Contacts of the helix formed by residues 59 - 84 (chain D) in PDB entry 2FO1
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 ASP 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLY* 1.3 66.1 - - - -
60D LEU* 1.3 56.0 + - - +
61D ASN* 2.9 28.8 + - - +
62D ALA* 3.1 25.5 + - + +
63D PHE* 3.8 4.0 + - - +
1105E ARG* 5.4 2.8 + - - -
1107E ARG* 4.9 2.8 - - - +
1139E ASP* 5.2 1.6 + - - -
1176E ARG* 2.8 29.4 + - - -
1177E ASP* 4.6 6.5 - - - +
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A ALA* 5.0 10.3 - - + -
57D ILE* 3.2 26.5 - - + -
58D GLY 2.3 21.7 + - - +
59D ASP* 1.3 66.7 - - - +
61D ASN* 1.3 63.8 + - - +
62D ALA 3.4 1.3 - - - -
63D PHE* 4.0 7.7 - - + +
64D HIS* 2.3 53.6 + - + +
1105E ARG* 4.6 28.7 - - + +
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Residues in contact with ASN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ASP* 2.9 13.8 + - - +
60D LEU* 1.3 88.0 - - - +
62D ALA* 1.3 60.4 + - - +
64D HIS* 4.3 8.1 + - - +
65D SER* 3.1 27.1 + - - -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ASP* 3.1 19.8 + - + +
61D ASN* 1.3 74.2 - - - +
63D PHE* 1.3 58.4 + - - +
64D HIS 2.9 1.5 + - - -
65D SER* 2.9 10.2 + - - -
66D GLY* 2.7 34.8 + - - -
1138E ARG* 5.1 11.6 + - + +
1175E GLY* 5.5 3.6 - - - -
1176E ARG* 4.2 16.4 - - + +
1177E ASP* 3.8 25.8 - - + +
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Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A ASP 5.4 0.7 - - - -
576A ALA* 3.3 38.8 - - + -
578A ARG* 3.8 33.9 - - + -
59D ASP 3.8 2.8 + - - +
60D LEU* 4.0 13.2 - - + +
62D ALA* 1.3 79.7 - - - +
64D HIS* 1.3 75.8 + + - +
67D GLU* 2.8 34.5 + - + +
1105E ARG* 3.7 35.9 - - - +
1137E ASN* 4.0 18.4 - - + +
1138E ARG* 3.4 41.5 + - - +
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Residues in contact with HIS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A GLU 5.5 5.7 + - - -
576A ALA* 5.8 2.5 - - + -
578A ARG* 5.6 6.3 + - - -
60D LEU* 2.3 45.8 + - + +
61D ASN* 4.3 9.7 + - - +
62D ALA 3.0 1.0 - - - -
63D PHE* 1.3 97.0 - + - +
65D SER* 1.3 56.5 + - - +
66D GLY 2.7 14.4 + - - -
67D GLU* 3.0 7.8 + - + +
68D GLU* 2.8 26.7 + - + +
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Residues in contact with SER 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ASN 3.1 18.3 + - - -
62D ALA* 2.9 17.3 + - - -
64D HIS* 1.3 76.5 - - - +
66D GLY* 1.3 51.1 + - - +
68D GLU* 3.1 14.2 - - - +
69D LEU* 2.8 36.8 - - - +
1175E GLY* 5.0 4.9 - - - -
1176E ARG* 4.4 13.2 - - - +
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ALA 2.7 14.6 + - - -
63D PHE 3.6 1.8 - - - -
64D HIS 2.7 0.6 - - - -
65D SER* 1.3 76.9 - - - +
67D GLU* 1.3 53.0 + - - -
68D GLU 2.4 16.6 + - - -
69D LEU* 2.8 17.8 + - - +
70D HIS* 3.0 14.8 + - - -
1138E ARG* 3.8 10.5 - - - -
1174E GLU 4.5 14.6 - - - -
1175E GLY* 4.9 5.2 - - - -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ARG* 3.2 49.9 + - - +
602A THR* 5.2 6.2 + - - +
610A HIS* 4.0 20.7 + - - +
63D PHE* 2.8 32.3 + - + +
64D HIS* 3.0 9.4 + - + +
66D GLY* 1.3 70.0 - - - +
68D GLU* 1.3 61.3 + - - +
70D HIS* 4.1 12.4 - - - +
71D ARG* 3.3 21.3 + - - +
1138E ARG* 3.1 26.1 + - - +
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Residues in contact with GLU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D HIS* 2.8 14.4 + - + +
65D SER* 3.1 18.6 - - - +
66D GLY 2.4 5.3 + - - -
67D GLU* 1.3 71.0 - - - +
69D LEU* 1.3 74.2 + - + +
70D HIS 2.7 3.3 + - - -
71D ARG* 2.7 10.6 + - - +
72D GLN* 2.7 39.8 + - + +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D SER* 2.8 28.3 - - - +
66D GLY* 2.8 8.8 + - - +
68D GLU* 1.3 81.2 - - + +
70D HIS* 1.3 59.1 + - - +
72D GLN* 2.8 29.5 - - + +
73D ARG* 3.1 22.3 + - - +
1174E GLU* 3.2 43.3 - - + +
1175E GLY* 4.3 12.8 - - - +
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Residues in contact with HIS 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A THR* 4.0 12.9 - - + +
603A PHE 4.9 0.3 - - - +
604A ARG* 3.0 44.6 + - - +
610A HIS* 5.1 1.8 - - - +
66D GLY 3.0 13.1 + - - +
67D GLU* 4.3 14.8 - - - +
68D GLU 2.7 4.8 + - - -
69D LEU* 1.3 70.1 - - - +
71D ARG* 1.3 63.7 + - - +
72D GLN 2.8 4.9 + - - -
73D ARG* 3.0 6.1 + - - +
74D SER* 3.0 21.5 + - - -
1138E ARG* 3.7 27.0 + - - -
1173E ASN* 3.9 15.7 + - - +
1174E GLU* 3.0 50.4 + - + +
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Residues in contact with ARG 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A GLU* 3.7 39.9 + - + +
602A THR* 4.5 13.2 - - - +
67D GLU 3.3 17.9 + - - +
68D GLU* 2.7 11.6 + - - +
70D HIS* 1.3 76.4 - - - +
72D GLN* 1.3 68.8 + - - +
74D SER* 3.3 8.8 + - - -
75D GLU* 3.2 47.5 + - + +
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Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLU* 2.7 30.1 + - + +
69D LEU* 2.8 25.6 - - + +
70D HIS 2.8 0.6 - - - -
71D ARG* 1.3 86.9 - - - +
73D ARG* 1.3 65.9 + - - +
75D GLU* 3.5 4.6 + - - +
76D LEU* 3.3 20.3 + - - +
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Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A PHE 4.7 2.0 - - - +
604A ARG* 5.2 7.0 - - - +
69D LEU* 3.3 20.0 + - - +
70D HIS* 3.0 8.1 + - - +
72D GLN* 1.3 79.8 - - - +
74D SER* 1.3 58.1 + - - +
76D LEU* 3.7 15.6 - - + +
77D ALA* 2.7 40.6 + - + +
1174E GLU* 3.1 36.0 + - - +
1217E VAL* 5.0 15.9 - - + -
1218E SER* 2.3 38.9 + - - +
1219E ASN 5.3 0.2 - - - +
1220E MSE 5.8 1.6 - - - +
1253E ARG* 5.0 9.4 - - - +
1255E GLU* 4.3 11.8 + - - -
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A THR 4.0 0.5 + - - -
602A THR* 3.7 15.4 - - - -
603A PHE* 3.2 32.3 + - - +
70D HIS 3.0 11.5 + - - -
71D ARG* 3.6 11.4 - - - -
72D GLN 3.3 0.2 - - - -
73D ARG* 1.3 78.8 - - - +
75D GLU* 1.3 58.2 + - - +
77D ALA* 3.7 2.8 - - - +
78D ARG* 2.9 55.3 + - - +
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Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A GLU* 6.0 2.0 - - - +
71D ARG* 3.2 36.5 + - + +
72D GLN* 3.9 4.9 - - - +
74D SER* 1.3 79.6 + - - +
76D LEU* 1.3 64.7 + - - +
78D ARG* 3.0 32.1 + - - +
79D ALA* 3.1 12.5 + - - +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLN 3.3 14.9 + - - +
73D ARG* 3.7 15.7 - - + +
75D GLU* 1.3 77.3 - - - +
77D ALA* 1.3 62.8 + - + +
79D ALA* 3.0 27.7 + - + +
80D ASN* 3.0 29.5 + - - +
1253E ARG* 3.2 39.0 - - - +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PRO* 4.1 6.5 - - + +
603A PHE* 4.3 24.5 - - + -
604A ARG 5.8 0.2 - - - +
73D ARG* 2.7 24.2 + - + +
74D SER 3.7 2.9 - - - +
76D LEU* 1.3 75.5 - - + +
78D ARG* 1.3 63.1 + - - +
79D ALA 3.1 1.8 - - - -
80D ASN* 3.4 13.3 - - - +
81D TYR* 3.4 22.0 + - - +
1217E VAL* 6.5 2.0 - - + -
1253E ARG* 5.0 3.8 - - - +
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Residues in contact with ARG 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A PRO* 2.4 49.8 + - - +
589A ASN* 4.5 4.2 - - - +
590A LEU 3.6 16.4 + - - +
591A LYS* 5.7 1.0 - - - +
600A GLU* 5.3 3.0 + - - -
601A THR* 3.1 24.9 + - - +
603A PHE* 4.1 5.1 - - - +
645A ASP* 5.9 1.6 - - - -
74D SER* 2.9 39.6 + - - +
75D GLU* 3.0 22.2 + - - +
77D ALA* 1.3 76.9 - - - +
79D ALA* 1.3 64.9 + - - +
81D TYR* 4.2 2.1 - - - +
82D GLU* 3.2 20.3 + - - +
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D GLU 3.1 9.2 + - - +
76D LEU* 3.0 16.4 - - + +
78D ARG* 1.3 75.6 - - - +
80D ASN* 1.3 59.4 + - - +
82D GLU* 2.5 32.1 + - - +
83D LYS* 2.9 11.1 + - - +
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Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 3.0 48.5 + - - +
77D ALA* 3.4 10.0 - - - +
79D ALA* 1.3 79.4 - - - +
81D TYR* 1.3 61.6 - - - +
83D LYS* 3.0 45.1 + - - +
84D ALA* 3.5 2.6 + - - +
1252E GLY 5.8 0.2 + - - -
1253E ARG* 4.2 6.9 - - - +
1286E HIS* 5.9 7.6 - - + -
1288E ASN* 5.3 5.5 + - - -
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Residues in contact with TYR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A PRO* 4.6 11.8 - - - +
587A LYS* 3.9 32.4 - - + +
588A PRO* 4.5 16.6 - - + -
589A ASN* 3.1 43.4 + - + -
77D ALA 3.4 14.0 + - - +
78D ARG 4.2 3.6 - - - +
79D ALA 2.9 1.2 + - - -
80D ASN* 1.3 74.6 - - - +
82D GLU* 1.3 63.0 + - - +
83D LYS 3.0 5.4 - - - -
84D ALA* 4.1 0.6 - - - -
85D ARG* 3.2 45.4 + - + +
88D MET* 4.7 21.2 - - + +
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A ASN* 6.1 0.5 - - - +
645A ASP* 5.3 4.5 - - - +
78D ARG* 3.2 13.2 + - + +
79D ALA* 2.5 19.4 + - - +
81D TYR* 1.3 76.3 - - - +
83D LYS* 1.3 60.0 + - - +
85D ARG* 2.8 38.6 + - - +
86D PRO* 4.3 2.9 - - - +
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Residues in contact with LYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ALA 2.9 6.2 + - - +
80D ASN* 3.0 33.1 + - - +
81D TYR 3.0 1.6 - - - -
82D GLU* 1.3 74.6 - - - +
84D ALA* 1.3 90.5 + - + +
85D ARG 2.8 9.5 + - - -
86D PRO* 3.0 18.5 - - - +
87D GLU* 5.2 1.8 - - - +
1285E ASN 4.4 10.2 + - - -
1286E HIS* 6.0 0.2 - - - +
1287E HIS* 5.4 7.6 - - + -
1288E ASN* 4.4 20.2 + - - +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ASN 3.5 3.3 + - - +
81D TYR* 4.1 1.3 - - - +
83D LYS* 1.3 98.5 - - - +
85D ARG* 1.3 54.2 + - - +
86D PRO* 3.3 2.2 - - - -
87D GLU* 2.9 28.0 + - - +
88D MET* 2.7 36.6 + - - +
1284E ASN 5.4 0.4 - - - +
1285E ASN* 3.8 22.2 - - + +
1287E HIS* 5.4 0.4 - - - +
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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