Contacts of the helix formed by residues 29 - 67 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 2.8 40.4 - - + +
28A ASP* 1.3 74.2 + - - +
30A ALA* 1.3 59.3 + - - +
31A PRO 3.3 2.7 - - - -
32A GLN* 3.3 13.4 + - - +
33A MET* 2.9 31.9 + - + +
27E MET 5.9 2.5 - - - +
30E ALA* 3.8 17.7 - - + +
31E PRO* 3.5 48.0 - - + -
34E LEU* 4.2 21.1 - - + -
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Residues in contact with ALA 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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28A ASP* 2.6 27.0 + - - +
29A LEU* 1.3 71.4 - - - +
31A PRO* 1.3 64.5 - - + +
33A MET* 3.1 14.7 + - - +
34A LEU* 2.9 23.6 + - - +
29B LEU* 3.7 19.5 - - + +
33B MET* 4.8 8.8 - - - +
30E ALA* 5.4 1.8 - - - +
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Residues in contact with PRO 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP* 3.3 27.1 - - + +
29A LEU 3.5 2.9 - - - -
30A ALA* 1.3 93.5 - - + +
32A GLN* 1.3 56.6 + - - +
34A LEU* 3.4 3.8 + - + +
35A ARG* 3.0 31.3 + - - +
29B LEU* 3.5 21.5 - - + -
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Residues in contact with GLN 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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27A MET* 6.2 2.0 - - - -
28A ASP 5.2 0.6 + - - +
29A LEU* 3.3 15.4 + - - +
30A ALA 3.2 0.4 - - - -
31A PRO* 1.3 77.2 - - - +
33A MET* 1.3 60.9 + - - +
35A ARG* 3.2 9.8 + - + +
36A GLU* 2.9 33.6 + - - +
34E LEU* 3.7 25.3 - - + +
38E GLN* 3.1 24.8 + - - -
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Residues in contact with MET 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 LEU 2.9 18.6 + - - +
30A ALA* 3.1 14.6 + - - +
32A GLN* 1.3 74.1 - - - +
34A LEU* 1.3 65.3 + - - +
36A GLU* 3.2 4.2 + - - +
37A LEU* 3.1 26.9 + - - +
33B MET* 3.6 28.3 - - + +
30E ALA* 4.1 28.3 - - - +
33E MET* 3.6 39.0 - - + +
34E LEU* 4.1 25.8 - - + -
37E LEU* 3.9 15.5 - - + +
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Residues in contact with LEU 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 2.9 12.0 + - - +
31A PRO* 3.6 9.6 - - + +
33A MET* 1.3 75.1 - - - +
35A ARG* 1.3 58.0 + - + +
37A LEU* 3.2 5.0 + - - +
38A GLN* 2.9 49.5 + - + +
29B LEU* 4.4 18.6 - - + -
32B GLN* 3.4 51.4 - - + +
33B MET* 4.0 16.3 - - + +
36B GLU* 3.7 27.4 - - + +
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Residues in contact with ARG 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO 3.0 18.7 + - - +
32A GLN* 3.5 13.7 - - + +
33A MET 3.2 0.2 - - - -
34A LEU* 1.3 78.0 - - + +
36A GLU* 1.3 64.4 + - + +
38A GLN* 3.2 32.5 + - - +
39A GLU* 2.9 60.1 + - - +
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Residues in contact with GLU 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 GLN* 2.9 24.3 + - - +
33A MET 3.2 7.1 + - - +
35A ARG* 1.3 78.5 - - - +
37A LEU* 1.3 58.5 + - - +
39A GLU* 3.2 6.1 + - - +
40A THR* 2.8 18.5 + - - -
34E LEU* 3.6 20.2 - - + -
37E LEU* 4.0 15.3 - - + -
38E GLN* 3.7 34.1 + - + -
41E ASN* 2.7 49.1 + - - +
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Residues in contact with LEU 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.6 36.3 - - + -
33A MET 3.1 14.8 + - - +
34A LEU* 3.5 7.2 - - - +
36A GLU* 1.3 77.5 - - - +
38A GLN* 1.3 62.3 + - - +
40A THR* 3.2 7.5 + - - +
41A ASN* 3.0 27.4 + - - -
33B MET* 3.8 56.5 - - + +
36B GLU* 3.9 14.6 - - + -
37B LEU* 4.0 14.4 - - + -
40B THR* 5.0 3.0 + - - +
37E LEU* 4.0 15.9 - - + -
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Residues in contact with GLN 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 2.9 33.4 + - + +
35A ARG* 3.2 44.8 + - - +
37A LEU* 1.3 75.3 - - - +
39A GLU* 1.3 59.1 + - - +
41A ASN* 3.4 3.1 + - - +
42A ALA* 3.0 25.5 + - - +
32B GLN* 5.1 3.4 + - - -
36B GLU* 3.5 33.6 + - + +
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Residues in contact with GLU 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG* 2.9 49.0 + - - +
36A GLU* 3.5 12.1 - - - +
38A GLN* 1.3 74.6 - - - +
40A THR* 1.3 65.8 + - - +
42A ALA* 3.2 11.8 + - - +
43A ALA* 3.0 24.1 + - - +
41E ASN* 3.7 10.9 - - - +
45E GLN* 5.6 7.5 + - - +
48E ARG* 5.3 2.3 + - - -
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Residues in contact with THR 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.6 41.4 - - + +
36A GLU 2.8 11.8 + - - -
37A LEU* 3.2 14.7 + - - +
39A GLU* 1.3 76.3 - - - +
41A ASN* 1.3 57.8 + - - +
43A ALA 3.3 1.2 + - - -
44A LEU* 2.8 29.2 + - + +
40B THR* 4.4 8.1 - - - +
37E LEU* 4.8 2.9 + - - +
40E THR* 4.8 3.6 - - + +
41E ASN* 2.4 35.6 + - - -
44E LEU* 3.2 18.0 - - + +
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Residues in contact with ASN 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.0 15.9 + - - +
38A GLN 3.8 5.2 - - - +
40A THR* 1.3 73.3 - - - +
42A ALA* 1.3 60.9 + - - +
44A LEU* 3.7 8.7 - - - +
45A GLN* 2.9 31.0 + - - +
36B GLU* 2.8 49.2 + - - +
39B GLU* 3.2 29.6 + - + +
40B THR* 2.5 35.1 + - - -
43B ALA* 5.2 1.0 - - - +
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Residues in contact with ALA 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN 3.0 13.6 + - - +
39A GLU* 3.4 22.2 - - - +
40A THR 3.2 0.2 - - - -
41A ASN* 1.3 78.7 - - - +
43A ALA* 1.3 63.2 + - - +
45A GLN* 3.2 7.2 + - - +
46A ASP* 3.1 27.2 + - - +
48E ARG* 5.2 2.9 - - - +
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Residues in contact with ALA 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU 3.0 13.2 + - - +
40A THR* 4.8 0.2 - - - -
42A ALA* 1.3 76.4 - - - +
44A LEU* 1.3 57.9 + - - +
46A ASP* 3.1 4.9 + - - +
47A VAL* 2.9 31.8 + - - +
41E ASN* 5.6 0.9 - - - +
44E LEU* 3.7 29.4 - - + +
45E GLN* 4.8 9.6 - - + -
48E ARG* 3.2 33.1 + - + +
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Residues in contact with LEU 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.9 36.3 - - + -
40A THR* 2.8 17.7 + - + +
41A ASN* 3.7 8.7 - - - +
43A ALA* 1.3 76.9 - - - +
45A GLN* 1.3 57.4 + - - +
47A VAL* 3.2 10.9 + - + +
48A ARG* 2.9 31.6 + - - +
40B THR* 3.6 33.0 - - + +
43B ALA* 3.5 28.9 - - + -
44B LEU* 4.2 8.1 - - + -
47B VAL* 4.2 18.4 - - + -
44E LEU* 3.7 7.1 - - + +
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Residues in contact with GLN 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN 2.9 18.1 + - - +
42A ALA* 3.5 7.4 - - - +
43A ALA 3.2 0.2 - - - -
44A LEU* 1.3 74.4 - - - +
46A ASP* 1.3 67.9 + - - +
48A ARG* 3.3 22.8 + - - +
49A GLU* 3.2 41.9 + - + +
39B GLU* 5.1 6.6 - - - +
43B ALA* 5.4 0.9 - - - +
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Residues in contact with ASP 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.1 14.6 + - - +
43A ALA 3.4 7.0 - - - +
45A GLN* 1.3 79.1 + - - +
47A VAL* 1.3 63.2 + - - +
49A GLU* 3.3 16.3 + - - +
50A LEU* 3.0 31.1 + - + +
48E ARG* 3.0 43.3 + - + +
52E ARG* 5.2 6.3 - - - +
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Residues in contact with VAL 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 4.0 26.5 - - + -
43A ALA 2.9 19.1 + - - +
44A LEU* 3.4 11.7 - - + +
46A ASP* 1.3 77.4 - - - +
48A ARG* 1.3 57.4 + - - +
50A LEU* 3.3 4.6 + - - +
51A LEU* 2.9 30.1 + - + +
47B VAL* 4.7 8.7 - - + -
44E LEU* 4.2 20.2 - - + -
47E VAL* 4.5 3.8 - - + -
48E ARG* 4.2 26.7 - - + +
51E LEU* 3.5 22.5 - - + +
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Residues in contact with ARG 48 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU 2.9 18.4 + - - +
45A GLN* 3.6 20.7 + - + +
46A ASP 3.3 0.2 - - - -
47A VAL* 1.3 77.5 - - - +
49A GLU* 1.3 56.5 + - + +
51A LEU* 3.5 4.2 + - - +
52A ARG* 2.9 42.5 + - - +
39B GLU* 6.3 0.8 - - - +
42B ALA* 4.7 4.2 + - - +
43B ALA* 3.5 37.7 - - + +
46B ASP* 2.9 40.8 + - - +
47B VAL* 3.5 25.8 - - + -
50B LEU* 3.8 6.7 - - + +
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Residues in contact with GLU 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 3.2 36.8 + - + +
46A ASP* 3.6 17.2 - - - +
48A ARG* 1.3 74.6 - - + +
50A LEU* 1.3 66.9 + - + +
52A ARG* 3.4 15.9 + - - +
53A GLN* 3.1 22.0 + - - +
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Residues in contact with LEU 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP* 3.0 22.8 + - + +
47A VAL* 3.6 6.5 - - - +
49A GLU* 1.3 74.4 - - + +
51A LEU* 1.3 61.0 + - - +
53A GLN* 3.0 9.0 + - + +
54A GLN* 2.8 29.9 + - - +
48E ARG* 3.7 33.7 - - + +
51E LEU* 4.2 20.4 - - + -
52E ARG* 4.1 42.8 - - - +
55E VAL* 4.0 16.6 - - + +
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Residues in contact with LEU 51 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.7 31.2 - - + -
47A VAL* 2.9 17.0 + - + +
48A ARG 3.8 4.3 - - - +
50A LEU* 1.3 76.2 - - - +
52A ARG* 1.3 63.1 + - - +
54A GLN* 3.2 8.7 + - - +
55A VAL* 3.0 31.2 + - + +
47B VAL* 3.6 45.8 - - + +
50B LEU* 3.6 20.0 - - + -
51B LEU* 4.2 7.6 - - + +
54B GLN* 3.7 24.2 - - - +
51E LEU* 4.4 8.2 - - + +
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Residues in contact with ARG 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 2.9 35.8 + - - +
49A GLU* 3.5 15.9 - - - +
51A LEU* 1.3 79.4 - - - +
53A GLN* 1.3 61.8 + - - +
55A VAL* 3.5 3.8 + - - +
56A LYS* 3.4 43.9 + - - +
46B ASP* 3.0 31.4 + - - -
50B LEU* 4.2 27.5 - - + +
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Residues in contact with GLN 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU 3.1 9.2 + - - +
50A LEU* 3.0 12.2 + - + +
52A ARG* 1.3 78.6 - - - +
54A GLN* 1.3 63.3 + - - +
56A LYS* 3.0 35.6 + - - +
57A GLU* 2.6 43.8 + - + +
55E VAL* 5.6 7.2 - - + -
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Residues in contact with GLN 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A STE 3.2 20.2 + - - -
50A LEU 2.8 12.6 + - - +
51A LEU* 3.5 12.1 - - - +
53A GLN* 1.3 74.6 - - - +
55A VAL* 1.3 66.1 + - - +
57A GLU* 3.0 9.7 + - - +
58A ILE* 2.8 28.5 + - + +
54B GLN* 2.9 33.2 + - - +
51E LEU* 3.5 6.5 - - - +
54E GLN* 3.0 23.1 + - - +
55E VAL* 3.2 29.9 - - + +
58E ILE* 3.5 27.4 - - + +
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Residues in contact with VAL 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.0 25.3 + - + +
52A ARG 3.8 4.9 - - - +
53A GLN 3.3 0.2 - - - -
54A GLN* 1.3 74.6 - - - +
56A LYS* 1.3 57.8 + - + +
58A ILE* 3.7 4.7 - - - +
59A THR* 2.9 43.2 + - - +
50B LEU* 3.9 32.5 - - + +
53B GLN* 3.5 28.3 - - + +
54B GLN* 3.7 26.2 - - + +
57B GLU* 4.9 5.4 - - + -
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Residues in contact with LYS 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.4 36.4 + - - +
53A GLN* 3.0 32.1 + - - +
55A VAL* 1.3 80.2 - - + +
57A GLU* 1.3 56.8 + - - +
59A THR* 3.4 6.2 + - - -
60A PHE* 3.0 28.6 + - - +
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Residues in contact with GLU 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN* 2.6 46.7 + - + +
54A GLN* 3.5 9.4 - - - +
56A LYS* 1.3 75.6 - - - +
58A ILE* 1.3 58.1 + - - +
60A PHE* 3.3 5.5 + - - +
61A LEU* 2.9 28.5 + - - +
55E VAL* 5.1 4.3 - - + +
58E ILE* 4.0 18.8 - - + -
59E THR* 3.7 21.8 + - - +
62E LYS* 2.6 44.5 + - + +
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Residues in contact with ILE 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 2.8 22.2 + - + +
55A VAL* 3.7 5.2 - - - +
57A GLU* 1.3 74.8 - - - +
59A THR* 1.3 59.6 + - - +
61A LEU* 3.2 9.9 + - + +
62A LYS* 2.8 27.1 + - + +
54B GLN* 3.3 40.8 - - + +
57B GLU* 3.8 25.1 - - + +
58B ILE* 4.0 26.0 - - + +
61B LEU* 5.1 8.6 - - + +
58E ILE* 4.2 24.5 - - + -
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Residues in contact with THR 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 2.9 23.3 + - - +
56A LYS* 3.8 6.7 - - - -
58A ILE* 1.3 76.2 - - - +
60A PHE* 1.3 63.0 + - - +
62A LYS* 3.3 5.9 + - - +
63A ASN* 3.0 44.0 + - - +
57B GLU* 3.0 35.8 + - - +
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Residues in contact with PHE 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS 3.0 17.5 + - - +
57A GLU* 3.5 7.2 - - - +
58A ILE 3.2 0.2 - - - -
59A THR* 1.3 78.3 - - - +
61A LEU* 1.3 62.2 + - - +
63A ASN* 3.4 7.3 + - - +
64A THR* 2.9 44.9 + - - -
62E LYS* 3.5 25.6 - - + -
66E MET* 3.4 39.3 - - + -
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Residues in contact with LEU 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU 2.9 14.5 + - - +
58A ILE* 3.2 13.9 + - + +
60A PHE* 1.3 79.0 - - - +
62A LYS* 1.3 62.4 + - - +
64A THR* 3.4 5.1 + - - -
65A VAL* 3.0 36.1 + - + +
61B LEU* 3.9 24.2 - - + -
61C LEU* 6.1 0.4 - - + -
58E ILE* 4.8 13.9 - - + -
61E LEU* 3.9 27.6 - - + +
62E LYS* 4.1 20.9 - - + +
65E VAL* 3.9 30.3 - - + -
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Residues in contact with LYS 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE 2.8 14.0 + - - +
59A THR* 3.4 9.9 - - - +
61A LEU* 1.3 77.4 - - - +
63A ASN* 1.3 81.0 + - - +
65A VAL* 3.1 5.7 + - - +
66A MET* 2.9 39.9 + - + +
57B GLU* 3.1 47.4 + - + +
60B PHE* 3.4 44.6 - - + +
61B LEU* 4.2 19.0 - - + +
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Residues in contact with ASN 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.0 34.0 + - - +
60A PHE* 3.9 6.2 - - - +
62A LYS* 1.3 96.8 + - - +
64A THR* 1.3 62.7 + - - +
66A MET* 3.2 14.2 + - - +
67A GLU* 2.7 35.5 + - - +
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Residues in contact with THR 64 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 2.9 40.6 + - - -
61A LEU* 3.7 7.6 - - - -
63A ASN* 1.3 76.2 - - - +
65A VAL* 1.3 63.3 + - - +
67A GLU* 3.2 15.5 + - - +
68A CYS* 3.2 12.0 + - - +
62E LYS* 5.9 0.7 - - - -
65E VAL* 3.7 24.7 - - + +
66E MET* 4.3 21.7 - - + +
71E CYS* 5.1 4.1 - - + +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.0 28.9 + - + +
62A LYS 3.4 7.0 - - - +
64A THR* 1.3 73.2 - - - +
66A MET* 1.3 65.0 + - - +
68A CYS* 3.1 23.9 + - + +
71A CYS* 4.5 13.7 - - - +
61B LEU* 3.6 27.8 - - + -
64B THR* 4.1 20.2 - - + +
65B VAL* 4.1 13.9 - - + -
65E VAL* 4.2 14.4 - - + -
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Residues in contact with MET 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 2.9 27.1 + - + +
63A ASN* 3.2 30.5 + - - +
65A VAL* 1.3 77.4 - - - +
67A GLU* 1.3 72.1 + - - +
68A CYS 3.3 2.3 + - - +
71A CYS* 5.4 2.8 - - - +
60B PHE* 3.4 39.5 - - + -
64B THR* 4.3 17.0 - - + +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 2.7 36.5 + - - +
64A THR* 3.2 7.4 + - - +
65A VAL 3.1 0.4 - - - -
66A MET* 1.3 92.3 - - - +
68A CYS* 1.3 61.3 + - - +
69A ASP* 3.1 13.2 + - - +
71E CYS* 5.0 2.3 - - - +
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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