Contacts of the helix formed by residues 3 - 35 (chain 3) 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 SER 3 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13 MET 3.9 1.6 + - - -
23 LEU* 1.3 76.2 - - - +
43 GLU* 1.3 59.4 + - - +
53 ARG* 4.0 2.9 + - - -
63 MET* 3.2 11.5 + - - +
73 LEU* 3.0 27.7 + - - +
1113 GLU* 2.8 35.3 + - - -
1133 ASP* 5.6 0.6 + - - -
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Residues in contact with GLU 4 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23 LEU 4.0 0.2 + - - -
33 SER* 1.3 73.0 - - - +
53 ARG* 1.3 61.9 + - - +
73 LEU* 3.6 12.1 + - + +
83 LYS* 3.2 26.8 + - + +
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Residues in contact with ARG 5 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33 SER* 3.2 2.3 + - - +
43 GLU* 1.3 74.7 - - - +
63 MET* 1.3 63.7 + - - +
83 LYS* 3.7 7.8 + - - +
93 ALA* 3.3 20.3 + - - +
1073 LEU* 4.2 21.1 - - + +
1113 GLU* 3.7 19.7 - - - +
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Residues in contact with MET 6 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23 LEU* 3.9 13.7 - - + -
33 SER* 3.2 25.9 + - - +
53 ARG* 1.3 78.0 - - - +
73 LEU* 1.3 59.1 + - - +
93 ALA* 3.1 3.8 + - - +
103 LEU* 3.0 31.0 + - + +
1043 LEU* 4.3 13.9 - - - +
1073 LEU* 3.7 22.0 - - + -
1083 ALA* 3.6 37.7 - - + +
1113 GLU* 3.5 15.6 + - - +
1133 ASP* 3.8 20.6 - - + +
1163 THR* 3.9 20.0 - - - +
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Residues in contact with LEU 7 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23 LEU* 3.9 21.2 - - + +
33 SER 3.0 17.1 + - - +
43 GLU* 3.9 11.0 - - + +
63 MET* 1.3 76.0 - - - +
83 LYS* 1.3 57.3 + - - +
103 LEU* 3.5 7.8 + - - +
113 ASN* 3.0 44.5 + - - +
613 ILE* 3.9 16.6 - - + -
663 GLY* 4.1 4.7 - - - -
673 ARG* 3.8 40.4 - - + +
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Residues in contact with LYS 8 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43 GLU* 3.2 19.6 + - + +
53 ARG* 3.8 8.1 - - + +
63 MET 3.2 0.2 - - - -
73 LEU* 1.3 79.0 - - - +
93 ALA* 1.3 58.2 + - - +
113 ASN* 3.6 6.3 + - + +
123 ASP* 3.0 54.1 + - - +
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Residues in contact with ALA 9 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53 ARG 3.3 11.2 + - - +
63 MET 3.1 9.9 + - - +
83 LYS* 1.3 78.3 - - - +
103 LEU* 1.3 58.2 + - - +
123 ASP* 3.6 8.1 + - - +
133 GLN* 3.2 26.3 + - - +
163 ARG* 4.3 2.3 + - - -
1043 LEU* 3.8 25.3 - - + +
1073 LEU* 3.9 16.6 - - + -
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Residues in contact with LEU 10 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23 LEU* 3.8 39.3 - - + -
63 MET* 3.0 26.4 + - + +
73 LEU* 3.8 4.5 - - - +
83 LYS 3.4 0.2 - - - -
93 ALA* 1.3 74.6 - - - +
113 ASN* 1.3 59.6 + - - +
133 GLN* 3.4 3.8 + - - +
143 LEU* 3.1 26.7 + - - +
573 PHE* 3.9 32.5 - - + -
603 TYR* 4.0 13.2 - - + -
613 ILE* 4.0 20.7 - - + +
1043 LEU* 4.1 10.1 - - + -
1163 THR* 3.9 20.2 - - + -
1193 PHE* 4.3 7.6 - - + -
1203 LEU* 5.4 0.4 - - + -
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Residues in contact with ASN 11 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73 LEU* 3.0 36.6 + - - +
83 LYS* 3.9 6.7 - - - +
103 LEU* 1.3 75.4 - - - +
123 ASP* 1.3 64.1 + - - +
143 LEU* 3.5 9.0 - - - +
153 ASN* 3.2 21.0 + - - +
613 ILE* 4.0 9.0 - - - +
673 ARG 3.2 20.4 + - - -
683 VAL* 3.3 11.4 - - - +
693 GLU* 2.8 47.8 + - + +
713 ASP* 4.6 4.1 - - - +
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Residues in contact with ASP 12 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 LYS* 3.0 46.9 + - - +
93 ALA* 3.7 9.6 - - - +
103 LEU 3.3 0.4 - - - -
113 ASN* 1.3 78.1 - - - +
133 GLN* 1.3 57.4 + - - +
153 ASN* 3.3 9.2 + - - +
163 ARG* 3.0 48.6 + - - +
713 ASP* 3.8 14.9 - - - +
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Residues in contact with GLN 13 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 ALA 3.2 9.1 + - - +
103 LEU 3.9 4.3 - - - +
113 ASN 3.4 0.2 - - - -
123 ASP* 1.3 73.6 - - - +
143 LEU* 1.3 56.7 + - - +
153 ASN 3.1 0.4 - - - -
163 ARG* 3.0 30.1 + - - +
173 GLU* 2.8 57.3 + - + +
573 PHE* 3.4 29.8 - - + -
973 ILE* 4.0 10.9 - - - +
1003 SER* 3.0 33.9 + - - +
1013 ILE* 3.8 14.1 - - + +
1043 LEU* 3.6 20.8 - - + +
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Residues in contact with LEU 14 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 LEU 3.1 11.6 + - - +
113 ASN* 3.5 13.2 - - - +
133 GLN* 1.3 75.3 - - - +
153 ASN* 1.3 61.6 + - - +
173 GLU* 3.7 6.6 + - - +
183 LEU* 3.3 39.4 + - + +
543 ALA* 3.5 19.6 - - + +
573 PHE* 3.9 12.2 - - + -
583 TYR* 3.5 34.1 - - + +
613 ILE* 4.0 15.5 - - + -
683 VAL* 4.1 13.5 - - + -
693 GLU 6.1 0.4 - - - +
703 LEU* 3.9 18.2 - - + -
25L PHE* 4.3 8.1 - - + -
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Residues in contact with ASN 15 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113 ASN 3.2 10.6 + - - +
123 ASP* 3.4 12.3 - - - +
133 GLN 3.1 0.4 - - - -
143 LEU* 1.3 77.8 - - - +
163 ARG* 1.3 61.3 + - - +
183 LEU* 3.4 8.4 + - - +
193 TYR* 3.0 26.2 + - - +
703 LEU* 6.4 0.4 - - - -
713 ASP* 3.1 48.6 + - + +
723 GLU 3.1 19.3 + - - +
733 ILE* 4.5 4.8 - - - +
743 PRO* 4.5 8.8 - - - +
22L TYR* 3.9 5.1 + - - -
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Residues in contact with ARG 16 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 ALA* 4.3 3.2 + - - +
123 ASP* 3.0 34.0 + - - +
133 GLN* 3.0 61.2 + - - +
153 ASN* 1.3 77.7 - - + +
173 GLU* 1.3 58.6 + - - +
193 TYR* 3.3 7.7 + - - +
203 SER* 2.9 32.1 + - - -
933 HIS* 4.7 1.0 + - - -
963 PHE* 4.5 24.7 - - + -
973 ILE* 4.0 8.5 - - + +
1003 SER* 3.9 21.9 + - - -
1043 LEU* 5.1 2.0 - - - +
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Residues in contact with GLU 17 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133 GLN* 2.8 38.0 + - - +
143 LEU 3.9 0.4 - - - +
163 ARG* 1.3 75.7 - - - +
183 LEU* 1.3 57.3 + - - +
203 SER* 3.4 4.8 + - - -
213 ALA* 3.2 20.3 + - - +
503 GLU* 3.0 51.3 - - - +
533 HIS* 3.5 19.8 + - + +
543 ALA* 3.9 13.2 - - + +
573 PHE* 3.9 17.8 - - + -
973 ILE* 4.3 12.4 - - - +
1013 ILE* 4.5 1.9 - - - +
1233 PHE* 3.9 19.6 - - - -
1273 GLN* 5.0 2.8 + - - -
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Residues in contact with LEU 18 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143 LEU* 3.3 36.1 + - + +
153 ASN* 3.7 7.0 - - - +
163 ARG 3.3 0.2 - - - -
173 GLU* 1.3 76.2 - - - +
193 TYR* 1.3 58.8 + - - +
213 ALA* 3.5 6.8 + - + +
223 TYR* 3.1 24.1 + - - +
513 ILE* 4.9 20.2 - - + -
543 ALA* 3.8 16.2 - - + -
703 LEU* 4.1 2.9 - - + -
733 ILE* 4.2 18.5 - - + +
22L TYR* 3.6 36.6 - - + +
25L PHE* 4.2 11.4 - - + -
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Residues in contact with TYR 19 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153 ASN* 3.0 18.1 + - - +
163 ARG* 3.3 7.6 + - - +
183 LEU* 1.3 74.0 - - - +
203 SER* 1.3 55.1 + - - +
223 TYR* 3.0 5.6 + - + -
233 LEU* 2.6 48.6 + - + +
733 ILE* 4.2 9.3 - - + +
743 PRO* 3.7 48.7 - - + -
753 LYS 4.4 3.1 + - - -
763 PRO* 3.8 16.9 - - + +
773 PRO* 3.7 23.9 - - - +
933 HIS* 3.7 30.1 - + - -
963 PHE* 6.0 1.6 - + - -
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Residues in contact with SER 20 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163 ARG 2.9 20.7 + - - -
173 GLU* 3.4 12.4 + - - -
183 LEU 3.3 0.2 - - - -
193 TYR* 1.3 76.6 - - - +
213 ALA* 1.3 60.9 + - - +
233 LEU* 3.8 2.7 - - - +
243 TYR* 3.1 34.5 + - - -
503 GLU* 3.5 23.2 + - - -
933 HIS* 3.0 29.0 + - - -
943 GLU* 5.6 0.7 - - - -
973 ILE* 3.4 14.6 - - - +
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Residues in contact with ALA 21 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173 GLU 3.2 6.5 + - - +
183 LEU* 3.5 11.9 - - + +
193 TYR 3.2 0.2 - - - -
203 SER* 1.3 77.5 - - - +
223 TYR* 1.3 57.9 - - - +
253 PHE* 3.1 25.8 + - - +
473 ALA* 3.3 37.3 - - + +
503 GLU* 3.6 12.7 - - + +
513 ILE* 3.7 20.4 - - + -
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Residues in contact with TYR 22 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183 LEU 3.1 15.7 + - - +
193 TYR* 3.0 7.4 + + + +
213 ALA* 1.3 73.2 - - - +
233 LEU* 1.3 59.9 + - - +
253 PHE* 3.7 8.4 + + - +
263 ALA* 3.2 24.6 + - - +
733 ILE* 3.7 25.1 - - + -
743 PRO 3.9 4.9 - - - -
763 PRO* 3.5 34.3 - - + +
15L ASN* 3.4 12.6 + - - -
18L LEU* 3.6 27.3 - - + +
70L LEU* 3.4 29.2 - - + +
71L ASP 2.6 30.0 + - - -
72L GLU* 4.7 0.7 - - - -
73L ILE* 3.8 20.2 - - + -
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Residues in contact with LEU 23 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193 TYR* 2.6 33.6 + - + +
203 SER 3.8 3.8 - - - +
223 TYR* 1.3 75.3 - - - +
243 TYR* 1.3 62.4 + - + +
263 ALA* 3.2 5.5 + - - +
273 MET* 2.9 43.1 + - + +
763 PRO* 4.1 7.2 - - + +
773 PRO* 3.8 30.3 - - + -
803 TRP* 4.1 17.9 - - + -
893 ALA* 5.3 0.9 - - + +
933 HIS* 3.5 47.1 - - + +
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Residues in contact with TYR 24 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203 SER* 3.1 24.1 + - - +
213 ALA 4.1 3.1 - - - +
233 LEU* 1.3 79.5 - - + +
253 PHE* 1.3 60.4 + - - +
273 MET* 3.6 13.8 - - + +
283 ALA* 2.9 23.4 + - - +
423 TRP* 5.9 0.9 - + - -
433 MET* 3.3 48.1 - - + +
463 GLN* 3.7 21.8 - - + -
473 ALA* 4.2 2.7 - - + -
503 GLU* 3.5 30.5 - - + -
903 ALA* 3.7 28.8 + - + +
933 HIS* 4.4 8.7 - + - -
943 GLU* 2.5 35.5 + - - +
1343 VAL* 4.8 5.6 - - + +
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Residues in contact with PHE 25 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213 ALA 3.1 18.3 + - - +
223 TYR* 3.9 15.3 - + - +
233 LEU 3.3 0.2 - - - -
243 TYR* 1.3 75.2 - - - +
263 ALA* 1.3 58.5 + - - +
283 ALA* 3.7 10.2 + - + +
293 ALA* 3.3 23.0 + - - +
433 MET 5.4 0.7 - - - -
443 LYS* 4.7 10.8 - - + -
473 ALA* 4.3 7.8 - - + +
14L LEU* 4.4 5.4 - - + -
18L LEU* 4.3 17.7 - - + -
54L ALA* 5.1 3.6 - - + -
55L LEU* 3.7 31.9 - - + -
58L TYR* 3.7 36.3 - + + -
70L LEU* 3.6 38.9 - - + +
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Residues in contact with ALA 26 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223 TYR 3.2 14.9 + - - +
233 LEU 3.2 10.4 + - - +
253 PHE* 1.3 76.7 - - - +
273 MET* 1.3 63.1 + - - +
293 ALA* 3.4 7.1 + - - +
303 TYR* 3.1 19.8 + - - +
763 PRO* 3.8 17.5 - - + -
773 PRO 3.7 21.5 - - - +
783 LYS* 4.4 4.3 - - - +
803 TRP* 4.0 6.1 - - + -
70L LEU* 3.6 12.1 - - + +
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Residues in contact with MET 27 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233 LEU* 2.9 33.0 + - + +
243 TYR* 3.3 19.5 + - + +
263 ALA* 1.3 74.8 - - - +
283 ALA* 1.3 58.2 + - - +
303 TYR* 3.0 3.3 + - - +
313 PHE* 2.9 40.9 + - + -
433 MET* 3.8 31.0 - - + -
803 TRP* 3.5 37.2 - - + -
863 ALA* 3.4 28.5 - - + +
893 ALA* 4.3 4.7 - - + -
903 ALA* 3.8 22.0 - - + +
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Residues in contact with ALA 28 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243 TYR 2.9 16.6 + - - +
253 PHE* 3.7 11.7 - - + +
273 MET* 1.3 76.2 - - - +
293 ALA* 1.3 56.6 + - - +
313 PHE* 3.5 0.6 + - - -
323 GLU* 3.0 23.4 + - - +
403 ALA* 3.5 32.0 - - - +
433 MET* 3.6 10.4 - - + +
443 LYS* 3.9 15.5 - - + -
58L TYR* 3.0 15.3 + - - +
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Residues in contact with ALA 29 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253 PHE 3.3 11.5 + - - +
263 ALA* 3.5 13.0 - - - +
273 MET 3.2 0.6 - - - -
283 ALA* 1.3 78.7 - - - +
303 TYR* 1.3 61.2 + - - +
333 ASP* 3.3 12.8 + - - +
58L TYR* 3.6 17.6 + - + -
62L TYR* 2.6 31.2 + - - +
67L ARG* 3.4 12.9 + - - +
68L VAL* 4.2 14.1 - - + +
70L LEU* 5.3 2.7 - - + -
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Residues in contact with TYR 30 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263 ALA 3.1 12.2 + - - +
273 MET* 3.0 10.6 + - - +
293 ALA* 1.3 76.1 - - - +
313 PHE* 1.3 73.0 + + - +
333 ASP* 3.4 18.3 + - - +
343 LEU* 3.5 37.3 + - + +
783 LYS 4.0 4.9 - - - +
793 GLU* 4.3 7.4 - - + -
803 TRP* 2.9 58.9 + + + -
813 GLU 3.8 2.1 + - - -
823 SER* 3.4 24.6 + - - -
833 PRO* 3.7 3.1 - - - +
863 ALA* 4.0 24.0 - - + -
67L ARG* 3.8 19.4 - - - +
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Residues in contact with PHE 31 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273 MET* 2.9 33.1 + - + +
283 ALA 4.0 2.2 - - - +
303 TYR* 1.3 81.7 - + - +
323 GLU* 1.3 65.0 + - - +
343 LEU* 3.1 13.1 + - + +
363 LEU* 3.1 47.7 + - + +
393 PHE* 3.5 33.2 - + + -
403 ALA 3.9 5.4 - - - +
433 MET* 4.0 32.1 - - + -
833 PRO* 3.8 25.4 - - + -
863 ALA* 3.9 20.2 - - + -
873 PHE* 3.8 22.4 - + - -
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Residues in contact with GLU 32 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283 ALA 3.0 8.1 + - - +
293 ALA 3.8 4.7 - - - +
303 TYR 3.3 0.2 - - - -
313 PHE* 1.3 76.4 - - - +
333 ASP* 1.3 61.8 + - - +
353 GLY* 3.1 13.9 + - - +
363 LEU 4.8 1.8 - - - +
373 GLU* 3.4 31.7 - - - +
403 ALA* 3.4 13.4 - - - +
413 ASN* 5.3 0.2 - - - +
443 LYS* 3.1 21.8 + - - -
58L TYR* 3.0 33.5 + - - +
62L TYR* 3.7 34.0 - - + -
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Residues in contact with ASP 33 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293 ALA 3.3 11.1 + - - +
303 TYR* 3.4 14.1 - - - +
313 PHE 3.2 0.2 - - - -
323 GLU* 1.3 80.9 - - - +
343 LEU* 1.3 65.6 + - - +
353 GLY* 3.5 0.5 + - - -
793 GLU* 5.1 4.5 - - - +
62L TYR* 3.8 8.0 - - + -
66L GLY 4.5 7.6 - - - +
67L ARG* 3.6 35.4 + - - +
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Residues in contact with LEU 34 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303 TYR* 3.5 49.1 + - + +
313 PHE* 3.1 10.3 + - - +
333 ASP* 1.3 82.1 - - - +
353 GLY* 1.3 57.5 + - - +
363 LEU* 3.3 20.6 + - + +
833 PRO* 4.1 20.4 - - + -
139Q ASP* 6.1 1.4 - - - +
143Q PHE* 5.8 3.8 - - - -
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Residues in contact with GLY 35 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313 PHE 3.1 0.4 + - - -
323 GLU 3.1 16.5 + - - -
333 ASP 3.2 1.2 + - - -
343 LEU* 1.3 78.0 - - - +
363 LEU* 1.3 60.4 - - - +
373 GLU* 3.0 19.5 + - - +
1553 ASP* 4.6 2.1 - - - +
136Q LYS* 5.9 1.4 - - - +
139Q ASP* 6.4 1.8 - - - -
140Q LYS* 4.8 13.3 - - - +
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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