Contacts of the helix formed by residues 36 - 64 (chain 6) 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 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316 PHE* 2.9 37.6 + - + +
326 GLU* 5.0 0.4 - - - -
346 LEU* 4.2 17.9 - - + +
356 GLY* 1.3 77.5 - - - +
376 GLU* 1.3 59.0 + - - +
396 PHE* 3.6 15.4 + - + -
406 ALA* 3.1 22.3 + - - +
836 PRO* 4.1 20.0 - - + -
1516 LEU* 4.3 29.4 - - + +
1526 PHE* 5.5 1.8 - - + -
1556 ASP* 3.2 31.4 - - + +
143M PHE* 5.1 9.9 - - + -
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Residues in contact with GLU 37 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326 GLU* 3.4 21.6 - - - +
356 GLY* 3.3 13.3 + - - +
366 LEU* 1.3 71.8 - - - +
386 GLY* 1.3 60.4 + - - +
406 ALA* 3.6 6.1 - - - +
416 ASN* 2.9 42.8 + - - +
1556 ASP* 3.4 4.4 + - - +
1596 SER* 5.4 0.7 - - - -
136M LYS* 3.2 46.8 + - + +
140M LYS* 6.5 0.2 - - - -
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Residues in contact with GLY 38 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376 GLU* 1.3 76.6 - - - +
396 PHE* 1.3 58.5 + - - +
416 ASN* 3.5 1.3 + - - +
426 TRP* 3.0 28.9 + - - +
1556 ASP* 2.9 30.8 + - - -
1586 LEU* 3.5 13.9 - - - +
1596 SER* 3.9 18.1 - - - -
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Residues in contact with PHE 39 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316 PHE* 3.5 33.7 - + + -
366 LEU* 3.8 12.1 - - + +
386 GLY* 1.3 74.3 - - - +
406 ALA* 1.3 57.3 + - - +
426 TRP* 3.5 7.2 + - - +
436 MET* 3.1 34.0 + - - +
876 PHE* 3.6 31.1 - + - -
1376 ILE* 4.3 4.3 - - + -
1416 LEU* 4.2 24.7 - - + -
1516 LEU* 4.0 18.2 - - + -
1546 LEU* 4.0 16.8 - - + -
1556 ASP* 3.2 40.4 + - + -
1586 LEU* 3.6 22.4 - - + -
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Residues in contact with ALA 40 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286 ALA* 3.4 26.6 - - - +
316 PHE* 3.8 3.1 - - - +
326 GLU* 3.4 34.5 - - - +
366 LEU 3.1 17.3 + - - +
376 GLU 3.6 5.2 - - - +
386 GLY 3.2 0.2 - - - -
396 PHE* 1.3 78.3 - - - +
416 ASN* 1.3 57.6 + - - +
436 MET 3.3 1.6 + - - -
446 LYS* 3.1 33.8 + - - +
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Residues in contact with ASN 41 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326 GLU* 5.1 0.2 - - - +
376 GLU* 2.9 28.1 + - - +
386 GLY* 4.0 4.4 - - - +
406 ALA* 1.3 73.6 - - - +
426 TRP* 1.3 60.4 + - - +
446 LYS* 3.5 26.0 + - - +
456 ALA* 3.0 28.9 + - - +
1596 SER* 5.3 9.2 + - - +
1616 ARG 3.6 13.6 - - - +
1626 ALA* 4.6 5.4 - - - +
1636 PRO* 3.4 20.4 - - + +
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Residues in contact with TRP 42 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246 TYR* 6.1 0.9 - + - -
386 GLY 3.0 18.6 + - - +
396 PHE* 3.6 6.7 - - - +
406 ALA 3.3 0.2 - - - -
416 ASN* 1.3 75.3 - - - +
436 MET* 1.3 87.5 + - + +
456 ALA* 3.4 3.1 + - - +
466 GLN* 3.0 42.9 + - + +
876 PHE* 4.3 10.1 - + + -
1336 SER* 3.7 19.3 - - - -
1346 VAL* 4.4 18.8 - - + -
1376 ILE* 3.5 25.4 - - + +
1586 LEU* 3.7 33.9 - - + +
1616 ARG* 3.2 57.7 + - + +
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Residues in contact with MET 43 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246 TYR* 3.4 49.8 - - + +
276 MET* 3.7 34.1 - - + -
286 ALA* 3.8 6.1 - - + -
316 PHE* 4.1 11.4 - - + -
396 PHE 3.1 20.2 + - - +
406 ALA 3.6 4.7 - - - +
416 ASN 3.3 0.2 - - - -
426 TRP* 1.3 90.1 - - + +
446 LYS* 1.3 55.3 + - - +
466 GLN* 3.3 3.4 + - - +
476 ALA* 2.8 33.3 + - - +
876 PHE* 3.7 39.3 - - + -
906 ALA* 4.7 2.5 - - + -
1346 VAL* 6.5 0.2 - - + -
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Residues in contact with LYS 44 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256 PHE* 4.7 12.1 - - + -
286 ALA* 3.8 10.1 - - + -
326 GLU* 3.0 28.2 + - - -
406 ALA 3.1 22.1 + - - +
416 ASN* 3.5 25.8 + - - +
426 TRP 3.4 0.2 - - - -
436 MET* 1.3 74.6 - - - +
456 ALA* 1.3 64.4 + - - +
476 ALA* 3.3 9.2 + - - +
486 GLU* 3.1 26.5 + - - +
1636 PRO* 3.9 19.5 - - + -
55O LEU* 4.9 13.8 - - + +
58O TYR* 3.4 29.8 - - - -
59O ASN* 4.4 7.5 + - - -
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Residues in contact with ALA 45 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416 ASN 3.0 17.7 + - - +
426 TRP 3.6 2.5 - - - +
436 MET 3.3 0.2 - - - -
446 LYS* 1.3 76.2 - - - +
466 GLN* 1.3 60.7 + - - +
486 GLU* 3.5 8.4 + - - +
496 GLU* 3.4 22.9 + - - +
1616 ARG* 3.6 33.3 + - + +
1626 ALA 3.8 17.9 - - - +
1636 PRO* 4.1 9.3 - - + +
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Residues in contact with GLN 46 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246 TYR* 3.7 25.6 - - + -
426 TRP* 3.0 39.7 + - + +
436 MET* 3.5 7.2 - - - +
446 LYS 3.3 0.2 - - - -
456 ALA* 1.3 75.2 - - - +
476 ALA* 1.3 62.8 + - - +
496 GLU* 3.1 18.4 + - - +
506 GLU* 3.0 25.5 + - - +
1306 GLU* 2.8 39.6 + - - +
1336 SER* 5.1 3.1 + - - -
1346 VAL* 5.6 4.0 - - + +
1616 ARG* 2.9 29.6 + - - +
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Residues in contact with ALA 47 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216 ALA* 3.3 50.1 - - + +
246 TYR* 4.2 7.1 - - + +
256 PHE* 4.2 11.2 - - + +
436 MET 2.8 16.8 + - - +
446 LYS* 3.3 10.9 + - - +
466 GLN* 1.3 75.6 - - - +
486 GLU* 1.3 60.9 + - - +
506 GLU* 3.5 1.0 + - - -
516 ILE* 3.4 14.4 + - + +
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Residues in contact with GLU 48 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446 LYS 3.1 13.4 + - - +
456 ALA* 3.6 9.9 - - - +
466 GLN 3.2 0.2 - - - -
476 ALA* 1.3 75.6 - - + +
496 GLU* 1.3 63.4 + - + +
516 ILE* 3.3 15.3 + - + +
526 GLY* 3.1 17.8 + - - -
1636 PRO* 3.3 21.4 - - + +
1646 LYS* 2.9 27.4 + - - +
1656 LEU* 3.0 35.2 + - + +
1666 PRO* 3.4 2.3 - - - +
55O LEU* 5.7 1.4 - - - +
165O LEU* 4.0 22.8 - - + +
169O LEU* 4.1 14.8 - - + +
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Residues in contact with GLU 49 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456 ALA 3.6 5.8 - - - +
466 GLN* 3.1 20.3 + - - +
486 GLU* 1.3 76.7 - - + +
506 GLU* 1.3 55.7 + - - +
526 GLY* 3.1 4.1 + - - +
536 HIS* 3.0 33.4 + - - -
1306 GLU* 4.4 2.0 - - - +
1616 ARG* 3.5 26.8 + - - +
1646 LYS* 5.4 3.8 + - - -
11726 AG 3.2 22.6 - - - -
169O LEU* 3.3 31.2 - - + +
170O MET* 3.5 25.7 + - - +
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Residues in contact with GLU 50 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176 GLU* 2.9 46.0 - - - +
206 SER* 3.5 14.3 + - - -
216 ALA* 3.5 23.1 - - + +
246 TYR* 3.7 15.3 - - + -
466 GLN* 3.0 35.2 + - - +
476 ALA 3.7 0.2 - - - +
486 GLU 3.2 0.8 - - - -
496 GLU* 1.3 74.3 - - - +
516 ILE* 1.3 58.0 + - - +
536 HIS* 3.3 14.3 + - - +
546 ALA* 3.1 23.6 + - - +
946 GLU* 4.7 2.0 - - - +
976 ILE* 5.7 1.6 - - - +
1276 GLN* 5.2 2.3 + - - -
1306 GLU* 3.0 17.7 - - - +
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Residues in contact with ILE 51 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186 LEU* 4.8 16.2 - - + -
216 ALA* 3.7 14.8 - - + -
476 ALA* 3.4 19.0 + - + +
486 GLU* 3.3 16.5 + - + +
506 GLU* 1.3 76.2 - - - +
526 GLY* 1.3 57.8 + - - +
546 ALA* 3.3 7.3 + - + +
556 LEU* 3.0 37.7 + - + +
1656 LEU* 6.2 1.1 - - + -
51O ILE* 4.7 27.4 - - + -
165O LEU* 4.3 19.7 - - + -
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Residues in contact with GLY 52 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486 GLU 3.1 12.8 + - - -
496 GLU* 3.1 6.4 + - - -
516 ILE* 1.3 75.7 - - - +
536 HIS* 1.3 62.3 + - - +
556 LEU* 3.4 12.6 + - - +
566 ARG* 3.2 28.5 + - - +
165O LEU* 5.4 0.8 - - - +
169O LEU* 4.2 21.8 - - - -
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Residues in contact with HIS 53 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176 GLU* 3.2 34.0 + - - +
496 GLU* 3.0 14.1 + - - -
506 GLU* 3.3 13.9 + - - +
526 GLY* 1.3 74.9 - - - +
546 ALA* 1.3 63.9 + - - +
566 ARG* 3.2 14.1 + - - +
576 PHE* 3.2 20.9 + - - -
1226 TRP* 3.8 23.1 - + - -
1236 PHE* 3.6 14.1 - + + -
1266 GLU* 3.1 26.5 + - - -
1276 GLN* 4.9 1.5 + - - -
1306 GLU* 3.2 15.5 - - - -
11726 AG 2.2 30.0 - - - -
170O MET* 5.8 0.4 - - + -
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Residues in contact with ALA 54 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 LEU* 3.5 27.5 - - + +
176 GLU* 3.9 7.8 - - + +
186 LEU* 3.8 33.4 - - + -
506 GLU 3.1 13.2 + - - +
516 ILE 3.5 9.0 - - - +
536 HIS* 1.3 75.6 - - - +
556 LEU* 1.3 57.8 + - - +
576 PHE* 3.5 2.0 + - - +
586 TYR* 3.0 25.3 + - - +
25O PHE* 5.0 4.0 - - + -
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Residues in contact with LEU 55 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516 ILE* 3.0 28.8 + - + +
526 GLY* 3.6 14.1 - - - +
536 HIS 3.2 0.4 - - - -
546 ALA* 1.3 76.4 - - - +
566 ARG* 1.3 60.0 + - + +
586 TYR* 3.4 10.5 - - + +
596 ASN* 2.9 43.8 + - - +
25O PHE* 3.8 28.9 - - + -
44O LYS* 4.8 17.3 - - + +
48O GLU* 5.7 1.1 - - - +
163O PRO* 6.2 0.7 - - + -
165O LEU* 5.3 5.6 - - + -
166O PRO* 4.0 34.1 - - + -
169O LEU* 6.0 0.2 - - + -
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Residues in contact with ARG 56 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526 GLY 3.2 16.0 + - - +
536 HIS* 3.2 10.9 + - - +
556 LEU* 1.3 76.5 - - + +
576 PHE* 1.3 58.8 + - - +
596 ASN* 3.4 9.6 + - - +
606 TYR* 3.0 29.5 + - - +
1196 PHE* 3.7 8.6 - - + -
1226 TRP* 3.3 63.8 - - - +
1236 PHE* 3.7 14.6 - - + -
169O LEU 5.1 1.4 + - - -
170O MET* 3.9 18.4 + - - +
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Residues in contact with PHE 57 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106 LEU* 3.8 35.0 - - + +
136 GLN* 3.3 33.0 - - + -
146 LEU* 4.0 21.1 - - + -
176 GLU* 4.3 12.3 - - + -
536 HIS 3.2 22.2 + - - -
546 ALA 3.7 6.7 - - - +
566 ARG* 1.3 75.4 - - - +
586 TYR* 1.3 64.9 + - - +
606 TYR* 4.0 1.3 - + - +
616 ILE* 3.1 31.0 + - - +
1016 ILE* 4.1 12.1 - - + -
1046 LEU* 4.5 0.4 - - + -
1196 PHE* 3.6 25.4 - + - -
1206 LEU* 4.2 8.7 - - + -
1236 PHE* 3.4 33.9 - + - -
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Residues in contact with TYR 58 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 LEU* 3.6 10.5 - - + +
546 ALA 3.0 15.6 + - - +
556 LEU* 3.4 16.2 - - + +
566 ARG 3.3 0.2 - - - -
576 PHE* 1.3 78.6 - - - +
596 ASN* 1.3 76.3 + - - +
616 ILE* 3.6 1.4 + - - +
626 TYR* 3.3 51.5 + + + -
686 VAL* 4.0 19.1 - - + -
25O PHE* 3.7 28.3 - + + -
28O ALA 3.0 23.1 + - - -
29O ALA* 3.9 17.9 - - + -
32O GLU* 2.9 25.2 + - - +
44O LYS* 3.4 30.4 - - - -
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Residues in contact with ASN 59 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556 LEU* 2.9 31.0 + - - +
566 ARG* 3.8 8.4 - - - +
576 PHE 3.3 0.2 - - - -
586 TYR* 1.3 90.4 - - - +
606 TYR* 1.3 59.6 + - - +
626 TYR* 3.6 4.9 + - - +
636 ASP* 3.1 36.5 + - - +
32O GLU* 6.0 0.3 - - - -
44O LYS* 4.2 8.5 + - - -
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Residues in contact with TYR 60 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281 VAL* 4.2 16.8 - - + -
26 LEU* 4.4 0.7 - - + -
106 LEU* 3.7 27.6 - - + -
566 ARG 3.0 17.2 + - - +
576 PHE 4.0 2.2 - - - +
596 ASN* 1.3 75.2 - - - +
616 ILE* 1.3 64.4 + - + +
636 ASP* 3.0 8.0 + - + +
646 ARG* 3.0 59.5 + - + +
1156 SER 3.1 6.7 - - - -
1166 THR* 2.7 45.9 + - + -
1196 PHE* 3.5 50.9 - + + -
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Residues in contact with ILE 61 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26 LEU* 4.6 4.9 - - - +
76 LEU* 3.6 12.1 - - + -
106 LEU* 3.8 51.4 - - + +
116 ASN* 4.2 12.8 - - - +
146 LEU* 4.2 3.8 - - + -
576 PHE 3.1 24.0 + - - +
586 TYR 3.9 4.0 - - - +
606 TYR* 1.3 78.1 - - - +
626 TYR* 1.3 59.4 + - + +
646 ARG* 3.4 8.3 + - - +
666 GLY* 2.8 25.5 + - - +
676 ARG 3.5 26.5 - - - +
686 VAL* 3.7 27.1 - - + +
----------------------------------------------------------
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Residues in contact with TYR 62 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1321 ALA* 5.2 1.4 - - - +
586 TYR* 3.3 44.3 + + + +
596 ASN* 4.2 4.0 - - - +
606 TYR 3.2 0.4 - - - -
616 ILE* 1.3 74.3 - - - +
636 ASP* 1.3 64.8 + - - +
646 ARG 3.2 0.4 - - - -
656 ASN* 3.4 11.8 + - - +
666 GLY 3.5 22.7 - - - +
676 ARG* 3.7 7.7 - - - -
686 VAL* 3.4 35.2 + - + -
29O ALA* 2.5 33.4 + - - +
32O GLU* 3.7 28.7 - - + -
33O ASP* 3.8 23.8 - - + -
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Residues in contact with ASP 63 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281 VAL* 4.0 26.8 - - + +
1291 GLU* 5.5 6.7 - - - +
1311 GLU* 5.2 2.9 - - - +
1321 ALA* 3.7 36.4 + - + +
596 ASN* 3.1 23.4 + - - +
606 TYR* 3.0 14.9 + - - +
626 TYR* 1.3 77.4 - - - +
646 ARG* 1.3 63.2 + - - +
656 ASN* 3.3 3.0 + - - +
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Residues in contact with ARG 64 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021 TYR* 3.4 11.1 + - - -
1281 VAL* 3.9 22.1 - - - +
1311 GLU* 3.9 27.7 + - - +
16 MET* 3.5 38.9 + - - +
26 LEU* 3.8 29.4 + - + +
606 TYR* 3.0 57.1 + - + +
616 ILE 3.4 0.6 + - - +
626 TYR 3.2 0.6 - - - -
636 ASP* 1.3 77.8 + - - +
656 ASN* 1.3 69.7 + - - +
666 GLY* 3.2 2.2 + - - -
1136 ASP* 4.2 8.3 + - - -
1156 SER* 3.4 28.3 + - - -
----------------------------------------------------------
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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