1 - - - +
488A ALA* 1.3 59.5 + - - +
490A VAL 3.5 0.2 + - - -
491A ALA* 3.1 26.0 + - - +
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Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 5.1 0.9 - - + -
50A ILE* 4.2 13.7 - - + -
298A GLY* 3.4 21.2 - - - +
301A TRP* 5.0 5.4 - - + -
302A MET* 3.4 28.9 - - + +
484A PHE* 3.1 16.1 + - + +
485A MET* 3.5 12.1 - - - +
486A LEU 3.2 0.4 - - - -
487A GLY* 1.3 77.5 - - - +
489A LEU* 1.3 56.5 + - - +
491A ALA 3.4 0.5 + - - -
492A MET* 2.9 27.0 + - - +
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 4.8 10.1 - - + -
344A LEU* 5.7 1.3 - - + -
347A PHE* 4.7 14.4 - - + -
406A LEU* 4.9 6.5 - - + -
476A ILE* 4.2 14.8 - - + -
478A PHE* 3.6 49.4 - - + -
481A LEU* 3.9 17.9 - - + -
485A MET* 3.0 31.0 + - + +
486A LEU* 3.7 6.5 - - + +
488A ALA* 1.3 73.7 - - - +
490A VAL* 1.3 63.4 + - - +
492A MET* 3.4 15.8 + - + +
493A TYR* 3.3 30.0 + - + -
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A MET* 4.2 15.0 - - + -
166A VAL* 5.5 1.8 - - + -
275A LEU* 4.5 5.4 - - + -
276A TRP* 3.5 29.4 - - + -
295A LEU* 5.6 0.7 - - + -
347A PHE* 4.2 6.1 - - + -
350A TYR* 4.0 16.8 - - + +
351A PHE* 3.5 22.0 - - + -
486A LEU* 3.0 37.5 + - + +
489A LEU* 1.3 73.0 - - - +
491A ALA* 1.3 66.7 + - - +
493A TYR 3.2 2.3 + - - -
494A GLU* 3.0 30.7 + - - +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 3.8 16.4 - - - +
276A TRP* 4.3 0.4 - - - -
299A ALA* 3.7 22.4 - - + +
302A MET* 3.8 12.3 - - + -
303A ASP* 4.3 2.0 - - - +
487A GLY 3.1 19.5 + - - +
488A ALA 3.8 3.4 - - - +
490A VAL* 1.3 77.0 - - - +
492A MET* 1.3 63.5 + - - +
494A GLU* 3.1 14.6 + - - +
495A HIS* 3.0 27.5 + - + -
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Residues in contact with MET 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.2 3.4 - - - -
52A VAL* 4.5 12.1 - - - -
302A MET* 3.5 24.6 - - + +
315A ALA* 4.2 15.7 - - - -
316A PRO* 3.7 23.3 - - + +
319A LEU* 3.6 31.2 - - + -
476A ILE* 4.0 16.8 - - + -
488A ALA 2.9 18.0 + - - +
489A LEU* 3.5 20.9 - - + +
490A VAL 3.2 0.4 - - - -
491A ALA* 1.3 78.3 - - - +
493A TYR* 1.3 79.8 + - + +
495A HIS 3.3 0.7 + - - -
496A LYS* 3.0 22.7 + - - +
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Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.5 5.6 - - + -
337A MET* 3.7 27.8 - - + +
347A PHE* 4.1 13.0 - + - -
351A PHE* 3.2 30.5 - + + -
404A ASP* 2.6 35.7 + - - +
406A LEU* 4.0 17.5 - - + +
476A ILE* 3.3 19.9 - - + +
489A LEU* 3.3 19.8 + - + -
490A VAL 3.2 2.0 + - - +
492A MET* 1.3 94.6 - - + +
494A GLU* 1.3 65.9 + - - +
496A LYS* 3.0 29.7 + - + +
497A ILE* 2.9 29.5 + - + +
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Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A HIS* 3.7 7.6 + - + -
103A ARG* 2.9 34.6 + - - -
272A ARG 4.6 0.6 - - - +
273A TYR* 3.5 43.7 + - + +
276A TRP* 2.9 29.5 + - - -
350A TYR* 4.4 5.3 + - + +
351A PHE* 4.2 5.6 - - + -
490A VAL* 3.0 27.8 + - + +
491A ALA* 3.1 7.8 + - - +
493A TYR* 1.3 75.9 - - - +
495A HIS* 1.3 61.6 + - + +
497A ILE* 3.3 12.8 + - + +
498A PHE* 3.0 24.8 + - - +
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Residues in contact with HIS 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 4.8 10.3 - - - -
84A PHE* 4.3 2.5 - + - -
99A HIS* 4.7 5.0 - + - -
100A VAL* 3.9 17.0 - - - +
103A ARG* 4.0 8.0 + - - -
302A MET* 4.3 3.8 + - - +
303A ASP* 2.7 38.9 + - - -
306A PHE* 3.4 44.4 - + + +
316A PRO* 3.6 21.8 - - + +
491A ALA* 3.0 16.4 + - + +
494A GLU* 1.3 79.8 - - + +
496A LYS* 1.3 66.0 + - - +
498A PHE* 3.5 6.9 - - + +
499A VAL* 3.0 28.1 + - - +
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Residues in contact with LYS 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PRO* 3.7 17.9 - - - +
319A LEU* 3.8 30.1 + - + +
320A ALA* 3.3 24.7 - - - +
323A GLY* 5.4 2.1 - - - -
335A HIS* 3.3 41.2 + - - -
337A MET* 6.0 0.2 - - - -
355A ASP* 4.7 9.0 + - - +
404A ASP* 4.4 1.4 + - - +
492A MET 3.0 12.3 + - - +
493A TYR* 3.0 33.2 + - + +
495A HIS* 1.3 76.0 - - - +
497A ILE* 1.3 67.0 + - + +
499A VAL 3.1 2.6 + - - -
500A GLN* 3.1 43.5 + - - +
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Residues in contact with ILE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A TYR* 3.8 11.2 - - + +
351A PHE* 4.0 19.7 - - + -
354A GLY* 3.6 9.9 - - - +
355A ASP* 3.6 41.5 - - + +
358A SER* 3.7 24.7 - - - -
359A ASN* 3.1 37.7 + - - +
493A TYR* 2.9 20.0 + - + +
494A GLU* 3.4 10.5 - - - +
496A LYS* 1.3 82.5 - - + +
498A PHE* 1.3 61.7 + - - +
500A GLN* 3.5 3.5 + - - -
501A GLY 3.1 9.0 + - - -
508A SER* 3.8 3.8 + - - +
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Residues in contact with PHE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 4.7 2.7 - - + -
79A ALA* 3.7 26.2 - - + -
80A ARG* 3.7 22.4 - - + -
83A MET* 3.5 27.1 - - + -
89A ILE* 3.9 12.1 - - + -
99A HIS* 6.4 0.7 - - + -
273A TYR* 5.8 0.4 - - - -
306A PHE* 3.8 28.3 - + - -
494A GLU 3.0 14.5 + - - +
495A HIS* 3.5 12.3 - - + +
496A LYS 3.1 0.4 - - - -
497A ILE* 1.3 78.5 - - - +
499A VAL* 1.3 64.1 + - + +
501A GLY* 3.3 2.3 + - - -
502A ILE* 3.1 49.2 + - + +
508A SER* 4.6 5.1 + - - -
509A PHE* 3.5 28.3 - + + -
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 4.0 25.4 - - + -
306A PHE* 3.9 28.3 - - + -
317A VAL* 4.1 16.2 - - + +
320A ALA* 3.6 16.4 - - + -
321A LEU* 4.1 9.0 - - + -
495A HIS 3.0 15.0 + - - +
496A LYS 3.1 6.3 + - - +
498A PHE* 1.3 74.8 - - + +
500A GLN* 1.3 65.5 + - - +
502A ILE* 3.2 7.8 + - - +
503A ILE* 3.0 37.5 + - + +
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Residues in contact with GLN 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA* 3.0 45.2 + - + +
323A GLY* 3.6 19.4 - - - -
324A ILE* 3.9 15.9 - - + +
327A ILE* 4.5 3.4 - - - +
355A ASP* 4.5 9.5 - - - +
359A ASN* 4.0 5.4 + - - +
376A PRO* 4.9 4.0 - - - +
496A LYS* 3.1 28.3 + - - +
497A ILE* 3.9 5.8 - - - +
499A VAL* 1.3 74.3 - - - +
501A GLY* 1.3 63.3 + - - +
503A ILE* 3.2 2.9 + - - +
504A TRP* 2.9 59.7 + - + -
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Residues in contact with GLY 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ASN* 3.8 4.6 - - - +
497A ILE 3.1 10.9 + - - -
498A PHE 3.8 0.7 - - - -
499A VAL 3.2 0.4 - - - -
500A GLN* 1.3 78.6 - - - +
502A ILE* 1.3 56.9 + - - +
504A TRP* 3.3 1.6 + - - -
505A ASP 2.9 23.7 + - - -
506A ILE* 3.1 30.1 + - - +
508A SER* 3.3 23.1 - - - -
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Residues in contact with ILE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.3 32.0 + - - +
75A GLY 4.2 3.8 - - - +
76A VAL* 4.2 12.3 - - + +
79A ALA* 3.7 34.3 - - + -
82A ARG* 5.7 1.1 - - - +
89A ILE* 6.0 3.1 - - + -
365A LYS* 6.2 3.6 - - - +
498A PHE* 3.1 39.7 + - + +
499A VAL* 3.6 8.3 - - - +
501A GLY* 1.3 76.3 - - - +
503A ILE* 1.3 63.9 + - - +
505A ASP* 3.0 12.7 + - - +
506A ILE 5.1 4.9 - - - +
509A PHE* 6.0 1.3 - - + -
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.7 29.6 - - + +
70A LEU* 4.2 14.6 - - + -
71A ALA* 4.8 6.1 - - - -
74A ARG* 2.8 37.6 + - + +
76A VAL* 4.0 16.4 - - + -
321A LEU* 3.7 24.2 - - + -
324A ILE* 3.2 38.8 - - + -
499A VAL* 3.0 21.9 + - + +
500A GLN 3.5 7.4 - - - +
502A ILE* 1.3 77.2 - - - +
504A TRP* 1.3 60.4 + - + +
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Residues in contact with TRP 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 5.7 0.2 - - - +
3A LEU* 3.5 23.6 + - + +
324A ILE* 4.3 14.1 - - + +
327A ILE* 3.9 23.8 - - + -
328A ASN* 2.7 25.6 + - - -
359A ASN* 3.6 13.7 - - + -
364A THR* 4.1 4.7 - - - +
372A HIS* 3.7 31.2 + + + -
373A GLN 3.4 4.0 + - - -
374A THR* 3.5 32.8 - - + -
375A GLY* 3.5 20.2 - - - -
376A PRO* 4.3 0.2 - - + -
500A GLN* 2.9 50.8 + - + +
501A GLY 3.9 4.9 - - - +
503A ILE* 1.3 76.9 - - + +
505A ASP* 1.3 70.1 + - - +
506A ILE* 3.5 24.8 + - + +
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Residues in contact with ASP 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 3.7 20.5 - - + +
74A ARG* 3.1 23.9 + - - +
91A TYR* 3.6 1.5 + - - -
364A THR* 3.1 23.3 + - + -
365A LYS* 2.9 55.9 + - - +
366A SER* 4.4 4.9 + - - -
501A GLY 2.9 4.8 + - - -
502A ILE* 3.0 11.5 + - - +
503A ILE 3.2 0.2 - - - -
504A TRP* 1.3 81.6 - - - +
506A ILE* 1.3 60.7 + - - +
----------------------------------------------------------
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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