Contacts of the helix formed by residues 55 - 87 (chain B) in PDB entry 4KNF
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 SER 55 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 1.3 78.0 - - - +
56B ALA* 1.3 65.1 + - - +
57B LYS* 3.5 21.1 + - - +
58B TRP* 3.0 27.7 + - - -
59B LYS* 3.1 11.5 + - - +
246B GLU* 3.7 5.9 + - - -
247B SER* 2.7 25.3 + - - -
250B ALA* 6.2 2.2 - - - -
251B LYS* 5.0 11.4 - - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 3.2 40.7 + - - +
248A SER* 6.5 1.6 - - - -
251A LYS* 5.3 11.0 - - + +
55B SER* 1.3 74.6 - - - +
57B LYS* 1.3 62.2 + - + +
58B TRP 3.2 0.9 + - - -
59B LYS* 3.7 8.3 + - - +
60B THR* 4.7 0.3 + - - -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 3.1 18.5 - - - +
56B ALA* 1.3 77.8 - - + +
58B TRP* 1.3 71.3 + - + +
60B THR* 5.4 0.9 + - - -
61B SER* 5.6 1.7 + - - -
246B GLU* 3.6 30.7 + - - +
250B ALA* 4.8 8.3 - - - +
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Residues in contact with TRP 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.8 11.4 - - + -
55B SER* 3.0 26.2 + - - -
57B LYS* 1.3 90.6 - - + +
59B LYS* 1.3 66.4 + - - +
60B THR 3.3 2.5 - - - -
61B SER* 3.1 24.2 + - - -
62B LEU* 3.2 12.3 + - - +
112B ILE* 5.3 5.8 - - + -
181B ALA* 4.0 26.0 - - + -
182B VAL* 4.7 10.1 - - + -
185B ALA* 4.1 16.8 - - + -
239B ILE* 4.6 21.3 - - + -
242B VAL* 3.6 28.9 - - + -
243B ALA* 3.4 34.1 - - + -
246B GLU* 3.0 27.1 + - + +
247B SER* 3.8 8.5 - - - -
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.6 37.4 + - - +
53A GLN* 3.4 25.4 - - - +
51B ARG* 2.9 42.6 + - + +
52B ASP* 4.3 6.7 - - - +
54B VAL* 2.8 33.6 + - + +
55B SER* 3.1 14.3 + - - +
56B ALA* 3.7 8.1 + - - +
58B TRP* 1.3 76.1 - - - +
60B THR* 1.3 57.3 + - - +
62B LEU* 3.1 5.4 + - - +
63B THR* 2.9 27.4 + - - -
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 4.3 7.2 - - + -
50A GLU* 2.6 29.5 + - - +
53A GLN* 3.0 14.3 + - - +
240A TRP* 3.6 27.5 - - + -
244A VAL* 5.9 0.3 - - - +
56B ALA 4.7 0.2 + - - -
57B LYS 5.4 0.9 - - - -
58B TRP 3.3 0.8 - - - -
59B LYS* 1.3 75.7 - - - +
61B SER* 1.3 53.5 + - - +
63B THR* 3.1 3.3 + - - -
64B VAL* 2.8 41.3 + - + +
111B LEU* 3.7 23.6 - - + -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS 5.6 0.9 + - - -
58B TRP* 3.1 22.3 + - - -
60B THR* 1.3 78.9 - - - +
62B LEU* 1.3 57.1 + - - +
64B VAL 3.4 0.3 + - - -
65B SER* 3.0 17.3 + - - -
108B GLU* 2.8 39.4 + - - +
111B LEU* 3.9 19.9 - - - +
112B ILE* 5.9 2.3 - - - +
239B ILE* 3.9 26.0 - - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.7 45.9 - - + +
50B GLU 4.0 13.2 - - - +
51B ARG* 3.6 15.7 - - + -
54B VAL* 3.4 42.8 - - + -
58B TRP 3.2 5.3 + - - +
59B LYS 3.1 8.7 + - - +
61B SER* 1.3 74.7 - - - +
63B THR* 1.3 66.7 + - - +
65B SER* 3.2 5.4 + - - -
66B GLY* 2.9 20.4 + - - -
236B GLY 4.7 1.3 - - - +
239B ILE* 5.0 5.2 - - + -
240B TRP* 4.1 29.6 - - + +
243B ALA* 4.9 2.0 - - + -
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.7 38.8 - - + -
49A VAL* 3.7 6.1 - - + +
50A GLU* 3.0 18.1 + - + -
48B PHE* 3.9 23.6 - - + -
51B ARG* 2.7 29.7 + - - +
59B LYS 2.9 8.0 + - - -
60B THR* 3.1 8.7 + - - -
62B LEU* 1.3 74.4 - - - +
64B VAL* 1.3 56.4 + - - +
66B GLY* 3.2 2.8 + - - -
67B LEU* 2.9 31.0 + - + +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 4.4 14.1 - - + -
60B THR* 2.8 29.1 + - + +
61B SER* 3.4 1.1 + - - -
62B LEU 3.2 0.2 - - - -
63B THR* 1.3 71.0 - - - +
65B SER* 1.3 63.3 + - - +
67B LEU* 3.1 13.0 + - + +
68B ILE* 3.0 25.9 + - + +
104B LEU* 3.5 42.2 - - + +
107B VAL* 5.0 8.5 - - + -
108B GLU* 3.8 19.3 - - + +
111B LEU* 4.2 16.6 - - + -
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.8 22.4 - - - -
61B SER 3.0 11.4 + - - -
62B LEU* 3.4 12.3 - - - -
64B VAL* 1.3 75.8 - - - +
66B GLY* 1.3 60.9 + - - +
68B ILE* 3.3 11.2 + - - +
69B THR* 3.2 26.3 + - - +
108B GLU* 3.5 19.2 + - - -
232B LYS 5.4 1.1 - - - +
235B PHE* 5.4 0.7 - - - -
236B GLY* 3.5 22.0 + - - -
239B ILE* 4.9 4.0 - - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR* 3.4 9.2 - - - +
47B PHE* 3.8 13.4 - - - +
48B PHE* 3.6 22.1 - - - -
62B LEU 2.9 17.1 + - - -
63B THR 3.6 2.9 - - - -
65B SER* 1.3 69.9 - - - +
67B LEU* 1.3 60.1 + - - +
69B THR* 2.7 21.2 + - - -
70B GLY* 2.8 14.2 + - - -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.5 44.2 - - + +
45A VAL* 4.0 22.9 - - + -
46A PHE* 4.0 26.5 - - + +
48B PHE* 3.8 2.4 - - + -
63B THR* 2.9 18.8 + - + +
64B VAL* 3.1 15.0 + - + +
66B GLY* 1.3 75.2 - - - +
68B ILE* 1.3 58.4 + - - +
70B GLY* 3.1 2.6 + - - -
71B ILE* 2.9 38.9 + - + +
104B LEU* 4.2 21.8 - - + -
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 3.0 26.2 + - + +
65B SER* 3.6 9.2 - - - +
67B LEU* 1.3 75.6 - - - +
69B THR* 1.3 62.9 + - + +
71B ILE 3.5 0.2 + - - -
72B ALA* 3.1 24.3 + - - +
101B THR* 3.8 23.8 - - - +
104B LEU* 3.7 24.0 - - + -
105B LEU* 3.7 45.1 - - + +
108B GLU* 4.3 4.0 - - - +
232B LYS* 3.8 35.2 - - + +
301B RET 4.8 1.1 - - + -
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.1 35.5 - - + +
43B ALA* 3.7 7.0 - - + -
44B THR* 2.7 33.7 + - - -
47B PHE* 3.7 26.2 - - + -
65B SER 3.2 8.5 + - - +
66B GLY* 2.7 14.2 + - - -
68B ILE* 1.3 75.7 - - - +
70B GLY* 1.3 51.5 + - - +
72B ALA* 3.2 1.7 + - - +
73B PHE* 2.7 35.7 + - - +
232B LYS* 4.2 12.8 - - + +
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR* 3.0 16.9 + - - -
66B GLY 2.8 15.2 + - - -
67B LEU* 3.1 4.7 + - - -
69B THR* 1.3 72.9 - - - +
71B ILE* 1.3 65.8 + - - +
73B PHE* 3.2 15.4 - - - +
74B TRP* 3.1 25.5 + - - -
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 5.1 10.8 - - + +
41A LEU* 6.4 2.5 - - + -
42A ALA* 4.4 21.5 - - + -
67B LEU* 2.9 22.6 + - + +
70B GLY* 1.3 74.2 - - - +
72B ALA* 1.3 64.1 + - - +
74B TRP* 3.2 9.2 + - + +
75B HIS* 3.0 53.5 + - + +
97B ASN* 3.9 6.5 - - - +
100B LEU* 3.9 27.1 - - + +
101B THR* 4.1 9.9 - - + -
104B LEU* 3.9 24.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.8 22.0 - - - -
68B ILE 3.1 19.6 + - - +
69B THR 3.4 4.0 - - - +
70B GLY 3.2 0.2 - - - -
71B ILE* 1.3 76.4 - - - +
73B PHE* 1.3 52.8 + - - +
75B HIS 3.1 2.4 + - - -
76B TYR* 2.6 45.3 + - + -
97B ASN* 3.5 25.1 + - - +
101B THR* 4.9 0.2 - - + -
232B LYS* 4.0 11.9 - - + -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 3.4 36.1 - - + +
40B MET* 3.7 13.9 - - + +
41B LEU* 3.9 45.1 - - + +
44B THR* 4.9 0.7 - - - +
69B THR 2.7 16.0 + - - +
70B GLY* 3.2 11.9 - - - +
72B ALA* 1.3 72.2 - - - +
74B TRP* 1.3 101.1 + + - +
76B TYR* 3.2 5.6 + - - +
77B LEU* 3.0 43.2 + - + +
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Residues in contact with TRP 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 6.2 1.6 - - + -
41A LEU* 4.0 28.7 - - + +
70B GLY* 3.1 28.3 + - - -
71B ILE* 3.2 10.4 + - + +
73B PHE* 1.3 94.1 - + - +
75B HIS* 1.3 67.2 + - + +
77B LEU* 3.1 38.2 + - + +
78B TYR* 3.2 32.8 + + + -
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 2.9 42.2 + + - -
38A ALA* 4.9 4.3 - - + -
71B ILE* 3.0 32.3 + - + +
72B ALA 3.6 2.5 - - - +
74B TRP* 1.3 79.1 - - + +
76B TYR* 1.3 55.0 + - - +
78B TYR* 3.3 5.5 + - - +
79B MET* 2.9 36.6 + - - +
93B PHE* 4.0 19.7 - + - +
96B ILE* 3.7 6.8 - - + +
97B ASN* 3.4 37.1 + - + +
100B LEU* 3.3 27.6 - - + -
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.7 18.6 - + - -
36B VAL* 2.9 41.3 - - + -
37B THR* 3.5 26.4 + - - +
40B MET* 4.6 4.0 - - + -
72B ALA* 2.6 37.2 + - + +
73B PHE* 3.6 5.8 - - - +
75B HIS* 1.3 70.8 - - - +
77B LEU* 1.3 59.0 + - - +
79B MET* 3.9 10.0 - - - +
80B ARG* 2.9 33.1 + - - +
94B ARG* 3.4 12.9 + - - -
97B ASN* 4.2 11.7 - - - -
225B ASN* 3.5 19.9 + - - -
228B ASP* 2.6 44.9 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 3.9 18.1 + - + -
73B PHE* 3.0 39.7 + - + +
74B TRP* 3.1 33.6 + - + +
76B TYR* 1.3 74.7 - - - +
78B TYR* 1.3 63.6 + - + +
80B ARG* 3.9 5.0 - - + +
81B GLY* 2.9 24.4 + - - -
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.6 32.8 - + - -
74B TRP* 3.2 39.0 + + + -
75B HIS 3.8 4.9 - - - +
76B TYR 3.3 0.4 - - - -
77B LEU* 1.3 79.6 - - + +
79B MET* 1.3 58.8 + - - +
81B GLY* 3.0 3.3 + - - -
82B VAL* 2.8 33.8 + - - +
93B PHE* 3.7 39.0 - + + -
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Residues in contact with MET 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.6 17.4 - - + -
75B HIS* 2.9 30.0 + - - +
76B TYR* 3.9 16.2 - - + +
78B TYR* 1.3 71.5 - - - +
80B ARG* 1.3 63.3 + - - +
82B VAL 3.5 0.3 + - - -
83B TRP* 3.1 19.2 + - - +
90B PRO* 3.3 36.9 - - + +
93B PHE* 3.8 13.4 - - + +
94B ARG* 2.6 80.1 - - + +
97B ASN* 5.1 2.9 - - - -
228B ASP* 5.2 0.2 - - - +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.1 28.9 - - - +
27B ASP* 5.3 0.2 + - - -
30B GLY* 2.7 25.6 + - - -
33B PHE* 3.6 31.0 - - + -
34B TRP* 3.6 41.3 - - - +
37B THR* 4.7 4.0 - - - +
76B TYR 2.9 19.2 + - - +
77B LEU* 3.9 5.4 - - + +
79B MET* 1.3 75.3 - - - +
81B GLY* 1.3 64.8 + - - +
83B TRP* 3.0 13.2 + - - +
84B ILE* 3.1 45.2 + - + +
----------------------------------------------------------
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU 2.9 17.6 + - - -
78B TYR* 3.0 5.5 + - - -
80B ARG* 1.3 77.3 - - - +
82B VAL* 1.3 60.9 + - - +
84B ILE* 3.5 3.1 + - - +
85B ASP* 3.0 35.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 3.2 41.5 - - - +
22A ASP* 3.4 17.9 - - + +
78B TYR 2.8 20.2 + - - +
79B MET 3.7 4.3 - - - +
81B GLY* 1.3 70.3 - - - +
83B TRP* 1.3 64.7 + - - +
85B ASP* 3.8 0.8 - - - -
86B THR* 2.9 34.5 + - - +
88B ASP* 3.4 23.8 - - + +
90B PRO* 4.1 13.7 - - + -
93B PHE* 3.8 11.4 - - + -
----------------------------------------------------------
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Residues in contact with TRP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 3.0 36.4 + - - -
29B VAL* 3.4 35.2 - - + +
30B GLY* 3.8 15.0 - - - -
33B PHE* 4.0 14.8 - + + -
79B MET 3.1 10.0 + - - +
80B ARG 3.0 9.7 + - - +
82B VAL* 1.3 78.8 - - - +
84B ILE* 1.3 61.7 + - + +
87B GLY* 2.8 53.2 + - - +
88B ASP 3.4 22.4 - - - +
89B THR* 4.0 7.4 - - - -
90B PRO* 4.7 0.9 - - + -
217B ALA* 4.4 13.7 - - + -
218B SER* 4.6 6.3 - - - -
221B ASN* 3.8 23.3 - - - -
----------------------------------------------------------
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 4.4 11.2 - - - +
30B GLY* 4.2 12.1 - - - -
80B ARG* 3.1 64.6 + - + +
81B GLY* 4.0 2.0 - - - +
83B TRP* 1.3 82.5 - - + +
85B ASP* 1.3 75.8 + - - +
86B THR 5.1 0.2 - - - -
87B GLY 4.8 0.5 + - - -
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 5.0 5.4 - - - +
81B GLY* 3.0 24.1 + - - +
82B VAL* 3.2 4.2 + - - +
84B ILE* 1.3 93.3 - - - +
86B THR* 1.3 67.1 + - + +
----------------------------------------------------------
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 4.2 26.0 - - - +
82B VAL* 2.9 16.3 + - - +
84B ILE 5.1 0.7 - - - -
85B ASP* 1.3 84.9 - - + +
87B GLY* 1.3 60.1 + - - +
88B ASP* 3.1 39.4 + - - +
----------------------------------------------------------
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 2.8 51.9 + - - -
84B ILE 4.8 0.2 - - - -
86B THR* 1.3 73.1 + - - +
88B ASP* 1.3 61.6 + - - +
89B THR 3.9 0.3 + - - -
217B ALA* 5.5 1.6 - - - +
----------------------------------------------------------
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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