Contacts of the helix formed by residues 35 - 72 (chain A) in PDB entry 4M8J
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 ALA 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 3.5 24.7 + - + +
34A ASP* 1.3 77.5 - - - +
36A SER* 1.3 63.7 + - - +
38A GLU* 3.0 21.1 + - - +
39A VAL* 3.1 16.8 + - - +
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 4.3 1.4 + - - -
29A THR* 3.2 29.9 + - - -
32A ASP 2.9 17.5 + - - -
33A LEU* 4.3 6.7 - - - -
34A ASP 3.2 0.4 - - - -
35A ALA* 1.3 78.7 - - - +
37A ASN* 1.3 52.0 + - - +
39A VAL* 3.0 13.4 + - - +
40A ILE* 2.5 42.4 + - - +
466A LEU* 4.1 20.9 - - - -
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Residues in contact with ASN 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 LEU 2.7 26.8 + - - +
34A ASP* 3.4 8.4 + - - +
35A ALA 3.4 0.4 - - - -
36A SER* 1.3 74.8 - - - +
38A GLU* 1.3 62.7 + - - +
39A VAL 3.4 0.2 - - - -
40A ILE* 3.9 10.4 - - + +
41A ASN* 3.3 25.3 + - - +
466A LEU* 3.4 46.9 + - - +
467A GLY 4.1 5.7 - - - +
470A LYS* 5.6 1.2 - - - +
471A PRO* 4.2 8.7 - - - +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP 3.1 18.5 - - - +
35A ALA* 3.0 15.4 + - - +
37A ASN* 1.3 83.4 - - - +
39A VAL* 1.3 58.5 + - - +
41A ASN* 4.4 2.9 - - - +
42A ALA* 3.3 18.1 + - - +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA 3.1 13.6 + - - +
36A SER* 3.1 21.1 - - - +
38A GLU* 1.3 78.3 - - - +
40A ILE* 1.3 58.1 + - + +
41A ASN 3.2 1.1 - - - -
42A ALA* 3.4 8.1 - - + -
43A VAL* 2.6 51.9 + - + +
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Residues in contact with ILE 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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29A THR* 6.0 1.6 - - - +
36A SER* 2.5 37.9 + - - +
37A ASN* 3.9 9.6 - - - +
39A VAL* 1.3 76.7 - - + +
41A ASN* 1.3 57.9 + - + +
42A ALA 3.3 2.4 + - - -
43A VAL* 4.9 0.9 - - + -
44A PHE* 3.3 13.2 + - - +
463A LEU* 6.4 0.9 - - + -
466A LEU* 4.0 20.6 - - + -
470A LYS* 3.7 26.2 - - + +
471A PRO* 3.8 14.6 - - + +
474A THR* 3.0 49.9 + - + +
475A ALA 5.6 0.7 - - - +
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN 3.3 19.5 + - - +
38A GLU* 4.6 2.2 - - - +
39A VAL 3.2 0.6 - - - -
40A ILE* 1.3 78.7 - - + +
42A ALA* 1.3 57.8 + - - +
44A PHE* 4.4 5.3 - - - -
45A SER* 2.9 29.4 + - - -
470A LYS* 3.8 33.4 - - + +
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Residues in contact with ALA 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 GLU 3.3 21.5 + - - +
39A VAL* 2.9 10.8 + - + +
41A ASN* 1.3 79.3 - - - +
43A VAL* 1.3 65.6 + - - +
44A PHE 3.3 0.7 - - - -
45A SER* 3.6 4.9 + - - +
46A TYR* 3.2 23.0 + - - +
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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
----------------------------------------------------------
39A VAL* 2.6 39.9 + - + +
40A ILE* 5.2 0.4 - - + -
42A ALA* 1.3 70.3 - - - +
44A PHE* 1.3 66.1 - - - +
46A TYR* 3.3 5.3 + - + +
47A VAL* 3.2 35.3 + - + +
474A THR* 3.8 20.6 - - + -
477A ILE* 6.5 0.4 - - + -
478A ALA* 5.3 11.4 - - + +
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Residues in contact with PHE 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 ILE 3.3 17.4 + - - +
41A ASN* 4.7 3.8 - - - -
43A VAL* 1.3 80.3 - - - +
45A SER* 1.3 70.6 + - - +
46A TYR 3.3 0.5 + - - -
47A VAL* 3.6 2.3 + - - +
48A THR* 3.1 41.0 + - + +
314A GLN* 3.9 19.3 - - + -
315A ALA* 4.2 15.9 - - + -
319A PHE* 4.5 0.4 - - + -
470A LYS* 3.2 35.4 - - - +
473A GLN* 3.6 27.6 - - + -
474A THR* 3.5 16.8 - - - +
477A ILE* 3.5 30.1 - - + -
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Residues in contact with SER 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 ASN* 2.9 29.9 + - - -
42A ALA* 3.6 7.0 + - - -
43A VAL 3.3 0.4 - - - -
44A PHE* 1.3 83.6 - - - +
46A TYR* 1.3 58.3 + - - +
48A THR* 4.2 2.2 - - - -
49A ASN* 2.7 45.2 + - - +
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Residues in contact with TYR 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 ALA 3.2 17.3 + - - +
43A VAL* 3.7 6.1 - - - +
44A PHE 3.2 0.6 - - - -
45A SER* 1.3 76.0 - - - +
47A VAL* 1.3 86.1 + - + +
49A ASN* 3.2 3.0 + - - +
50A VAL* 3.1 41.3 + - + +
51A TRP* 3.3 36.1 + + - -
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Residues in contact with VAL 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* 3.2 27.9 + - + +
44A PHE 4.3 0.9 - - - +
46A TYR* 1.3 89.7 - - + +
48A THR* 1.3 57.9 + - - +
51A TRP* 2.7 49.8 + - + +
52A GLY 3.3 0.9 + - - -
55A PHE* 4.0 17.3 - - + -
477A ILE* 3.7 28.3 - - + -
478A ALA* 6.1 1.3 - - - -
481A CYS* 4.2 20.4 - - - -
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Residues in contact with THR 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 PHE* 3.1 30.2 + - + +
45A SER* 3.7 4.5 + - - -
47A VAL* 1.3 75.1 - - - +
49A ASN* 1.3 67.6 + - - +
52A GLY* 3.1 23.9 + - - +
314A GLN* 3.4 39.7 + - - +
318A VAL* 3.5 27.4 - - + -
477A ILE* 3.6 24.5 - - + -
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Residues in contact with ASN 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 SER* 2.7 34.3 + - - +
46A TYR 3.2 3.3 + - - +
48A THR* 1.3 83.3 + - - +
50A VAL* 1.3 60.2 + - + +
53A TRP* 6.1 0.2 - - - -
311A GLY* 5.6 1.2 - - - -
314A GLN* 3.1 31.9 + - - +
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Residues in contact with VAL 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 TYR* 3.1 38.3 + - + +
49A ASN* 1.3 79.3 - - + +
51A TRP* 1.3 92.6 + - + +
52A GLY 3.6 1.6 - - - -
53A TRP* 2.7 32.8 + - - +
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Residues in contact with TRP 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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46A TYR* 3.3 34.4 + + - -
47A VAL* 2.7 32.5 + - + +
50A VAL* 1.3 103.6 - - + +
52A GLY* 1.3 63.8 + - - +
53A TRP* 3.3 30.3 - + - +
54A ALA* 3.2 21.7 + - + +
55A PHE* 3.1 18.0 - - + -
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Residues in contact with GLY 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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47A VAL 3.3 1.2 + - - -
48A THR* 3.1 24.2 + - - -
50A VAL 3.6 1.2 - - - -
51A TRP* 1.3 78.3 - - - +
53A TRP* 1.3 62.0 + - - +
55A PHE* 3.3 23.6 + - - +
56A GLU* 3.3 18.4 + - - +
304A THR* 5.4 1.8 - - - -
318A VAL* 3.9 17.4 - - - +
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Residues in contact with TRP 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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49A ASN 6.0 0.2 - - - -
50A VAL* 2.7 29.0 + - - -
51A TRP* 4.0 28.3 - + - -
52A GLY* 1.3 74.4 - - - +
54A ALA* 1.3 92.2 + - + +
56A GLU* 3.1 9.7 + - - +
57A TRP* 3.0 52.1 + + + +
304A THR* 4.3 22.1 - - + +
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Residues in contact with ALA 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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51A TRP* 3.2 26.2 + - + +
52A GLY 3.2 0.6 - - - -
53A TRP* 1.3 103.0 - - + +
55A PHE* 1.3 63.9 + - + +
57A TRP* 3.6 3.1 + - - +
58A TYR 3.2 14.0 + - - -
484A PHE* 3.0 32.4 - - + -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.0 26.9 - - + -
51A TRP* 3.1 30.5 - - + -
52A GLY* 3.3 14.6 + - - +
53A TRP 3.3 0.2 - - - -
54A ALA* 1.3 78.2 - - + +
56A GLU* 1.3 57.7 + - - +
58A TYR* 3.2 6.3 - - - +
59A MET* 3.0 32.0 + - - +
318A VAL* 4.4 14.6 - - + +
321A TRP* 4.0 17.5 - - + -
322A ALA* 4.2 20.0 - - + -
325A VAL* 4.4 13.2 - - + -
477A ILE* 4.6 15.5 - - + -
480A GLY 4.0 20.4 - - - -
481A CYS* 4.7 8.3 - - - -
484A PHE* 3.8 20.0 - + - -
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Residues in contact with GLU 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 GLY 3.3 16.6 - - - +
53A TRP* 3.1 10.3 + - - +
55A PHE* 1.3 75.8 - - - +
57A TRP* 1.3 61.2 + - + +
59A MET* 3.2 4.6 + - - +
60A VAL* 3.0 27.4 + - - +
300A MET 4.6 0.5 - - - +
301A LEU* 3.7 21.1 - - - +
302A PHE* 4.0 6.6 - - + -
303A TYR 2.8 35.9 + - - +
304A THR* 4.0 9.2 - - - +
317A THR* 3.2 32.6 - - - +
318A VAL* 4.2 9.1 - - + +
321A TRP* 3.8 18.9 + - + +
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Residues in contact with TRP 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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53A TRP* 3.0 53.5 + + + +
54A ALA* 4.1 4.5 - - - +
56A GLU* 1.3 74.3 - - + +
58A TYR* 1.3 60.6 + - - +
60A VAL* 3.2 23.3 - - + +
61A ILE* 2.8 52.1 + - + +
302A PHE* 3.4 37.5 - + - -
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Residues in contact with TYR 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 ALA 3.2 15.2 + - - +
55A PHE 3.2 9.4 - - - +
57A TRP* 1.3 77.8 - - - +
59A MET* 1.3 78.4 + - + +
61A ILE* 4.1 4.4 - - - +
62A MET* 3.1 66.6 + - + +
149A THR* 5.0 5.0 + - - -
153A LEU* 4.7 3.3 - - - +
325A VAL* 3.7 23.5 - - + -
328A ALA* 4.9 1.4 - - - +
484A PHE* 3.7 42.8 - + + -
487A ASN* 3.0 34.5 + - + +
488A ILE* 3.9 19.7 - - + -
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Residues in contact with MET 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 PHE 3.0 19.2 + - - +
56A GLU 3.2 8.2 + - - +
58A TYR* 1.3 93.5 - - + +
60A VAL* 1.3 57.4 + - - +
63A PHE* 3.2 18.6 - - - +
145A LEU* 4.6 7.3 - - + +
146A PRO* 3.7 13.9 - - + -
149A THR* 3.2 45.7 - - + +
301A LEU* 4.8 5.6 - - + +
321A TRP* 3.6 61.9 - - + +
324A TRP* 4.4 13.9 - - + -
325A VAL* 4.9 0.9 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU 3.0 9.9 + - - +
57A TRP* 3.2 44.4 + - + +
59A MET* 1.3 76.9 - - - +
61A ILE* 1.3 66.6 - - + +
63A PHE* 3.5 11.0 - - + +
64A GLY* 3.4 15.8 + - - -
301A LEU* 3.6 26.9 - - + -
302A PHE* 3.6 27.8 - - + -
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Residues in contact with ILE 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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57A TRP* 2.8 34.6 + - + +
58A TYR* 4.1 5.4 - - - +
60A VAL* 1.3 83.8 - - + +
62A MET* 1.3 67.4 + - + +
63A PHE 3.0 1.3 - - - -
64A GLY* 2.8 18.0 + - - +
65A GLY* 3.2 8.7 + - - -
152A PHE* 5.9 0.2 - - - -
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Residues in contact with MET 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.1 57.7 + - + +
61A ILE* 1.3 82.1 - - + +
63A PHE* 1.3 60.5 - - - +
65A GLY* 3.3 11.1 + - - +
66A TRP 3.4 8.0 + - - -
148A ALA 4.0 9.0 - - - +
149A THR* 3.6 26.5 - - - +
152A PHE* 4.3 22.6 - - + +
153A LEU* 3.9 20.0 - - - -
487A ASN 5.5 0.4 - - - +
488A ILE* 5.2 7.2 - - + -
491A THR* 3.6 32.3 - - + +
495A ILE* 6.4 0.2 - - + -
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Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A MET 3.2 21.8 + - - +
60A VAL* 3.5 11.4 - - + +
61A ILE 3.0 0.2 - - - -
62A MET* 1.3 79.1 - - - +
64A GLY* 1.3 61.0 + - - +
66A TRP* 3.4 9.3 - + + +
67A PHE* 3.2 46.8 - + - -
144A PRO 4.7 1.6 - - - -
145A LEU* 3.9 40.4 - - + -
148A ALA* 3.6 29.8 - - + -
149A THR* 3.9 4.9 - - + +
297A MET* 6.0 2.2 - - - -
301A LEU* 4.5 13.5 - - + -
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Residues in contact with GLY 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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60A VAL 3.4 8.4 + - - -
61A ILE* 2.8 10.6 + - - -
63A PHE* 1.3 78.3 - - - +
65A GLY* 1.3 63.3 + - - +
66A TRP 3.1 0.2 - - - -
67A PHE* 3.2 11.5 + - - +
68A TRP* 3.0 20.6 + - - +
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Residues in contact with GLY 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 ILE 3.2 10.0 + - - -
62A MET 3.3 2.3 + - - -
64A GLY* 1.3 74.0 - - - +
66A TRP* 1.3 54.2 + - - +
68A TRP* 3.9 8.1 - - - -
69A LEU* 2.6 45.4 + - - +
152A PHE* 3.6 31.6 - - - -
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Residues in contact with TRP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MET 3.4 5.7 + - - -
63A PHE* 3.4 14.6 - + - +
64A GLY 3.1 0.4 - - - -
65A GLY* 1.3 75.9 - - - +
67A PHE* 1.3 97.0 - + + +
69A LEU* 3.2 9.5 + - - +
70A VAL* 3.0 54.4 + - + +
71A PHE* 4.8 3.4 - + - -
148A ALA* 3.4 45.8 - - + +
151A SER* 3.8 15.0 - - - -
152A PHE* 4.8 1.5 - - - +
348A CYS* 3.5 14.1 + - + +
349A LEU* 3.9 25.6 - - + -
352A VAL* 3.3 27.8 - - + +
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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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63A PHE* 3.2 61.7 - + - -
64A GLY* 3.2 9.4 + - - +
66A TRP* 1.3 105.0 - + - +
68A TRP* 1.3 59.1 + - - +
71A PHE* 2.9 53.4 + + + +
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Residues in contact with TRP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 3.0 14.3 + - - +
65A GLY* 3.4 9.2 - - - +
67A PHE* 1.3 76.0 - - - +
69A LEU* 1.3 85.3 + - + +
71A PHE* 5.0 0.4 - - - -
72A GLY* 2.7 46.1 + - - +
73A ARG* 4.4 28.9 - - + +
74A TYR* 3.5 40.2 + + + +
152A PHE* 3.9 21.5 - + - -
494A PHE* 4.7 3.1 - + - -
495A ILE* 5.1 12.8 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 2.6 30.6 + - - +
66A TRP* 3.5 5.2 - - - +
68A TRP* 1.3 102.8 - - + +
70A VAL* 1.3 62.6 + - - +
74A TYR* 4.1 6.2 - - + -
75A ALA* 3.3 25.8 + - - +
151A SER* 3.7 10.8 - - - +
152A PHE* 4.0 25.4 - - + +
155A VAL* 3.6 39.5 - - + -
344A VAL* 3.9 13.8 - - + +
348A CYS* 3.6 18.4 - - - -
494A PHE* 4.9 4.3 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 3.0 46.3 + - + +
69A LEU* 1.3 75.3 - - - +
71A PHE* 1.3 79.1 + - + +
75A ALA* 3.2 3.1 - - - +
345A ARG* 2.7 67.4 + - + +
348A CYS* 4.0 12.8 - - + -
349A LEU* 4.0 17.5 - - + -
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TRP* 4.8 3.6 - + - -
67A PHE* 2.9 48.0 + + + +
68A TRP* 3.7 1.6 - - - -
70A VAL* 1.3 99.5 - - + +
72A GLY* 1.3 62.3 + - - +
75A ALA* 4.6 0.4 - - - -
345A ARG* 4.1 15.3 - - - +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TRP* 2.7 37.6 + - - -
69A LEU 3.6 2.4 + - - -
70A VAL 3.6 0.2 - - - -
71A PHE* 1.3 77.8 - - - +
73A ARG* 1.3 59.1 + - - -
74A TYR 3.0 10.3 + - - -
75A ALA* 3.2 17.1 + - - +
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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