Contacts of the helix formed by residues 42 - 71 (chain U) 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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U ARG* 3.5 3.6 + - - +
40U LYS* 4.8 5.2 - - - +
41U TYR* 1.3 81.3 - - - +
43U ASP* 1.3 64.4 + - - +
44U GLU* 3.8 5.4 - - + +
45U SER* 2.9 29.8 + - - +
46U GLU 3.0 10.2 + - - -
157U ASN* 3.5 45.3 - - + +
159U ASP* 4.9 0.6 + - - -
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Residues in contact with ASP 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U ARG* 3.0 24.8 + - - +
42U VAL* 1.3 73.7 - - - +
44U GLU* 1.3 56.8 + - - +
46U GLU* 3.4 12.9 + - - +
47U SER* 2.9 31.6 + - - -
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Residues in contact with GLU 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42U VAL* 3.2 5.4 - - + +
43U ASP* 1.3 77.6 - - - +
45U SER* 1.3 57.7 + - - +
47U SER* 3.5 5.8 + - - -
48U ALA* 3.0 28.6 + - - +
153U VAL* 3.7 11.7 - - + +
156U LYS* 3.3 28.2 + - - +
157U ASN* 3.0 28.0 + - - +
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Residues in contact with SER 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41U TYR* 4.1 14.8 - - - -
42U VAL* 2.9 24.8 + - - +
44U GLU* 1.3 76.7 - - - +
46U GLU* 1.3 60.7 + - - +
48U ALA* 3.1 3.1 + - - +
49U VAL* 2.9 33.8 + - - +
153U VAL* 4.1 11.1 + - - +
157U ASN* 3.8 15.2 + - - +
159U ASP* 4.2 7.9 + - - +
162U LEU* 3.9 22.9 - - - +
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Residues in contact with GLU 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U ARG* 3.2 29.6 + - - +
41U TYR* 3.7 21.0 + - + -
42U VAL 3.0 11.2 + - - +
43U ASP* 3.4 17.1 - - - +
45U SER* 1.3 76.1 - - - +
47U SER* 1.3 63.6 + - - +
49U VAL 3.3 0.2 + - - -
50U ASN* 3.1 13.0 + - - +
102U GLN* 3.0 37.5 + - - +
107U GLY* 3.6 2.9 - - - -
108U LYS* 2.8 37.1 + - - +
110U LYS* 5.4 3.9 + - - -
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Residues in contact with SER 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43U ASP 2.9 18.5 + - - -
44U GLU* 3.7 7.0 - - - -
46U GLU* 1.3 78.5 - - - +
48U ALA* 1.3 56.2 + - - +
50U ASN* 3.1 11.5 + - - +
51U GLU* 2.9 27.8 + - - +
112U GLN* 5.2 0.5 - - - +
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Residues in contact with ALA 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44U GLU 3.0 18.8 + - - +
45U SER 3.1 4.7 + - - +
47U SER* 1.3 72.5 - - - +
49U VAL* 1.3 65.4 + - - +
51U GLU* 3.2 9.7 + - - +
52U GLN* 3.0 23.9 + - - +
150U LEU* 3.6 22.3 - - + +
153U VAL* 3.9 25.4 - - + -
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Residues in contact with VAL 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41U TYR* 3.4 20.6 - - - +
45U SER 2.9 16.4 + - - +
46U GLU 3.7 4.3 - - - +
48U ALA* 1.3 76.4 - - - +
50U ASN* 1.3 62.9 + - - +
52U GLN* 3.2 5.3 + - - +
53U ILE* 2.9 26.3 + - + +
98U LEU* 3.8 31.1 - - + +
101U TYR* 4.7 3.8 - - + -
102U GLN* 3.6 22.7 - - + +
150U LEU* 3.9 19.5 - - + -
162U LEU* 3.9 20.4 - - + -
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Residues in contact with ASN 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U GLU* 3.1 17.4 + - - +
47U SER* 3.1 11.3 + - - +
49U VAL* 1.3 76.6 - - - +
51U GLU* 1.3 61.3 + - - +
53U ILE* 3.4 15.8 + - - +
54U ASN* 3.2 18.0 + - - +
102U GLN* 3.0 17.8 + - - +
108U LYS 3.1 20.0 + - - -
109U VAL* 3.4 4.3 - - - -
110U LYS* 3.0 48.7 + - + +
112U GLN* 3.8 15.6 - - - +
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Residues in contact with GLU 51 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ILE* 3.9 27.9 - - - +
15P PHE* 4.2 11.3 - - - +
47U SER* 2.9 13.5 + - - +
48U ALA* 3.2 12.5 + - - +
50U ASN* 1.3 76.0 - - - +
52U GLN* 1.3 60.4 + - - +
54U ASN* 3.1 6.3 + - - +
55U VAL* 3.0 40.5 + - + +
112U GLN* 3.6 22.1 + - - +
146U LYS* 4.8 10.5 + - + -
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Residues in contact with GLN 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48U ALA 3.0 15.2 + - - +
49U VAL 3.2 4.0 + - - +
51U GLU* 1.3 74.8 - - - +
53U ILE* 1.3 66.3 + - - +
55U VAL* 3.1 16.5 + - - +
56U GLU* 2.8 58.8 + - - +
98U LEU* 3.6 20.9 - - + -
143U THR* 4.0 3.0 - - - +
146U LYS* 3.3 29.6 - - - +
147U LEU* 3.3 31.1 - - + +
150U LEU* 3.9 18.2 - - + -
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Residues in contact with ILE 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49U VAL* 2.9 24.7 + - + +
50U ASN* 3.5 26.5 - - - +
52U GLN* 1.3 75.8 - - - +
54U ASN* 1.3 58.8 + - - +
56U GLU* 3.4 2.4 + - - +
57U TYR* 2.9 32.9 + - + +
95U ALA* 3.9 9.2 - - + +
98U LEU* 3.6 28.9 - - + +
99U MET* 3.8 38.1 - - + +
102U GLN* 4.8 0.2 - - + -
109U VAL* 4.5 8.3 - - + -
110U LYS 5.8 0.7 - - - +
111U LEU* 3.7 29.4 - - + -
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Residues in contact with ASN 54 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ILE 5.3 0.9 + - - -
15P PHE* 3.6 21.5 + - - +
61Q TYR* 4.1 6.9 + - - -
50U ASN 3.2 4.9 + - - +
51U GLU* 3.1 8.3 + - - +
52U GLN 3.1 0.6 - - - -
53U ILE* 1.3 79.0 - - - +
55U VAL* 1.3 60.4 + - - +
57U TYR* 3.9 4.0 - - - +
58U ASN* 2.9 51.7 + - - +
112U GLN* 3.3 49.3 + - + +
113U SER 3.0 26.2 + - - +
114U ILE* 4.3 3.0 - - - +
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Residues in contact with VAL 55 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P PHE* 3.9 28.0 - - + -
51U GLU* 3.0 34.2 + - + +
52U GLN* 3.1 33.6 + - - +
54U ASN* 1.3 75.5 - - - +
56U GLU* 1.3 63.0 + - - +
58U ASN* 3.2 3.6 + - - +
59U VAL* 3.0 24.6 + - + +
142U LEU* 6.0 0.2 - - + -
143U THR* 4.3 18.8 - - + +
146U LYS* 4.0 28.0 - - + -
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Residues in contact with GLU 56 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52U GLN* 2.8 43.6 + - - +
55U VAL* 1.3 76.0 - - - +
57U TYR* 1.3 59.1 + - - +
59U VAL* 3.3 3.4 + - - +
60U SER* 2.9 28.1 + - - -
91U GLU* 3.2 15.6 - - - +
94U HIS* 3.6 11.5 - - + +
95U ALA* 3.7 24.5 - - + +
98U LEU* 4.0 15.3 - - + -
143U THR* 3.7 11.7 - - - +
147U LEU* 3.8 10.4 - - - +
170U TYR* 4.3 5.9 - - - -
213U CA 2.5 27.9 - - - -
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Residues in contact with TYR 57 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 5.3 13.7 - + - -
60Q SER* 4.9 2.9 + - - -
61Q TYR* 3.5 39.1 - + - +
64Q HIS* 2.7 41.1 + + - +
88Q SER* 4.6 1.2 + - - -
114Q ILE* 6.4 0.2 - - + -
53U ILE* 2.9 24.2 + - + +
54U ASN* 3.9 7.6 - - - +
55U VAL 3.3 0.2 - - - -
56U GLU* 1.3 76.9 - - - +
58U ASN* 1.3 58.0 + - - +
60U SER* 3.3 12.6 + - - -
61U TYR* 3.0 27.5 + - + +
92U ARG* 3.8 23.8 + - + -
95U ALA* 3.8 22.6 - - + +
99U MET* 4.4 7.0 - - - -
111U LEU* 4.5 2.2 - - + -
114U ILE* 3.5 26.1 - - + +
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Residues in contact with ASN 58 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P PHE* 3.7 24.2 + - + +
17P PRO* 3.8 9.9 - - + +
54U ASN* 2.9 46.7 + - - +
55U VAL 3.2 4.5 + - - +
57U TYR* 1.3 74.7 - - - +
59U VAL* 1.3 59.4 + - - +
61U TYR* 3.1 7.4 + - - +
62U VAL* 2.9 34.0 + - - +
113U SER 4.1 4.3 - - - +
114U ILE* 3.5 22.7 - - - +
115U VAL* 3.5 28.5 + - - +
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Residues in contact with VAL 59 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P PHE* 5.1 6.5 - - + -
17P PRO* 6.0 0.4 - - + -
55U VAL* 3.0 26.3 + - + +
56U GLU* 3.7 1.1 - - - +
58U ASN* 1.3 73.1 - - - +
60U SER* 1.3 67.5 + - - +
62U VAL* 3.3 7.6 + - - +
63U TYR* 2.9 48.3 + - + -
91U GLU* 3.2 25.1 - - - +
139U LEU* 4.6 22.9 - - + +
140U GLU* 4.5 3.8 - - - +
142U LEU* 6.3 0.7 - - + -
143U THR* 3.4 24.9 - - - +
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Residues in contact with SER 60 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 4.9 2.5 + - - -
92Q ARG* 4.5 3.8 + - - -
56U GLU 2.9 13.8 + - - -
57U TYR* 3.4 17.0 - - - -
59U VAL* 1.3 77.6 - - - +
61U TYR* 1.3 57.3 + - - +
63U TYR 3.3 0.2 + - - -
64U HIS* 3.0 15.6 + - - +
88U SER* 2.7 45.8 + - - +
91U GLU* 3.6 19.9 - - - +
92U ARG* 3.7 17.0 + - - +
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Residues in contact with TYR 61 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q ASN* 4.1 5.0 + - - -
57Q TYR* 3.6 49.8 - + - +
111Q LEU* 3.6 21.4 - - + +
112Q GLN 2.6 36.8 + - - -
114Q ILE* 3.8 18.6 - - + +
57U TYR* 3.0 14.5 + + + +
58U ASN* 3.1 8.7 + - - +
60U SER* 1.3 71.8 - - - +
62U VAL* 1.3 66.2 + - + +
64U HIS* 3.1 5.8 + - - +
65U ALA* 3.0 21.7 + - - +
114U ILE* 3.5 28.0 - - + -
115U VAL 3.9 4.9 - - - -
117U PRO* 3.6 31.9 - - + -
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Residues in contact with VAL 62 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P PRO* 4.2 21.3 - - + -
18P PHE* 3.8 37.5 - - + -
58U ASN* 2.9 22.2 + - - +
59U VAL* 3.7 5.6 - - - +
61U TYR* 1.3 77.3 - - + +
63U TYR* 1.3 55.4 + - - +
65U ALA* 3.1 4.3 + - - +
66U MET* 2.9 35.8 + - + +
117U PRO* 4.2 13.2 - - + -
121U PHE* 5.1 0.7 - - + -
139U LEU* 3.4 30.5 - - + -
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Residues in contact with TYR 63 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59U VAL* 2.9 34.5 + - + +
60U SER 3.7 4.5 - - - +
62U VAL* 1.3 75.4 - - - +
64U HIS* 1.3 58.5 + - - +
66U MET* 3.2 12.4 + - - +
67U PHE* 2.8 25.8 + - - +
83U PHE* 5.6 1.8 - + - -
84U PHE* 3.6 44.1 - + - +
87U SER* 3.7 20.0 - - - -
88U SER 3.8 4.9 - - - +
91U GLU* 3.6 21.1 - - + -
136U ALA* 3.7 25.6 + - + -
139U LEU* 4.4 10.0 - - + +
140U GLU* 2.6 40.1 + - - +
181U ILE* 3.9 8.2 - - + +
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Residues in contact with HIS 64 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 2.7 36.0 + + - +
92Q ARG* 3.7 18.4 + - + -
96Q GLU* 2.7 41.4 + - + +
99Q MET* 3.6 31.2 - - + +
111Q LEU* 4.1 8.5 - - + -
60U SER 3.0 8.4 + - - +
61U TYR 3.1 8.9 + - - +
63U TYR* 1.3 76.7 - - - +
65U ALA* 1.3 57.1 + - - +
67U PHE* 3.3 15.6 + + + +
68U ALA* 2.9 28.8 + - - +
85U LYS* 5.0 2.7 - - + -
88U SER* 3.5 20.1 + - - +
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Residues in contact with ALA 65 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Q VAL* 6.1 0.2 - - - -
111Q LEU* 3.7 12.6 - - + +
61U TYR 3.0 12.2 + - - +
62U VAL 3.1 8.9 + - - +
64U HIS* 1.3 77.2 - - - +
66U MET* 1.3 61.4 + - - +
68U ALA* 3.3 7.5 + - - +
69U TYR* 3.1 18.2 + - - +
117U PRO* 3.9 17.5 - - + -
118U LEU 3.5 24.7 - - - +
119U SER* 4.5 4.5 - - - +
121U PHE* 3.8 10.3 - - + -
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Residues in contact with MET 66 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62U VAL* 2.9 34.2 + - - +
63U TYR* 3.2 22.6 + - - +
65U ALA* 1.3 74.6 - - - +
67U PHE* 1.3 66.4 + - - +
69U TYR* 3.2 1.6 + - - +
70U PHE* 3.1 31.9 + - + -
84U PHE* 3.6 31.9 - - + -
121U PHE* 3.3 35.2 - - + -
132U ALA* 3.1 40.4 - - + +
135U LEU* 4.5 3.4 - - + -
136U ALA* 4.4 6.1 - - + +
139U LEU* 4.4 5.6 - - - -
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Residues in contact with PHE 67 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Q GLU* 4.6 9.6 - - + -
99Q MET* 4.0 17.7 - - + -
100Q GLU* 3.9 29.2 - - + -
103Q ASN* 5.4 0.2 - - - -
63U TYR 2.8 13.5 + - - +
64U HIS* 3.5 25.1 - + - +
66U MET* 1.3 75.3 - - - +
68U ALA* 1.3 77.1 + - - +
69U TYR 3.1 0.2 + - - -
70U PHE 3.2 1.6 + - - -
71U ASP* 2.9 51.5 + - + +
81U ALA* 3.4 27.9 - - + +
82U LYS* 5.9 0.2 - - - -
84U PHE* 3.7 7.0 - - - +
85U LYS* 3.7 42.8 - - + +
----------------------------------------------------------
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Residues in contact with ALA 68 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Q MET* 4.0 8.7 - - + -
103Q ASN* 2.9 27.2 + - - +
109Q VAL* 3.7 39.3 - - + +
64U HIS 2.9 17.2 + - - +
65U ALA* 3.6 7.9 - - - +
66U MET 3.2 0.4 - - - -
67U PHE* 1.3 83.6 - - + +
69U TYR* 1.3 63.3 + - - +
71U ASP 3.7 0.3 + - - -
72U ARG* 3.6 8.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65U ALA 3.1 6.0 + - - +
66U MET 3.6 6.5 - - - +
67U PHE 3.1 0.4 - - - -
68U ALA* 1.3 77.6 - - - +
70U PHE* 1.3 93.9 + + - +
71U ASP 3.1 0.4 - - - -
72U ARG* 3.1 54.9 + - - +
75U VAL* 3.6 28.1 - - + +
119U SER 3.7 10.5 + - - +
120U ASP* 3.0 21.7 + - - -
121U PHE* 3.5 34.5 - + + -
122U ASP* 3.3 31.7 - - - +
128U ASP* 4.1 12.1 + - + +
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Residues in contact with PHE 70 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U MET* 3.1 28.6 + - + +
67U PHE 3.8 0.2 - - - -
69U TYR* 1.3 98.3 - + - +
71U ASP* 1.3 58.5 + - - +
72U ARG 3.2 2.5 + - - -
75U VAL* 3.6 16.6 - - + -
76U ALA* 3.8 4.9 + - - -
77U LEU* 3.5 49.7 + - + +
78U ARG* 5.2 0.3 - - - +
80U LEU* 3.8 17.3 - - + -
81U ALA* 3.8 24.2 - - - +
84U PHE* 3.8 19.1 - + - -
121U PHE* 4.5 6.3 - - + -
128U ASP* 3.6 19.3 - - + -
132U ALA* 3.4 33.4 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179N LYS* 3.1 35.2 + - - -
183N GLU* 4.6 2.2 - - - +
100Q GLU* 4.2 11.5 - - - +
103Q ASN* 2.9 34.5 + - - +
67U PHE* 2.9 45.9 + - + +
69U TYR 3.1 0.4 - - - -
70U PHE* 1.3 76.9 - - - +
72U ARG* 1.3 63.7 + - - +
76U ALA* 5.8 0.2 - - - -
81U ALA* 3.9 8.3 - - + +
----------------------------------------------------------
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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