Contacts of the helix formed by residues 23 - 55 (chain B) in PDB entry 1TKP
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 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU 5.6 0.2 - - - -
21B ARG 4.0 1.2 - - - -
22B MET* 1.3 76.0 - - - +
24B ALA* 1.3 54.3 + - - +
25B ASP* 3.2 14.8 - - + +
26B ARG* 3.2 50.0 + - - +
27B ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.5 21.5 - - - +
15B GLU* 3.7 14.5 + - - +
16B GLY* 3.7 14.1 - - - +
22B MET 3.8 1.0 + - - -
23B ASP* 1.3 70.1 - - - +
25B ASP* 1.3 60.2 + - - +
27B ALA* 3.7 1.1 - - - -
28B GLU* 2.8 34.2 + - - +
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Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASP* 3.1 13.5 + - + +
24B ALA* 1.3 81.7 - - - +
26B ARG* 1.3 69.1 + - - +
28B GLU* 3.4 8.0 + - - +
29B GLN* 3.5 26.1 + - - +
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG 3.1 26.5 + - - -
22B MET* 3.3 24.5 - - + -
23B ASP* 3.2 30.0 + - - +
25B ASP* 1.3 85.1 + - - +
27B ALA* 1.3 64.3 + - - +
29B GLN* 3.1 14.5 + - - +
30B CYS* 3.5 13.8 + - - -
143B LEU* 2.9 54.1 + - + +
144B GLY* 4.1 12.1 + - - -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 4.1 3.8 - - + -
16B GLY* 3.7 12.6 - - - -
22B MET* 4.0 14.1 - - + +
23B ASP 2.9 17.1 + - - +
24B ALA* 3.9 2.9 - - - +
25B ASP 3.2 0.4 - - - -
26B ARG* 1.3 78.1 - - - +
28B GLU* 1.3 52.1 + - - +
30B CYS* 2.9 6.8 + - - +
31B VAL* 2.8 36.6 + - - +
88B LEU* 3.4 36.3 - - + +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 3.6 20.3 - - - +
14B VAL* 3.8 29.2 + - + +
24B ALA* 2.8 18.8 + - - +
25B ASP* 4.0 4.0 - - - +
26B ARG 3.3 0.2 - - - -
27B ALA* 1.3 73.7 - - - +
29B GLN* 1.3 66.2 + - + +
31B VAL* 4.2 2.5 - - - -
32B ASP* 2.9 50.6 + - - +
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Residues in contact with GLN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASP* 3.5 24.2 + - - +
26B ARG 3.1 7.7 + - - +
28B GLU* 1.3 80.7 - - + +
30B CYS* 1.3 61.8 + - - +
32B ASP* 4.1 5.2 - - - +
33B ALA* 3.6 11.1 + - - +
139B LEU* 3.5 30.4 - - + +
143B LEU* 3.3 34.6 - - + +
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B MET* 5.8 1.3 - - - -
26B ARG 3.5 6.9 + - - -
27B ALA* 2.9 4.1 + - - +
29B GLN* 1.3 73.6 - - - +
31B VAL* 1.3 61.2 + - - +
33B ALA* 3.2 6.7 + - - +
34B LEU* 2.8 39.3 + - + +
88B LEU* 3.8 20.4 - - + -
139B LEU* 4.8 2.0 - - - -
140B ALA* 4.4 10.8 - - - -
143B LEU* 3.5 26.5 - - - -
145B ASP* 3.4 30.7 - - - +
148B THR* 4.6 5.6 - - + -
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.7 33.9 - - + -
27B ALA 2.8 18.3 + - - +
28B GLU 4.1 2.5 - - - +
30B CYS* 1.3 77.6 - - - +
32B ASP* 1.3 63.0 + - - +
34B LEU* 3.8 7.1 - - - +
35B ASN* 2.8 38.2 + - - +
85B VAL* 3.8 30.9 - - + +
88B LEU* 3.6 25.8 - - + -
90B GLY* 4.3 2.2 - - - -
91B VAL 5.1 0.7 - - - +
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 5.6 0.3 - - - +
14B VAL* 4.9 1.0 - - - +
28B GLU* 2.9 46.0 + - - +
29B GLN* 4.1 5.1 - - - +
31B VAL* 1.3 81.7 - - - +
33B ALA* 1.3 59.8 - - - +
35B ASN* 4.1 5.0 - - - +
36B ALA* 3.4 20.1 + - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLN 3.6 11.2 + - - +
30B CYS* 3.2 9.0 + - - +
32B ASP* 1.3 76.3 - - - +
34B LEU* 1.3 63.3 + - + +
36B ALA* 3.3 2.7 + - - +
37B ASP* 3.1 22.7 + - - -
136B HIS* 3.3 52.2 - - + +
139B LEU* 4.3 10.1 - - + -
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B CYS* 2.8 33.9 + - + +
31B VAL* 4.3 1.8 - - - -
33B ALA* 1.3 73.4 - - + +
35B ASN* 1.3 56.7 + - - +
37B ASP* 3.2 7.4 - - - +
38B LEU* 2.6 35.3 + - - +
81B LEU* 4.0 16.6 - - + +
84B ARG* 4.0 30.3 - - + -
85B VAL* 3.6 21.1 - - + +
88B LEU* 4.5 3.8 - - + -
136B HIS* 5.7 0.2 - - + -
148B THR* 4.0 19.3 - - + -
151B MET* 5.4 1.1 - - - -
152B LEU* 3.7 33.4 - - + -
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Residues in contact with ASN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 2.8 22.8 + - - +
32B ASP* 4.1 5.4 - - - +
34B LEU* 1.3 78.2 - - - +
36B ALA* 1.3 61.8 + - - +
38B LEU* 3.2 10.9 + - - +
39B ALA* 3.1 12.0 + - - +
85B VAL* 3.9 10.5 - - - +
91B VAL 2.8 27.1 + - - +
92B PRO* 3.2 8.9 - - - +
93B HIS* 3.1 64.7 + - + +
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASP 3.4 12.4 + - - +
33B ALA* 3.3 9.8 + - - +
34B LEU 3.1 0.8 - - - -
35B ASN* 1.3 79.5 - - - +
37B ASP* 1.3 67.4 + - - +
39B ALA* 3.3 5.0 + - - +
40B ASN* 3.3 27.9 + - - +
93B HIS* 5.0 2.0 - - - -
102B GLU 4.9 8.5 - - - +
136B HIS* 4.9 4.5 - - + -
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA 3.1 10.5 + - - +
34B LEU* 3.2 12.8 - - - +
36B ALA* 1.3 77.5 - - - +
38B LEU* 1.3 63.7 + - - +
40B ASN* 3.1 8.4 + - - +
41B VAL* 2.9 28.8 + - + +
81B LEU* 3.9 15.9 - - + +
129B ILE* 5.3 3.7 - - - +
132B ALA* 4.1 11.8 - - - +
133B THR* 4.0 14.4 + - - -
136B HIS* 3.0 31.2 + - - +
152B LEU* 3.8 22.7 - - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP* 4.6 1.1 - - + -
34B LEU 2.6 19.4 + - - +
35B ASN* 3.2 26.9 + - - +
37B ASP* 1.3 72.9 - - - +
39B ALA* 1.3 57.7 + - - +
41B VAL* 3.3 0.7 + - - -
42B TYR* 2.8 39.4 + - + +
78B ALA* 3.4 41.1 - - + +
81B LEU* 3.9 10.5 - - + +
82B ALA* 3.6 15.5 - - + +
85B VAL* 5.1 0.4 - - + -
92B PRO* 3.6 23.3 - - + -
93B HIS* 3.7 12.6 - - + +
99B LEU* 4.2 9.6 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN 3.1 11.6 + - - +
36B ALA* 3.3 3.1 + - - +
37B ASP 3.2 0.2 - - - -
38B LEU* 1.3 79.4 - - - +
40B ASN* 1.3 65.2 + - - +
42B TYR* 3.4 1.4 + - - +
43B VAL* 3.0 26.7 + - - +
93B HIS* 4.0 5.4 - - + -
99B LEU* 3.2 35.4 - - - +
102B GLU* 3.8 16.8 - - + +
103B ALA* 3.6 14.1 - - - +
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA* 3.3 15.1 + - - +
37B ASP* 3.1 11.8 + - - +
39B ALA* 1.3 81.5 - - - +
41B VAL* 1.3 57.7 + - - +
43B VAL* 3.1 6.7 + - - +
44B LEU* 2.9 27.4 + - - +
103B ALA* 3.4 6.2 - - - +
104B SER* 2.9 42.6 + - - -
105B VAL* 3.2 21.7 + - + +
128B ASP* 5.5 1.4 + - - +
129B ILE* 3.8 25.7 - - + +
132B ALA* 5.3 7.3 - - - +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASP* 2.9 21.0 + - + +
38B LEU* 4.0 2.7 - - - +
40B ASN* 1.3 77.0 - - - +
42B TYR* 1.3 58.3 + - - +
44B LEU* 3.3 5.4 + - + +
45B TYR* 2.9 24.8 + - - +
74B ALA* 3.1 39.1 - - + +
77B VAL* 4.0 18.6 - - + -
78B ALA* 3.8 12.8 - - + +
81B LEU* 4.3 8.1 - - + -
129B ILE* 3.8 32.5 - - + -
159B LEU* 4.3 6.3 - - + -
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 2.7 29.5 + - - -
46A HIS* 3.5 26.7 - + + -
49A LYS* 3.8 16.6 - - - +
53A TRP* 3.9 21.1 - + - -
96A PRO* 5.1 1.1 - - - -
38B LEU* 2.8 24.1 + - + +
39B ALA 4.0 1.1 - - - +
41B VAL* 1.3 75.2 - - - +
43B VAL* 1.3 63.7 + - - +
45B TYR* 3.3 30.9 + + + -
46B HIS* 3.2 23.7 + + + -
75B GLU* 4.1 8.7 + - + +
78B ALA* 3.7 26.1 - - + +
79B ASP 5.5 0.3 + - - -
99B LEU* 3.7 30.1 - - + -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO* 4.5 17.4 - - + +
39B ALA 3.0 15.8 + - - +
40B ASN 3.1 3.6 + - - +
42B TYR* 1.3 72.2 - - - +
44B LEU* 1.3 69.3 + - - +
46B HIS* 2.9 3.5 + - - +
47B GLN* 2.9 23.1 + - - +
99B LEU* 3.8 10.5 - - + +
100B GLN* 3.8 19.1 - - + -
103B ALA* 3.6 16.8 - - + -
105B VAL* 3.0 36.8 - - + -
107B VAL* 4.4 17.7 - - + +
125B ILE* 4.9 2.7 - - + -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASN 2.9 13.8 + - - +
41B VAL* 3.4 10.3 - - + +
42B TYR 3.3 0.2 - - - -
43B VAL* 1.3 76.2 - - - +
45B TYR* 1.3 51.1 + - - +
47B GLN* 3.0 4.2 + - - +
48B LEU* 2.8 51.1 + - + +
74B ALA* 4.0 19.3 - - + -
122B ASP* 4.3 5.2 - - + +
125B ILE* 3.6 37.0 - - + -
126B TYR* 3.7 51.8 - - + -
129B ILE* 4.1 13.5 - - + -
159B LEU* 4.8 6.3 - - + -
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 2.8 32.4 + + - -
45A TYR* 4.1 8.3 + + - -
75A GLU* 3.0 35.5 + - - +
316A FE 4.5 0.2 - - - -
41B VAL 2.9 13.8 + - - +
42B TYR* 3.5 37.9 - + + +
43B VAL 3.1 0.2 - - - -
44B LEU* 1.3 76.1 - - - +
46B HIS* 1.3 77.2 + + - +
48B LEU* 3.4 5.4 + - - +
49B LYS* 3.0 41.5 + - + +
71B ALA* 3.1 30.1 - - + -
74B ALA* 4.1 13.0 - - + -
75B GLU* 3.8 13.9 - - + +
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.4 44.7 + + - -
46A HIS* 2.8 32.8 + + - -
94A ALA* 3.8 17.4 + - - +
95A SER* 5.8 0.4 - - - -
96A PRO* 3.4 38.1 - - + +
99A LEU* 3.6 20.2 - - + +
42B TYR* 3.2 13.5 + + + +
43B VAL 2.9 5.4 + - - +
45B TYR* 1.3 93.3 - + - +
47B GLN* 1.3 55.9 + - - +
49B LYS* 3.4 6.8 + - - +
50B LYS* 3.0 24.8 + - - +
53B TRP* 5.4 1.3 - - - -
99B LEU* 5.7 0.2 - - + -
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 6.1 0.2 - - - -
43B VAL 2.9 12.3 + - - +
44B LEU* 3.6 7.0 - - + +
46B HIS* 1.3 75.7 - - - +
48B LEU* 1.3 63.6 + - - +
50B LYS* 3.3 9.3 + - + +
51B HIS* 3.0 41.9 + - + +
106B ASP 4.9 1.0 + - - -
107B VAL* 3.7 12.7 - - + +
108B GLU* 3.0 36.1 + - - +
121B ASN* 3.8 18.6 - - - +
122B ASP* 2.8 25.2 + - - +
125B ILE* 3.4 24.7 - - + +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 2.8 42.6 + - + +
45B TYR 3.7 4.7 - - - +
47B GLN* 1.3 70.9 - - - +
49B LYS* 1.3 59.9 + - - +
51B HIS* 3.4 2.7 + - - +
52B HIS* 2.9 31.3 + - - +
67B LEU* 3.8 30.7 - - + +
70B ALA* 3.5 28.7 - - + +
71B ALA* 3.6 14.6 - - + +
74B ALA* 4.3 3.1 - - + -
122B ASP* 3.9 18.6 - - + +
126B TYR* 3.3 31.9 - - + +
166B ILE* 5.0 0.2 - - + -
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.6 20.4 + - - +
75A GLU* 4.1 15.4 + - - -
79A ASP* 3.0 38.7 + - - +
304A FE 4.3 2.2 - - - -
45B TYR* 3.0 32.7 + - + +
46B HIS* 3.4 11.7 - - - +
48B LEU* 1.3 74.6 - - - +
50B LYS* 1.3 65.3 + - - +
52B HIS* 3.2 14.2 + - + +
53B TRP* 2.9 55.6 + - + +
68B GLY* 5.7 3.0 + - - -
71B ALA* 3.7 20.9 - - + -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL* 6.0 0.9 - - - -
94A ALA* 3.3 29.2 - - + -
46B HIS 3.0 10.4 + - - +
47B GLN* 3.4 14.4 - - + +
48B LEU 3.2 0.2 - - - -
49B LYS* 1.3 81.8 - - - +
51B HIS* 1.3 65.0 + - + +
53B TRP* 3.4 11.5 + - + +
54B ASN* 2.7 51.6 + - - +
108B GLU* 3.0 28.3 + - + +
109B ASP 2.8 19.4 + - - -
110B GLU* 4.1 6.1 + - - +
111B ASP 2.7 32.5 + - - -
112B VAL* 4.5 7.9 - - - +
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 3.0 20.9 + - + +
48B LEU 3.9 2.0 - - - +
50B LYS* 1.3 87.9 - - + +
52B HIS* 1.3 59.0 + - - +
54B ASN* 4.7 3.6 - - + -
55B VAL* 2.8 38.2 + - - +
67B LEU* 3.8 18.4 - - + -
108B GLU* 2.9 34.2 + - - -
113B TYR 6.2 0.2 - - - -
115B ILE* 5.2 3.4 - - + -
118B SER* 3.2 36.9 + - - -
119B LEU* 5.5 0.4 - - + -
122B ASP* 2.4 45.7 + - - +
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Residues in contact with HIS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP* 3.7 2.0 + - - -
83A GLU* 3.1 2.9 + - - -
304A FE 2.1 31.2 - - - -
48B LEU 2.9 19.3 + - - +
49B LYS* 3.2 14.1 + - - +
51B HIS* 1.3 76.3 - - - +
53B TRP* 1.3 85.4 + + - +
55B VAL* 3.7 6.1 - - - +
64B HIS* 2.7 75.8 + + - -
65B LEU* 5.4 0.7 - - - -
67B LEU* 3.7 18.3 - - + +
68B GLY* 3.3 20.2 + - - +
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Residues in contact with TRP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.6 1.3 - - + -
42A TYR* 3.8 28.9 - + - -
79A ASP* 2.8 27.1 + - - -
82A ALA* 3.2 36.0 - - + +
83A GLU* 3.7 21.6 - - + +
86A GLN* 3.7 14.0 + - + +
92A PRO* 3.7 19.7 - - + -
93A HIS 3.7 22.2 - - - -
94A ALA* 4.5 7.0 - - - -
99A LEU* 5.9 0.4 - - + -
46B HIS* 5.6 1.8 - - - -
49B LYS* 2.9 40.5 + - + +
50B LYS* 3.5 17.9 - - + +
51B HIS 3.2 0.2 - - - -
52B HIS* 1.3 91.8 - + - +
54B ASN* 1.3 63.8 + - - +
64B HIS* 5.0 0.2 - - - -
327B FE 3.0 22.0 - - - -
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Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 5.7 1.7 + - - -
86A GLN* 3.2 28.8 - - - +
90A GLY 4.8 1.0 - - - +
91A VAL* 5.4 0.6 - - - +
92A PRO* 3.9 15.2 + - - +
50B LYS* 2.7 42.2 + - - +
51B HIS* 4.2 4.3 - - + +
53B TRP* 1.3 83.8 - - - +
55B VAL* 1.3 67.5 + - - +
56B GLU* 3.2 17.6 + - - +
112B VAL* 3.8 43.5 - - + +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS* 2.8 24.3 + - - +
52B HIS* 3.7 13.7 - - - +
54B ASN* 1.3 74.2 - - - +
56B GLU* 1.3 67.6 + - - +
60B PHE* 3.5 35.6 - - + +
63B LEU* 3.9 19.1 - - + -
64B HIS* 3.7 16.6 - - + +
67B LEU* 4.7 1.1 - - + -
115B ILE* 3.1 41.5 - - + -
327B FE 4.1 5.7 - - - -
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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) + - + + + + + -
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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