Contacts of the helix formed by residues 5 - 34 (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 ARG 5 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36 SER 3.1 1.0 + - - -
46 GLU* 1.3 75.8 + - + +
66 MET* 1.3 59.7 + - - +
76 LEU* 3.0 6.2 - - - +
86 LYS* 3.5 23.3 - - + +
96 ALA* 2.8 27.6 + - + +
1076 LEU* 4.6 24.3 - - + +
1116 GLU* 3.3 28.5 + - - +
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Residues in contact with MET 6 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26 LEU* 3.6 27.1 - - + -
36 SER* 3.0 30.0 + - - +
46 GLU 3.4 1.6 - - - -
56 ARG* 1.3 76.6 - - - +
76 LEU* 1.3 52.0 + - - +
96 ALA* 3.3 4.2 + - - +
106 LEU* 2.8 40.6 + - + +
1046 LEU* 4.1 11.2 - - - -
1076 LEU* 3.7 26.5 - - + +
1086 ALA* 3.7 33.2 - - + +
1116 GLU* 3.5 17.5 - - - +
1136 ASP* 3.6 12.1 - - + +
1166 THR* 3.8 18.8 - - + +
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Residues in contact with LEU 7 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26 LEU* 3.8 24.3 - - + +
36 SER 3.7 7.7 + - - +
46 GLU* 5.5 1.3 - - - -
56 ARG 4.6 4.7 - - - +
66 MET* 1.3 76.8 - - - +
86 LYS* 1.3 53.4 + - - +
106 LEU* 3.1 5.8 + - - +
116 ASN* 2.6 50.3 + - - +
616 ILE* 3.6 32.8 - - + -
666 GLY* 4.0 5.8 - - - -
676 ARG* 3.7 28.3 - - + +
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Residues in contact with LYS 8 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 ARG* 3.2 24.1 + - + +
76 LEU* 1.3 78.2 - - - +
96 ALA* 1.3 58.8 + - - +
116 ASN* 4.3 6.5 - - + +
126 ASP* 2.8 66.2 + - - +
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Residues in contact with ALA 9 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 ARG* 2.8 18.3 + - + +
66 MET 3.5 5.2 - - - +
86 LYS* 1.3 76.2 - - - +
106 LEU* 1.3 61.2 + - - +
126 ASP* 3.7 6.7 + - - +
136 GLN* 3.2 23.6 + - - +
166 ARG* 4.6 2.0 + - - +
1046 LEU* 3.6 28.5 - - + +
1076 LEU* 3.7 17.5 - - + -
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Residues in contact with LEU 10 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26 LEU* 3.7 28.9 - - + -
66 MET* 2.8 28.2 + - + +
76 LEU 3.5 4.9 - - - +
96 ALA* 1.3 73.7 - - - +
116 ASN* 1.3 58.1 + - - +
136 GLN 3.6 0.2 + - - -
146 LEU* 3.2 25.5 + - - +
576 PHE* 3.8 34.2 - - + -
606 TYR* 3.7 29.8 - - + -
616 ILE* 3.8 20.0 - - + +
1046 LEU* 3.9 16.8 - - + -
1166 THR* 4.1 14.1 - - + -
1196 PHE* 4.4 5.8 - - + -
1206 LEU* 5.2 0.7 - - + -
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Residues in contact with ASN 11 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76 LEU* 2.6 39.4 + - - +
86 LYS* 3.8 8.2 - - + +
106 LEU* 1.3 72.7 - - - +
126 ASP* 1.3 67.1 + - - +
146 LEU* 3.6 7.6 + - - +
156 ASN* 3.2 20.8 + - - +
616 ILE* 4.2 6.4 - - - +
676 ARG 3.2 22.6 + - - -
686 VAL* 3.4 12.8 - - - +
696 GLU* 2.8 45.0 + - + +
716 ASP* 4.7 4.1 - - - +
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Residues in contact with ASP 12 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86 LYS* 2.8 57.3 + - - +
96 ALA* 4.0 5.4 - - - +
116 ASN* 1.3 78.4 - - - +
136 GLN* 1.3 58.5 + - - +
156 ASN* 3.3 8.9 + - - +
166 ARG* 2.9 53.8 + - - +
716 ASP* 3.9 13.7 - - - +
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Residues in contact with GLN 13 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96 ALA 3.2 16.6 + - - +
106 LEU 4.0 0.9 - - - +
126 ASP* 1.3 77.0 - - - +
146 LEU* 1.3 59.3 + - - +
166 ARG* 3.1 28.5 + - - +
176 GLU* 2.9 56.3 + - - +
576 PHE* 3.3 34.5 - - + -
976 ILE* 4.1 8.7 - - - +
1006 SER* 3.1 32.3 + - - +
1016 ILE* 3.7 15.1 - - + +
1046 LEU* 3.7 12.2 - - + +
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Residues in contact with LEU 14 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106 LEU 3.2 12.5 + - - +
116 ASN* 3.6 12.3 - - - +
136 GLN* 1.3 75.4 - - - +
156 ASN* 1.3 61.8 + - - +
176 GLU* 3.4 7.2 + - - +
186 LEU* 3.2 41.8 + - + +
546 ALA* 3.5 19.8 - - + +
576 PHE* 4.0 13.1 - - + -
586 TYR* 3.6 33.4 - - + +
616 ILE* 4.2 5.2 - - + -
686 VAL* 3.9 23.6 - - + -
696 GLU 6.1 0.4 - - - +
706 LEU* 3.8 18.4 - - + -
25O PHE* 4.2 6.5 - - + -
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Residues in contact with ASN 15 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 ASN 3.2 10.8 + - - +
126 ASP* 3.4 12.1 - - - +
146 LEU* 1.3 80.9 - - - +
166 ARG* 1.3 59.2 + - + +
186 LEU* 3.5 6.5 + - - +
196 TYR* 3.1 26.5 + - - +
706 LEU* 5.2 0.6 - - - +
716 ASP* 3.2 49.4 + - - +
726 GLU 3.7 13.5 + - - +
736 ILE* 4.3 6.3 - - - +
746 PRO* 4.8 5.9 - - - +
22O TYR* 3.4 11.1 + - - -
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Residues in contact with ARG 16 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 ALA* 4.6 3.2 + - - +
126 ASP* 2.9 31.9 + - - +
136 GLN* 3.1 52.8 + - - +
156 ASN* 1.3 73.9 - - + +
176 GLU* 1.3 62.0 + - - +
196 TYR* 3.6 8.3 + - - +
206 SER* 3.0 29.5 + - - -
966 PHE* 4.2 27.1 - - + -
976 ILE* 4.0 9.5 - - + +
1006 SER* 3.9 24.8 + - - -
1036 GLU* 5.8 1.8 + - - -
1046 LEU* 5.3 1.6 - - - +
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Residues in contact with GLU 17 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136 GLN* 2.9 40.1 + - - +
146 LEU 3.7 5.2 - - - +
156 ASN 3.3 0.2 - - - -
166 ARG* 1.3 77.0 - - - +
186 LEU* 1.3 57.9 + - - +
206 SER* 3.4 3.2 + - - -
216 ALA* 3.2 20.8 + - - +
506 GLU* 2.9 51.5 - - - +
536 HIS* 3.2 28.5 + - + +
546 ALA* 3.9 9.6 - - + +
576 PHE* 4.3 12.1 - - + -
976 ILE* 3.9 15.0 - - - +
1016 ILE* 4.7 1.4 - - - +
1236 PHE* 4.4 12.0 - - - -
1276 GLN* 4.8 2.4 + - - -
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Residues in contact with LEU 18 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 LEU* 3.2 38.8 + - + +
156 ASN* 3.8 7.0 - - - +
166 ARG 3.3 0.2 - - - -
176 GLU* 1.3 74.7 - - - +
196 TYR* 1.3 59.9 + - - +
216 ALA* 3.4 7.2 - - + +
226 TYR* 3.1 23.7 + - - +
506 GLU 5.2 0.2 - - - -
516 ILE* 4.8 22.9 - - + -
546 ALA* 3.8 17.7 - - + -
706 LEU* 4.2 0.4 - - + -
736 ILE* 4.1 17.3 - - + +
22O TYR* 3.6 37.7 - - + +
25O PHE* 4.2 12.6 - - + -
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Residues in contact with TYR 19 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 ASN* 3.1 17.2 + - - +
166 ARG* 3.9 7.4 - - - +
186 LEU* 1.3 73.6 - - - +
206 SER* 1.3 57.4 + - - +
226 TYR* 3.0 3.5 + - + -
236 LEU* 2.7 48.5 + - + +
736 ILE* 3.9 16.3 - - + +
746 PRO* 3.7 46.4 - - + -
756 LYS 4.6 2.3 + - - -
766 PRO* 4.0 15.1 - - + +
776 PRO* 3.7 24.3 - - - +
936 HIS* 3.7 30.5 - + - -
966 PHE* 6.1 1.3 - + - -
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Residues in contact with SER 20 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166 ARG 3.0 18.5 + - - -
176 GLU* 3.4 12.1 + - - -
186 LEU 3.3 0.2 - - - -
196 TYR* 1.3 76.7 - - - +
216 ALA* 1.3 60.0 + - - +
236 LEU* 3.4 3.1 + - - +
246 TYR* 3.0 36.2 + - - -
506 GLU* 3.5 24.3 + - - -
936 HIS* 3.1 27.5 + - - -
946 GLU* 5.6 0.7 - - - -
976 ILE* 3.4 14.0 - - - +
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Residues in contact with ALA 21 (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 6.1 + - - +
186 LEU* 3.4 12.3 - - + +
206 SER* 1.3 79.6 - - - +
226 TYR* 1.3 56.9 + - - +
256 PHE* 3.1 24.6 + - - +
476 ALA* 3.3 37.2 - - + +
506 GLU* 3.5 13.1 - - + +
516 ILE* 3.7 20.6 - - + +
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Residues in contact with TYR 22 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186 LEU 3.1 13.4 + - - +
196 TYR* 3.0 13.9 + + + +
216 ALA* 1.3 74.3 - - - +
236 LEU* 1.3 60.2 + - - +
256 PHE* 3.6 8.9 + + + -
266 ALA* 3.1 25.5 + - - +
736 ILE* 4.0 12.3 - - + -
746 PRO 3.9 12.8 - - - -
766 PRO* 3.6 33.1 - - + +
15O ASN* 3.4 12.8 + - - -
18O LEU* 3.6 28.2 - - + +
70O LEU* 3.4 30.5 - - + +
71O ASP 2.7 29.0 + - - -
72O GLU* 4.8 1.1 - - - -
73O ILE* 3.7 19.6 - - + +
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Residues in contact with LEU 23 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196 TYR* 2.7 33.6 + - + +
206 SER* 3.8 4.5 - - - +
226 TYR* 1.3 73.0 - - - +
246 TYR* 1.3 63.9 + - + +
266 ALA* 3.2 5.2 + - - +
276 MET* 2.9 45.3 + - + +
766 PRO* 4.2 7.1 - - + +
776 PRO* 3.8 29.8 - - + -
806 TRP* 4.1 17.3 - - + -
896 ALA 5.1 0.7 - - - +
936 HIS* 3.6 46.4 - - + +
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Residues in contact with TYR 24 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206 SER* 3.0 24.8 + - - +
216 ALA 4.1 3.1 - - - +
236 LEU* 1.3 78.9 - - + +
256 PHE* 1.3 60.6 + - - +
276 MET* 3.6 13.2 - - + -
286 ALA* 2.8 27.5 + - - +
426 TRP* 6.1 1.1 - + - -
436 MET* 3.4 46.3 - - + +
466 GLN* 3.7 22.0 - - + -
476 ALA* 4.2 2.9 - - + -
506 GLU* 3.7 29.6 - - + -
906 ALA* 3.8 30.0 + - + +
936 HIS* 4.3 9.3 - + - -
946 GLU* 2.7 35.4 + - - +
1346 VAL* 4.9 4.0 - - + +
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Residues in contact with PHE 25 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216 ALA 3.1 18.8 + - - +
226 TYR* 3.8 16.6 - + + +
246 TYR* 1.3 76.5 - - - +
266 ALA* 1.3 56.3 + - - +
286 ALA* 3.6 8.9 - - + +
296 ALA* 3.2 25.3 + - - +
446 LYS* 4.7 9.4 - - + -
476 ALA* 4.2 9.4 - - + +
14O LEU* 4.2 11.2 - - + -
18O LEU* 4.4 11.9 - - + -
54O ALA* 5.0 3.8 - - + -
55O LEU* 3.9 28.3 - - + -
58O TYR* 3.7 37.6 - + + -
70O LEU* 3.5 39.2 - - + +
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Residues in contact with ALA 26 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226 TYR 3.1 14.6 + - - +
236 LEU 3.3 9.4 - - - +
256 PHE* 1.3 76.7 - - - +
276 MET* 1.3 61.5 + - - +
296 ALA* 3.6 5.3 + - - +
306 TYR* 3.2 20.1 + - - +
766 PRO* 3.7 18.4 - - + -
776 PRO 3.7 21.3 - - - +
786 LYS* 4.4 4.7 - - - +
806 TRP* 3.8 7.5 - - + -
67O ARG* 5.2 0.3 + - - -
70O LEU* 3.5 11.8 - - + +
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Residues in contact with MET 27 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236 LEU* 2.9 34.5 + - + +
246 TYR* 3.7 11.9 - - + +
256 PHE 3.3 0.2 - - - -
266 ALA* 1.3 73.8 - - - +
286 ALA* 1.3 60.5 + - - +
306 TYR* 3.2 2.5 + - - +
316 PHE* 2.9 40.4 + - + -
436 MET* 3.7 31.4 - - + -
806 TRP* 3.5 37.7 - - + -
866 ALA* 3.4 31.9 - - + +
896 ALA* 4.2 5.2 - - + -
906 ALA* 3.8 23.1 - - + +
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Residues in contact with ALA 28 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246 TYR 2.8 18.3 + - - +
256 PHE* 3.6 11.7 - - + +
266 ALA 3.3 0.2 - - - -
276 MET* 1.3 76.8 - - - +
296 ALA* 1.3 55.7 + - - +
316 PHE 3.4 0.5 + - - -
326 GLU* 2.9 24.4 + - - +
406 ALA* 3.4 30.6 - - - +
436 MET* 3.8 9.6 - - + +
446 LYS* 3.8 17.5 - - + +
58O TYR* 3.1 13.1 + - - +
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Residues in contact with ALA 29 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256 PHE 3.2 14.2 + - - +
266 ALA* 3.8 8.5 - - - +
276 MET 3.3 0.2 - - - -
286 ALA* 1.3 76.5 - - - +
306 TYR* 1.3 65.6 + - - +
336 ASP* 3.1 14.4 + - - +
58O TYR* 3.5 20.3 + - + -
62O TYR* 2.5 31.1 + - - +
67O ARG* 3.8 10.3 + - - +
68O VAL* 4.2 13.7 - - + +
70O LEU* 5.3 2.5 - - + -
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Residues in contact with TYR 30 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266 ALA 3.2 11.5 + - - +
276 MET 3.2 10.4 + - - +
296 ALA* 1.3 80.2 - - - +
316 PHE* 1.3 76.4 + + - +
336 ASP* 3.4 6.4 + - + +
346 LEU* 3.4 50.6 + - + +
786 LYS 4.1 4.0 - - - +
796 GLU* 4.3 5.4 - - + -
806 TRP* 2.8 62.9 + + + -
816 GLU 3.8 1.7 + - - -
826 SER* 3.3 31.6 - - - -
836 PRO* 3.9 0.2 - - - +
866 ALA* 4.2 12.6 - - + -
67O ARG* 4.0 20.1 - - - +
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Residues in contact with PHE 31 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276 MET* 2.9 30.9 + - + +
286 ALA 3.9 1.6 - - - +
306 TYR* 1.3 83.1 - + - +
326 GLU* 1.3 61.8 + - - +
346 LEU* 3.4 3.9 + - + +
356 GLY 3.3 3.1 + - - -
366 LEU* 2.9 56.8 + - + +
396 PHE* 3.5 25.6 - + + -
406 ALA 3.8 9.2 - - - +
436 MET* 4.1 21.1 - - + -
836 PRO* 3.6 29.2 - - + -
866 ALA* 4.0 20.4 - - + -
876 PHE* 3.7 35.9 - + - -
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Residues in contact with GLU 32 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286 ALA 2.9 7.2 + - - +
296 ALA 3.6 5.2 - - - +
306 TYR 3.3 0.2 - - - -
316 PHE* 1.3 77.6 - - - +
336 ASP* 1.3 61.7 + - - +
356 GLY* 3.2 14.3 + - - -
366 LEU 4.6 1.8 - - - +
376 GLU* 3.4 31.5 - - - +
406 ALA* 3.4 13.8 - - - +
416 ASN* 5.1 0.2 - - - +
446 LYS* 3.0 22.9 + - - -
58O TYR* 2.9 34.8 + - - +
62O TYR* 3.7 34.6 - - + -
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Residues in contact with ASP 33 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296 ALA 3.1 13.2 + - - +
306 TYR* 3.6 10.3 - - + +
316 PHE 3.3 0.2 - - - -
326 GLU* 1.3 73.7 - - - +
346 LEU* 1.3 63.2 + - + +
356 GLY* 3.1 5.9 + - - -
62O TYR* 3.7 7.6 - - + -
66O GLY 4.2 10.4 - - - +
67O ARG* 3.5 37.5 + - - +
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Residues in contact with LEU 34 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306 TYR* 3.4 50.1 + - + +
316 PHE* 3.8 9.6 - - + +
326 GLU 3.3 0.4 - - - -
336 ASP* 1.3 81.6 - - + +
356 GLY* 1.3 60.0 + - - +
366 LEU* 3.6 17.7 + - + +
836 PRO* 4.1 21.3 - - + -
139M ASP* 6.0 1.6 - - - +
143M PHE* 5.5 8.7 - - - -
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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