Contacts of the helix formed by residues 3 - 34 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14 MET 4.0 0.2 + - - -
24 LEU* 1.3 76.0 - - - +
44 GLU* 1.3 65.1 + - - +
54 ARG* 3.9 2.6 + - - -
64 MET* 3.1 16.0 + - - +
74 LEU* 3.1 22.3 + - - +
1114 GLU* 2.7 35.0 + - - -
1134 ASP* 5.5 1.0 + - - -
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Residues in contact with GLU 4 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24 LEU 4.0 0.2 + - - -
34 SER* 1.3 73.4 - - - +
54 ARG* 1.3 59.9 + - - +
74 LEU* 3.8 10.6 + - + +
84 LYS* 3.5 22.2 + - - +
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Residues in contact with ARG 5 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34 SER* 3.2 2.1 + - - +
44 GLU* 1.3 79.2 - - - +
64 MET* 1.3 59.8 + - - +
84 LYS* 3.6 6.4 + - - +
94 ALA* 3.1 27.1 + - - +
1074 LEU* 4.4 20.8 - - + +
1114 GLU* 3.9 21.8 - - - +
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Residues in contact with MET 6 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24 LEU* 3.8 24.7 - - + -
34 SER* 3.1 25.0 + - - +
54 ARG* 1.3 77.8 - - - +
74 LEU* 1.3 55.1 + - - +
94 ALA* 3.1 4.1 + - - +
104 LEU* 2.8 39.0 + - + +
1044 LEU* 4.2 19.1 - - - +
1074 LEU* 3.9 21.3 - - + +
1084 ALA* 3.7 37.7 - - + +
1114 GLU* 3.9 8.0 + - - +
1134 ASP* 3.8 13.5 - - + +
1164 THR* 3.8 16.8 - - - +
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Residues in contact with LEU 7 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24 LEU* 4.2 22.8 - - + +
34 SER 3.1 14.9 + - - +
44 GLU* 4.0 10.1 - - + +
54 ARG 3.4 0.2 - - - -
64 MET* 1.3 75.1 - - - +
84 LYS* 1.3 55.8 + - - +
104 LEU* 3.5 2.6 + - - +
114 ASN* 2.8 50.0 + - - +
614 ILE* 3.8 22.4 - - + -
664 GLY* 4.3 4.3 - - - -
674 ARG* 3.6 35.9 - - + +
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Residues in contact with LYS 8 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44 GLU 3.5 15.9 + - - +
54 ARG* 3.8 6.5 - - + +
64 MET 3.2 0.6 - - - -
74 LEU* 1.3 78.2 - - - +
94 ALA* 1.3 57.8 + - - +
114 ASN* 3.7 7.4 - - + +
124 ASP* 2.9 56.2 + - - +
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Residues in contact with ALA 9 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 ARG 3.1 17.0 + - - +
64 MET 3.1 6.6 + - - +
84 LYS* 1.3 77.8 - - - +
104 LEU* 1.3 60.1 + - - +
124 ASP* 3.6 9.3 + - - +
134 GLN* 3.3 21.0 + - - +
164 ARG* 4.4 2.6 + - - -
1044 LEU* 3.7 20.1 - - + +
1074 LEU* 3.7 23.8 - - + -
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Residues in contact with LEU 10 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24 LEU* 3.8 27.6 - - + -
64 MET* 2.8 34.3 + - + +
74 LEU* 3.9 3.8 - - - +
94 ALA* 1.3 74.4 - - - +
114 ASN* 1.3 61.4 + - - +
134 GLN* 3.5 4.0 + - - +
144 LEU* 3.1 27.4 + - - +
574 PHE* 3.7 33.4 - - + -
604 TYR* 4.0 19.7 - - + -
614 ILE* 4.0 19.1 - - + +
1044 LEU* 4.2 10.1 - - + -
1164 THR* 4.1 17.9 - - + -
1194 PHE* 4.3 7.2 - - + -
1204 LEU* 5.0 1.1 - - + -
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Residues in contact with ASN 11 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 LEU* 2.8 37.6 + - - +
84 LYS* 3.7 8.1 - - + +
104 LEU* 1.3 75.4 - - - +
124 ASP* 1.3 64.5 - - - +
144 LEU* 3.4 8.5 - - - +
154 ASN* 3.1 21.8 + - - +
614 ILE* 3.9 9.4 - - - +
674 ARG 3.6 17.4 + - - -
684 VAL* 3.4 11.4 - - - +
694 GLU* 3.1 43.6 + - + +
714 ASP* 4.6 5.7 - - - +
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Residues in contact with ASP 12 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84 LYS* 2.9 47.1 + - - +
94 ALA* 3.7 9.7 - - - +
104 LEU 3.3 0.2 - - - -
114 ASN* 1.3 78.5 - - - +
134 GLN* 1.3 57.0 + - - +
154 ASN* 3.2 8.9 + - - +
164 ARG* 2.8 49.7 + - - +
714 ASP* 3.6 15.4 - - - +
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Residues in contact with GLN 13 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 ALA 3.3 7.6 + - - +
104 LEU 3.9 4.5 - - - +
114 ASN 3.3 0.2 - - - -
124 ASP* 1.3 74.9 - - - +
144 LEU* 1.3 61.3 + - - +
154 ASN 3.1 0.2 - - - -
164 ARG* 3.0 27.0 + - - +
174 GLU* 2.8 59.6 + - - +
574 PHE* 3.4 29.4 - - + -
974 ILE* 3.9 8.3 - - - +
1004 SER* 2.9 32.5 + - - +
1014 ILE* 3.7 14.7 - - + +
1044 LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 14 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104 LEU 3.1 12.9 + - - +
114 ASN* 3.4 12.8 - - - +
134 GLN* 1.3 75.2 - - - +
154 ASN* 1.3 58.4 + - - +
174 GLU* 3.6 4.4 + - - +
184 LEU* 3.2 44.7 + - + +
544 ALA* 3.6 19.9 - - + +
574 PHE* 4.0 11.3 - - + -
584 TYR* 3.7 30.7 - - + +
614 ILE* 3.9 18.2 - - + -
684 VAL* 3.9 17.0 - - + -
694 GLU 5.8 1.1 - - - +
704 LEU* 3.8 17.9 - - + -
25M PHE* 4.4 7.4 - - + -
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Residues in contact with ASN 15 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114 ASN 3.1 13.2 + - - +
124 ASP* 3.3 11.9 - - - +
144 LEU* 1.3 76.2 - - - +
164 ARG* 1.3 59.9 + - - +
184 LEU* 3.3 8.2 + - - +
194 TYR* 3.0 27.5 + - - +
704 LEU* 6.4 0.2 - - - -
714 ASP* 3.1 45.9 + - + +
724 GLU 3.2 18.4 + - - +
734 ILE* 4.1 6.1 - - - +
744 PRO* 4.9 5.9 - - - +
22M TYR* 3.8 8.1 + - - -
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Residues in contact with ARG 16 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 ALA 4.4 2.8 + - - -
124 ASP* 2.8 34.5 + - - +
134 GLN* 3.0 57.8 + - - +
154 ASN* 1.3 76.3 - - + +
174 GLU* 1.3 58.4 + - - +
194 TYR* 3.4 8.4 + - - +
204 SER* 3.0 30.4 + - - -
934 HIS* 5.5 0.2 - - - -
964 PHE* 4.1 27.3 - - + -
974 ILE* 4.0 8.4 - - + +
1004 SER* 3.7 25.5 + - - -
1034 GLU* 5.7 2.8 + - - -
1044 LEU* 5.2 1.8 - - - +
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Residues in contact with GLU 17 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134 GLN* 2.8 39.7 + - - +
144 LEU 3.9 4.7 - - - +
164 ARG* 1.3 74.4 - - - +
184 LEU* 1.3 62.8 + - - +
204 SER* 3.4 7.0 + - - -
214 ALA* 3.2 16.6 + - - +
504 GLU* 2.9 49.6 - - - +
534 HIS* 3.6 18.9 + - + +
544 ALA* 4.0 7.6 - - + +
574 PHE* 4.2 15.7 - - + -
974 ILE* 3.9 15.2 - - - +
1014 ILE* 4.4 1.9 - - - +
1234 PHE* 4.1 16.5 - - - -
1274 GLN* 4.6 4.4 + - - -
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Residues in contact with LEU 18 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144 LEU* 3.2 39.7 + - + +
154 ASN* 3.6 8.1 - - - +
164 ARG 3.3 0.4 - - - -
174 GLU* 1.3 75.8 - - - +
194 TYR* 1.3 61.6 + - - +
214 ALA* 3.5 7.0 - - + +
224 TYR* 3.2 20.3 + - - +
504 GLU 5.3 0.2 - - - -
514 ILE* 4.9 21.3 - - + -
544 ALA* 3.8 17.5 - - + -
704 LEU* 4.0 3.1 - - + -
734 ILE* 4.1 17.8 - - + +
22M TYR* 3.6 39.3 - - + +
25M PHE* 4.3 10.3 - - + -
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Residues in contact with TYR 19 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154 ASN* 3.0 17.6 + - - +
164 ARG* 3.8 7.2 - - - +
184 LEU* 1.3 74.8 - - - +
204 SER* 1.3 55.8 + - - +
224 TYR* 2.9 3.2 + - + -
234 LEU* 2.7 49.2 + - + +
734 ILE* 4.0 15.4 - - + +
744 PRO* 3.5 48.2 - - + -
754 LYS 4.4 2.3 + - - -
764 PRO* 3.7 15.6 - - + +
774 PRO* 3.5 27.5 - - - +
934 HIS* 3.7 31.6 - + - -
964 PHE* 6.2 0.2 - + - -
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Residues in contact with SER 20 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164 ARG 3.0 15.6 + - - -
174 GLU* 3.4 12.4 - - - -
184 LEU 3.3 0.2 - - - -
194 TYR* 1.3 76.8 - - - +
214 ALA* 1.3 61.7 + - - +
234 LEU* 3.3 3.7 + - - +
244 TYR* 2.9 40.5 + - - -
504 GLU* 3.5 22.4 + - - -
934 HIS* 3.5 13.8 + - - -
944 GLU* 5.8 0.4 - - - -
974 ILE* 3.4 24.6 - - - +
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Residues in contact with ALA 21 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174 GLU 3.2 6.1 + - - +
184 LEU* 3.5 12.6 - - + +
194 TYR 3.2 0.2 - - - -
204 SER* 1.3 78.7 - - - +
224 TYR* 1.3 56.2 + - - +
254 PHE* 3.1 24.4 + - - +
474 ALA* 3.3 38.1 - - + +
504 GLU* 3.6 14.3 - - + +
514 ILE* 3.7 19.3 - - + -
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Residues in contact with TYR 22 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184 LEU 3.2 11.2 + - - +
194 TYR* 2.9 9.2 + - + +
214 ALA* 1.3 76.7 - - - +
234 LEU* 1.3 60.9 + - - +
254 PHE* 3.5 10.6 + + - +
264 ALA* 3.1 24.3 + - - +
734 ILE* 3.7 25.1 - - + -
744 PRO 3.8 5.4 - - - -
764 PRO* 3.6 28.9 - - + +
15M ASN* 3.8 8.8 + - - -
18M LEU* 3.7 27.9 - - + +
70M LEU* 3.4 32.7 - - + +
71M ASP 2.6 31.0 + - - -
73M ILE* 3.6 22.2 - - + +
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Residues in contact with LEU 23 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194 TYR* 2.7 36.3 + - + +
204 SER* 3.3 5.1 + - - +
224 TYR* 1.3 73.4 - - - +
244 TYR* 1.3 64.3 + - + +
264 ALA* 3.1 5.4 + - - +
274 MET* 3.0 53.3 + - + +
764 PRO* 4.1 7.6 - - + +
774 PRO* 3.9 29.4 - - + -
804 TRP* 4.0 4.7 - - + -
894 ALA* 5.0 1.1 - - + +
934 HIS* 3.6 45.5 - - + +
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Residues in contact with TYR 24 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204 SER* 2.9 35.0 + - - +
214 ALA 4.1 3.6 - - - +
234 LEU* 1.3 77.0 - - + +
254 PHE* 1.3 60.3 + - - +
264 ALA 3.3 0.2 - - - -
274 MET* 3.8 11.6 - - + +
284 ALA* 3.0 25.8 + - - +
424 TRP* 5.8 0.7 - + - -
434 MET* 3.4 46.6 - - + +
464 GLN* 4.1 15.9 - - + -
474 ALA* 4.2 4.0 - - + +
504 GLU* 3.8 30.3 - - + -
904 ALA* 3.8 28.4 + - + +
934 HIS* 4.7 10.5 - + - -
944 GLU* 2.5 35.9 + - - +
1344 VAL* 4.8 5.8 - - + +
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Residues in contact with PHE 25 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214 ALA 3.1 18.4 + - - +
224 TYR* 3.6 16.8 - + + +
244 TYR* 1.3 78.3 - - - +
264 ALA* 1.3 57.1 + - - +
284 ALA* 3.5 8.1 - - + +
294 ALA* 3.1 24.8 + - - +
444 LYS* 4.8 8.7 - - + -
474 ALA* 4.3 7.8 - - + +
14M LEU* 4.4 5.6 - - + -
18M LEU* 4.3 18.4 - - + -
54M ALA* 5.1 4.3 - - + -
55M LEU* 3.9 27.8 - - + -
58M TYR* 3.6 39.9 - + + -
70M LEU* 3.7 34.9 - - + +
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Residues in contact with ALA 26 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224 TYR 3.1 13.1 + - - +
234 LEU* 3.1 10.8 + - - +
254 PHE* 1.3 75.2 - - - +
274 MET* 1.3 59.3 + - - +
294 ALA* 3.4 7.2 + - - +
304 TYR* 3.1 23.9 + - - +
764 PRO* 3.7 23.3 - - + -
774 PRO 3.7 16.8 - - - +
784 LYS* 4.5 4.7 - - - +
804 TRP* 4.0 6.0 - - + -
67M ARG* 5.1 0.2 + - - -
70M LEU* 3.6 11.6 - - + +
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Residues in contact with MET 27 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234 LEU* 3.0 36.3 + - + +
244 TYR* 3.9 14.1 - - - +
254 PHE 3.3 0.2 - - - -
264 ALA* 1.3 72.1 - - - +
284 ALA* 1.3 60.0 + - - +
304 TYR* 3.1 2.5 + - - +
314 PHE* 2.9 43.3 + - + -
434 MET* 3.8 28.5 - - + -
804 TRP* 3.5 40.2 - - + -
864 ALA* 3.5 27.6 - - + +
894 ALA* 4.3 3.6 - - + -
904 ALA* 3.8 24.7 - - + +
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Residues in contact with ALA 28 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244 TYR 3.0 18.8 + - - +
254 PHE* 3.5 11.7 - - + +
274 MET* 1.3 75.9 - - - +
294 ALA* 1.3 56.0 + - - +
314 PHE 3.5 0.2 + - - -
324 GLU* 3.0 23.2 + - - +
404 ALA* 3.4 29.9 - - - +
434 MET* 3.7 9.8 - - + +
444 LYS* 3.8 17.5 - - + +
58M TYR* 3.0 14.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 29 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254 PHE 3.1 13.6 + - - +
264 ALA* 3.5 11.9 - - - +
284 ALA* 1.3 75.2 - - - +
304 TYR* 1.3 62.9 + - - +
324 GLU 3.4 0.3 + - - -
334 ASP* 3.1 14.6 + - - +
58M TYR* 3.6 19.0 + - + -
62M TYR* 2.5 31.4 + - - +
67M ARG* 3.8 10.1 - - - +
68M VAL* 4.2 14.6 - - + +
70M LEU* 5.6 2.0 - - + -
----------------------------------------------------------
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Residues in contact with TYR 30 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264 ALA 3.1 12.4 + - - +
274 MET 3.1 9.1 + - - +
294 ALA* 1.3 77.0 - - - +
314 PHE* 1.3 74.6 + + - +
334 ASP* 3.4 13.6 + - + +
344 LEU* 3.4 42.3 + - + +
784 LYS 4.1 5.2 - - - +
794 GLU* 4.4 8.7 - - + -
804 TRP* 2.9 59.2 + + + -
814 GLU 3.7 2.3 + - - -
824 SER* 3.3 23.6 - - - -
834 PRO* 3.6 1.4 - - - +
864 ALA* 3.9 24.7 - - + -
67M ARG* 3.9 19.2 - - - +
----------------------------------------------------------
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Residues in contact with PHE 31 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274 MET* 2.9 34.7 + - + +
284 ALA 4.0 1.6 - - - +
304 TYR* 1.3 81.6 - + - +
324 GLU* 1.3 62.5 + - - +
344 LEU* 3.3 5.0 + - + +
354 GLY 3.3 3.6 + - - -
364 LEU* 2.8 44.9 + - + +
394 PHE* 3.5 35.9 - + + -
404 ALA 3.8 9.4 - - - +
434 MET* 4.0 31.0 - - + -
834 PRO* 3.7 27.8 - - + -
864 ALA* 3.7 20.9 - - + -
874 PHE* 3.7 21.3 - + - -
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Residues in contact with GLU 32 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284 ALA 3.0 16.6 + - - +
294 ALA 3.6 5.4 - - - +
304 TYR 3.3 0.2 - - - -
314 PHE* 1.3 76.0 - - - +
334 ASP* 1.3 62.1 + - - +
354 GLY* 3.2 13.3 + - - +
364 LEU 4.6 2.2 - - - +
374 GLU* 3.6 29.3 - - - +
404 ALA* 3.4 13.6 - - - +
444 LYS* 2.8 30.4 + - - -
58M TYR* 2.9 19.7 + - - +
59M ASN* 5.9 0.4 - - - -
62M TYR* 3.7 33.9 - - + -
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Residues in contact with ASP 33 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294 ALA 3.1 12.2 + - - +
304 TYR* 3.5 12.1 - - + +
314 PHE 3.2 0.2 - - - -
324 GLU* 1.3 76.0 - - - +
344 LEU* 1.3 63.0 + - - +
354 GLY 3.1 2.7 + - - -
794 GLU* 5.2 4.3 - - - +
62M TYR* 3.7 7.3 - - + -
66M GLY 4.4 9.4 - - - +
67M ARG* 3.5 36.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304 TYR* 3.4 49.9 + - + +
314 PHE* 3.3 9.1 + - + +
324 GLU 3.3 0.4 - - - -
334 ASP* 1.3 80.7 - - + +
354 GLY* 1.3 60.2 + - - +
364 LEU* 3.3 27.9 - - + +
834 PRO* 4.2 11.9 - - + -
139P ASP* 6.1 1.3 - - - +
143P PHE* 5.1 15.6 - - + -
----------------------------------------------------------
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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