Contacts of the helix formed by residues 32 - 56 (chain A) in PDB entry 1VF5
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 ILE 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASN* 1.3 83.7 - - + +
33A PHE* 1.3 71.7 + - + +
34A TYR* 2.7 8.7 + - - +
35A CYS* 3.1 29.0 + - - +
36A LEU* 5.3 0.2 - - - +
303A HEM 4.4 1.2 - - - +
101E BCR 4.5 20.2 - - + +
28G GLN* 6.3 6.1 - - + -
29G TYR* 6.0 9.6 - - + -
31G ARG* 4.4 24.9 - - + +
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Residues in contact with PHE 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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31A ASN 3.3 6.4 + - - -
32A ILE* 1.3 81.1 - - + +
34A TYR* 1.3 60.6 + - + +
35A CYS 2.9 10.3 + - - -
36A LEU* 3.3 21.5 + - + +
103A ARG* 3.0 24.1 - - + +
14E LEU* 3.2 61.0 - - + -
17E GLY* 3.2 34.5 - - - -
18E ILE* 3.3 22.2 - - + -
22E ILE* 5.3 3.8 - - + -
101E BCR 3.5 30.1 - - + -
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A HIS* 4.7 11.5 + + - -
30A VAL* 3.5 28.5 + - + +
31A ASN* 3.3 58.6 - - + +
32A ILE 2.7 0.8 - - - -
33A PHE* 1.3 86.3 - + + +
35A CYS* 1.3 54.6 + - - +
103A ARG* 3.7 32.5 - - - +
107A THR* 3.7 18.8 + - + -
209A GLN 6.5 0.7 - - - -
211A ILE* 6.1 0.9 - - - +
302A HEM 2.6 38.9 - - - +
303A HEM 3.0 26.5 - - + +
22E ILE* 4.5 20.0 - - + +
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Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.1 19.6 + - - +
33A PHE 2.9 1.4 - - - -
34A TYR* 1.3 77.3 - - - +
36A LEU* 1.3 66.5 + - + +
37A GLY 3.2 3.3 + - - -
38A GLY* 3.2 5.1 + - - -
39A ILE* 3.0 24.0 + - + +
303A HEM 1.8 66.4 - - + +
43B VAL* 4.6 3.6 - - - -
101E BCR 4.2 21.5 - - + -
28G GLN* 5.4 3.6 - - - -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE 5.3 0.2 - - - +
33A PHE* 3.3 27.3 + - + +
34A TYR 3.4 0.2 - - - -
35A CYS* 1.3 79.1 - - + +
37A GLY* 1.3 63.3 + - - +
39A ILE* 3.2 10.7 + - + +
40A THR* 2.9 31.3 + - - -
96A MET* 4.3 6.5 - - - +
99A LEU* 3.0 40.6 - - + +
100A HIS* 3.7 22.4 - - + +
103A ARG* 3.3 14.8 - - + +
14E LEU* 4.5 23.1 - - + -
101E BCR 5.3 14.8 - - + -
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS 3.2 1.4 - - - -
36A LEU* 1.3 78.1 - - - +
38A GLY* 1.3 59.6 + - - +
40A THR* 3.6 1.0 + - - -
41A LEU* 3.2 18.4 + - - +
100A HIS* 3.6 14.9 + - - -
302A HEM 3.3 54.1 + - - +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS 3.2 5.2 + - - -
37A GLY* 1.3 73.1 - - - +
39A ILE* 1.3 53.2 + - - +
41A LEU* 3.2 7.0 + - - +
42A THR* 2.7 41.2 + - - -
302A HEM 3.6 5.3 - - - +
303A HEM 3.5 45.0 + - - +
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS 3.0 24.8 + - - +
36A LEU* 3.2 11.9 + - + +
38A GLY* 1.3 70.9 - - - +
40A THR* 1.3 69.2 + - - +
42A THR* 2.7 19.3 + - - +
43A CYS* 2.8 18.0 + - - -
96A MET* 3.4 33.4 - - + -
43B VAL* 2.9 38.4 - - + -
47B THR* 3.5 21.1 - - + +
101E BCR 3.3 24.0 - - + -
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 2.9 15.7 + - - -
37A GLY 3.8 4.3 - - - -
39A ILE* 1.3 78.5 - - - +
41A LEU* 1.3 62.9 + - - +
43A CYS* 3.3 7.8 + - - +
44A PHE* 3.1 17.7 + - - +
93A MET* 3.4 34.7 - - + +
96A MET* 3.3 28.4 + - - +
97A MET* 3.3 17.2 + - + -
100A HIS* 4.3 2.5 - - - +
302A HEM 3.7 23.1 - - + +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 3.2 12.8 + - - +
38A GLY* 3.3 7.2 - - - +
39A ILE 3.0 0.4 - - - -
40A THR* 1.3 78.7 - - - +
42A THR* 1.3 56.4 + - - +
44A PHE* 2.8 28.3 + - + +
45A LEU* 2.9 33.8 + - + +
199A MET* 3.8 24.0 - - + -
203A PHE* 4.1 24.2 - - + -
302A HEM 3.5 12.3 - - + +
303A HEM 3.6 37.2 - - + -
305A PL9 4.8 10.1 - - + -
306D OPC 5.5 5.4 - - + -
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 2.7 21.7 + - - -
39A ILE* 2.7 17.5 + - - +
41A LEU* 1.3 68.6 - - - +
43A CYS* 1.3 65.0 + - - +
44A PHE 2.9 1.8 - - - -
45A LEU* 3.0 13.8 + - + +
46A ILE* 2.9 35.9 + - + +
303A HEM 4.2 5.9 - - - +
44B ILE* 3.9 39.0 - - + +
47B THR* 3.8 27.1 + - + -
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Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 2.8 25.3 + - - -
40A THR 3.5 8.1 - - - +
42A THR* 1.3 76.6 - - - +
44A PHE* 1.3 60.8 + - - +
46A ILE* 3.8 4.0 - - - -
47A GLN* 2.8 32.2 + - - +
89A SER* 2.9 12.7 + - - +
92A MET* 3.9 17.5 - - - -
93A MET* 3.5 34.9 - - + +
96A MET* 4.4 1.1 - - - -
47B THR* 4.0 18.8 - - - -
51B ILE* 4.2 3.6 - - - -
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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 THR 3.1 6.7 + - - +
41A LEU* 2.8 21.6 + - + +
43A CYS* 1.3 74.4 - - - +
45A LEU* 1.3 64.6 + - + +
46A ILE 3.0 1.8 - - - -
47A GLN* 2.7 22.2 + - - +
48A PHE* 2.9 34.0 + + + -
93A MET* 3.6 22.4 - - + -
131A PHE* 4.4 6.5 - + - -
192A PRO* 5.0 3.8 - - + -
195A ILE* 3.8 28.7 - - + -
199A MET* 4.2 18.4 - - + -
301A HEM 3.1 43.1 - - + -
306D OPC 4.1 28.0 - - + -
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Residues in contact with LEU 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 LEU* 2.9 36.0 + - + +
42A THR* 3.5 13.9 - - + +
44A PHE* 1.3 86.0 - - + +
46A ILE* 1.3 61.6 + - + +
48A PHE* 3.4 7.4 + - + +
49A ALA* 3.3 22.3 + - - +
303A HEM 5.5 4.5 - - + -
305A PL9 4.4 41.7 - - + -
44B ILE* 6.4 2.2 - - + -
306D OPC 4.4 22.0 - - + -
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Residues in contact with ILE 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 THR* 2.9 33.1 + - + +
43A CYS* 3.5 2.5 - - - +
44A PHE 3.0 0.2 - - - -
45A LEU* 1.3 78.1 - - + +
47A GLN* 1.3 56.5 + - - +
49A ALA* 3.9 3.2 - - - +
50A THR* 2.8 33.4 + - + +
85A ILE* 3.6 27.8 - - + -
89A SER* 3.3 19.5 - - - +
47B THR* 4.2 3.1 - - + -
48B PHE* 3.8 31.2 - - + -
51B ILE* 3.4 28.9 - - + -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A CYS 2.8 8.8 + - - -
44A PHE 2.7 15.4 + - - +
46A ILE* 1.3 70.9 - - - +
48A PHE* 1.3 56.1 + - - +
50A THR* 3.7 2.5 - - - -
51A GLY* 2.7 34.0 + - - -
86A HIS* 2.4 46.3 - - + +
89A SER* 2.5 35.1 + - - -
90A ALA* 2.8 17.9 + - - +
301A HEM 3.2 53.1 - - + -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 2.9 30.3 + + + +
45A LEU* 3.7 13.9 - - + +
47A GLN* 1.3 76.6 - - - +
49A ALA* 1.3 59.0 + - + +
52A PHE* 3.0 30.7 + - - +
192A PRO* 5.5 0.9 - - + -
301A HEM 3.5 22.3 - - + +
306D OPC 3.4 64.4 - - + -
189N PHE* 3.6 28.9 - + - -
193N TRP* 3.8 42.8 - + + -
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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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45A LEU 3.3 13.4 + - - +
46A ILE* 3.9 5.6 - - - +
47A GLN 3.2 0.4 - - - -
48A PHE* 1.3 82.1 - - + +
50A THR* 1.3 61.4 + - + +
52A PHE* 3.4 4.6 - - - +
53A ALA* 2.9 27.9 + - - +
38D LEU* 5.2 15.9 - - + +
306D OPC 4.1 24.2 - - - +
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 2.8 23.5 + - + +
47A GLN* 3.7 0.7 - - - -
49A ALA* 1.3 76.7 - - + +
51A GLY* 1.3 61.3 + - - +
53A ALA* 3.5 3.5 - - - +
54A MET* 3.1 27.9 + - - +
82A ILE* 3.4 39.3 - - + +
85A ILE* 4.1 24.0 - - + -
86A HIS* 2.8 31.5 + - - +
48B PHE* 6.1 1.3 - - + -
38D LEU* 6.0 3.8 - - + +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN 2.7 24.6 + - - -
50A THR* 1.3 72.0 + - - +
52A PHE* 1.3 66.3 + - - +
54A MET* 2.9 18.7 + - - +
55A THR* 3.4 3.3 + - - +
86A HIS* 3.2 18.6 - - - -
301A HEM 3.3 26.1 - - - +
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE 3.0 21.9 + - - +
49A ALA 3.4 4.5 - - - +
51A GLY* 1.3 73.6 - - - +
53A ALA* 1.3 59.6 + - - +
55A THR* 2.5 43.3 + - - -
56A PHE* 3.3 32.0 + + - -
301A HEM 3.3 11.3 - - - +
42D PHE* 3.7 23.6 - + - -
306D OPC 3.8 27.4 - - - +
185N SER* 3.6 0.7 - - - -
189N PHE* 3.4 30.3 - + + -
190N VAL* 3.2 30.7 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 2.9 13.4 + - - +
50A THR* 3.5 12.8 - - - +
51A GLY 3.2 0.2 - - - -
52A PHE* 1.3 75.2 - - - +
54A MET* 1.3 54.7 + - - +
55A THR 3.5 0.5 + - - -
56A PHE* 3.5 10.5 + - - +
82A ILE* 4.0 9.4 - - + -
38D LEU* 4.3 18.2 - - + -
41D TYR* 2.3 46.3 + - + -
42D PHE* 4.2 15.0 - - + -
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Residues in contact with MET 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR 3.1 11.2 - - - +
51A GLY 2.9 9.6 + - - +
52A PHE 2.8 0.2 + - - -
53A ALA* 1.3 72.8 - - - +
55A THR* 1.3 56.9 + - - +
56A PHE 2.9 6.2 + - - -
57A TYR 3.2 1.5 + - - -
58A TYR* 2.7 32.1 + - + +
72A ILE* 4.5 14.5 - - + +
82A ILE* 3.7 11.7 - - + -
83A ARG* 3.8 31.0 - - + -
86A HIS* 3.4 44.2 - - + +
301A HEM 3.5 47.1 - - + -
41D TYR* 3.3 7.9 - - - +
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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
----------------------------------------------------------
51A GLY 3.7 2.9 - - - +
52A PHE* 2.5 30.2 + - - +
54A MET* 1.3 71.7 - - - +
56A PHE* 1.3 60.3 + - - +
57A TYR 3.3 0.4 - - - -
58A TYR* 4.2 4.9 - - - +
184A TYR* 3.4 25.9 + - - +
188A THR* 4.9 0.9 - - - -
301A HEM 3.2 40.4 - - + -
181N THR* 3.5 23.6 - - - +
185N SER* 2.7 31.4 + - - -
189N PHE* 5.1 4.3 - - + -
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.3 30.3 - + - -
53A ALA 3.6 11.2 - - - +
54A MET 2.9 0.6 - - - -
55A THR* 1.3 84.6 - - - +
57A TYR* 1.3 78.1 + - + +
42D PHE* 3.6 27.8 - + + -
168N LEU 5.0 2.0 - - - -
178N ALA* 5.1 4.5 - - - +
181N THR* 3.4 16.2 - - - +
182N ARG* 3.7 49.4 + - + +
185N SER* 3.0 32.5 - - - -
190N VAL* 4.6 4.7 - - + -
1304N TDS 4.3 22.7 - + - -
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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