Contacts of the helix formed by residues 42 - 71 (chain H) in PDB entry 3A68
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 VAL 42 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 3.5 2.6 + - - +
40H LYS* 4.0 3.8 - - - -
41H TYR* 1.3 81.4 - - - +
43H ASP* 1.3 66.1 + - - +
44H GLU* 3.8 9.2 - - + +
45H SER* 3.0 30.3 + - - +
46H GLU 3.1 9.7 + - - -
157H ASN* 3.7 35.4 - - + +
159H ASP* 4.9 0.4 + - - -
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Residues in contact with ASP 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 3.0 24.7 + - - +
42H VAL* 1.3 73.8 - - - +
44H GLU* 1.3 57.2 + - - +
46H GLU* 3.2 12.2 + - - +
47H SER* 2.8 36.5 + - - +
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Residues in contact with GLU 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H VAL* 3.2 6.4 - - + +
43H ASP* 1.3 78.1 - - - +
45H SER* 1.3 57.7 + - - +
47H SER* 3.7 6.8 - - - -
48H ALA* 3.0 27.7 + - - +
153H VAL* 3.7 20.2 - - + +
156H LYS* 6.3 0.7 - - - -
157H ASN* 2.8 32.8 + - - +
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Residues in contact with SER 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H TYR* 4.0 17.3 - - - -
42H VAL* 3.0 23.1 + - - +
44H GLU* 1.3 76.5 - - - +
46H GLU* 1.3 66.4 + - - +
48H ALA* 3.2 3.2 + - - +
49H VAL* 3.0 28.2 + - - +
153H VAL* 4.1 12.5 + - - +
157H ASN* 4.1 12.0 - - - +
159H ASP* 4.2 9.6 + - - +
162H LEU* 3.9 23.8 - - - +
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 3.7 26.1 + - - +
41H TYR* 3.8 21.6 - - + -
42H VAL 3.1 11.0 + - - +
43H ASP* 3.5 17.7 - - - +
45H SER* 1.3 78.0 - - - +
47H SER* 1.3 63.7 + - - +
49H VAL 3.4 0.3 + - - -
50H ASN* 3.1 16.5 + - - +
102H GLN* 3.0 36.7 + - - +
107H GLY* 3.5 4.3 - - - -
108H LYS* 2.7 35.5 + - - +
110H LYS* 5.5 2.0 + - - -
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Residues in contact with SER 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ASP* 2.8 24.7 + - - +
44H GLU* 3.7 7.4 - - - -
46H GLU* 1.3 76.7 + - - +
48H ALA* 1.3 57.2 + - - +
50H ASN* 3.2 10.7 + - - +
51H GLU* 2.9 27.1 + - - +
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H GLU 3.0 18.5 + - - +
45H SER 3.2 3.1 + - - +
47H SER* 1.3 76.0 - - - +
49H VAL* 1.3 57.6 + - - +
51H GLU* 3.2 8.4 + - - +
52H GLN* 3.0 24.4 + - - +
150H LEU* 3.5 28.7 - - + +
153H VAL* 3.8 25.8 - - + -
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Residues in contact with VAL 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H TYR* 3.3 20.4 - - - +
45H SER 3.0 15.4 + - - +
46H GLU 3.7 5.2 - - - +
48H ALA* 1.3 75.5 - - - +
50H ASN* 1.3 63.6 + - - +
52H GLN* 3.2 5.9 + - - +
53H ILE* 3.0 25.3 + - + +
98H LEU* 3.8 32.9 - - + +
101H TYR* 4.6 3.8 - - + -
102H GLN* 3.7 20.9 - - + +
150H LEU* 4.1 12.1 - - + -
162H LEU* 4.0 26.2 - - + -
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Residues in contact with ASN 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H GLU* 3.1 17.2 + - - +
47H SER* 3.2 11.1 + - - +
49H VAL* 1.3 77.2 - - - +
51H GLU* 1.3 61.9 + - - +
53H ILE* 3.4 15.0 + - - +
54H ASN* 3.2 20.1 + - - +
102H GLN* 3.1 19.0 + - - +
108H LYS 3.1 21.2 + - - -
109H VAL* 3.4 4.3 - - - -
110H LYS* 3.0 48.4 + - + +
112H GLN* 5.6 4.3 - - + +
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Residues in contact with GLU 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.5 40.7 - - - +
15A PHE* 3.8 17.3 - - - +
47H SER 2.9 12.3 + - - +
48H ALA* 3.4 12.8 - - - +
49H VAL 3.2 0.2 - - - -
50H ASN* 1.3 76.5 - - - +
52H GLN* 1.3 60.2 + - - +
54H ASN* 3.1 8.9 + - - +
55H VAL* 3.0 33.4 + - + +
112H GLN* 6.0 1.0 - - - +
146H LYS* 5.0 8.3 - - + -
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Residues in contact with GLN 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ALA 3.0 16.2 + - - +
49H VAL* 3.8 4.3 - - - +
51H GLU* 1.3 74.1 - - - +
53H ILE* 1.3 66.9 + - - +
55H VAL* 3.1 16.8 + - - +
56H GLU* 2.9 45.3 + - - +
98H LEU* 3.5 22.2 - - + -
143H THR* 4.0 2.8 - - - +
146H LYS* 3.4 37.8 + - - +
147H LEU* 3.4 27.0 - - + +
150H LEU* 3.9 18.2 - - + +
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Residues in contact with ILE 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H VAL* 3.0 23.2 + - + +
50H ASN* 3.5 25.8 - - - +
51H GLU 3.3 0.2 - - - -
52H GLN* 1.3 76.0 - - - +
54H ASN* 1.3 59.1 + - - +
56H GLU 3.4 0.2 + - - -
57H TYR* 3.0 29.3 + - + +
95H ALA* 3.9 14.4 - - + +
98H LEU* 3.5 27.8 - - + +
99H MET* 3.7 38.1 - - + +
102H GLN* 4.8 0.4 - - + -
109H VAL* 4.4 9.0 - - + -
110H LYS 5.9 1.1 - - - +
111H LEU* 3.7 28.7 - - + -
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Residues in contact with ASN 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.9 9.8 - - + +
15A PHE* 3.9 17.7 + - - +
61D TYR* 4.1 6.7 + - - -
50H ASN 3.2 8.5 + - - +
51H GLU* 3.1 15.9 + - - +
53H ILE* 1.3 79.3 - - - +
55H VAL* 1.3 64.3 + - - +
57H TYR* 3.9 3.7 - - - +
58H ASN* 2.9 49.5 + - - +
112H GLN* 3.5 33.3 + - + +
113H SER 3.0 26.2 + - - +
114H ILE* 4.2 2.6 - - - +
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Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.1 29.2 - - + -
51H GLU* 3.0 33.8 + - + +
52H GLN* 3.1 33.0 + - - +
54H ASN* 1.3 76.4 - - - +
56H GLU* 1.3 63.8 + - - +
58H ASN* 3.3 4.2 + - - +
59H VAL* 3.0 22.8 + - + +
143H THR* 4.3 20.6 - - + +
146H LYS* 4.1 26.9 - - + -
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Residues in contact with GLU 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLN* 2.9 41.4 + - - +
55H VAL* 1.3 73.9 - - - +
57H TYR* 1.3 64.8 + - - +
59H VAL* 3.2 4.5 + - - +
60H SER* 2.9 22.5 + - - -
91H GLU* 3.1 16.7 - - - +
94H HIS* 3.6 13.2 - - + +
95H ALA* 3.8 21.8 - - + +
98H LEU* 3.9 17.0 - - + -
143H THR* 3.7 13.2 - - - +
147H LEU* 3.9 10.7 - - - +
170H TYR* 4.2 7.2 - - - -
214H CA 2.4 28.7 - - - -
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Residues in contact with TYR 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D TYR* 5.3 13.5 - + - -
60D SER* 5.0 2.4 + - - -
61D TYR* 3.6 40.9 - + - +
64D HIS* 2.7 42.0 + + - +
88D SER* 4.6 1.7 + - - -
53H ILE* 3.0 24.3 + - + +
54H ASN* 3.9 6.5 - - - +
56H GLU* 1.3 76.0 - - - +
58H ASN* 1.3 62.8 + - - +
60H SER* 3.2 13.1 + - - -
61H TYR* 3.0 22.0 + + + +
92H ARG* 3.7 22.9 + - + -
95H ALA* 3.7 21.5 - - + +
99H MET* 4.6 6.1 - - - -
111H LEU* 4.6 2.0 - - + -
114H ILE* 3.5 26.2 - - + -
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Residues in contact with ASN 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.0 26.6 + - + -
17A PRO* 4.3 7.2 - - + +
54H ASN* 2.9 53.3 + - - +
55H VAL 3.6 4.3 - - - +
57H TYR* 1.3 77.6 - - - +
59H VAL* 1.3 61.8 + - - +
61H TYR* 3.1 3.3 + - - +
62H VAL* 2.9 28.4 + - - +
113H SER 4.0 6.1 + - - -
114H ILE* 3.1 28.1 - - - +
115H VAL* 3.4 23.2 + - - +
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Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 5.3 2.9 - - + -
55H VAL* 3.0 19.2 + - + +
56H GLU* 3.2 4.0 + - - +
58H ASN* 1.3 76.0 - - + +
60H SER* 1.3 63.7 + - - +
62H VAL* 3.3 1.7 + - - +
63H TYR* 2.9 51.7 + - + +
91H GLU* 3.5 20.6 - - - +
139H LEU* 3.7 35.7 - - + -
140H GLU* 4.4 3.6 - - - +
143H THR* 3.5 24.0 - - + +
----------------------------------------------------------
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Residues in contact with SER 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D TYR* 4.9 2.6 + - - -
92D ARG* 4.5 4.3 + - - -
56H GLU 2.9 10.0 + - - -
57H TYR* 3.3 16.5 - - - -
59H VAL* 1.3 78.5 - - - +
61H TYR* 1.3 55.5 + - - +
64H HIS* 3.1 14.7 + - - +
88H SER* 2.7 50.7 + - - +
91H GLU* 3.5 19.0 - - - +
92H ARG* 3.7 18.7 - - - +
----------------------------------------------------------
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Residues in contact with TYR 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ILE* 6.0 0.2 - - - +
54D ASN* 4.1 5.2 + - - -
57D TYR* 3.6 45.8 - + - +
111D LEU* 3.6 20.5 - - + +
112D GLN 2.6 38.0 + - - -
113D SER* 5.1 0.2 - - - -
114D ILE* 3.7 22.9 - - + +
57H TYR* 3.0 14.6 + + + +
58H ASN 3.1 7.8 + - - +
60H SER* 1.3 74.7 - - - +
62H VAL* 1.3 65.7 + - + +
64H HIS* 3.1 5.9 + - - +
65H ALA* 3.0 21.5 + - - +
114H ILE* 3.6 28.0 - - + -
115H VAL 3.8 4.5 - - - -
117H PRO* 3.6 31.1 - - + +
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Residues in contact with VAL 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO* 4.0 20.6 - - + -
18A PHE* 3.8 39.3 - - + -
58H ASN 2.9 21.8 + - - +
59H VAL 3.7 4.0 - - - +
61H TYR* 1.3 76.6 - - + +
63H TYR* 1.3 57.3 + - + +
65H ALA* 3.1 4.3 + - - +
66H MET* 2.9 44.0 + - + +
117H PRO* 4.2 12.1 - - + -
121H PHE* 5.1 0.9 - - + -
139H LEU* 3.8 23.6 - - + -
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Residues in contact with TYR 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H VAL* 2.9 35.1 + - + +
60H SER 3.8 4.3 - - - +
62H VAL* 1.3 77.0 - - - +
64H HIS* 1.3 57.8 + - - +
66H MET* 3.2 11.5 + - + -
67H PHE* 2.9 25.8 + - - +
83H PHE* 6.0 1.8 - + - -
84H PHE* 3.5 43.5 - + - +
87H SER* 3.7 21.3 - - - -
88H SER 3.8 3.8 - - - +
91H GLU* 3.6 20.4 - - + -
136H ALA* 3.8 30.6 + - + +
139H LEU* 4.5 8.9 - - + +
140H GLU* 2.4 42.5 + - - +
181H ILE* 3.9 4.6 - - + +
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Residues in contact with HIS 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D TYR* 2.6 35.3 + + - +
92D ARG* 3.5 23.0 + - + -
96D GLU* 2.7 38.5 + - + +
99D MET* 3.7 20.5 - - + +
111D LEU* 4.1 8.7 - - + -
60H SER 3.1 8.0 + - - +
61H TYR 3.1 8.9 + - - +
63H TYR* 1.3 76.3 - - - +
65H ALA* 1.3 58.5 + - - +
67H PHE* 3.3 26.0 + + + +
68H ALA* 2.9 28.8 + - - +
85H LYS* 5.1 2.5 - - - -
88H SER* 3.5 18.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU* 3.6 18.3 - - + +
61H TYR 3.0 11.4 + - - +
62H VAL 3.1 9.2 + - - +
64H HIS* 1.3 78.3 - - - +
66H MET* 1.3 61.3 + - - +
68H ALA* 3.3 6.8 + - - +
69H TYR* 3.0 22.5 + - - +
117H PRO* 3.9 11.0 - - + -
118H LEU 3.4 24.7 - - - +
119H SER* 4.5 4.3 - - - +
121H PHE* 3.7 7.4 - - + -
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Residues in contact with MET 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 5.3 1.3 - - + -
62H VAL* 2.9 31.0 + - + +
63H TYR* 3.2 18.8 + - + +
65H ALA* 1.3 73.5 - - - +
67H PHE* 1.3 65.4 + - - +
69H TYR* 3.2 1.7 + - - +
70H PHE* 3.0 32.2 + - + -
84H PHE* 3.6 44.4 - - + -
121H PHE* 3.5 40.8 - - + -
132H ALA* 4.0 8.5 - - + +
135H LEU* 3.8 26.9 - - + -
136H ALA* 4.3 6.3 - - - +
139H LEU* 5.5 1.3 - - + -
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Residues in contact with PHE 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLU* 4.3 17.7 - - + -
99D MET* 4.1 14.6 - - + -
100D GLU* 3.9 25.4 - - + -
103D ASN* 5.6 0.2 - - - -
63H TYR 2.9 14.2 + - - +
64H HIS* 3.4 25.6 - + - +
66H MET* 1.3 76.3 - - - +
68H ALA* 1.3 69.1 + - - +
70H PHE 3.3 1.9 + - - -
71H ASP* 3.0 48.0 + - + +
81H ALA* 3.4 28.6 - - + +
84H PHE* 3.6 7.5 - - - +
85H LYS* 3.7 45.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D MET* 3.9 9.6 - - + -
103D ASN* 3.0 27.8 + - - +
109D VAL* 3.7 39.3 - - + +
64H HIS 2.9 17.1 + - - +
65H ALA* 3.6 7.9 - - - +
66H MET 3.2 0.2 - - - -
67H PHE* 1.3 82.3 - - + +
69H TYR* 1.3 62.0 + - - +
71H ASP 3.7 0.2 + - - -
72H ARG* 3.7 8.9 + - - +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLN* 6.1 0.3 - - - +
65H ALA 3.0 9.1 + - - +
66H MET 3.6 6.7 - - - +
67H PHE 3.2 0.4 - - - -
68H ALA* 1.3 77.0 - - - +
70H PHE* 1.3 91.4 - + - +
71H ASP 3.1 0.9 - - - -
72H ARG* 3.1 65.1 + - - +
75H VAL* 3.6 24.5 - - + +
119H SER 3.6 7.4 + - - +
120H ASP* 3.9 2.9 - - - -
121H PHE* 3.5 40.6 - + + -
122H ASP* 3.5 31.0 + - - +
128H ASP* 3.9 17.0 + - + -
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Residues in contact with PHE 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H MET* 3.0 31.9 + - + +
67H PHE 3.8 0.2 - - - -
69H TYR* 1.3 98.2 - + - +
71H ASP* 1.3 57.9 + - - +
72H ARG 3.2 1.5 + - - -
75H VAL* 3.6 17.7 - - + -
76H ALA* 3.8 4.9 + - - -
77H LEU* 3.4 39.7 + - + +
78H ARG* 5.2 0.3 - - - -
80H LEU* 3.7 20.0 - - + -
81H ALA* 3.8 23.8 - - - +
84H PHE* 3.7 20.9 - + - -
121H PHE* 4.7 4.0 - - + -
128H ASP* 3.7 26.5 - - + -
132H ALA* 3.4 35.2 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLU* 4.1 16.5 - - - +
103D ASN* 2.9 33.9 + - - +
67H PHE* 3.0 40.7 + - + +
69H TYR 3.1 0.4 - - - -
70H PHE* 1.3 75.6 - - - +
72H ARG* 1.3 66.2 + - - +
76H ALA* 5.7 0.2 - - - -
81H ALA* 4.0 7.6 - - + +
179I LYS* 3.1 34.0 + - - -
183I GLU* 4.5 2.7 - - - +
----------------------------------------------------------
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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