Contacts of the helix formed by residues 42 - 71 (chain Q) 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 Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q ARG* 3.5 3.0 + - - +
40Q LYS* 4.3 4.7 + - - -
41Q TYR* 1.3 81.7 - - - +
43Q ASP* 1.3 66.5 + - - +
44Q GLU* 4.0 5.4 - - + +
45Q SER* 3.0 27.8 + - - +
46Q GLU* 3.1 10.0 + - - +
157Q ASN* 3.7 41.7 - - + +
159Q ASP* 5.0 0.4 + - - -
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Residues in contact with ASP 43 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q ARG* 3.0 24.8 + - - +
42Q VAL* 1.3 74.7 - - - +
44Q GLU* 1.3 57.5 + - - +
46Q GLU* 3.3 14.3 + - - +
47Q SER* 2.9 34.4 + - - +
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Residues in contact with GLU 44 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q VAL* 3.1 6.0 + - + +
43Q ASP* 1.3 78.7 - - - +
45Q SER* 1.3 58.3 + - - +
47Q SER* 3.5 7.5 + - - -
48Q ALA* 3.0 26.7 + - - +
153Q VAL* 3.9 17.0 - - + +
156Q LYS* 2.8 25.5 + - - -
157Q ASN* 2.8 28.7 + - - +
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Residues in contact with SER 45 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q TYR* 4.1 15.9 - - - -
42Q VAL* 3.0 23.4 + - - +
44Q GLU* 1.3 74.8 - - - +
46Q GLU* 1.3 66.9 + - - +
48Q ALA* 3.1 3.0 + - - +
49Q VAL* 2.9 27.9 + - - +
153Q VAL* 4.1 11.6 + - - +
157Q ASN* 3.7 16.5 + - - +
159Q ASP* 4.3 9.3 + - - +
162Q LEU* 4.0 21.2 - - - +
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Residues in contact with GLU 46 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q ARG* 3.7 23.0 + - - +
41Q TYR* 3.7 19.8 - - + -
42Q VAL 3.1 10.4 + - - +
43Q ASP* 3.5 18.4 - - - +
45Q SER* 1.3 78.4 - - - +
47Q SER* 1.3 61.9 + - - +
49Q VAL 3.4 0.3 + - - -
50Q ASN* 3.1 24.8 + - - +
102Q GLN* 3.1 28.9 + - - +
107Q GLY* 3.4 6.5 - - - -
108Q LYS* 2.7 36.4 + - - +
110Q LYS* 5.7 2.3 + - - -
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Residues in contact with SER 47 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q ASP* 2.9 21.3 + - - +
44Q GLU* 3.7 7.4 - - - -
46Q GLU* 1.3 77.9 + - - +
48Q ALA* 1.3 58.3 + - - +
50Q ASN* 3.2 10.5 + - - +
51Q GLU* 2.9 28.7 + - - +
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Residues in contact with ALA 48 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q GLU 3.0 17.9 + - - +
45Q SER* 3.1 4.9 + - - +
47Q SER* 1.3 77.3 - - - +
49Q VAL* 1.3 57.0 + - - +
51Q GLU* 3.3 12.0 + - - +
52Q GLN* 3.0 27.5 + - - +
149Q ASN* 5.8 2.2 - - - +
150Q LEU* 3.6 23.8 - - + +
153Q VAL* 3.9 25.1 - - + -
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Residues in contact with VAL 49 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q TYR* 3.3 21.3 - - - +
45Q SER 2.9 15.0 + - - +
46Q GLU 3.7 3.8 - - - +
47Q SER 3.3 0.2 - - - -
48Q ALA* 1.3 76.8 - - - +
50Q ASN* 1.3 62.7 + - - +
52Q GLN* 3.2 5.6 + - - +
53Q ILE* 3.0 25.1 + - + +
98Q LEU* 3.8 33.2 - - + +
101Q TYR* 4.7 3.1 - - + -
102Q GLN* 3.7 20.2 - - + +
150Q LEU* 4.1 11.4 - - + -
162Q LEU* 3.9 28.9 - - + -
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Residues in contact with ASN 50 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q GLU* 3.1 17.8 + - - +
47Q SER* 3.2 11.4 + - - +
49Q VAL* 1.3 77.2 - - - +
51Q GLU* 1.3 61.5 + - - +
53Q ILE* 3.4 15.1 + - - +
54Q ASN* 3.2 20.4 + - - +
102Q GLN* 3.0 19.0 + - - +
108Q LYS 3.1 20.8 + - - -
109Q VAL* 3.4 4.2 - - - -
110Q LYS* 3.0 48.6 + - + +
112Q GLN* 5.5 4.5 - - + +
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Residues in contact with GLU 51 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J ILE* 4.8 27.8 - - + +
15J PHE* 6.1 0.9 - - + -
47Q SER 2.9 13.8 + - - +
48Q ALA* 3.5 13.2 - - - +
50Q ASN* 1.3 76.6 - - - +
52Q GLN* 1.3 59.2 + - - +
54Q ASN* 3.1 9.8 + - - +
55Q VAL* 3.0 32.9 + - + +
112Q GLN* 6.5 0.2 - - - -
146Q LYS* 3.8 25.2 + - + +
149Q ASN* 4.7 14.1 + - - -
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Residues in contact with GLN 52 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q ALA 3.0 16.4 + - - +
49Q VAL 3.2 4.2 + - - +
51Q GLU* 1.3 75.0 - - - +
53Q ILE* 1.3 66.5 + - - +
55Q VAL* 3.1 19.7 + - - +
56Q GLU* 2.9 54.6 + - - +
98Q LEU* 3.6 22.0 - - + -
143Q THR* 4.1 3.6 - - - +
146Q LYS* 3.4 30.1 - - - +
147Q LEU* 3.4 30.1 - - + +
150Q LEU* 3.9 17.9 - - + +
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Residues in contact with ILE 53 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49Q VAL* 3.0 24.7 + - + +
50Q ASN* 3.6 26.0 - - - +
52Q GLN* 1.3 75.6 - - - +
54Q ASN* 1.3 57.4 + - - +
56Q GLU 3.4 0.2 + - - -
57Q TYR* 3.0 33.0 + - + +
95Q ALA* 3.9 10.6 - - - +
98Q LEU* 3.6 28.4 - - + +
99Q MET* 3.7 38.6 - - + +
102Q GLN* 4.7 0.2 - - + -
109Q VAL* 4.4 8.7 - - + -
110Q LYS 5.9 1.3 - - - +
111Q LEU* 3.7 29.2 - - + -
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Residues in contact with ASN 54 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J ILE* 3.4 28.4 + - + +
15J PHE* 3.6 7.4 + - - +
50Q ASN 3.2 9.0 + - - +
51Q GLU* 3.1 11.9 + - - +
53Q ILE* 1.3 78.8 - - - +
55Q VAL* 1.3 58.7 + - - +
57Q TYR* 3.9 3.5 - - - +
58Q ASN* 2.9 53.9 + - - +
111Q LEU* 6.4 0.2 - - - -
112Q GLN* 3.5 28.5 + - + +
113Q SER 3.1 25.5 + - - +
114Q ILE* 4.2 2.8 - - - +
61U TYR* 4.1 7.1 + - - -
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Residues in contact with VAL 55 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PHE* 3.8 31.4 - - + -
51Q GLU* 3.0 27.0 + - + +
52Q GLN* 3.1 30.0 + - - +
54Q ASN* 1.3 77.0 - - - +
56Q GLU* 1.3 62.9 + - - +
58Q ASN* 3.2 4.0 + - - +
59Q VAL* 3.0 23.4 + - + +
143Q THR* 4.3 18.8 - - + +
146Q LYS* 4.0 35.4 - - + -
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Residues in contact with GLU 56 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q GLN* 2.9 42.6 + - - +
55Q VAL* 1.3 75.9 - - - +
57Q TYR* 1.3 57.7 + - - +
59Q VAL* 3.3 4.4 + - - +
60Q SER* 2.9 27.7 + - - -
91Q GLU* 3.0 16.7 - - - +
94Q HIS* 3.6 13.4 - - + +
95Q ALA* 3.8 22.2 - - + +
98Q LEU* 3.9 17.0 - - + -
143Q THR* 3.7 12.3 - - - +
147Q LEU* 3.9 10.0 - - - +
170Q TYR* 4.2 6.6 - - - -
214Q CA 2.5 28.3 - - - -
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Residues in contact with TYR 57 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q ILE* 3.0 23.5 + - + +
54Q ASN* 3.9 6.7 - - - +
56Q GLU* 1.3 75.6 - - - +
58Q ASN* 1.3 62.6 + - - +
60Q SER* 3.3 13.1 + - - -
61Q TYR* 3.0 23.4 + + + +
92Q ARG* 3.9 23.4 + - + -
95Q ALA* 3.7 22.6 - - + +
99Q MET* 4.4 6.3 - - - -
111Q LEU* 4.5 2.5 - - + -
114Q ILE* 3.6 24.0 - - + +
57U TYR* 5.3 13.7 - + - -
60U SER* 4.9 2.4 + - - -
61U TYR* 3.6 38.8 - + - +
64U HIS* 2.7 41.0 + + - +
88U SER* 4.6 1.9 + - - -
114U ILE* 6.2 0.2 - - + -
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Residues in contact with ASN 58 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PHE* 3.7 27.8 + - + +
17J PRO* 3.7 20.1 - - + +
54Q ASN* 2.9 50.9 + - - +
55Q VAL 3.5 5.2 - - - +
57Q TYR* 1.3 78.0 - - - +
59Q VAL* 1.3 56.6 - - - +
61Q TYR* 3.1 3.3 + - - +
62Q VAL* 2.9 33.1 + - - +
113Q SER 4.2 6.5 + - - -
114Q ILE* 3.4 24.3 - - - +
115Q VAL* 3.8 11.4 + - - +
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Residues in contact with VAL 59 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J PHE* 5.0 7.6 - - + -
17J PRO* 6.0 0.9 - - + -
55Q VAL* 3.0 23.4 + - + +
56Q GLU* 3.7 3.6 - - - +
58Q ASN* 1.3 71.9 - - - +
60Q SER* 1.3 66.4 + - - +
62Q VAL* 3.3 6.8 + - - +
63Q TYR* 2.9 49.7 + - + -
91Q GLU* 3.5 23.6 - - - +
139Q LEU* 4.8 22.2 - - + +
140Q GLU* 4.4 4.7 - - - +
143Q THR* 3.4 26.5 - - + +
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Residues in contact with SER 60 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q GLU 2.9 10.3 + - - -
57Q TYR* 3.4 16.3 - - - -
58Q ASN 3.2 0.2 - - - -
59Q VAL* 1.3 77.9 - - - +
61Q TYR* 1.3 56.5 + - - +
63Q TYR 3.4 0.3 + - - -
64Q HIS* 3.0 14.9 + - - +
88Q SER* 2.7 51.2 + - - +
91Q GLU* 3.6 19.4 - - - +
92Q ARG* 3.7 17.8 - - - +
57U TYR* 4.9 2.8 + - - -
92U ARG* 4.5 4.2 + - - -
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Residues in contact with TYR 61 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 3.0 14.2 + + + +
58Q ASN 3.1 7.8 + - - +
60Q SER* 1.3 73.3 - - - +
62Q VAL* 1.3 65.9 + - + +
64Q HIS* 3.2 5.9 + - - +
65Q ALA* 3.0 18.4 + - - +
114Q ILE* 3.5 28.5 - - + -
115Q VAL 3.9 5.2 - - - -
117Q PRO* 3.6 32.4 - - + +
53U ILE* 5.9 0.2 - - - +
54U ASN* 4.1 4.9 + - - -
57U TYR* 3.5 50.4 - + - +
111U LEU* 3.6 22.3 - - + +
112U GLN 2.7 38.2 + - - -
114U ILE* 3.8 17.5 - - + +
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Residues in contact with VAL 62 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J PRO* 4.2 21.3 - - + -
18J PHE* 3.8 37.0 - - + -
58Q ASN* 2.9 20.5 + - - +
59Q VAL* 3.8 6.1 - - - +
61Q TYR* 1.3 76.8 - - + +
63Q TYR* 1.3 58.1 + - - +
65Q ALA* 3.1 3.8 + - - +
66Q MET* 2.9 36.6 + - + +
117Q PRO* 4.2 12.8 - - + -
121Q PHE* 5.1 0.2 - - + -
139Q LEU* 3.5 31.4 - - + -
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Residues in contact with TYR 63 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Q VAL* 2.9 34.4 + - + +
60Q SER 3.8 4.0 - - - +
62Q VAL* 1.3 76.4 - - - +
64Q HIS* 1.3 58.6 + - - +
66Q MET* 3.2 11.9 + - - +
67Q PHE* 2.9 28.1 + - - +
83Q PHE* 5.6 1.1 - + - -
84Q PHE* 3.6 42.0 - + - +
87Q SER* 3.7 20.0 - - - -
88Q SER* 3.8 4.9 - - - -
91Q GLU* 3.7 20.2 - - + -
136Q ALA* 3.8 28.1 + - + +
139Q LEU* 4.7 7.0 - - + +
140Q GLU* 2.5 42.2 + - - +
181Q ILE* 3.9 8.3 - - + +
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Residues in contact with HIS 64 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q SER 3.0 8.8 + - - +
61Q TYR* 3.2 9.4 + - - +
63Q TYR* 1.3 77.1 - - - +
65Q ALA* 1.3 57.8 + - - +
67Q PHE* 3.4 15.8 + + + +
68Q ALA* 3.0 27.7 + - - +
85Q LYS* 5.1 2.7 - - + -
88Q SER* 3.5 21.4 + - - +
57U TYR* 2.7 36.0 + + - +
92U ARG* 3.6 18.6 + - + -
96U GLU* 2.7 41.0 + - + +
99U MET* 3.7 30.8 - - + +
111U LEU* 4.1 9.0 - - + -
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Residues in contact with ALA 65 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q TYR 3.0 12.3 + - - +
62Q VAL 3.1 8.9 + - - +
64Q HIS* 1.3 77.6 - - - +
66Q MET* 1.3 61.2 + - - +
68Q ALA* 3.2 6.7 + - - +
69Q TYR* 3.1 18.2 + - - +
117Q PRO* 4.0 11.2 - - + -
118Q LEU 3.5 24.0 - - - +
119Q SER* 4.5 5.3 - - - +
121Q PHE* 3.8 9.8 - - + -
109U VAL* 6.1 0.2 - - - -
111U LEU* 3.7 17.2 - - + +
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Residues in contact with MET 66 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q VAL* 2.9 30.0 + - - +
63Q TYR* 3.2 24.0 + - - +
65Q ALA* 1.3 73.9 - - - +
67Q PHE* 1.3 65.8 + - - +
69Q TYR* 3.2 1.7 + - - +
70Q PHE* 3.1 31.2 + - + -
84Q PHE* 3.7 24.5 - - + -
121Q PHE* 3.3 35.2 - - + -
132Q ALA* 3.2 48.0 - - + +
135Q LEU* 4.6 3.1 - - + -
136Q ALA 4.5 3.8 - - - +
139Q LEU* 4.5 6.7 - - - -
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Residues in contact with PHE 67 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q TYR 2.9 14.4 + - - +
64Q HIS* 3.5 24.5 - + - +
66Q MET* 1.3 74.7 - - - +
68Q ALA* 1.3 65.1 + - - +
70Q PHE* 3.2 1.7 + - - +
71Q ASP* 2.9 56.6 + - + +
81Q ALA* 3.3 28.9 - - + +
84Q PHE* 3.6 7.0 - - - +
85Q LYS* 3.6 47.6 - - + +
96U GLU* 4.5 6.7 - - + -
99U MET* 4.1 16.2 - - + -
100U GLU* 3.9 28.5 - - + -
103U ASN* 5.5 0.7 - - - -
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Residues in contact with ALA 68 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Q HIS 3.0 16.7 + - - +
65Q ALA* 3.6 8.1 - - - +
66Q MET 3.2 0.2 - - - -
67Q PHE* 1.3 82.7 - - + +
69Q TYR* 1.3 61.4 + - - +
72Q ARG* 3.6 5.9 + - - +
99U MET* 4.0 8.3 - - + -
103U ASN* 2.9 32.5 + - - +
109U VAL* 3.7 39.3 - - + +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65Q ALA 3.1 7.4 + - - +
66Q MET 3.6 7.2 - - - +
67Q PHE 3.2 0.4 - - - -
68Q ALA* 1.3 78.3 - - - +
70Q PHE* 1.3 89.5 - + - +
72Q ARG* 3.1 59.9 + - - +
75Q VAL* 3.6 34.2 - - + +
119Q SER 3.7 8.3 + - - +
120Q ASP* 3.7 8.3 - - - -
121Q PHE* 3.5 39.9 - + + -
122Q ASP* 3.3 32.3 - - - +
128Q ASP* 4.1 12.6 + - + +
33U GLN* 6.1 0.5 - - - +
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Residues in contact with PHE 70 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q MET* 3.1 29.7 + - + +
69Q TYR* 1.3 92.1 - + - +
71Q ASP* 1.3 58.2 + - - +
72Q ARG 3.2 1.9 + - - -
75Q VAL* 3.6 16.2 - - + -
76Q ALA* 3.8 5.2 + - - -
77Q LEU* 3.5 49.6 + - + +
78Q ARG* 5.3 0.2 - - - -
80Q LEU* 3.6 19.7 - - + -
81Q ALA* 3.8 26.0 - - - +
84Q PHE* 3.8 17.7 - + - -
121Q PHE* 4.5 5.4 - - + -
128Q ASP* 3.6 26.0 - - + -
132Q ALA* 3.4 35.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K LYS* 3.0 34.4 + - - -
183K GLU* 4.6 2.0 - - - +
67Q PHE* 2.9 46.7 + - + +
69Q TYR 3.2 0.4 - - - -
70Q PHE* 1.3 75.9 - - - +
72Q ARG* 1.3 64.3 + - - +
81Q ALA* 3.9 7.3 - - + +
100U GLU* 4.2 12.4 - - - +
103U ASN* 2.9 33.1 + - - +
----------------------------------------------------------
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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