Contacts of the helix formed by residues 483 - 506 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.3 21.8 - - + -
48B HIS 4.7 1.9 + - - -
171B LEU* 3.9 3.1 - - - -
174B TYR* 3.6 15.3 - - + +
481B LYS* 3.0 29.5 + - + +
482B LEU* 1.3 75.8 - - - +
484B PRO* 1.3 70.4 - - - +
485B PHE* 3.6 7.3 + - - +
486B ILE* 3.1 24.8 + - - +
487B LEU* 2.8 28.6 + - - +
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Residues in contact with PRO 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.8 28.9 - - + -
174B TYR* 3.7 25.8 - - + -
292B HIS* 3.5 42.0 - - + +
295B GLN* 4.0 18.4 - - + +
296B LEU* 3.4 17.9 - - - +
483B THR* 1.3 87.5 - - - +
485B PHE* 1.3 61.4 + - - +
487B LEU* 4.6 0.2 - - + -
488B GLY 3.0 18.5 + - - -
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Residues in contact with PHE 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 3.3 34.8 - - + -
48B HIS* 3.5 45.5 - + + -
295B GLN* 3.3 26.6 + - + +
298B SER* 3.6 26.5 - - - -
299B GLY* 3.3 24.7 - - - -
302B TRP* 3.7 25.1 - + + -
483B THR* 3.2 7.7 + - - +
484B PRO* 1.3 78.8 - - - +
486B ILE* 1.3 73.1 + - + +
488B GLY 3.1 1.9 + - - -
489B ALA* 3.0 20.8 + - + +
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Residues in contact with ILE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 5.1 2.2 - - + -
46B THR* 4.0 13.9 - - + +
48B HIS 3.6 23.1 - - - +
49B GLY* 4.2 11.2 - - - -
50B HIS 4.7 2.2 - - - +
51B ILE* 4.1 22.4 - - + -
479B PHE* 3.8 31.0 - - + -
481B LYS 3.4 26.2 - - - +
482B LEU* 4.8 1.1 - - - -
483B THR* 3.1 17.1 + - + +
485B PHE* 1.3 80.6 - - + +
487B LEU* 1.3 63.5 + - - +
489B ALA* 3.2 4.8 + - - +
490B LEU* 3.0 28.7 + - + +
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 4.4 11.0 - - - -
167B VAL* 4.0 18.8 - - + -
170B ALA* 3.7 20.2 - - + -
171B LEU* 3.7 33.9 - - + -
296B LEU* 4.2 3.1 - - + -
345B MET* 5.4 1.3 - - + -
348B PHE* 4.4 13.5 - - + -
482B LEU* 4.1 23.7 - - + +
483B THR 2.8 17.8 + - - +
484B PRO 3.8 2.7 - - - +
486B ILE* 1.3 77.5 - - - +
488B GLY* 1.3 62.3 + - - +
490B LEU* 3.2 4.6 + - + +
491B ILE* 3.0 48.1 + - + +
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Residues in contact with GLY 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TRP* 3.6 10.0 - - - -
296B LEU* 3.5 32.9 - - - +
300B ALA* 3.5 9.5 - - - -
484B PRO 3.0 11.3 + - - -
485B PHE 3.1 2.0 + - - -
487B LEU* 1.3 76.4 - - - +
489B ALA* 1.3 62.4 + - - +
491B ILE* 3.5 0.4 + - - -
492B ALA* 3.1 25.3 + - - +
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Residues in contact with ALA 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.8 22.2 - - + -
299B GLY* 3.4 23.0 - - - +
302B TRP* 5.0 3.4 - - + -
303B MET* 3.5 20.0 - - + +
485B PHE* 3.0 18.3 + - + +
486B ILE* 3.2 9.4 + - - +
488B GLY* 1.3 76.8 - - - +
490B LEU* 1.3 55.7 + - - +
492B ALA 3.5 0.5 + - - -
493B MET* 2.9 28.8 + - - +
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Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.2 15.3 - - + -
345B MET* 4.8 8.1 - - + -
348B PHE* 4.8 11.9 - - + -
407B LEU* 4.9 4.9 - - + -
477B ILE* 3.8 28.7 - - + -
479B PHE* 3.6 37.9 - - + -
482B LEU* 4.0 16.2 - - + -
486B ILE* 3.0 22.2 + - + +
487B LEU* 3.2 7.6 + - + +
489B ALA* 1.3 74.1 - - - +
491B ILE* 1.3 66.6 + - - +
493B MET* 3.3 17.1 + - + +
494B TYR* 3.2 29.4 + - + -
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Residues in contact with ILE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.8 24.9 - - + -
167B VAL* 4.0 14.4 - - + -
276B LEU* 4.6 2.2 - - + -
277B TRP* 3.5 32.1 - - + -
296B LEU* 4.6 2.9 - - + -
348B PHE* 4.4 5.2 - - + -
351B TYR* 4.0 16.6 - - + +
352B PHE* 3.7 21.4 - - + -
487B LEU* 3.0 46.0 + - + +
490B LEU* 1.3 73.7 - - - +
492B ALA* 1.3 63.4 + - - +
494B TYR* 3.1 4.2 + - - -
495B GLU* 2.9 28.9 + - - +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 3.8 16.8 - - - +
277B TRP* 4.3 0.8 - - - -
300B ALA* 3.8 22.2 - - + +
303B MET* 3.8 13.2 - - + -
304B ASP* 4.2 2.0 - - - +
488B GLY 3.1 18.4 + - - +
489B ALA 3.7 3.6 - - - +
491B ILE* 1.3 77.7 - - - +
493B MET* 1.3 60.9 + - - +
495B GLU* 3.4 12.7 + - - +
496B HIS* 3.0 29.8 + - - -
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Residues in contact with MET 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 5.4 0.2 - - - -
51B ILE* 5.0 4.3 - - - -
53B VAL* 4.1 18.6 - - + -
303B MET* 3.5 28.4 - - + +
316B ALA* 4.2 9.2 - - - -
317B PRO* 3.4 23.4 - - - +
320B LEU* 3.8 31.2 - - + -
477B ILE* 4.0 21.5 - - + -
489B ALA 2.9 14.9 + - - +
490B LEU* 3.4 24.5 - - + +
491B ILE 3.2 0.2 - - - -
492B ALA* 1.3 74.9 - - - +
494B TYR* 1.3 73.5 + - + +
497B LYS* 3.0 23.7 + - - +
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Residues in contact with TYR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 4.6 7.0 - - + -
338B LEU* 3.9 17.4 - - + +
348B PHE* 4.0 28.9 - + - -
352B PHE* 3.3 29.8 - + + -
405B ASP* 2.6 36.8 + - - +
407B LEU* 3.9 11.4 - - + +
477B ILE* 3.2 19.1 - - + +
490B LEU* 3.2 19.4 + - + -
491B ILE 3.1 1.8 + - - -
493B MET* 1.3 92.7 - - + +
495B GLU* 1.3 65.3 - - - +
497B LYS* 3.2 29.2 + - + +
498B ILE* 3.0 32.2 + - + +
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Residues in contact with GLU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B HIS* 3.8 4.5 + - - +
104B ARG* 2.7 37.3 + - - -
273B ARG 4.5 0.6 - - - +
274B TYR* 3.5 45.1 - - + -
277B TRP* 2.9 31.2 + - - -
351B TYR* 4.1 8.9 + - + +
352B PHE* 4.2 6.4 - - + -
491B ILE* 2.9 21.3 + - + +
492B ALA* 3.4 7.9 + - - +
494B TYR* 1.3 75.1 - - - +
496B HIS* 1.3 64.3 + - - +
498B ILE* 3.3 12.5 + - + +
499B PHE* 3.0 24.4 + - - +
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Residues in contact with HIS 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET* 4.6 9.5 - - - -
85B PHE* 4.4 2.7 - + - -
100B HIS* 4.7 6.5 + - - -
101B VAL* 3.8 19.3 - - + -
104B ARG* 3.7 8.7 + - - -
303B MET* 4.3 8.5 - - + -
304B ASP* 2.7 33.4 + - - -
307B PHE* 3.3 47.2 - + + -
317B PRO* 3.6 20.0 - - + -
492B ALA 3.0 22.9 + - - +
495B GLU* 1.3 75.3 + - - +
497B LYS* 1.3 65.8 + - - +
499B PHE* 3.2 7.3 + - - +
500B VAL* 2.9 27.9 + - - +
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Residues in contact with LYS 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 3.6 16.5 - - - +
320B LEU* 3.6 25.5 + - + +
321B ALA* 3.5 21.0 - - - +
324B GLY* 5.1 3.3 - - - -
336B HIS* 3.6 38.4 + - - -
356B ASP* 4.7 12.5 + - - +
405B ASP* 4.7 1.2 + - - -
493B MET 3.0 15.0 + - - +
494B TYR* 3.4 32.1 - - + +
496B HIS* 1.3 75.7 - - - +
498B ILE* 1.3 64.8 + - + +
500B VAL 3.3 0.3 + - - -
501B GLN* 3.0 50.6 + - - +
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Residues in contact with ILE 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B TYR* 3.6 13.5 - - + +
352B PHE* 4.0 16.8 - - + -
355B GLY* 3.8 22.9 - - - +
356B ASP* 3.8 27.8 - - + +
359B SER* 3.6 26.5 - - - -
360B ASN* 2.9 36.0 + - - +
494B TYR* 3.0 27.4 + - + +
495B GLU* 3.4 9.0 - - - +
497B LYS* 1.3 78.9 - - + +
499B PHE* 1.3 63.5 + - - +
501B GLN* 3.4 4.9 + - - +
502B GLY 3.1 8.5 + - - -
509B SER* 3.8 2.7 + - - +
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Residues in contact with PHE 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 5.1 2.7 - - + -
80B ALA* 3.6 25.6 - - + -
81B ARG* 3.6 22.4 - - + -
84B MET* 3.7 27.6 - - + -
90B ILE* 3.8 13.5 - - + -
100B HIS* 6.3 0.2 - - - +
307B PHE* 3.7 30.5 - + - -
495B GLU 3.0 13.7 + - - +
496B HIS* 3.2 10.0 + - - +
498B ILE* 1.3 78.4 - - - +
500B VAL* 1.3 62.9 + - - +
502B GLY* 3.2 2.9 + - - -
503B ILE* 3.1 49.0 + - + +
509B SER* 4.5 6.2 + - - -
510B PHE* 3.5 27.4 - + + -
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Residues in contact with VAL 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.9 28.0 - - + -
307B PHE* 3.7 29.6 - - + -
318B VAL* 4.0 25.1 - - + +
321B ALA* 3.6 23.6 - - + -
496B HIS 2.9 20.5 + - - +
499B PHE* 1.3 76.0 - - + +
501B GLN* 1.3 64.0 + - - +
503B ILE* 3.3 7.2 + - - +
504B MET* 3.1 33.2 + - - +
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Residues in contact with GLN 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ALA* 3.2 31.7 + - + +
324B GLY* 3.5 23.8 - - - -
325B ILE* 3.9 12.3 - - + +
328B ILE* 4.4 5.7 - - - +
356B ASP* 4.6 10.6 - - - +
360B ASN* 3.8 5.5 + - - +
377B PRO* 4.8 4.0 - - - +
497B LYS* 3.0 44.0 + - - +
498B ILE* 3.8 6.6 - - - +
499B PHE 3.3 0.2 - - - -
500B VAL* 1.3 77.3 - - - +
502B GLY* 1.3 61.8 + - - +
504B MET* 3.2 3.7 + - - +
505B TRP* 3.0 56.5 + - + -
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Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ASN* 3.7 3.2 - - - +
498B ILE 3.1 11.1 + - - -
499B PHE 3.2 0.8 + - - -
501B GLN* 1.3 74.5 - - - +
503B ILE* 1.3 62.5 + - - +
505B TRP* 3.3 1.3 + - - -
506B ASP 3.0 17.8 + - - -
507B ILE* 3.0 33.6 + - - +
509B SER* 3.4 22.2 - - - -
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 3.0 38.6 + - - +
76B GLY 4.2 1.6 - - - +
77B VAL* 4.2 16.8 - - + -
80B ALA* 3.7 32.1 - - + -
90B ILE* 5.7 3.1 - - + -
499B PHE* 3.1 42.0 + - + +
500B VAL* 3.3 7.8 + - - +
502B GLY* 1.3 77.0 - - - +
504B MET* 1.3 62.3 + - - +
506B ASP* 3.0 7.5 + - - +
507B ILE 5.0 7.0 - - - +
509B SER* 6.2 0.2 - - - +
510B PHE* 5.8 1.6 - - + -
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Residues in contact with MET 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.7 16.5 - - + +
71B LEU* 3.5 38.4 - - + -
72B ALA* 3.8 11.7 - - - +
75B ARG* 2.8 35.3 + - + +
77B VAL* 3.8 13.9 - - + -
322B LEU* 3.4 34.5 - - + -
325B ILE* 4.2 26.2 - - + -
500B VAL* 3.1 29.7 + - - +
501B GLN 3.2 4.0 + - - +
503B ILE* 1.3 74.3 - - - +
505B TRP* 1.3 61.0 + - - +
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Residues in contact with TRP 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.6 21.4 + - + +
325B ILE* 3.5 20.5 - - + +
328B ILE* 3.8 19.7 - - + -
329B ASN* 2.8 23.2 + - - -
360B ASN* 3.7 26.9 - - + -
365B THR* 4.0 5.0 - - - +
373B HIS* 3.8 26.0 + + + -
374B GLN 3.5 14.6 + - - -
375B THR* 3.6 35.7 - - + -
376B GLY* 3.5 20.0 - - - -
377B PRO* 4.9 0.2 - - + -
501B GLN* 3.0 40.1 + - + +
502B GLY* 3.3 6.9 + - - +
503B ILE 3.2 0.2 - - - -
504B MET* 1.3 75.0 - - - +
506B ASP* 1.3 69.7 + - - +
507B ILE* 3.5 15.9 + - + +
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Residues in contact with ASP 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 3.7 23.7 - - + +
75B ARG* 2.9 24.6 + - - +
92B TYR* 3.5 2.4 + - - -
365B THR* 3.0 14.7 + - + -
366B LYS* 2.9 57.7 + - - +
367B SER* 4.4 4.7 + - - -
502B GLY 3.0 4.0 + - - -
503B ILE* 3.0 10.4 + - - +
504B MET 3.2 0.6 - - - -
505B TRP* 1.3 81.1 - - - +
507B 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