Contacts of the helix formed by residues 486 - 509 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 2.8 27.4 + - + +
175B LEU* 3.8 5.6 - - - -
178B TYR* 3.3 16.8 - - - +
484B LYS* 3.8 28.0 - - + +
485B PHE* 1.3 77.3 - - - +
487B PRO* 1.3 77.7 - - - +
488B PHE 3.1 1.7 + - - -
489B THR* 3.0 19.8 + - + +
490B LEU* 2.8 22.3 + - - +
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Residues in contact with PRO 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.0 26.7 - - + -
178B TYR* 3.6 26.0 - - + -
295B ASN* 3.5 46.0 - - + +
298B LYS* 3.8 10.3 - - + -
299B LEU* 3.4 19.4 - - - +
486B THR* 1.3 88.3 - - - +
488B PHE* 1.3 57.7 + - - +
490B LEU* 3.8 0.4 - - + +
491B GLY 2.9 24.6 + - - -
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Residues in contact with PHE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 3.7 25.4 - - + -
50B PRO* 4.0 20.6 - - + -
51B ASN* 6.0 1.3 - - + -
52B ASP* 3.4 35.7 - - + +
298B LYS* 3.4 21.8 + - + +
301B ASP* 3.8 24.2 - - + -
302B GLY* 3.2 21.6 - - - -
305B PHE* 3.5 31.9 - + + -
486B THR* 3.2 1.0 + - - -
487B PRO* 1.3 80.6 - - - +
489B THR* 1.3 62.2 + - - +
491B GLY 3.2 1.4 + - - -
492B ALA* 2.9 26.9 + - + +
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Residues in contact with THR 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 5.4 0.7 - - + -
52B ASP* 3.6 31.2 - - + +
55B ILE* 5.0 9.4 - - + -
482B VAL* 4.3 20.4 - - + -
484B LYS 2.7 27.4 + - - +
485B PHE* 3.3 7.2 - - - -
486B THR* 3.0 24.9 + - - +
488B PHE* 1.3 77.4 - - + +
490B LEU* 1.3 62.4 + - - +
492B ALA* 3.3 6.0 + - - +
493B LEU* 3.0 29.6 + - - +
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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
----------------------------------------------------------
170B MET* 4.8 1.8 - - - -
171B VAL* 4.2 15.0 - - + -
174B ALA* 3.8 31.0 - - + -
175B LEU* 3.8 25.6 - - + -
299B LEU* 4.4 2.0 - - + -
348B LEU* 4.8 11.9 - - + -
351B PHE* 4.3 21.3 - - + -
485B PHE* 5.2 8.3 - - + -
486B THR 2.8 19.1 + - - +
487B PRO 3.8 2.5 - - - +
489B THR* 1.3 78.6 + - - +
491B GLY* 1.3 56.5 + - - +
493B LEU* 3.1 7.8 + - + -
494B ILE* 2.9 57.6 + - + +
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Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TRP* 3.7 9.0 - - - -
299B LEU* 3.5 34.6 - - - +
303B ALA* 3.5 17.7 - - - +
487B PRO 2.9 11.3 + - - -
488B PHE 3.7 1.6 - - - -
490B LEU* 1.3 75.9 - - - +
492B ALA* 1.4 62.4 + - - +
494B ILE 3.5 0.3 + - - -
495B ALA 3.1 18.7 + - - -
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 4.0 24.7 - - + -
302B GLY* 3.2 21.6 - - - +
305B PHE* 4.5 7.4 - - + -
306B MET* 3.3 24.4 - - + +
488B PHE* 2.9 18.0 + - + +
489B THR* 3.6 5.6 - - - +
491B GLY* 1.4 76.7 - - - +
493B LEU* 1.3 56.6 + - - +
496B MET* 3.0 24.8 + - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 4.4 17.0 - - + -
306B MET* 5.7 0.9 - - + -
348B LEU* 5.8 0.9 - - + -
351B PHE* 4.9 13.7 - - + -
410B LEU* 4.4 13.2 - - + -
480B ILE* 4.0 17.7 - - + -
482B VAL* 4.0 13.2 - - + -
485B PHE* 3.6 33.4 - - + -
489B THR 3.0 20.8 + - - +
490B LEU* 3.1 6.9 + - + +
492B ALA* 1.3 75.9 - - + +
494B ILE* 1.3 65.8 + - - +
496B MET* 3.1 38.1 + - + +
497B TYR* 3.2 20.7 + - + -
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Residues in contact with ILE 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B MET* 3.8 26.2 - - + -
171B VAL* 4.0 14.1 - - + -
279B LEU* 4.5 4.5 - - + -
280B TRP* 3.6 31.4 - - + -
299B LEU* 4.6 3.8 - - + -
351B PHE* 4.5 5.2 - - + -
354B TYR* 4.0 15.3 - - + +
355B PHE* 3.6 23.1 - - + -
490B LEU* 2.9 43.3 + - + +
493B LEU* 1.3 76.8 - - - +
495B ALA* 1.3 56.8 + - - +
496B MET 3.2 0.3 + - - -
497B TYR 3.2 2.4 + - - -
498B GLU* 2.9 32.5 + - - +
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Residues in contact with ALA 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 3.7 19.5 - - - +
280B TRP* 4.4 0.6 - - - -
303B ALA* 3.8 19.5 - - + +
306B MET* 3.8 12.8 - - + -
307B ASP* 4.1 2.9 - - - +
491B GLY 3.1 18.5 + - - +
492B ALA 3.8 4.0 - - - +
494B ILE* 1.3 75.7 - - - +
496B MET* 1.3 62.2 + - - +
498B GLU* 3.2 14.4 + - - +
499B HIS* 2.9 26.3 + - - -
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Residues in contact with MET 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 6.1 0.7 - - - -
55B ILE* 5.8 4.0 - - - -
57B LEU* 5.4 4.5 - - - -
306B MET* 3.7 26.9 - - + -
319B ALA* 4.2 14.1 - - - -
320B PRO* 3.7 17.0 - - + +
323B LEU* 3.7 31.2 - - + -
480B ILE* 3.8 20.0 - - + -
492B ALA 3.0 14.4 + - - +
493B LEU* 3.3 29.8 - - + +
494B ILE 3.1 0.2 - - - -
495B ALA* 1.3 76.7 - - - +
497B TYR* 1.3 84.0 + - + +
499B HIS* 3.2 2.9 + - - -
500B LYS* 2.9 24.8 + - - +
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Residues in contact with TYR 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 4.5 7.6 - - + -
341B LEU* 3.6 18.3 - - + +
351B PHE* 3.9 29.6 - + - -
355B PHE* 3.3 30.7 - + + -
408B ASP* 2.7 41.8 + - - +
410B LEU* 4.2 9.1 - - + +
480B ILE* 3.6 10.4 - - + +
493B LEU* 3.2 19.1 + - + -
494B ILE 3.7 0.2 - - - +
496B MET* 1.3 97.0 - - + +
498B GLU* 1.3 64.9 + - - +
500B LYS* 3.2 27.5 + - + +
501B ILE* 3.0 33.3 + - + +
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Residues in contact with GLU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B HIS* 3.7 5.1 - - - +
108B ARG* 2.8 34.1 + - - -
276B ARG 5.8 0.2 - - - +
277B TYR* 3.7 40.9 + - + -
280B TRP* 2.9 30.6 + - - -
354B TYR* 4.3 4.7 + - - +
355B PHE* 4.3 6.7 - - + -
494B ILE* 2.9 25.3 + - + +
495B ALA* 3.3 8.8 - - - +
497B TYR* 1.3 75.6 - - - +
499B HIS* 1.3 66.0 + - + +
501B ILE* 3.3 10.3 + - + +
502B PHE* 3.0 26.3 + - - +
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Residues in contact with HIS 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 4.0 14.7 - - + +
89B PHE* 4.2 1.6 - + - -
104B HIS* 4.8 4.2 + - - -
105B VAL* 3.8 17.0 - - - +
108B ARG* 3.8 9.3 + - - -
306B MET* 4.6 3.6 + - - +
307B ASP* 2.7 38.8 + - - -
310B PHE* 3.2 44.4 - + + +
320B PRO* 3.5 22.0 - - + -
495B ALA* 2.9 19.5 + - + +
497B TYR 3.1 0.2 - - - -
498B GLU* 1.3 81.2 - - + +
500B LYS* 1.3 59.2 + - - +
502B PHE* 3.7 4.9 - - + +
503B THR* 2.8 34.5 + - - -
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Residues in contact with LYS 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PRO* 3.6 16.2 - - + +
323B LEU* 3.7 30.9 - - + +
324B ALA* 3.5 19.9 - - - +
327B GLY* 5.2 3.5 - - - -
339B HIS* 3.7 36.8 + - - -
359B ASP* 4.6 10.2 + - - +
408B ASP* 4.6 1.2 + - - -
496B MET 2.9 12.9 + - - +
497B TYR* 3.2 31.1 + - + +
499B HIS* 1.3 76.1 - - - +
501B ILE* 1.3 59.8 + - + +
503B THR 3.2 1.7 + - - -
504B GLN* 2.9 55.4 + - - +
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Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TYR* 3.5 23.6 - - + +
355B PHE* 4.0 18.8 - - + -
358B GLY* 3.8 5.2 - - - +
359B ASP* 3.7 46.0 - - + +
362B SER* 3.6 21.5 - - - -
363B ASN* 3.0 29.3 + - - +
497B TYR* 3.0 21.4 + - + +
498B GLU* 3.5 7.0 - - - +
500B LYS* 1.3 79.2 - - + +
502B PHE* 1.3 64.2 + - - +
504B GLN* 3.3 4.5 + - - +
505B GLY 3.0 10.4 + - - -
512B SER* 3.8 3.3 + - - +
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Residues in contact with PHE 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 4.5 4.5 - - + -
84B ALA* 3.6 26.7 - - + -
85B ARG* 3.6 25.1 - - + -
88B MET* 3.9 18.4 - - + -
94B ILE* 3.9 23.8 - - + -
104B HIS* 6.3 0.4 - - - +
277B TYR* 5.3 0.2 + - - -
310B PHE* 3.8 21.8 - + - -
498B GLU 3.0 15.9 + - - +
499B HIS* 3.7 6.7 - - + +
501B ILE* 1.3 79.1 - - - +
503B THR* 1.3 66.2 + - - +
505B GLY* 3.2 2.8 + - - -
506B VAL* 3.0 43.9 + - + +
512B SER* 4.4 6.6 + - - -
513B PHE* 3.8 29.2 - + + -
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Residues in contact with THR 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.9 28.9 - - + +
310B PHE* 3.6 22.9 - - - -
321B VAL* 4.2 17.8 - - + +
324B ALA* 3.5 20.6 - - + -
325B LEU* 5.6 0.2 - - + -
499B HIS 2.8 21.4 + - - -
500B LYS* 3.6 4.9 - - - -
502B PHE* 1.3 80.4 - - - +
504B GLN* 1.3 64.5 + - - +
506B VAL* 3.4 6.8 + - - +
507B ILE* 3.1 29.0 + - + +
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Residues in contact with GLN 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ALA* 3.1 36.7 + - + +
327B GLY* 3.7 22.4 - - - -
328B VAL* 3.9 4.6 - - + +
359B ASP* 4.7 9.4 - - - +
363B ASN* 3.9 5.8 + - - +
380B PRO* 5.1 5.0 - - - +
500B LYS* 2.9 40.0 + - - +
501B ILE* 3.7 6.4 - - - +
502B PHE 3.3 0.2 - - - -
503B THR* 1.3 76.8 - - - +
505B GLY* 1.3 57.2 + - - +
507B ILE* 3.1 8.9 + - - +
508B TRP* 2.9 68.3 + - + -
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Residues in contact with GLY 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ASN* 3.9 3.9 - - - +
501B ILE 3.0 10.7 + - - -
502B PHE 3.2 1.5 + - - -
504B GLN* 1.3 75.6 - - - +
506B VAL* 1.3 57.0 + - - +
508B TRP 3.5 0.2 + - - -
509B ASP* 2.9 23.4 + - - -
510B ILE* 3.1 31.5 + - - +
512B SER* 3.4 23.6 - - - -
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Residues in contact with VAL 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS* 3.4 35.4 + - - +
79B ARG 3.5 9.0 - - - +
81B VAL* 4.1 15.0 - - + -
84B ALA* 3.7 30.1 - - + -
502B PHE* 3.0 34.7 + - + +
503B THR* 3.6 9.4 - - - +
504B GLN 3.2 0.2 - - - -
505B GLY* 1.3 71.2 - - - +
507B ILE* 1.3 67.9 + - - +
509B ASP* 3.1 15.2 + - - +
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Residues in contact with ILE 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.8 17.8 - - + +
13B TYR* 6.0 0.2 - - + -
75B LEU* 4.1 23.8 - - + +
76B ALA* 4.7 3.1 - - - -
79B ARG* 2.8 48.2 + - + -
81B VAL* 4.1 15.7 - - + -
324B ALA* 5.3 1.8 - - + -
325B LEU* 4.0 27.1 - - + -
328B VAL* 4.4 22.9 - - + -
503B THR* 3.1 28.3 + - + +
504B GLN* 3.1 7.8 + - - +
506B VAL* 1.3 73.9 - - - +
508B TRP* 1.3 58.8 + - + +
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Residues in contact with TRP 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.7 19.9 - - + +
79B ARG* 4.5 0.2 - - - -
327B GLY 5.3 2.2 - - - -
328B VAL* 4.0 20.9 - - + +
331B GLY* 6.2 0.9 - - - -
332B ASN* 2.9 32.1 - - - +
363B ASN* 3.7 13.9 - - + -
376B TYR* 2.5 35.3 + + + -
377B SER 3.5 12.1 + - - -
378B THR* 3.5 33.0 - - + -
379B GLY* 3.5 19.1 - - - -
380B PRO* 4.5 4.9 - - + -
504B GLN* 2.9 51.7 + - + +
505B GLY 4.2 0.2 - - - -
507B ILE* 1.3 76.3 - - + +
509B ASP* 1.3 65.7 + - - +
510B ILE* 3.4 28.9 + - + +
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Residues in contact with ASP 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU 5.1 0.5 - - - +
3B PRO* 4.4 1.9 - - - +
4B LYS* 3.5 48.3 + - + +
5B VAL 5.4 0.2 - - - +
79B ARG* 3.7 17.5 - - - +
96B PHE* 5.3 0.7 - - - -
368B THR* 3.1 14.9 - - + -
369B ARG* 2.9 50.8 + - - +
370B SER* 4.7 1.0 + - - -
376B TYR* 4.5 2.7 - - - +
505B GLY 2.9 7.1 + - - -
506B VAL* 3.1 10.3 + - - +
507B ILE 3.2 0.2 - - - -
508B TRP* 1.3 79.1 - - - +
510B ILE* 1.3 58.6 + - - +
----------------------------------------------------------
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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