Contacts of the helix formed by residues 36 - 64 (chain 5) in PDB entry 2X17
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 LEU 36 (chain 5).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315 PHE* 3.0 40.8 + - + +
325 GLU* 5.0 0.4 - - - -
345 LEU* 4.0 26.9 - - + +
355 GLY* 1.3 75.8 - - - +
375 GLU* 1.3 63.2 + - - +
385 GLY 3.5 0.2 + - - -
395 PHE* 4.1 15.5 - - + -
405 ALA* 3.1 18.5 + - - +
835 PRO* 4.2 14.1 - - + -
1515 LEU* 4.3 26.9 - - + +
1525 PHE* 5.6 0.9 - - - -
1555 ASP* 3.3 29.4 - - + +
143L PHE* 5.0 10.8 - - + -
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Residues in contact with GLU 37 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325 GLU* 3.6 20.6 - - - +
355 GLY* 3.2 13.0 + - - +
365 LEU* 1.3 71.5 - - - +
385 GLY* 1.3 60.0 + - - +
405 ALA* 3.4 7.4 + - - +
415 ASN* 3.0 38.9 + - - +
1555 ASP* 3.5 5.0 + - - +
1595 SER* 5.4 0.4 - - - -
136L LYS* 2.9 36.6 + - + +
140L LYS* 6.4 0.4 - - - -
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Residues in contact with GLY 38 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375 GLU* 1.3 77.4 - - - +
395 PHE* 1.3 63.0 + - - +
415 ASN* 4.0 0.7 - - - +
425 TRP* 3.1 24.1 + - - +
1555 ASP* 2.9 34.1 + - - -
1585 LEU* 3.4 12.3 - - - +
1595 SER* 3.7 18.7 - - - -
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Residues in contact with PHE 39 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315 PHE* 3.5 34.8 - + + -
365 LEU* 3.8 13.5 - - + +
375 GLU 3.4 0.2 - - - -
385 GLY* 1.3 74.8 - - - +
405 ALA* 1.3 63.1 + - - +
425 TRP* 3.5 6.1 + - - +
435 MET* 3.2 28.2 + - - +
875 PHE* 3.8 27.4 - + - -
1375 ILE* 4.3 4.5 - - + -
1415 LEU* 4.1 26.0 - - + -
1515 LEU* 4.1 17.7 - - + -
1545 LEU* 4.0 17.0 - - + -
1555 ASP* 3.2 46.3 + - - -
1585 LEU* 3.6 24.2 - - + -
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Residues in contact with ALA 40 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285 ALA* 3.6 27.1 - - - +
315 PHE* 3.8 3.1 - - - +
325 GLU* 3.4 33.2 - - - +
365 LEU 3.1 17.3 + - - +
375 GLU 3.5 5.8 - - - +
385 GLY 3.3 0.2 - - - -
395 PHE* 1.3 77.4 - - - +
415 ASN* 1.3 57.9 + - - +
435 MET 3.3 1.0 + - - -
445 LYS* 3.1 33.6 + - - +
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Residues in contact with ASN 41 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325 GLU* 5.1 0.2 - - - +
375 GLU* 3.0 24.7 + - - +
385 GLY* 4.1 4.9 - - - +
405 ALA* 1.3 73.5 - - - +
425 TRP* 1.3 64.3 + - - +
445 LYS* 3.5 24.8 + - - +
455 ALA* 3.0 24.6 + - - +
1595 SER* 5.2 9.0 + - - +
1615 ARG 3.6 14.2 - - - +
1625 ALA* 4.4 7.5 - - - +
1635 PRO* 3.5 21.5 - - + +
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Residues in contact with TRP 42 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245 TYR* 6.0 0.9 - + - -
385 GLY 3.1 18.0 + - - +
395 PHE* 3.6 6.5 - - - +
405 ALA 3.3 0.2 - - - -
415 ASN* 1.3 76.2 - - - +
435 MET* 1.3 84.5 + - + +
455 ALA* 3.4 4.5 + - - +
465 GLN* 3.0 45.1 + - + +
875 PHE* 4.3 10.5 - + - -
1335 SER* 3.5 23.1 + - - -
1345 VAL* 4.3 18.8 - - + -
1375 ILE* 3.6 25.5 - - + +
1585 LEU* 3.8 32.0 - - + +
1615 ARG* 3.3 53.0 + - + +
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Residues in contact with MET 43 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245 TYR* 3.4 48.0 - - + +
275 MET* 3.8 29.2 - - + -
285 ALA* 3.7 6.3 - - + -
315 PHE* 4.2 16.8 - - + -
395 PHE 3.2 17.2 + - - +
405 ALA 3.7 4.7 - - - +
415 ASN 3.3 0.2 - - - -
425 TRP* 1.3 91.1 - - + +
445 LYS* 1.3 58.2 + - - +
465 GLN* 3.3 3.3 + - - +
475 ALA* 2.8 29.3 + - - +
875 PHE* 3.7 40.2 - - + -
905 ALA* 4.6 5.6 - - + -
1345 VAL* 6.3 0.2 - - + -
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Residues in contact with LYS 44 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245 TYR 5.3 0.2 - - - -
255 PHE* 4.8 11.4 - - + -
285 ALA* 3.9 9.6 - - + -
325 GLU* 3.0 28.7 + - - -
405 ALA 3.1 23.2 + - - +
415 ASN* 3.6 25.5 + - - +
425 TRP 3.4 0.2 - - - -
435 MET* 1.3 75.8 - - - +
455 ALA* 1.3 57.4 + - - +
475 ALA* 3.2 9.0 + - - +
485 GLU* 3.1 31.4 + - - +
1635 PRO* 4.1 21.1 - - + -
55N LEU* 4.9 12.1 - - + +
58N TYR* 3.4 29.7 - - - -
59N ASN* 4.2 9.3 + - - -
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Residues in contact with ALA 45 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415 ASN 3.0 17.9 + - - +
425 TRP 3.6 2.0 - - - +
445 LYS* 1.3 75.2 - - - +
465 GLN* 1.3 61.8 + - - +
485 GLU* 3.6 7.8 + - - +
495 GLU* 3.4 24.9 + - - +
1615 ARG* 3.4 30.1 + - + +
1625 ALA 3.7 22.4 - - - +
1635 PRO* 4.2 7.5 - - - +
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Residues in contact with GLN 46 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245 TYR* 3.7 24.7 - - + -
425 TRP* 3.0 36.6 + - + +
435 MET* 3.5 9.9 - - - +
445 LYS 3.2 0.4 - - - -
455 ALA* 1.3 76.3 - - - +
475 ALA* 1.3 61.6 + - - +
495 GLU* 3.3 8.1 + - - +
505 GLU* 2.8 43.6 + - - +
1305 GLU* 3.2 27.1 + - - +
1335 SER* 5.2 3.3 + - - -
1345 VAL* 5.6 4.1 - - + +
1615 ARG* 3.1 28.4 + - - +
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Residues in contact with ALA 47 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215 ALA* 3.4 42.1 - - + +
245 TYR* 4.2 7.6 - - + +
255 PHE* 4.2 10.5 - - + +
435 MET 2.8 14.5 + - - +
445 LYS* 3.2 13.2 + - - +
465 GLN* 1.3 77.8 - - - +
485 GLU* 1.3 60.9 + - + +
505 GLU* 3.3 2.1 + - - -
515 ILE* 3.3 21.7 + - + +
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Residues in contact with GLU 48 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445 LYS 3.1 13.2 + - - +
455 ALA* 3.8 9.5 - - - +
465 GLN 3.3 0.2 - - - -
475 ALA* 1.3 73.6 - - + +
495 GLU* 1.3 64.9 + - - +
515 ILE* 3.3 16.9 + - + +
525 GLY 3.1 16.6 + - - -
1635 PRO* 3.3 22.8 - - - +
1645 LYS* 2.9 28.9 + - - +
1655 LEU* 3.2 35.5 + - + +
1665 PRO* 3.6 2.3 - - - +
55N LEU* 5.6 2.8 - - - +
165N LEU* 4.2 14.0 - - + +
169N LEU* 3.9 19.9 - - + +
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Residues in contact with GLU 49 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 ALA 3.4 14.6 + - - +
465 GLN* 3.3 19.4 + - - +
475 ALA 3.3 0.6 - - - -
485 GLU* 1.3 76.7 - - - +
505 GLU* 1.3 56.4 + - - +
525 GLY* 3.2 2.9 + - - -
535 HIS* 2.9 35.3 + - - +
1305 GLU* 4.6 0.2 - - - +
1615 ARG* 3.4 18.1 + - - +
1645 LYS* 5.0 8.1 + - - +
11735 AG 3.3 22.0 - - - -
169N LEU* 3.6 19.0 - - + +
170N MET* 3.3 32.2 + - - +
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Residues in contact with GLU 50 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175 GLU* 2.9 44.1 - - - +
205 SER* 3.4 17.6 + - - -
215 ALA* 3.6 6.7 - - - +
245 TYR* 3.8 22.0 - - + -
465 GLN* 2.8 36.9 + - - +
475 ALA 3.5 6.5 - - - +
485 GLU 3.2 0.6 - - - -
495 GLU* 1.3 74.1 - - - +
515 ILE* 1.3 59.1 + - - +
535 HIS* 3.2 10.4 + - - +
545 ALA* 2.9 27.4 + - - +
945 GLU* 4.7 1.9 - - - +
975 ILE* 5.6 1.0 - - - +
1275 GLN* 5.1 2.9 + - - -
1305 GLU* 2.9 18.0 - - - +
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Residues in contact with ILE 51 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185 LEU* 5.0 14.1 - - + -
215 ALA* 3.8 14.8 - - + -
475 ALA* 3.3 18.3 + - + +
485 GLU* 3.3 18.1 + - + +
505 GLU* 1.3 75.1 - - - +
525 GLY* 1.3 59.1 + - - +
545 ALA* 3.2 7.6 + - + +
555 LEU* 2.9 41.4 + - + +
1655 LEU* 6.0 1.6 - - + -
51N ILE* 4.7 28.9 - - + -
165N LEU* 4.3 18.6 - - + -
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Residues in contact with GLY 52 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485 GLU 3.1 13.2 + - - -
495 GLU 3.2 5.3 + - - -
515 ILE* 1.3 77.4 - - - +
535 HIS* 1.3 60.5 + - - +
555 LEU* 3.4 9.7 + - - +
565 ARG* 3.2 30.8 + - - +
165N LEU* 5.2 0.2 - - - +
166N PRO* 6.1 0.2 - - - -
169N LEU* 4.0 23.7 - - - +
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Residues in contact with HIS 53 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175 GLU* 3.4 21.5 - - - +
495 GLU* 2.9 29.2 + - - +
505 GLU* 3.2 15.2 + - - +
525 GLY* 1.3 77.0 - - - +
545 ALA* 1.3 59.8 + - - +
565 ARG* 3.5 5.1 + - - -
575 PHE* 3.3 21.8 - - - -
1225 TRP* 3.3 23.3 - + - -
1235 PHE* 3.4 20.1 - + + -
1265 GLU* 3.4 24.6 + - + -
1275 GLN* 5.5 0.2 - - - -
1305 GLU* 3.0 24.2 + - - -
11735 AG 2.0 33.0 - - - -
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Residues in contact with ALA 54 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145 LEU* 3.6 22.8 - - + +
175 GLU* 3.8 14.8 - - + +
185 LEU* 3.8 33.4 - - + -
505 GLU 2.9 13.4 + - - +
515 ILE* 3.2 8.5 + - + +
535 HIS* 1.3 75.7 - - - +
555 LEU* 1.3 59.7 + - + +
575 PHE* 3.4 3.3 + - - -
585 TYR* 3.1 22.4 + - - +
25N PHE* 5.5 2.9 - - + -
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Residues in contact with LEU 55 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515 ILE* 2.9 35.0 + - + +
525 GLY* 3.8 9.9 - - - +
545 ALA* 1.3 74.5 - - + +
565 ARG* 1.3 59.8 + - + +
585 TYR* 3.3 10.7 - - + +
595 ASN* 2.9 40.6 + - - +
25N PHE* 3.7 30.7 - - + -
44N LYS* 5.0 14.8 - - + -
48N GLU* 5.6 1.8 - - - +
163N PRO* 6.3 0.2 - - + -
165N LEU* 5.3 5.4 - - + -
166N PRO* 4.1 32.1 - - + -
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Residues in contact with ARG 56 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525 GLY 3.2 17.0 + - - +
535 HIS* 3.6 9.6 - - - +
545 ALA 3.2 0.4 - - - -
555 LEU* 1.3 74.5 - - - +
575 PHE* 1.3 59.0 + - - +
595 ASN* 3.5 9.4 + - - +
605 TYR 3.1 21.1 + - - -
1195 PHE* 3.6 16.8 - - + -
1225 TRP* 3.4 62.7 - - - +
1235 PHE* 3.7 11.2 - - + -
170N MET 3.6 21.8 + - - -
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Residues in contact with PHE 57 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 LEU* 3.7 34.3 - - + +
135 GLN* 3.4 32.5 - - + -
145 LEU* 4.0 20.2 - - + -
175 GLU* 4.3 13.2 - - + -
535 HIS 3.3 19.6 + - - -
545 ALA 3.4 7.5 + - - +
555 LEU 3.3 0.4 - - - -
565 ARG* 1.3 75.0 - - - +
585 TYR* 1.3 65.2 + - - +
605 TYR* 3.4 1.4 + - - +
615 ILE* 3.1 29.6 + - + +
1015 ILE* 4.1 4.7 - - + -
1045 LEU* 4.3 0.7 - - + -
1195 PHE* 3.5 29.2 - + - -
1205 LEU* 4.1 17.9 - - + -
1235 PHE* 3.4 29.2 - + - -
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Residues in contact with TYR 58 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145 LEU* 3.6 11.8 - - + +
545 ALA 3.1 13.0 + - - +
555 LEU* 3.3 16.4 - - + +
565 ARG 3.3 0.2 - - - -
575 PHE* 1.3 78.3 - - - +
595 ASN* 1.3 75.3 + - - +
615 ILE* 3.6 1.6 + - - +
625 TYR* 3.3 50.2 + + + -
685 VAL* 4.0 18.2 - - + -
25N PHE* 3.6 32.1 - + + -
28N ALA 2.9 28.9 + - - -
29N ALA* 3.4 17.9 - - + -
32N GLU* 3.1 28.0 + - - +
44N LYS* 3.6 21.2 - - - -
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Residues in contact with ASN 59 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555 LEU* 2.9 28.0 + - - +
565 ARG* 3.9 9.3 - - - +
585 TYR* 1.3 90.7 - - - +
605 TYR* 1.3 64.8 + - - +
625 TYR* 3.6 4.3 + - - +
635 ASP* 3.1 32.7 + - - +
44N LYS* 4.4 7.8 + - - -
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Residues in contact with TYR 60 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 LEU* 4.3 2.1 - - + +
105 LEU* 3.9 23.6 - - + -
565 ARG 3.1 8.7 + - - +
575 PHE 3.9 2.0 - - - +
585 TYR 3.4 0.2 - - - -
595 ASN* 1.3 75.0 - - - +
615 ILE* 1.3 67.0 + - + +
635 ASP* 3.1 7.0 + - + +
645 ARG* 3.1 52.1 + - + +
1155 SER* 3.0 14.0 - - - -
1165 THR* 2.8 45.3 + - + -
1195 PHE* 3.6 63.0 - + + -
1286 VAL* 4.3 17.5 - - + -
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Residues in contact with ILE 61 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 LEU* 4.4 5.1 - - + +
75 LEU* 3.8 11.0 - - + -
105 LEU* 3.9 40.6 - - + +
115 ASN* 3.6 22.9 - - - +
145 LEU* 4.1 9.9 - - + -
575 PHE 3.1 18.8 + - - +
585 TYR 3.9 4.5 - - - +
605 TYR* 1.3 78.3 - - + +
625 TYR* 1.3 59.0 + - - +
645 ARG* 3.3 8.7 + - - +
665 GLY* 2.8 26.1 + - - -
675 ARG 3.5 35.2 - - - +
685 VAL* 3.8 13.9 - - + +
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Residues in contact with TYR 62 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585 TYR* 3.3 47.0 + + - +
595 ASN* 4.2 4.3 - - - +
605 TYR 3.3 0.4 - - - -
615 ILE* 1.3 75.1 - - - +
635 ASP* 1.3 65.6 + - - +
645 ARG 3.2 0.2 - - - -
655 ASN* 3.3 12.0 + - - +
665 GLY 3.5 21.5 - - - -
675 ARG* 3.3 16.5 + - - -
685 VAL* 3.5 28.4 + - + -
1326 ALA* 5.3 1.0 - - - +
29N ALA* 2.5 30.7 + - - +
32N GLU* 3.8 28.7 - - + -
33N ASP* 3.8 24.9 - - + -
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Residues in contact with ASP 63 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595 ASN* 3.1 25.3 + - - +
605 TYR* 3.1 13.2 + - - +
625 TYR* 1.3 77.2 - - - +
645 ARG* 1.3 62.2 + - - +
655 ASN* 3.2 2.9 + - - +
1286 VAL* 3.9 25.6 - - + +
1296 GLU* 5.6 4.8 - - - +
1316 GLU* 5.1 2.6 - - - +
1326 ALA* 3.6 37.7 + - + +
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Residues in contact with ARG 64 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15 MET* 4.1 36.7 - - - +
25 LEU* 3.8 27.3 + - + +
605 TYR* 3.1 50.5 + - + +
615 ILE 3.3 2.7 + - - +
625 TYR 3.2 0.4 - - - -
635 ASP* 1.3 77.2 + - - +
655 ASN* 1.3 68.9 + - - +
665 GLY* 3.2 3.7 + - - -
1135 ASP* 4.6 5.1 + - - -
1155 SER* 3.3 22.8 + - - -
1026 TYR* 3.1 21.8 + - - -
1276 GLN 5.0 0.4 + - - -
1286 VAL* 4.1 26.0 - - - +
1316 GLU* 3.9 29.2 + - - +
----------------------------------------------------------
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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) + - + + + + + -
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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