Contacts of the helix formed by residues 36 - 64 (chain Q) 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 LEU 36 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439 PHE* 5.1 11.7 - - + -
31Q PHE* 2.9 37.7 + - + +
32Q GLU* 4.3 1.5 + - - -
34Q LEU* 4.1 21.5 - - + +
35Q GLY* 1.3 79.8 - - - +
37Q GLU* 1.3 61.2 + - - +
39Q PHE* 3.6 16.6 + - + -
40Q ALA* 3.1 23.8 + - - +
83Q PRO* 4.3 17.0 - - + -
151Q LEU* 4.5 25.6 - - + +
152Q PHE* 5.6 1.6 - - - -
155Q ASP* 3.3 30.3 - - + +
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Residues in contact with GLU 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1369 LYS* 3.0 44.4 + - + +
32Q GLU* 3.5 19.5 - - - +
35Q GLY* 3.6 10.3 + - - +
36Q LEU* 1.3 70.9 - - - +
38Q GLY* 1.3 61.0 + - - +
40Q ALA* 3.7 5.5 - - - +
41Q ASN* 2.8 45.1 + - - +
155Q ASP* 3.4 5.6 + - - +
159Q SER* 5.3 0.4 - - - -
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Residues in contact with GLY 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q GLU* 1.3 76.1 - - - +
39Q PHE* 1.3 63.7 + - - +
41Q ASN* 4.0 0.6 - - - +
42Q TRP* 3.1 21.0 + - - +
155Q ASP* 2.9 31.4 + - - -
158Q LEU* 3.2 17.8 - - - +
159Q SER* 3.7 18.3 - - - -
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Residues in contact with PHE 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q PHE* 3.5 34.5 - + + -
36Q LEU* 3.9 12.6 - - + +
37Q GLU 3.4 0.2 - - - -
38Q GLY* 1.3 75.2 - - - +
40Q ALA* 1.3 58.2 + - - +
42Q TRP* 3.6 6.6 + - - +
43Q MET* 3.1 32.9 + - - +
87Q PHE* 3.7 27.7 - + - -
137Q ILE* 4.4 3.6 - - + -
141Q LEU* 4.1 16.8 - - + -
151Q LEU* 3.9 30.5 - - + -
154Q LEU* 3.9 17.5 - - + -
155Q ASP* 3.2 46.0 + - + -
158Q LEU* 3.7 21.1 - - + -
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Residues in contact with ALA 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588 TYR* 4.5 0.4 - - - +
28Q ALA* 3.4 32.3 - - - +
31Q PHE* 3.8 3.5 - - - +
32Q GLU* 3.4 28.7 - - - +
36Q LEU 3.1 18.6 + - - +
37Q GLU 3.7 4.3 - - - +
39Q PHE* 1.3 75.1 - - - +
41Q ASN* 1.3 60.6 + - - +
43Q MET 3.2 1.7 + - - -
44Q LYS* 2.9 33.8 + - - +
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Residues in contact with ASN 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q GLU* 5.1 0.7 - - - +
37Q GLU* 2.8 32.8 + - - +
38Q GLY* 4.0 5.7 - - - +
40Q ALA* 1.3 69.9 - - - +
42Q TRP* 1.3 59.9 + - - +
44Q LYS* 3.3 24.0 + - - +
45Q ALA* 2.9 30.3 + - - +
158Q LEU 5.0 0.2 - - - +
159Q SER* 5.0 10.7 + - - +
161Q ARG 3.6 14.8 - - - +
162Q ALA* 4.4 5.4 - - - +
163Q PRO* 3.5 21.1 - - + +
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Residues in contact with TRP 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q TYR* 5.9 0.9 - + - -
38Q GLY 3.1 19.3 + - - +
39Q PHE* 3.6 6.3 - - - +
41Q ASN* 1.3 74.3 - - - +
43Q MET* 1.3 84.8 + - + +
45Q ALA* 3.3 3.3 + - - +
46Q GLN* 2.9 43.8 + - + +
87Q PHE* 4.3 9.4 - + - -
133Q SER* 3.6 20.2 - - - -
134Q VAL* 4.3 19.3 - - + -
137Q ILE* 3.5 24.5 - - + +
158Q LEU* 3.6 36.5 - - + +
161Q ARG* 3.3 55.8 + - + +
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Residues in contact with MET 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q TYR* 3.4 50.1 - - + +
27Q MET* 3.7 32.8 - - + -
28Q ALA* 3.8 6.5 - - + +
31Q PHE* 4.1 11.7 - - + -
39Q PHE 3.1 20.6 + - - +
40Q ALA 3.2 4.7 + - - +
42Q TRP* 1.3 88.9 - - + +
44Q LYS* 1.3 59.8 + - - +
46Q GLN* 3.4 1.0 + - - +
47Q ALA* 2.9 28.2 + - - +
87Q PHE* 3.6 41.7 - - + -
90Q ALA* 4.7 4.0 - - + -
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Residues in contact with LYS 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558 LEU* 4.7 14.6 - - + +
588 TYR* 3.4 30.9 - - - -
598 ASN* 4.3 8.5 + - - -
25Q PHE* 4.7 12.1 - - + -
28Q ALA* 3.8 10.1 - - + -
32Q GLU* 3.1 28.3 + - - -
40Q ALA 2.9 19.7 + - - +
41Q ASN* 3.6 27.5 + - - +
43Q MET* 1.3 74.3 - - - +
45Q ALA* 1.3 62.9 + - - +
47Q ALA* 3.3 8.7 + - - +
48Q GLU* 3.1 26.3 + - - +
163Q PRO* 3.9 20.6 - - + -
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Residues in contact with ALA 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q ASN 2.9 16.2 + - - +
42Q TRP 3.6 2.2 - - - +
44Q LYS* 1.3 72.9 - - - +
46Q GLN* 1.3 64.1 + - - +
48Q GLU* 3.4 8.3 + - - +
49Q GLU* 3.4 23.6 + - - +
161Q ARG* 3.6 32.7 + - + +
162Q ALA 3.8 18.2 - - - +
163Q PRO* 4.1 8.9 - - + +
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Residues in contact with GLN 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q TYR* 3.8 25.3 - - + -
42Q TRP* 2.9 40.0 + - + +
43Q MET* 3.7 6.1 - - - +
45Q ALA* 1.3 73.9 - - - +
47Q ALA* 1.3 64.2 + - - +
49Q GLU* 3.2 14.1 + - - +
50Q GLU* 2.8 38.4 + - - +
94Q GLU* 5.5 0.4 - - - -
130Q GLU* 2.9 29.3 + - - +
133Q SER* 5.3 2.3 + - - -
134Q VAL* 5.6 4.6 - - + +
161Q ARG* 3.1 30.1 + - - +
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Residues in contact with ALA 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ALA* 3.3 43.1 - - + +
24Q TYR* 4.0 7.2 - - + +
25Q PHE* 4.1 10.1 - - + +
43Q MET 2.9 18.0 + - - +
44Q LYS* 3.4 10.1 - - - +
46Q GLN* 1.3 78.6 - - - +
48Q GLU* 1.3 60.3 + - + +
50Q GLU* 3.3 2.1 + - - -
51Q ILE* 3.3 22.2 + - + +
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Residues in contact with GLU 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558 LEU* 5.5 2.6 - - - +
1658 LEU* 3.8 17.5 - - + +
1698 LEU* 3.9 17.7 - - + +
44Q LYS 3.1 14.4 + - - +
45Q ALA* 3.5 9.4 - - - +
46Q GLN 3.2 0.2 - - - -
47Q ALA* 1.3 74.5 - - + +
49Q GLU* 1.3 60.2 + - - +
51Q ILE* 3.2 17.4 + - + +
52Q GLY 3.1 21.0 + - - -
163Q PRO* 3.3 20.0 - - - +
164Q LYS* 2.9 26.1 + - - +
165Q LEU* 3.2 37.8 + - + +
166Q PRO* 3.4 2.3 - - - +
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Residues in contact with GLU 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688 LEU 5.0 0.7 - - - +
1698 LEU* 3.4 24.7 - - + +
1708 MET* 3.3 35.2 + - + +
45Q ALA 3.4 13.9 + - - +
46Q GLN* 3.2 17.8 + - - +
48Q GLU* 1.3 77.1 - - - +
50Q GLU* 1.3 56.5 + - - +
52Q GLY* 3.1 3.3 + - - -
53Q HIS* 3.0 35.6 + - + -
130Q GLU* 4.5 0.9 - - - +
161Q ARG* 3.5 18.8 + - - +
164Q LYS* 5.2 6.1 + - - +
1173Q AG 3.3 21.5 - - - -
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Residues in contact with GLU 50 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q GLU* 2.9 46.8 - - - +
20Q SER* 3.4 14.3 + - - -
21Q ALA* 3.6 10.8 - - - +
24Q TYR* 3.8 23.3 - - + -
46Q GLN* 2.8 36.6 + - - +
47Q ALA 3.6 6.1 - - - +
48Q GLU 3.3 0.4 - - - -
49Q GLU* 1.3 74.0 - - - +
51Q ILE* 1.3 60.2 + - - +
53Q HIS* 3.3 10.7 + - - +
54Q ALA* 3.1 23.2 + - - +
94Q GLU* 3.9 2.8 - - - +
97Q ILE* 5.5 1.9 - - - +
127Q GLN* 5.2 2.8 + - - -
130Q GLU* 3.0 17.6 - - - +
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Residues in contact with ILE 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518 ILE* 4.6 29.4 - - + -
1658 LEU* 4.2 19.1 - - + -
18Q LEU* 4.9 15.3 - - + -
21Q ALA* 3.8 14.6 - - + -
47Q ALA* 3.3 17.4 + - + +
48Q GLU* 3.2 20.1 + - + +
50Q GLU* 1.3 75.0 - - - +
52Q GLY* 1.3 58.3 + - - +
54Q ALA* 3.3 8.7 + - - +
55Q LEU* 3.1 37.4 + - + +
165Q LEU* 6.2 1.1 - - + -
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Residues in contact with GLY 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698 LEU* 3.9 27.1 - - - +
48Q GLU 3.1 10.3 + - - -
49Q GLU 3.1 5.7 + - - -
51Q ILE* 1.3 77.6 - - - +
53Q HIS* 1.3 61.6 - - - +
55Q LEU* 3.4 10.8 + - - +
56Q ARG* 3.2 28.6 + - - +
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Residues in contact with HIS 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q GLU* 3.4 28.5 + - - +
49Q GLU* 3.0 19.7 + - + -
50Q GLU* 3.5 12.7 + - - +
51Q ILE 3.3 0.4 - - - -
52Q GLY* 1.3 74.3 - - - +
54Q ALA* 1.3 64.7 + - - +
56Q ARG* 3.2 14.7 + - - +
57Q PHE* 3.3 21.4 + - - -
122Q TRP* 3.6 24.9 - + - -
123Q PHE* 3.6 16.5 - + + -
126Q GLU* 3.1 24.0 + - - -
127Q GLN* 5.2 0.6 + - - -
130Q GLU* 3.1 14.1 - - - -
1173Q AG 2.2 32.2 - - - -
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Residues in contact with ALA 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 PHE* 5.3 3.8 - - + -
14Q LEU* 3.6 27.2 - - + +
17Q GLU* 4.0 9.6 - - + +
18Q LEU* 3.8 33.2 - - + -
50Q GLU 3.1 13.8 + - - +
51Q ILE 3.3 9.8 + - - +
53Q HIS* 1.3 77.4 - - - +
55Q LEU* 1.3 56.0 + - + +
57Q PHE* 3.4 3.3 + - - +
58Q TYR* 3.1 23.6 + - - +
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Residues in contact with LEU 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 PHE* 3.8 28.9 - - + -
448 LYS* 4.9 17.3 - - + -
488 GLU* 5.8 0.7 - - - +
1638 PRO* 6.4 0.4 - - + -
1658 LEU* 5.2 4.9 - - + -
1668 PRO* 4.1 34.8 - - + -
51Q ILE* 3.1 34.2 + - + +
52Q GLY* 3.6 12.1 - - - +
54Q ALA* 1.3 72.8 - - + +
56Q ARG* 1.3 60.5 + - - +
57Q PHE 3.4 0.2 - - - -
58Q TYR* 3.3 10.0 - - + +
59Q ASN* 2.8 43.5 + - - +
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Residues in contact with ARG 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1708 MET 3.0 26.9 + - - -
1718 GLN* 3.8 0.6 - - - +
1728 GLY 3.7 27.1 + - - +
52Q GLY 3.2 16.6 + - - +
53Q HIS* 3.4 9.8 - - - +
54Q ALA 3.2 0.6 - - - -
55Q LEU* 1.3 75.4 - - + +
57Q PHE* 1.3 58.7 + - - +
59Q ASN* 3.4 9.1 + - - +
60Q TYR* 3.0 29.6 + - - +
119Q PHE* 3.7 8.3 - - + -
122Q TRP* 3.4 57.6 - - - +
123Q PHE* 3.7 14.8 - - + -
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Residues in contact with PHE 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q LEU* 3.8 33.7 - - + +
13Q GLN* 3.4 33.9 - - + -
14Q LEU* 4.0 21.1 - - + -
17Q GLU* 4.1 12.3 - - + -
53Q HIS 3.3 21.9 + - - -
54Q ALA* 3.7 6.7 - - - +
55Q LEU 3.4 0.2 - - - -
56Q ARG* 1.3 76.0 - - - +
58Q TYR* 1.3 65.1 + - - +
60Q TYR* 3.9 0.7 - - - +
61Q ILE* 3.0 31.8 + - + +
101Q ILE* 4.2 11.9 - - + -
104Q LEU* 4.5 0.7 - - + -
119Q PHE* 3.6 26.2 - + - -
120Q LEU* 4.2 9.6 - - + -
123Q PHE* 3.4 33.7 - + - -
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Residues in contact with TYR 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 PHE* 3.7 30.3 - + + -
288 ALA 3.0 23.5 + - - -
298 ALA* 3.9 16.6 - - + -
328 GLU* 3.0 24.4 + - - +
448 LYS* 3.4 30.9 - - - -
14Q LEU* 3.6 11.4 - - + +
54Q ALA 3.1 14.5 + - - +
55Q LEU* 3.3 15.9 - - + +
57Q PHE* 1.3 78.1 - - - +
59Q ASN* 1.3 75.2 + - - +
61Q ILE* 3.5 1.0 + - - +
62Q TYR* 3.4 50.5 + + + -
68Q VAL* 3.9 19.1 - - + -
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Residues in contact with ASN 59 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328 GLU* 6.0 0.2 - - - -
448 LYS* 4.4 6.6 + - - -
1668 PRO* 6.3 0.8 - - - +
55Q LEU* 2.8 33.6 + - - +
56Q ARG* 3.8 9.1 - - - +
58Q TYR* 1.3 91.1 - - - +
60Q TYR* 1.3 59.3 + - - +
62Q TYR* 3.7 3.4 + - - +
63Q ASP* 3.1 35.8 + - - +
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Residues in contact with TYR 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128N VAL* 4.2 18.2 - - + -
2Q LEU* 4.3 1.3 - - + +
10Q LEU* 4.1 22.2 - - + -
56Q ARG 3.0 18.3 + - - +
57Q PHE 3.9 2.0 - - - +
58Q TYR 3.4 0.2 - - - -
59Q ASN* 1.3 74.4 - - - +
61Q ILE* 1.3 66.8 + - + +
63Q ASP* 3.0 17.3 + - + +
64Q ARG* 3.1 43.3 + - + +
115Q SER* 3.1 13.9 - - - -
116Q THR* 2.9 44.7 + - + -
119Q PHE* 3.5 52.9 - + + -
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Residues in contact with ILE 61 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q LEU* 4.5 4.8 - - + +
7Q LEU* 3.8 10.5 - - + -
10Q LEU* 4.0 40.4 - - + +
11Q ASN* 3.8 21.1 - - - +
14Q LEU* 3.9 11.4 - - + -
57Q PHE* 3.0 23.2 + - + +
58Q TYR 3.8 4.0 - - - +
59Q ASN 3.4 0.2 - - - -
60Q TYR* 1.3 79.8 - - + +
62Q TYR* 1.3 58.9 + - + +
64Q ARG* 3.3 9.0 + - - +
66Q GLY* 2.8 25.9 + - - -
67Q ARG 3.6 28.0 - - - +
68Q VAL* 3.8 21.5 - - + +
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Residues in contact with TYR 62 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298 ALA* 2.6 33.9 + - - +
328 GLU* 3.7 31.6 - - + -
338 ASP* 3.6 25.8 - - + -
132N ALA* 5.3 0.9 - - - +
58Q TYR* 3.4 44.7 + + + +
59Q ASN* 4.3 4.3 - - - +
60Q TYR 3.3 0.4 - - - -
61Q ILE* 1.3 74.2 - - - +
63Q ASP* 1.3 64.7 + - - +
64Q ARG 3.2 0.9 - - - -
65Q ASN* 3.4 11.1 + - - +
66Q GLY 3.5 21.8 - - - +
67Q ARG* 3.4 13.0 + - - -
68Q VAL* 3.5 31.8 + - + -
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Residues in contact with ASP 63 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128N VAL* 4.2 24.2 - - + +
129N GLU* 5.7 5.8 - - - +
131N GLU* 5.3 1.7 - - - +
132N ALA* 3.5 37.8 + - + +
59Q ASN* 3.1 27.1 + - - +
60Q TYR* 3.0 15.0 + - - +
62Q TYR* 1.3 77.8 - - - +
64Q ARG* 1.3 62.1 + - - +
65Q ASN* 3.3 2.8 + - - +
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Residues in contact with ARG 64 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N TYR* 3.5 19.0 + - - -
127N GLN 4.9 0.4 + - - -
128N VAL* 3.8 35.3 + - - +
131N GLU* 4.1 27.5 + - - +
1Q MET* 3.5 35.8 - - - +
2Q LEU* 3.8 27.2 + - + +
60Q TYR* 3.1 56.6 + - + +
61Q ILE 3.3 2.7 + - - +
62Q TYR 3.2 0.4 - - - -
63Q ASP* 1.3 75.7 + - - +
65Q ASN* 1.3 70.1 + - - +
66Q GLY* 3.2 2.2 + - - -
113Q ASP* 5.0 4.8 + - - -
115Q SER* 3.6 13.3 + - - -
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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