Contacts of the helix formed by residues 29 - 67 (chain E) in PDB entry 3V2P
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 29 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MET* 4.0 9.2 - - + -
30D ALA* 3.4 13.7 - - + +
31D PRO* 3.4 42.8 - - + -
34D LEU* 4.0 23.3 - - + -
28E ASP* 1.3 88.1 + - - +
30E ALA* 1.3 58.1 + - - +
31E PRO* 3.3 2.5 - - - -
32E GLN* 3.1 23.0 + - + +
33E MET* 2.9 34.5 + - + +
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Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.8 25.7 - - + +
30A ALA 5.4 0.7 - - - +
33A MET* 4.1 16.9 - - - +
27E MET 3.3 20.0 - - - +
28E ASP* 2.6 14.5 + - + -
29E LEU* 1.3 72.3 - - - +
31E PRO* 1.3 65.5 - - + +
33E MET* 3.9 3.0 - - - +
34E LEU* 2.9 27.0 + - - +
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Residues in contact with PRO 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.5 23.6 - - + -
27E MET 4.3 2.9 - - - +
28E ASP 3.2 12.3 - - - +
29E LEU 3.4 3.1 - - - -
30E ALA* 1.3 95.4 - - + +
32E GLN* 1.3 71.8 + - - +
34E LEU* 3.6 3.5 + - + +
35E ARG* 3.2 22.3 + - - +
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Residues in contact with GLN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 3.7 29.2 - - + -
28E ASP 4.6 0.4 + - - -
29E LEU* 3.4 35.4 - - - +
31E PRO* 1.3 85.4 - - - +
33E MET* 1.3 63.3 + - - +
35E ARG* 3.3 7.1 + - - +
36E GLU* 3.2 26.9 + - - +
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Residues in contact with MET 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A MET* 3.6 26.9 - - + +
33B MET* 5.6 2.7 - - + -
37C LEU* 4.9 1.3 - - + -
30D ALA* 4.6 8.1 - - - +
33D MET* 3.7 43.1 - - + +
34D LEU* 4.0 18.4 - - + -
37D LEU* 3.5 30.1 - - + +
28E ASP* 4.5 12.3 - - - +
29E LEU* 2.9 21.0 + - + +
30E ALA* 3.9 1.8 - - - +
32E GLN* 1.3 73.6 - - - +
34E LEU* 1.3 66.4 + - - +
36E GLU* 3.2 3.8 + - - +
37E LEU* 3.0 27.8 + - - +
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Residues in contact with LEU 34 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.2 24.0 - - + -
32A GLN* 3.7 42.0 - - + +
33A MET* 4.1 19.9 - - + +
36A GLU* 3.6 27.6 - - + -
30E ALA 2.9 18.4 + - - +
31E PRO 3.7 4.0 - - - +
33E MET* 1.3 77.1 - - - +
35E ARG* 1.3 57.8 + - - +
37E LEU* 3.1 5.7 + - - +
38E GLN* 2.9 45.6 + - + +
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Residues in contact with ARG 35 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PRO 3.2 12.0 + - - +
32E GLN* 3.5 10.8 - - - +
33E MET 3.2 0.2 - - - -
34E LEU* 1.3 79.9 - - - +
36E GLU* 1.3 68.2 + - - +
38E GLN* 3.2 16.8 + - - +
39E GLU* 2.5 53.9 + - - +
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 3.7 18.5 - - + +
37D LEU* 3.7 22.0 - - + +
38D GLN* 3.5 39.4 + - + +
41D ASN* 3.8 20.5 + - - +
32E GLN 3.2 15.7 + - - +
33E MET 3.6 6.3 - - - +
35E ARG* 1.3 83.7 - - - +
37E LEU* 1.3 59.2 + - - +
39E GLU* 3.4 9.2 + - - +
40E THR* 2.9 32.8 + - - -
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Residues in contact with LEU 37 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.6 34.3 - - + -
33A MET* 3.9 50.3 - - + +
36A GLU* 4.0 13.2 - - + -
37A LEU* 4.0 15.5 - - + -
40A THR* 4.8 2.5 + - - +
33B MET* 5.3 0.4 - - + -
37D LEU* 3.6 20.4 - - + -
33E MET 3.0 19.3 + - - +
34E LEU* 3.4 6.5 - - - +
36E GLU* 1.3 77.3 - - - +
38E GLN* 1.3 58.0 + - - +
40E THR* 3.2 6.6 + - - +
41E ASN* 2.9 34.8 + - - +
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Residues in contact with GLN 38 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.1 26.3 + - - -
36A GLU* 3.7 31.7 + - + +
34E LEU* 2.9 31.1 + - + +
35E ARG* 3.2 17.5 + - - +
37E LEU* 1.3 77.9 - - - +
39E GLU* 1.3 62.1 + - + +
41E ASN* 3.4 2.4 + - - +
42E ALA* 3.0 23.2 + - - +
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Residues in contact with GLU 39 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN* 2.8 35.6 + - - +
45D GLN* 4.8 3.5 + - - +
35E ARG* 2.5 60.6 + - - +
36E GLU* 3.8 11.2 - - - +
38E GLN* 1.3 77.0 - - + +
40E THR* 1.3 64.1 + - - +
42E ALA* 3.3 7.6 + - - +
43E ALA* 3.0 22.7 + - - +
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Residues in contact with THR 40 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 4.3 45.9 - - + +
40A THR* 4.8 6.5 - - + +
37D LEU* 4.7 2.1 + - - +
40D THR* 4.3 10.0 - - + +
41D ASN* 4.1 21.4 - - - +
44D LEU* 4.7 7.1 - - + +
36E GLU 2.9 22.6 + - - -
37E LEU* 3.5 8.6 - - - +
39E GLU* 1.3 77.8 - - - +
41E ASN* 1.3 57.8 + - - +
43E ALA* 3.2 5.6 + - - +
44E LEU* 2.9 27.9 + - + +
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Residues in contact with ASN 41 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU* 2.7 53.7 + - - +
39A GLU* 3.7 8.2 - - + +
40A THR* 2.4 41.2 + - - +
43A ALA* 5.6 0.9 - - - +
37E LEU 2.9 17.8 + - - +
38E GLN 3.7 4.0 - - - +
40E THR* 1.3 76.2 - - - +
42E ALA* 1.3 59.2 + - - +
44E LEU* 3.7 5.6 - - - +
45E GLN* 2.9 48.7 + - - +
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Residues in contact with ALA 42 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ARG* 3.8 12.8 + - - +
38E GLN 3.0 13.6 + - - +
39E GLU* 3.5 11.4 - - - +
40E THR 3.2 0.2 - - - -
41E ASN* 1.3 76.8 - - - +
43E ALA* 1.3 62.5 + - - +
45E GLN* 3.6 11.0 + - - +
46E ASP* 3.3 15.1 + - - +
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Residues in contact with ALA 43 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.4 20.4 - - + +
45D GLN* 3.9 21.3 - - - +
48D ARG* 3.9 22.0 + - - +
39E GLU 3.0 13.8 + - - +
40E THR* 3.6 8.5 - - - +
42E ALA* 1.3 75.1 - - - +
44E LEU* 1.3 59.5 + - - +
46E ASP* 3.2 4.2 + - - +
47E VAL* 2.8 33.3 + - + +
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Residues in contact with LEU 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 4.0 38.8 - - + -
40A THR* 3.2 46.0 - - + +
43A ALA* 3.7 17.9 - - + -
44A LEU* 3.7 10.5 - - + +
47A VAL* 4.2 16.6 - - + -
44D LEU* 4.8 3.5 - - + +
40E THR* 2.9 17.2 + - + +
41E ASN* 3.2 7.2 + - - +
43E ALA* 1.3 74.9 - - - +
45E GLN* 1.3 59.4 + - - +
47E VAL* 3.1 11.4 + - + +
48E ARG* 2.8 29.7 + - - +
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Residues in contact with GLN 45 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 5.6 7.3 + - - +
43A ALA* 4.8 7.4 - - + -
41E ASN* 2.9 39.1 + - - +
42E ALA* 3.8 9.2 - - - +
44E LEU* 1.3 75.5 - - - +
46E ASP* 1.3 61.5 + - - +
48E ARG* 3.3 29.5 + - - +
49E GLU* 3.1 29.0 + - + +
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Residues in contact with ASP 46 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ARG* 2.4 50.0 + - - +
52D ARG* 2.8 17.2 + - - -
42E ALA 3.3 3.6 + - - +
43E ALA 3.2 4.4 + - - +
44E LEU 3.2 0.2 - - - -
45E GLN* 1.3 75.1 - - - +
47E VAL* 1.3 68.7 + - - +
49E GLU* 3.1 9.0 + - - +
50E LEU* 2.9 37.4 + - - +
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Residues in contact with VAL 47 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.8 30.7 - - + -
47A VAL* 4.5 11.7 - - + -
44D LEU* 4.2 21.1 - - + -
47D VAL* 4.6 6.1 - - + -
48D ARG* 4.5 22.9 - - + -
51D LEU* 3.8 12.9 - - + +
43E ALA 2.8 19.3 + - - +
44E LEU* 3.4 12.6 - - + +
46E ASP* 1.3 76.7 - - - +
48E ARG* 1.3 62.5 + - - +
50E LEU* 3.2 9.1 + - - +
51E LEU* 2.9 24.0 + - + +
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Residues in contact with ARG 48 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 5.3 2.2 + - - -
42A ALA* 4.4 2.6 - - - +
43A ALA* 3.2 31.4 - - + +
46A ASP* 3.0 34.8 + - + +
47A VAL* 4.2 16.4 - - + -
50A LEU* 3.7 12.2 - - + +
44E LEU 2.8 16.0 + - - +
45E GLN* 3.4 26.4 - - - +
46E ASP 3.2 0.2 - - - -
47E VAL* 1.3 74.7 - - - +
49E GLU* 1.3 68.1 + - - +
51E LEU* 3.3 5.4 + - - +
52E ARG* 3.0 56.4 + - - +
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Residues in contact with GLU 49 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLN 3.1 13.1 + - - +
46E ASP* 3.1 10.7 + - - +
48E ARG* 1.3 106.4 + - - +
50E LEU* 1.3 66.2 + - - +
52E ARG* 3.2 25.2 + - - +
53E GLN* 3.1 24.0 + - - +
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Residues in contact with LEU 50 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ARG* 4.2 9.9 - - + +
51D LEU* 3.5 31.6 - - + -
52D ARG* 3.8 40.8 - - + -
55D VAL* 4.1 12.6 - - + +
46E ASP* 2.9 37.0 + - - +
47E VAL* 4.1 6.1 - - - -
49E GLU* 1.3 76.5 - - - +
51E LEU* 1.3 59.0 + - - +
53E GLN* 3.2 18.2 + - - +
54E GLN* 2.8 30.0 + - - +
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Residues in contact with LEU 51 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.5 35.4 - - + +
47A VAL* 3.5 45.5 - - + +
50A LEU* 4.2 14.6 - - + -
51A LEU* 4.4 8.5 - - + +
54A GLN* 3.5 28.9 - - - +
51D LEU* 4.2 6.7 - - + +
47E VAL* 2.9 15.2 + - + +
48E ARG 3.6 4.9 - - - +
50E LEU* 1.3 72.8 - - - +
52E ARG* 1.3 66.2 + - - +
54E GLN* 3.5 5.1 - - - +
55E VAL* 2.9 37.3 + - + +
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Residues in contact with ARG 52 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP* 5.2 6.9 + - - +
50A LEU* 4.1 29.5 - - - +
48E ARG* 3.0 50.5 + - - +
49E GLU* 3.2 29.3 + - - +
51E LEU* 1.3 75.8 - - - +
53E GLN* 1.3 60.3 + - - +
55E VAL* 2.9 27.6 - - + +
56E LYS* 3.4 12.5 + - - +
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Residues in contact with GLN 53 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 3.5 25.0 - - + +
59D THR* 4.7 1.2 + - - -
49E GLU 3.1 10.3 + - - +
50E LEU* 3.6 18.7 + - - +
52E ARG* 1.3 79.4 - - - +
54E GLN* 1.3 63.3 - - - +
56E LYS* 3.1 23.0 + - + +
57E GLU* 3.0 37.8 + - + +
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Residues in contact with GLN 54 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 2.6 30.2 + - - -
54A GLN* 3.0 20.5 + - - +
51D LEU* 3.5 13.0 - - - +
54D GLN* 3.0 27.5 + - - +
55D VAL* 3.5 19.6 - - + +
58D ILE* 3.5 27.4 - - + +
50E LEU 2.8 17.8 + - - +
51E LEU* 3.2 7.2 + - - +
53E GLN* 1.3 77.6 - - - +
55E VAL* 1.3 61.3 + - - +
57E GLU* 3.2 9.3 + - - +
58E ILE* 2.9 27.2 + - + +
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Residues in contact with VAL 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.0 24.0 - - + +
53A GLN* 5.6 5.4 - - + -
54A GLN* 3.2 43.7 - - + +
57A GLU* 5.1 3.4 - - + +
51E LEU* 2.9 25.0 + - + +
52E ARG* 2.9 30.1 - - + +
54E GLN* 1.3 71.7 - - - +
56E LYS* 1.3 58.2 + - + +
58E ILE* 3.7 6.7 - - - +
59E THR* 2.8 36.0 + - - +
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Residues in contact with LYS 56 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ARG* 3.8 10.1 - - - +
53E GLN* 3.1 26.9 - - + +
55E VAL* 1.3 84.1 - - + +
57E GLU* 1.3 60.1 + - - +
59E THR* 3.0 8.8 + - - -
60E PHE* 2.9 64.8 + - + -
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Residues in contact with GLU 57 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL* 5.1 2.7 - - + -
58D ILE* 3.9 18.6 - - + -
59D THR* 2.9 33.5 + - - +
62D LYS* 2.8 35.4 + - + +
53E GLN* 3.0 32.0 + - + +
54E GLN* 3.5 7.9 - - - +
56E LYS* 1.3 78.0 - - + +
58E ILE* 1.3 57.9 + - - +
60E PHE* 3.1 17.1 + - - +
61E LEU* 2.9 28.5 + - - +
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Residues in contact with ILE 58 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.5 39.5 - - + +
57A GLU* 4.0 27.1 - - + +
58A ILE* 4.2 21.8 - - + -
61A LEU* 4.8 11.6 - - + +
58D ILE* 3.9 24.7 - - + -
54E GLN* 2.9 25.3 + - + +
55E VAL* 3.7 5.2 - - - +
57E GLU* 1.3 75.5 - - - +
59E THR* 1.3 59.5 + - - +
61E LEU* 3.2 9.8 + - + +
62E LYS* 2.8 28.3 + - + +
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Residues in contact with THR 59 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.7 22.1 + - - +
55E VAL* 2.8 24.2 + - - +
56E LYS* 3.3 8.2 - - - -
58E ILE* 1.3 78.4 - - - +
60E PHE* 1.3 65.8 + - + +
62E LYS* 3.4 22.9 + - - +
63E ASN* 3.1 36.3 + - - +
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Residues in contact with PHE 60 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LYS* 4.2 17.9 - - + -
66D MET* 4.7 7.9 - - + -
56E LYS* 2.9 53.3 + - + -
57E GLU* 3.4 24.7 - - - +
59E THR* 1.3 79.5 - - + +
61E LEU* 1.3 65.7 + - - +
63E ASN* 3.1 14.3 + - + +
64E THR* 2.9 27.2 + - - -
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Residues in contact with LEU 61 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 3.9 27.8 - - + -
58D ILE* 5.1 8.1 - - + -
61D LEU* 3.9 37.2 - - + +
62D LYS* 3.9 16.1 - - + +
65D VAL* 3.7 37.7 - - + -
57E GLU 2.9 12.6 + - - +
58E ILE* 3.2 14.3 + - + +
60E PHE* 1.3 74.4 - - - +
62E LYS* 1.3 62.8 + - - +
64E THR* 3.2 6.1 + - - -
65E VAL* 3.1 31.0 + - + +
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Residues in contact with LYS 62 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 2.6 39.7 + - - +
60A PHE* 3.5 45.3 - - + -
61A LEU* 4.1 21.7 - - + +
64A THR* 5.4 0.6 - - - +
58E ILE* 2.8 21.4 + - + +
59E THR* 3.5 15.5 - - - +
61E LEU* 1.3 72.7 - - - +
63E ASN* 1.3 76.8 + - - +
65E VAL* 3.2 4.7 + - - +
66E MET* 3.0 36.2 + - + +
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Residues in contact with ASN 63 (chain E).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E THR* 3.1 29.0 + - - +
60E PHE* 3.1 14.4 + - - +
62E LYS* 1.3 94.0 + - - +
64E THR* 1.3 62.4 + - - +
66E MET* 3.5 14.0 + - - +
67E GLU* 3.3 30.0 + - + +
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Residues in contact with THR 64 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LYS 5.6 0.7 - - - -
65D VAL* 3.8 18.6 - - + +
66D MET* 3.6 51.2 - - + +
71D CYS* 4.8 3.8 - - + +
60E PHE 2.9 15.7 + - - -
61E LEU* 3.6 8.6 - - - -
62E LYS 3.2 0.2 - - - -
63E ASN* 1.3 77.5 - - - +
65E VAL* 1.3 62.3 + - - +
67E GLU* 3.5 5.1 + - - +
68E CYS* 3.3 19.6 + - - +
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Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.9 16.6 - - + -
64A THR* 3.7 23.0 - - + +
65A VAL* 4.2 20.0 - - + +
65D VAL* 3.9 22.7 - - + -
61E LEU* 3.1 19.2 + - + +
62E LYS 3.2 7.2 + - - +
64E THR* 1.3 74.3 - - - +
66E MET* 1.3 62.8 + - - +
67E GLU 3.1 1.8 - - - -
68E CYS* 3.1 20.9 + - + +
71E CYS* 4.3 19.3 - - - +
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Residues in contact with MET 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.4 41.7 - - + -
64A THR* 4.3 15.5 - - + +
62E LYS* 3.0 26.0 + - - +
63E ASN* 3.7 22.9 - - - +
64E THR 3.4 0.2 - - - -
65E VAL* 1.3 77.5 - - - +
67E GLU* 1.3 74.9 + - - +
68E CYS 3.4 1.4 + - - +
71E CYS* 6.2 0.2 - - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D CYS 4.1 1.9 - - - +
63E ASN* 3.3 19.1 + - + +
64E THR* 3.8 5.8 - - - +
65E VAL 3.1 0.2 - - - -
66E MET* 1.3 100.4 - - - +
68E CYS* 1.3 62.9 + - - +
69E ASP* 3.3 14.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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