Contacts of the helix formed by residues 23 - 55 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLU 5.8 0.2 - - - -
16A GLY* 4.2 0.4 - - - -
21A ARG 4.1 0.8 - - - -
22A MET* 1.3 78.4 - - - +
24A ALA* 1.3 59.5 + - - +
25A ASP* 3.4 12.7 - - + +
26A ARG* 3.2 52.1 + - - +
27A ALA* 3.1 22.7 + - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.8 20.1 - - - +
15A GLU* 3.9 12.5 + - - +
16A GLY* 3.8 13.2 - - - +
22A MET 3.9 0.2 + - - -
23A ASP* 1.3 71.3 - - - +
25A ASP* 1.3 65.6 + - - +
27A ALA* 3.8 0.7 - - - +
28A GLU* 2.9 28.9 + - - +
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 3.4 11.6 - - + +
24A ALA* 1.3 81.8 - - - +
26A ARG* 1.3 65.3 + - - +
28A GLU* 3.4 9.6 + - - +
29A GLN* 3.6 26.2 + - - +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG 3.1 25.7 + - - -
22A MET* 3.6 26.6 - - + +
23A ASP* 3.2 32.6 + - - +
25A ASP* 1.3 80.9 + - - +
27A ALA* 1.3 64.8 + - - +
29A GLN* 3.1 17.5 + - - +
30A CYS* 3.3 9.6 + - - -
143A LEU* 3.2 59.1 + - + +
144A GLY* 4.0 12.9 + - - -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.6 9.2 - - + -
16A GLY* 3.7 9.9 - - - -
22A MET* 4.1 11.4 - - + +
23A ASP 3.1 15.7 + - - +
24A ALA 3.8 1.3 - - - +
26A ARG* 1.3 78.9 - - - +
28A GLU* 1.3 53.4 + - - +
30A CYS* 3.0 5.3 + - - +
31A VAL* 2.8 36.9 + - - +
88A LEU* 3.4 38.1 - - + +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 5.0 6.3 - - - +
14A VAL* 3.8 26.1 - - + +
24A ALA 2.9 18.4 + - - +
25A ASP* 3.8 6.6 - - - +
26A ARG 3.1 0.4 - - - -
27A ALA* 1.3 76.2 - - - +
29A GLN* 1.3 60.8 + - + +
32A ASP* 2.8 51.7 + - - +
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASP* 3.7 26.5 + - - +
26A ARG* 3.1 8.2 + - - +
28A GLU* 1.3 83.0 - - + +
30A CYS* 1.3 61.4 + - - +
32A ASP* 3.9 5.7 - - - +
33A ALA* 3.4 14.2 + - - +
139A LEU* 3.6 29.0 - - + +
143A LEU* 3.4 33.6 - - + +
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Residues in contact with CYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A MET* 6.1 1.3 - - - -
26A ARG* 3.3 5.1 + - - -
27A ALA* 3.0 7.8 + - - +
29A GLN* 1.3 77.6 - - - +
31A VAL* 1.3 63.2 + - - +
33A ALA* 3.0 3.9 + - - +
34A LEU* 2.8 39.8 + - + +
88A LEU* 3.7 17.9 - - + -
139A LEU* 4.3 7.6 - - - -
140A ALA* 4.3 16.4 - - - -
143A LEU* 4.0 19.7 - - - -
145A ASP* 3.6 29.6 - - - -
148A THR* 4.4 2.2 - - + -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.5 35.4 - - + -
27A ALA 2.8 18.4 + - - +
28A GLU 4.0 0.2 - - - +
30A CYS* 1.3 72.9 - - - +
32A ASP* 1.3 70.9 + - - +
34A LEU* 4.4 6.5 - - - +
35A ASN* 2.9 33.1 + - - +
85A VAL* 3.9 34.3 - - + +
88A LEU* 3.8 26.0 - - + -
90A GLY* 4.4 2.9 - - - +
91A VAL 5.1 0.2 - - - +
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 5.8 0.2 - - - +
14A VAL* 4.9 2.4 - - - +
28A GLU* 2.8 47.2 + - - +
29A GLN* 3.9 5.3 - - - +
31A VAL* 1.3 83.5 - - - +
33A ALA* 1.3 62.3 + - - +
35A ASN* 4.3 3.2 - - - +
36A ALA* 3.3 21.0 + - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN 3.4 3.4 + - - +
30A CYS* 3.0 12.1 + - - +
32A ASP* 1.3 75.1 - - - +
34A LEU* 1.3 65.5 + - + +
36A ALA* 3.2 3.7 + - - +
37A ASP* 3.1 16.6 + - - -
136A HIS* 3.2 52.7 - - + +
139A LEU* 3.8 20.2 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A CYS* 2.8 28.1 + - + +
31A VAL* 4.5 0.2 - - - -
33A ALA* 1.3 74.2 - - + +
35A ASN* 1.4 52.4 + - - +
37A ASP* 2.8 10.6 + - - +
38A LEU* 2.7 35.7 + - - +
81A LEU* 4.0 15.4 - - + +
84A ARG* 3.8 33.4 - - + -
85A VAL* 3.5 21.3 - - + -
88A LEU* 4.1 17.5 - - + -
148A THR* 4.1 7.4 - - + -
151A MET* 5.7 0.4 - - - -
152A LEU* 3.6 40.2 - - + -
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Residues in contact with ASN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 6.1 1.0 - - - +
31A VAL* 2.9 24.5 + - - +
32A ASP* 4.3 3.6 - - - +
34A LEU* 1.4 73.8 - - - +
36A ALA* 1.3 64.9 + - - +
38A LEU* 3.6 11.0 - - - +
39A ALA* 3.1 18.5 + - - +
85A VAL* 3.8 12.1 - - - +
91A VAL 2.9 26.3 + - - +
92A PRO* 3.2 8.6 - - - +
93A HIS* 3.1 59.8 + - + +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP 3.3 15.9 + - - +
33A ALA* 3.2 7.1 + - - +
34A LEU 3.1 1.0 - - - -
35A ASN* 1.3 81.3 - - - +
37A ASP* 1.3 66.1 + - - +
39A ALA* 3.6 5.5 + - - +
40A ASN* 3.4 26.9 + - - +
93A HIS* 5.1 2.0 - - - -
102A GLU* 4.7 9.2 - - - +
136A HIS* 4.9 4.5 - - + +
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA 3.1 8.7 + - - +
34A LEU* 2.8 10.5 + - - +
36A ALA* 1.3 78.7 - - - +
38A LEU* 1.3 62.1 + - - +
40A ASN* 3.2 8.2 + - - +
41A VAL* 2.8 36.2 + - + +
81A LEU* 3.9 15.4 - - + +
129A ILE* 5.7 4.1 - - + +
132A ALA* 4.0 10.2 - - - +
133A THR* 4.2 15.7 + - - +
136A HIS* 2.8 45.7 + - - +
152A LEU* 4.3 13.9 - - - +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 2.7 18.4 + - - +
35A ASN* 3.6 23.3 - - - +
37A ASP* 1.3 73.7 - - - +
39A ALA* 1.3 57.2 + - - +
41A VAL* 4.6 0.4 - - - -
42A TYR* 2.8 44.8 + - + +
78A ALA* 3.4 39.7 - - + +
81A LEU* 3.8 14.8 - - + +
82A ALA* 3.8 12.3 - - + -
85A VAL* 5.4 0.2 - - + -
92A PRO* 3.7 16.8 - - + -
93A HIS* 3.7 22.0 - - + +
99A LEU* 4.0 6.3 - - + -
53B TRP* 4.6 0.4 - - + -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASN 3.1 16.9 + - - +
36A ALA 3.8 4.3 - - - +
37A ASP 3.2 0.2 - - - -
38A LEU* 1.3 78.0 - - - +
40A ASN* 1.3 56.0 + - - +
42A TYR* 3.6 1.7 + - - +
43A VAL* 3.0 33.4 + - - +
93A HIS* 4.2 4.5 - - + -
99A LEU* 3.2 32.4 - - - +
102A GLU* 3.7 27.6 - - + +
103A ALA* 4.1 2.0 - - - -
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ALA* 3.4 17.9 + - - +
37A ASP* 3.2 11.4 + - - +
39A ALA* 1.3 75.3 - - - +
41A VAL* 1.3 59.4 + - - +
43A VAL* 3.3 4.3 + - - +
44A LEU* 2.9 26.3 + - - +
103A ALA* 3.3 4.6 - - - +
104A SER* 2.8 42.9 + - - +
105A VAL* 3.1 26.5 + - + +
128A ASP* 5.8 2.0 + - - +
129A ILE* 3.7 24.8 - - + +
132A ALA* 5.6 5.1 - - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASP* 2.8 20.9 + - + +
38A LEU 3.9 2.2 - - - +
40A ASN* 1.3 74.5 - - - +
42A TYR* 1.3 61.8 + - - +
44A LEU* 3.1 8.9 - - + +
45A TYR* 2.8 25.6 + - - +
74A ALA* 3.2 37.4 - - + +
77A VAL* 4.2 11.4 - - + -
78A ALA* 3.8 13.9 - - + +
81A LEU* 4.1 14.4 - - + -
129A ILE* 4.0 26.9 - - + -
159A LEU* 4.4 5.2 - - + -
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 2.8 32.2 + - + +
39A ALA 4.1 2.5 - - - +
41A VAL* 1.3 74.7 - - - +
43A VAL* 1.3 64.2 + - - +
45A TYR* 3.4 24.4 + + + -
46A HIS* 3.1 30.2 + - + -
75A GLU* 4.3 9.3 + - + +
78A ALA* 3.7 19.5 - - + -
79A ASP 5.3 0.2 + - - -
99A LEU* 3.6 26.5 - - + -
45B TYR* 2.8 30.2 + - - -
46B HIS* 3.4 28.7 - + + -
49B LYS* 3.6 18.5 + - - +
53B TRP* 3.8 22.7 - + - -
96B PRO* 4.9 1.1 - - + -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA 3.0 24.0 + - - +
40A ASN 3.3 1.1 + - - +
42A TYR* 1.3 73.4 - - - +
44A LEU* 1.3 68.2 + - - +
46A HIS* 3.2 2.4 + - - +
47A GLN* 2.9 22.9 + - - +
99A LEU* 4.1 0.9 - - + +
100A GLN* 3.8 27.4 - - + +
103A ALA* 3.5 18.4 - - + -
105A VAL* 3.3 30.7 - - + -
107A VAL* 4.3 21.4 - - + +
125A ILE* 4.9 5.2 - - + -
96B PRO* 4.3 17.0 - - + +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASN 2.9 14.8 + - - +
41A VAL* 3.1 11.0 - - + +
43A VAL* 1.3 78.2 - - - +
45A TYR* 1.3 66.3 + - - +
47A GLN* 3.1 3.2 + - - -
48A LEU* 2.9 47.5 + - + +
74A ALA* 4.2 14.6 - - + -
122A ASP* 4.5 5.2 - - + +
125A ILE* 4.0 26.5 - - + -
126A TYR* 3.6 44.9 - - + +
129A ILE* 3.8 21.1 - - + -
159A LEU* 4.9 6.1 - - + -
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL 2.8 16.9 + - - +
42A TYR* 3.7 29.2 - + + +
43A VAL 3.2 0.4 - - - -
44A LEU* 1.3 76.7 - - - +
46A HIS* 1.3 83.2 + + - +
48A LEU* 3.2 5.4 + - - +
49A LYS* 2.9 41.1 + - + +
71A ALA* 3.1 29.4 - - + -
74A ALA* 3.9 15.7 - - + -
75A GLU* 3.5 22.0 - - + +
42B TYR* 2.7 32.6 + + - -
45B TYR* 4.1 6.4 + - - -
75B GLU* 2.2 39.3 + - - +
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Residues in contact with HIS 46 (chain A).
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 3.1 20.1 + - - +
43A VAL 3.9 1.6 - - - +
45A TYR* 1.3 86.6 - + - +
47A GLN* 1.3 56.5 + - - +
49A LYS* 3.5 6.1 + - - +
50A LYS* 3.0 26.0 + - - +
53A TRP* 5.4 1.9 - - - -
42B TYR* 3.5 36.6 + + - -
46B HIS* 2.8 32.0 + + - -
94B ALA* 3.7 18.1 + - - +
95B SER* 5.8 0.2 - - - -
96B PRO* 3.4 35.3 - - + +
99B LEU* 3.2 30.5 - - + +
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL 2.9 17.3 + - - +
44A LEU* 3.7 3.4 - - + +
46A HIS* 1.3 72.9 - - - +
48A LEU* 1.3 60.6 + - - +
50A LYS* 3.1 12.4 + - + +
51A HIS* 2.8 46.5 + - + +
106A ASP 4.5 1.2 + - - -
107A VAL* 3.9 11.3 - - + +
108A GLU* 3.0 36.9 + - - +
121A ASN* 3.8 19.6 - - - +
122A ASP* 3.0 25.4 + - - +
125A ILE* 3.2 27.4 - - + +
94B ALA* 6.0 0.2 - - - -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 2.9 38.8 + - + +
45A TYR 3.6 3.4 - - - +
47A GLN* 1.3 74.5 - - - +
49A LYS* 1.3 66.9 + - - +
51A HIS* 3.2 4.3 + - - +
52A HIS* 2.8 25.1 + - - +
67A LEU* 4.0 23.2 - - + +
70A ALA* 3.7 25.6 - - + +
71A ALA* 3.8 14.6 - - + +
74A ALA* 4.4 2.2 - - + -
122A ASP* 3.8 29.8 - - + +
126A TYR* 3.6 27.6 - - + +
166A ILE* 4.9 1.6 - - + -
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Residues in contact with LYS 49 (chain A).
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* 2.9 32.3 + - + +
46A HIS* 3.5 9.9 - - - +
48A LEU* 1.3 76.3 - - - +
50A LYS* 1.3 65.8 + - - +
52A HIS* 3.1 15.9 + - + +
53A TRP* 2.8 51.4 + - + +
68A GLY* 5.6 3.6 + - - -
71A ALA* 3.5 20.5 - - + +
42B TYR* 3.8 21.3 + - - +
75B GLU* 4.1 15.6 + - - +
79B ASP* 3.3 34.9 + - - +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A HIS 3.0 15.5 + - - +
47A GLN* 3.1 15.9 + - + +
49A LYS* 1.3 77.8 - - - +
51A HIS* 1.3 66.4 + - + +
53A TRP* 3.4 13.0 - - - +
54A ASN* 2.9 48.3 + - - +
108A GLU* 3.1 25.1 + - + +
109A ASP 2.8 20.2 + - - -
110A GLU* 3.8 9.9 + - - +
111A ASP 2.6 33.5 + - - -
112A VAL* 4.4 9.4 - - - +
91B VAL* 5.7 0.9 - - - -
92B PRO 5.7 0.9 - - - -
94B ALA* 3.6 27.2 - - + +
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN* 2.8 21.6 + - + +
48A LEU* 3.7 3.8 - - - +
50A LYS* 1.3 88.5 - - + +
52A HIS* 1.3 59.2 + - - +
54A ASN* 4.3 3.8 - - + +
55A VAL* 3.0 34.6 + - - +
67A LEU* 3.6 17.0 - - + -
108A GLU* 3.0 31.8 + - - -
112A VAL* 6.4 1.6 - - + -
113A TYR 6.2 0.4 - - - -
115A ILE* 5.1 2.9 - - + +
118A SER* 3.3 35.7 + - - -
119A LEU* 5.0 0.6 - - + +
122A ASP* 2.4 44.4 + - - +
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU 2.8 20.4 + - - +
49A LYS* 3.3 15.4 + - - +
51A HIS* 1.3 72.3 - - - +
53A TRP* 1.4 86.3 + + - +
54A ASN 3.3 0.2 + - - -
55A VAL* 3.6 8.5 - - - +
64A HIS* 2.6 71.4 + + - +
65A LEU* 5.2 2.0 - - + -
67A LEU* 3.7 18.0 - - + +
68A GLY* 3.3 21.4 + - - +
79B ASP* 3.6 4.2 + - - -
83B GLU* 3.3 1.3 + - - -
303B FE 2.3 31.1 - - - -
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Residues in contact with TRP 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A HIS* 5.4 2.7 - - - -
49A LYS* 2.8 40.0 + - + +
50A LYS* 3.4 23.1 - - + +
52A HIS* 1.4 82.8 - + - +
54A ASN* 1.3 67.6 + - - +
55A VAL 3.8 1.9 + - - +
64A HIS* 4.9 1.5 + - - -
38B LEU* 4.6 1.6 - - + -
42B TYR* 3.9 28.5 - + - -
78B ALA 4.6 0.4 - - - -
79B ASP* 3.0 26.3 + - - -
82B ALA* 3.3 27.9 - - + +
83B GLU* 3.5 26.7 - - + +
86B GLN* 3.6 18.3 + - + +
92B PRO* 3.4 24.5 - - + -
93B HIS 3.5 24.9 - - - -
94B ALA* 4.4 7.6 - - - -
326B FE 3.8 10.2 - - - -
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS* 2.9 41.9 + - + +
51A HIS* 4.6 3.6 - - + +
52A HIS 3.2 0.4 - - - -
53A TRP* 1.3 84.1 - - - +
55A VAL* 1.3 68.9 + - - +
56A GLU* 3.3 18.8 + - - +
112A VAL* 3.7 42.7 - - + +
8B ARG* 5.5 1.7 + - - -
86B GLN* 3.1 31.5 - - - +
90B GLY 4.5 2.1 - - - +
91B VAL* 5.2 0.4 - - - +
92B PRO* 3.7 18.5 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 3.0 19.3 + - - +
52A HIS* 3.6 11.9 - - - +
53A TRP 3.6 2.1 - - - +
54A ASN* 1.3 79.7 - - - +
56A GLU* 1.3 68.7 + - - +
60A PHE* 3.6 38.5 - - + +
63A LEU* 3.7 24.9 - - + -
64A HIS* 4.0 14.4 - - + +
67A LEU* 4.6 0.9 - - + -
115A ILE* 3.6 32.5 - - + -
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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