Contacts of the helix formed by residues 47 - 77 (chain A) in PDB entry 2Q7M
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 THR 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLN* 3.0 47.5 - - - +
46A GLY* 1.3 67.6 - - - -
48A LEU* 1.3 57.0 + - - +
49A ALA* 3.1 11.2 - - + +
50A PHE* 4.0 19.2 - - - +
51A GLU* 2.5 40.1 + - - +
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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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45A THR* 5.6 4.3 - - + -
46A GLY 2.8 23.8 - - - +
47A THR* 1.3 75.8 - - - +
49A ALA* 1.3 56.9 + - - +
51A GLU* 4.3 9.9 - - + -
52A ARG* 2.8 56.7 - - - +
43B GLN* 5.4 6.1 - - - +
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Residues in contact with ALA 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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33A GLU* 3.7 20.5 - - + +
37A GLN* 4.5 6.5 - - - +
47A THR* 3.1 5.3 - - + +
48A LEU* 1.3 76.4 - - - +
50A PHE* 1.3 61.5 + - - +
51A GLU 3.4 0.2 - - - -
52A ARG* 3.6 3.9 + - - +
53A VAL* 3.2 31.2 + - - +
102A LEU* 5.4 3.1 - - + +
104A GLU* 5.7 5.8 - - - +
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Residues in contact with PHE 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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30A VAL* 4.3 11.0 - - + -
33A GLU* 3.3 48.4 - - + +
34A SER* 3.8 5.2 - - - -
37A GLN* 4.2 2.5 - - + -
42A PHE* 2.9 57.0 - + + -
44A ARG 5.6 1.3 - - - -
46A GLY* 5.1 2.7 - - - -
47A THR* 3.3 25.0 + - - -
49A ALA* 1.3 78.4 - - - +
51A GLU* 1.3 77.3 + - - +
52A ARG 3.2 1.6 - - - -
53A VAL* 3.8 1.3 - - + +
54A TYR* 3.0 43.4 + + + +
112C TYR* 6.2 0.2 - + - -
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Residues in contact with GLU 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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42A PHE 6.0 0.3 - - - -
44A ARG 3.8 3.6 - - - +
45A THR* 3.3 24.7 + - + +
46A GLY* 3.0 31.2 + - - +
47A THR 2.5 25.6 + - - +
48A LEU* 4.3 9.2 - - + -
50A PHE* 1.3 84.5 - - - +
52A ARG* 1.3 58.9 + - - +
53A VAL 3.3 0.2 - - - -
54A TYR* 4.3 1.6 - - - +
55A THR* 2.2 35.8 + - - +
44B ARG* 2.3 48.1 + - + -
44C ARG* 4.3 2.4 + - - -
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Residues in contact with ARG 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 44.8 + - - +
49A ALA* 3.8 6.1 - - - +
50A PHE 3.2 0.6 - - - -
51A GLU* 1.3 83.7 + - - +
53A VAL* 1.3 58.2 + - + +
55A THR* 3.8 4.8 + - - -
56A ALA* 3.2 18.4 + - - +
101A TYR* 3.4 34.8 - - + +
102A LEU* 4.3 14.1 - - + +
104A GLU* 6.3 1.6 - - - +
105A ARG 6.4 0.2 - - - +
106A THR 5.5 0.4 + - - -
108A SER* 3.1 27.8 - - - +
41B SER* 2.9 52.0 + - - -
42B PHE 5.2 2.4 + - - -
43B GLN* 4.7 8.5 + - - +
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Residues in contact with VAL 53 (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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26A PHE 4.8 1.1 - - - +
29A LYS* 3.2 34.1 - - + +
30A VAL* 3.0 28.0 - - + -
33A GLU* 4.8 6.3 - - + -
49A ALA 3.2 18.9 + - - +
50A PHE* 4.2 4.5 - - + +
52A ARG* 1.3 76.0 - - + +
54A TYR* 1.3 57.6 + - - +
55A THR 2.9 4.5 - - - -
56A ALA* 3.1 4.8 + - + +
57A ASN* 2.8 29.1 + - - +
98A PHE* 4.9 9.4 - - + -
101A TYR 5.4 0.4 - - - +
102A LEU* 4.0 27.8 - - + -
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Residues in contact with TYR 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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30A VAL* 3.7 13.2 - - + -
42A PHE* 3.9 19.3 - - + -
43A GLN* 6.1 0.4 - - - -
50A PHE* 3.0 37.4 + + + +
51A GLU* 4.9 0.7 - - - +
53A VAL* 1.3 76.8 - - - +
55A THR* 1.3 57.2 + - - +
57A ASN* 4.1 11.7 - - - -
58A GLN* 3.0 63.8 + - + +
44B ARG* 3.2 28.3 - - - +
44C ARG* 4.6 2.2 - - - -
58C GLN* 3.5 21.5 + - - +
62C ASP* 4.1 2.7 - - - -
112C TYR* 3.3 39.7 + + - -
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Residues in contact with THR 55 (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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51A GLU* 2.2 28.6 + - - +
52A ARG* 3.8 6.9 + - - -
53A VAL 2.9 0.6 - - - -
54A TYR* 1.3 76.9 - - - +
56A ALA* 1.3 67.9 + - - +
57A ASN 3.1 0.5 + - - -
58A GLN* 3.1 8.5 + - - -
59A ASN* 2.8 32.9 - - - +
101A TYR* 3.5 26.2 - - - +
42B PHE* 4.4 5.4 - - + +
44B ARG* 3.8 44.8 - - + +
54B TYR* 5.5 0.9 - - + +
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Residues in contact with ALA 56 (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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52A ARG 3.2 15.0 + - - +
53A VAL* 3.1 6.2 + - + +
55A THR* 1.3 78.4 - - - +
57A ASN* 1.3 64.8 + - - +
59A ASN* 3.3 12.9 - - - +
60A CYS* 3.4 15.9 + - - -
97A TYR* 5.1 1.3 - - - -
98A PHE* 3.9 23.5 - - + +
101A TYR* 3.6 42.1 - - + +
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Residues in contact with ASN 57 (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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26A PHE* 3.4 35.3 - - + +
27A ALA* 4.2 3.2 - - - +
30A VAL* 3.7 25.0 - - + +
53A VAL 2.8 16.7 + - - +
54A TYR* 3.9 12.7 - - - +
56A ALA* 1.3 72.4 - - - +
58A GLN* 1.3 53.6 + - - +
59A ASN 2.5 17.3 + - - -
60A CYS* 2.8 15.5 + - - -
61A VAL* 3.0 31.0 + - - +
98A PHE* 4.3 8.9 - - + -
502A 2CS 4.5 9.8 - - - -
62C ASP* 4.3 5.9 - - - +
112C TYR* 5.4 1.6 - - - -
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Residues in contact with GLN 58 (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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54A TYR* 3.0 49.1 + - + +
55A THR* 4.1 1.6 - - - +
57A ASN* 1.3 73.7 - - - +
59A ASN* 1.3 62.6 + - - +
61A VAL* 4.3 7.6 - - - +
62A ASP* 2.7 30.8 - - - +
44B ARG* 5.5 3.6 - - - +
54B TYR* 3.4 10.6 + - + +
58B GLN* 3.1 20.6 - - + +
61B VAL* 4.9 2.4 - - - +
58C GLN* 2.9 25.5 + - + +
61C VAL* 5.0 0.7 - - - +
62C ASP* 2.9 37.9 + - - +
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Residues in contact with ASN 59 (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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55A THR* 2.8 31.6 + - - +
56A ALA 3.3 7.9 - - - +
57A ASN 2.5 6.9 + - - -
58A GLN* 1.3 81.4 - - - +
60A CYS* 1.3 60.4 + - - +
61A VAL 3.4 0.7 - - - -
62A ASP* 3.7 11.7 - - - +
63A ALA* 3.9 15.4 + - - +
97A TYR* 3.2 18.4 + - + +
101A TYR* 3.1 32.1 - - - -
112A TYR* 3.3 34.2 - - + +
114A PHE* 4.6 1.4 - - - -
503A 2CS 4.4 1.0 - - - -
42B PHE* 3.6 4.8 - - - -
54B TYR* 3.3 14.6 + - - -
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Residues in contact with CYS 60 (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 ASN* 6.0 1.1 - - - +
26A PHE* 3.6 25.8 - - + -
56A ALA 3.6 12.6 - - - -
57A ASN 2.8 6.6 + - - +
59A ASN* 1.3 79.6 - - - +
61A VAL* 1.3 60.6 + - + +
62A ASP 3.1 2.7 - - - -
63A ALA* 3.1 6.8 + - - -
64A TYR* 3.0 25.5 + - - +
94A ARG* 3.4 40.4 + - - +
97A TYR* 4.4 8.5 - - - -
98A PHE* 4.0 13.2 - - - -
114A PHE* 4.2 9.4 - - - -
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Residues in contact with VAL 61 (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 ASN* 5.6 6.7 - - - +
26A PHE* 6.2 0.2 - - + -
57A ASN* 3.0 41.2 + - - +
58A GLN* 4.3 8.1 - - - +
59A ASN 3.4 0.2 - - - -
60A CYS* 1.3 79.8 - - + +
62A ASP* 1.3 61.8 + - - +
63A ALA 3.3 0.2 - - - -
64A TYR* 4.2 7.4 - - + +
65A PRO* 3.7 12.6 - - - +
502A 2CS 4.5 12.1 - - + -
61B VAL* 4.6 5.1 - - - +
61C VAL* 4.6 4.7 - - + +
62C ASP* 3.6 45.8 - - + +
65C PRO* 4.8 7.7 - - + +
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Residues in contact with ASP 62 (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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58A GLN* 2.7 34.4 - - - +
59A ASN* 3.9 6.5 - - - -
60A CYS 3.1 0.2 - - - -
61A VAL* 1.3 76.9 - - - +
63A ALA* 1.3 59.7 + - - +
65A PRO* 3.3 17.7 - - - +
66A THR* 3.4 9.2 + - - -
112A TYR* 2.9 26.0 - - - -
503A 2CS 3.2 30.7 - - + -
54B TYR* 4.1 0.2 + - - -
58B GLN* 3.0 22.4 + - - +
61B VAL* 3.7 20.4 - - + +
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Residues in contact with ALA 63 (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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59A ASN 3.9 3.5 + - - +
60A CYS 3.1 8.8 + - - +
62A ASP* 1.3 78.2 - - - +
64A TYR* 1.3 65.6 + - - +
65A PRO* 3.1 4.4 - - - +
66A THR* 3.5 3.3 + - - -
67A PHE* 3.0 24.9 + - - +
90A TYR* 3.0 24.9 + - - +
94A ARG* 4.1 1.1 - - - +
114A PHE* 3.8 13.5 - - + -
503A 2CS 3.4 29.1 - - + +
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Residues in contact with TYR 64 (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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16A THR* 3.9 3.6 + - - +
19A SER* 3.0 27.7 + - - -
20A VAL* 3.7 20.3 + - - +
23A ASN* 3.3 27.8 - - - +
60A CYS 3.0 14.8 + - - +
61A VAL* 4.3 7.4 - - + +
63A ALA* 1.3 72.9 - - - +
65A PRO* 1.3 62.6 - - + +
67A PHE* 3.4 6.3 - + - +
68A LEU* 2.8 62.6 + - + +
94A ARG* 3.3 22.9 - - - +
65C PRO* 3.6 27.4 - - + -
66C THR* 3.6 22.2 - - + -
69C ALA* 4.3 4.9 - - + +
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Residues in contact with PRO 65 (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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61A VAL 3.7 7.4 - - - +
62A ASP* 3.3 20.2 - - - +
63A ALA 3.1 4.0 - - - -
64A TYR* 1.3 95.2 - - + +
66A THR* 1.3 64.2 + - - +
67A PHE 2.9 5.1 + - - -
68A LEU* 3.1 6.9 + - + +
69A ALA* 2.9 30.8 + - - +
61B VAL* 5.4 7.4 - - + +
64B TYR* 3.8 28.6 - - + -
65B PRO* 5.4 10.1 - - + -
68B LEU* 5.7 1.8 - - + +
65C PRO* 5.5 7.8 - - + -
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Residues in contact with THR 66 (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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62A ASP 3.4 18.4 + - - -
63A ALA 3.5 3.2 + - - -
65A PRO* 1.3 78.2 - - - +
67A PHE* 1.3 57.4 + - - +
69A ALA* 3.9 10.7 - - - +
70A VAL* 4.1 10.4 - - - +
119A ILE* 4.4 6.2 - - - +
503A 2CS 4.2 22.3 - - - +
20B VAL* 3.4 26.2 - - + +
23B ASN* 2.9 46.4 + - + +
24B GLY 4.9 0.9 - - - +
61B VAL* 5.8 0.5 - - - +
64B TYR* 4.2 5.4 - - + -
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Residues in contact with PHE 67 (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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15A VAL* 5.5 2.5 - - + -
19A SER* 4.7 7.2 - - - -
63A ALA 3.0 16.8 + - - +
64A TYR* 4.0 16.8 - + - -
65A PRO 2.9 0.4 - - - -
66A THR* 1.3 77.5 - - - +
68A LEU* 1.3 76.7 + - + +
69A ALA 2.9 1.7 + - - -
70A VAL* 3.2 4.3 + - - +
71A LEU* 2.9 40.6 + - + -
87A GLY* 3.6 31.9 - - - -
90A TYR* 3.4 56.1 - + + -
91A LEU* 3.8 14.8 - - + -
94A ARG* 4.3 1.1 - - - -
119A ILE* 4.0 9.2 - - + -
122A LEU* 4.0 9.9 - - + -
503A 2CS 6.4 0.2 - - - -
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Residues in contact with LEU 68 (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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15A VAL* 5.9 0.2 - - + -
16A THR* 3.8 25.1 - - + +
19A SER* 4.8 2.2 - - - +
64A TYR* 2.8 61.4 + - + +
65A PRO* 3.6 6.5 - - + +
67A PHE* 1.3 86.7 - - + +
69A ALA* 1.3 67.3 + - - +
71A LEU* 3.2 22.1 + - + -
72A TRP* 2.9 35.4 + - + +
65C PRO* 6.2 0.4 - - + -
69C ALA* 5.9 2.5 - - + -
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Residues in contact with ALA 69 (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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65A PRO 2.9 16.3 + - - +
66A THR* 3.9 5.2 - - - +
67A PHE 2.9 0.6 - - - -
68A LEU* 1.3 82.6 - - - +
70A VAL* 1.3 61.9 + - - +
71A LEU 3.0 0.2 + - - -
72A TRP* 3.0 2.1 + - - +
73A SER* 3.0 23.7 + - - -
16B THR* 4.5 13.7 - - + -
17B LEU* 5.3 0.4 - - - -
20B VAL* 3.4 27.8 - - + -
64B TYR* 4.6 5.8 - - + +
68B LEU* 5.5 3.6 - - + -
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Residues in contact with VAL 70 (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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66A THR 4.1 8.5 - - - +
67A PHE 3.2 9.1 + - - +
69A ALA* 1.3 77.0 - - - +
71A LEU* 1.3 59.7 + - - +
72A TRP 3.2 0.4 - - - -
73A SER* 3.0 8.5 - - - +
74A ALA* 2.9 32.2 + - - +
119A ILE* 3.8 19.5 - - + +
122A LEU* 3.4 29.7 - - + +
123A PHE* 3.7 23.8 - - + +
17B LEU* 3.6 24.5 - - + -
20B VAL* 3.9 16.8 - - + -
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Residues in contact with LEU 71 (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 LEU* 3.9 23.8 - - + +
15A VAL* 4.1 15.3 - - + -
16A THR* 4.1 7.9 - - - +
67A PHE* 2.9 25.4 + - + +
68A LEU* 3.3 19.7 - - + +
69A ALA 3.0 0.4 + - - -
70A VAL* 1.3 77.5 - - - +
72A TRP* 1.3 78.1 + - + +
75A GLY* 3.4 15.9 + - - -
83A ALA* 3.5 29.2 - - - +
84A ALA* 4.8 0.7 - - - -
87A GLY* 3.6 22.9 - - - -
122A LEU* 3.5 7.2 - - + -
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Residues in contact with TRP 72 (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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9A VAL* 3.7 17.0 - - + -
12A LEU* 3.1 51.4 - - + -
13A ALA* 3.8 7.6 - - + -
16A THR* 3.5 32.6 + - + +
68A LEU* 2.9 35.8 - - + +
69A ALA* 3.0 4.0 + - - +
71A LEU* 1.3 83.2 - - + +
73A SER* 1.3 56.6 + - - +
74A ALA 2.9 1.8 - - - -
75A GLY* 2.4 23.4 + - - +
76A LEU* 2.7 38.0 + - + +
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Residues in contact with SER 73 (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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69A ALA 3.0 12.2 + - - -
70A VAL* 3.0 20.2 - - - -
72A TRP* 1.3 75.4 - - - +
74A ALA* 1.3 65.2 + - - +
76A LEU* 4.1 4.7 - - - +
77A LEU* 2.7 45.6 + - - +
126A SER* 2.9 24.3 + - - -
13B ALA* 5.9 2.2 - - - -
16B THR* 5.7 3.6 - - - -
17B LEU* 3.7 18.4 - - - +
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Residues in contact with ALA 74 (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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70A VAL 2.9 15.6 + - - +
72A TRP 2.9 0.8 - - - -
73A SER* 1.3 79.3 + - - +
75A GLY* 1.3 52.3 + - - +
78A CYS 2.3 27.8 - - - +
79A SER 3.4 0.2 - - - +
83A ALA* 2.9 13.5 - - + +
122A LEU* 2.8 38.1 - - + +
125A MET* 3.3 20.8 - - + +
126A SER 3.8 8.1 - - - +
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Residues in contact with GLY 75 (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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8A ASN 5.1 0.2 - - - +
12A LEU* 3.9 10.1 - - - -
71A LEU 3.4 6.8 + - - -
72A TRP 2.4 24.6 + - - -
74A ALA* 1.3 69.0 - - - +
76A LEU* 1.3 68.3 + - - +
78A CYS 3.6 4.5 - - - +
79A SER 4.6 0.2 + - - -
80A GLN* 3.5 25.5 + - - +
83A ALA* 3.4 17.0 - - - -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN 4.9 6.7 - - - +
9A VAL* 5.5 2.2 - - + -
12A LEU* 3.7 20.4 - - + -
72A TRP* 2.7 52.5 + - + +
73A SER* 4.1 2.9 - - - +
75A GLY* 1.3 82.3 - - - +
77A LEU* 1.3 61.0 + - + +
78A CYS* 2.7 17.3 + - - -
1B MET* 3.3 44.2 + - + +
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Residues in contact with LEU 77 (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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73A SER* 2.7 24.8 + - - +
76A LEU* 1.3 88.0 - - + +
78A CYS* 1.3 63.5 + - - +
126A SER* 3.4 27.8 - - - +
129A GLY* 2.9 23.0 + - - -
130A ILE* 3.7 28.5 - - + +
1B MET* 5.1 1.1 - - + -
6B VAL* 4.3 25.1 - - + -
9B VAL* 5.1 8.3 - - + -
10B VAL* 6.1 1.8 - - + -
13B ALA* 3.9 22.9 - - + -
17B LEU* 4.5 5.8 - - + -
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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