Contacts of the helix formed by residues 57 - 87 (chain C) in PDB entry 3LSU
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 57 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 4.2 2.0 - - - -
52C LEU* 4.1 0.5 - - - +
55C GLU* 2.9 19.2 + - - +
56C PRO* 1.3 75.3 - - - +
58C PRO* 1.3 70.1 - - - +
59C ALA* 3.5 11.2 + - - +
60C ASN* 3.0 31.4 + - - +
61C ALA* 2.9 27.2 + - - +
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Residues in contact with PRO 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 4.1 9.6 - - + -
79B THR* 4.0 20.0 + - + +
82B CYS* 3.6 35.4 - - + -
83B LEU* 5.4 3.8 - - + -
207B ILE* 4.2 10.1 - - + -
56C PRO 4.4 0.9 - - - +
57C SER* 1.3 88.0 - - - +
59C ALA* 1.3 56.4 + - - +
61C ALA* 3.6 9.4 - - + +
62C ARG* 2.8 32.7 + - - +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 4.0 34.5 - - + +
57C SER* 3.1 11.6 + - - +
58C PRO* 1.3 81.0 - - - +
60C ASN* 1.3 64.9 + - - +
62C ARG* 3.4 6.2 + - - +
63C MLY 3.2 33.0 + - - +
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Residues in contact with ASN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 5.2 4.0 - - + +
51C LEU* 3.5 25.5 - - + +
52C LEU* 3.9 13.5 - - + +
55C GLU* 2.8 50.8 + - - +
57C SER* 3.0 15.1 + - - +
59C ALA* 1.3 73.6 - - - +
61C ALA* 1.3 66.4 + - - +
63C MLY 2.9 39.5 + - - +
64C MET* 3.1 21.3 + - - +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 19.9 - - + -
75B GLY 4.8 1.6 - - - +
78B PHE* 3.8 19.7 - - + -
79B THR* 3.4 18.8 - - - +
52C LEU* 3.6 9.5 - - + +
57C SER 2.9 16.5 + - - +
58C PRO 3.6 1.6 - - - +
60C ASN* 1.3 75.8 - - - +
62C ARG* 1.3 62.7 + - - +
64C MET* 3.1 4.4 + - - +
65C ILE* 3.0 28.8 + - - +
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 4.1 8.2 + - + -
83B LEU* 6.0 0.2 - - - -
156B THR* 5.0 4.5 - - + -
157B VAL 2.8 16.4 + - - +
158B THR* 3.4 24.1 - - + +
159B GLY* 3.0 28.0 + - - +
161B LEU 2.7 30.3 + - - -
162B VAL* 3.8 8.4 - - - +
163B PRO* 3.9 11.3 - - - +
206B MLY 5.8 3.0 - - - +
207B ILE* 3.4 31.5 - - + +
58C PRO 2.8 17.4 + - - +
59C ALA* 3.4 7.7 + - - +
60C ASN 3.2 0.2 - - - -
61C ALA* 1.3 77.2 - - - +
63C MLY 1.3 64.4 + - + +
65C ILE* 3.4 13.9 + - - +
66C ALA* 3.1 22.0 + - - +
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Residues in contact with MLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B MLY 6.2 4.5 - - - -
48C LEU* 3.5 33.0 - - + +
51C LEU* 4.2 11.4 - - + +
55C GLU* 6.0 0.7 - - - -
59C ALA* 3.2 20.4 + - - +
60C ASN* 2.9 35.3 + - - +
62C ARG* 1.3 79.4 + - + +
64C MET* 1.3 63.3 + - - +
66C ALA* 3.3 16.1 + - - +
67C ILE* 3.5 9.5 + - - +
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Residues in contact with MET 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 4.2 14.8 - - + -
42B VAL* 4.9 8.3 - - + -
71B ILE* 4.0 13.2 - - + -
45C PHE* 3.5 35.2 - - + -
48C LEU* 3.6 19.9 - - + +
49C SER* 3.4 35.2 - - - +
52C LEU* 4.9 7.4 - - + -
60C ASN 3.1 12.2 + - - +
61C ALA* 3.4 11.9 - - - +
63C MLY 1.3 74.6 + - - +
65C ILE* 1.3 64.8 + - - +
67C ILE* 3.2 15.8 - - - +
68C GLN* 2.9 38.5 + - - +
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 5.4 1.1 - - + -
71B ILE* 4.6 3.8 - - - +
72B MLY 4.3 28.2 - - + +
75B GLY* 3.4 40.4 - - - +
76B GLY* 3.4 9.9 - - - +
79B THR* 3.7 10.5 - - - +
154B GLN 6.1 0.2 - - - +
156B THR* 4.0 19.7 - - + +
158B THR* 4.3 12.8 - - + -
61C ALA 3.0 19.3 + - - +
62C ARG* 3.6 9.9 - - - +
64C MET* 1.3 75.2 - - + +
66C ALA* 1.3 64.3 + - - +
68C GLN* 3.1 26.7 + - - +
69C GLN* 4.4 1.4 + - - +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B THR* 3.9 26.2 - - - +
159B GLY* 5.2 3.1 - - - +
62C ARG 3.1 13.8 + - - +
63C MLY 3.6 12.3 - - - +
64C MET 3.2 0.6 - - - -
65C ILE* 1.3 77.8 - - - +
67C ILE* 1.3 60.1 + - + +
68C GLN 3.7 0.2 + - - -
69C GLN* 4.3 11.3 + - - +
70C ASN* 5.0 4.9 + - - -
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA* 3.9 8.7 - - + +
44C GLN* 3.8 24.2 - - + +
45C PHE* 3.4 44.6 - - + +
48C LEU* 3.7 25.8 - - + -
63C MLY 3.7 3.8 - - - +
64C MET* 3.2 18.8 + - - +
66C ALA* 1.3 76.2 - - + +
68C GLN* 1.3 72.7 + - - +
69C GLN 3.2 3.1 - - - -
70C ASN* 3.0 23.8 + - + +
71C ILE* 3.1 16.9 + - + +
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN* 3.1 42.2 - - - +
71B ILE* 3.3 36.1 - - + +
72B MLY 4.2 19.7 - - - +
45C PHE* 4.8 0.2 - - - -
64C MET* 2.9 34.1 + - - +
65C ILE* 3.1 18.9 + - - +
67C ILE* 1.3 83.5 - - - +
69C GLN* 1.3 62.8 + - - +
71C ILE* 3.3 15.2 + - - +
72C MLY 2.9 24.8 + - - +
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MLY 3.3 33.5 + - - +
65C ILE 4.4 1.4 + - - -
66C ALA 4.3 8.7 + - - +
67C ILE 3.2 0.8 - - - -
68C GLN* 1.3 77.8 - - - +
70C ASN* 1.3 60.3 + - - +
72C MLY 3.3 12.2 + - - +
73C PHE* 2.9 38.0 + - - +
129D GLN* 2.7 36.1 + - - +
152D TYR* 4.7 6.7 + - - -
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Residues in contact with ASN 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA* 4.1 16.6 - - + -
44C GLN* 4.8 9.7 + - - -
66C ALA 5.0 3.4 + - - -
67C ILE* 3.0 19.3 + - + +
69C GLN* 1.3 77.6 - - - +
71C ILE* 1.3 66.0 + - - +
73C PHE* 4.5 1.3 - - - +
74C HIS* 2.9 42.1 + - + +
129D GLN* 3.1 25.5 + - - +
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.6 44.0 - - + -
64B MET 4.6 5.2 - - - +
65B ILE* 4.6 2.6 - - + +
68B GLN* 4.1 13.0 - - + -
38C PHE* 4.0 12.2 - - + -
41C ALA* 3.8 24.7 - - + +
42C VAL* 4.9 2.5 - - + +
45C PHE* 4.3 5.8 - - + -
67C ILE* 3.1 23.2 + - + +
68C GLN* 3.6 35.7 - - - +
70C ASN* 1.3 75.4 - - - +
72C MLY 1.3 58.5 + - - +
75C GLY* 2.9 29.6 + - - -
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Residues in contact with MLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.2 17.0 - - + +
68B GLN* 3.5 34.3 + - - +
72B MLY 4.0 27.3 - - - -
68C GLN 2.9 17.0 + - - +
69C GLN* 3.7 13.0 - - - +
71C ILE* 1.3 78.9 + - - +
73C PHE* 1.3 57.2 + - - +
76C GLY* 2.9 24.9 + - - -
154C GLN 4.2 3.5 - - - +
155C ASP* 3.1 47.1 - - - +
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Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR* 6.2 0.2 - - + -
34C TYR* 3.7 27.6 - + - -
69C GLN* 2.9 23.5 + - - +
70C ASN 4.2 1.1 - - - +
72C MLY 1.3 79.5 + - - +
74C HIS* 1.3 76.6 + + - +
76C GLY 3.3 0.2 + - - -
77C GLY* 2.8 24.1 + - - -
153C ASN* 4.8 1.8 - - + -
154C GLN* 3.2 41.8 - - + +
155C ASP* 6.1 0.2 - - - -
170C TRP* 3.9 13.5 - + - -
129D GLN* 3.4 73.4 - - + +
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Residues in contact with HIS 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR* 4.1 15.9 - - + -
34C TYR* 3.6 26.9 - + - +
37C GLY* 3.5 30.1 - - - -
38C PHE* 3.3 22.9 - - - +
70C ASN* 2.9 36.4 + - + +
73C PHE* 1.3 93.1 - + - +
75C GLY* 1.3 61.6 + - - +
77C GLY 3.7 0.6 - - - +
78C PHE* 2.8 31.4 + - - +
129D GLN* 3.9 12.7 + - - -
182D MLY 6.5 0.4 - - - -
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Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 4.6 0.8 - - - +
65B ILE* 3.5 12.1 - - - -
38C PHE* 3.3 26.9 - - - -
71C ILE 2.9 20.4 + - - -
74C HIS* 1.3 78.8 - - - +
76C GLY* 1.3 55.0 + - - +
78C PHE* 3.4 2.9 + - - +
79C THR* 2.9 33.6 + - - -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.3 15.7 - - - +
72C MLY 2.9 14.0 + - - -
73C PHE 3.7 0.2 - - - -
75C GLY* 1.3 73.5 - - - +
77C GLY* 1.3 54.9 + - - +
79C THR* 4.5 1.3 - - - -
80C ASN* 2.7 39.8 + - - -
154C GLN* 3.2 26.9 - - - -
156C THR* 4.9 2.0 - - - -
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS* 4.0 0.3 - - - -
34C TYR* 3.6 23.7 - - - -
73C PHE 2.8 16.7 + - - -
76C GLY* 1.3 71.8 - - - +
78C PHE* 1.3 63.2 + - - +
81C HIS* 2.7 30.5 + - - +
154C GLN* 3.5 24.7 - - - +
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Residues in contact with PHE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO 4.1 8.7 - - - -
57B SER 4.2 4.0 - - - -
58B PRO* 4.0 28.3 - - + -
61B ALA* 4.0 16.2 - - + -
2C VAL* 3.7 37.0 - - + -
3C THR 3.5 24.9 - - - -
31C HIS* 3.2 25.3 + - - -
34C TYR* 3.6 11.7 - - + +
35C VAL* 3.7 19.5 - - + -
38C PHE* 4.7 5.6 - + + -
74C HIS 2.8 17.8 + - - +
75C GLY* 3.6 5.4 - - - +
77C GLY* 1.3 75.8 - - - +
79C THR* 1.3 64.9 + - - +
82C CYS* 3.2 32.0 + - - -
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 3.9 24.2 + - + +
61B ALA* 3.5 21.3 - - - +
62B ARG* 4.0 19.9 + - + -
65B ILE* 4.1 3.9 - - - +
75C GLY 2.9 18.4 + - - -
76C GLY* 3.8 4.7 - - - -
78C PHE* 1.3 80.8 - - - +
80C ASN* 1.3 64.3 + - - +
82C CYS* 3.2 6.9 + - - +
83C LEU* 3.1 36.1 + - + +
156C THR* 4.7 9.4 - - + +
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Residues in contact with ASN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLY 2.7 21.1 + - - +
77C GLY 4.5 0.2 - - - +
79C THR* 1.3 73.8 - - - +
81C HIS* 1.3 57.8 + - - +
83C LEU* 3.3 9.7 + - - +
84C PHE* 2.9 27.0 + - - +
133C TRP* 3.4 34.8 - - + +
135C PHE* 3.3 15.1 - - - -
154C GLN* 3.2 25.2 + - - +
155C ASP 3.4 22.4 + - - -
156C THR* 2.6 27.8 + - - -
166C ALA* 4.6 0.2 - - - +
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Residues in contact with HIS 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C HIS* 3.2 21.3 + + - -
31C HIS* 3.4 34.8 - + + +
34C TYR* 3.2 28.3 - + - -
77C GLY* 2.7 20.6 + - - -
79C THR 3.3 0.2 - - - -
80C ASN* 1.3 73.6 - - - +
82C CYS* 1.3 65.9 + - - +
84C PHE* 3.2 5.9 + + - +
85C TRP* 3.0 39.9 + + - +
133C TRP* 3.7 12.0 - + - -
154C GLN* 3.6 15.0 - - - -
168C ASP* 3.5 2.2 + - - -
208C MN 2.2 35.1 + - - -
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Residues in contact with CYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 3.6 29.6 - - + -
5C PRO* 3.8 19.6 - - + +
31C HIS* 3.6 16.1 - - - -
78C PHE* 3.2 40.5 + - - +
79C THR 3.2 7.2 + - - +
81C HIS* 1.3 78.5 - - - +
83C LEU* 1.3 62.3 + - - +
85C TRP* 3.6 5.6 + - - +
86C GLU* 3.3 27.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 5.5 7.2 - - + -
62B ARG* 6.0 1.8 - - - -
79C THR* 3.1 34.2 + - + +
80C ASN* 3.5 10.8 - - - +
82C CYS* 1.3 76.5 - - + +
84C PHE* 1.3 64.3 + - - +
86C GLU 3.2 1.2 + - - -
87C ASN* 3.0 15.0 + - - -
135C PHE* 4.3 14.6 - - + -
156C THR* 4.8 2.2 - - - +
163C PRO* 3.7 36.3 - - + -
166C ALA* 4.1 9.6 - - + -
201C ARG* 2.9 43.8 + - - +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 5.0 4.3 - - + -
23C ASN* 5.7 0.7 - - - -
26C HIS* 3.7 27.6 - + - -
80C ASN 2.9 16.7 + - - +
81C HIS* 3.2 9.2 + + - +
83C LEU* 1.3 76.8 - - - +
85C TRP* 1.3 89.6 + + - +
87C ASN* 3.1 18.5 + - - +
88C LEU* 3.3 40.7 + - + +
133C TRP* 4.0 9.6 - + + -
166C ALA* 3.3 21.1 - - - +
167C ILE* 4.0 0.7 - - + -
168C ASP* 3.6 25.8 - - + -
173C ALA* 5.3 0.2 - - + -
185C TYR* 3.9 18.2 - - - -
189C ILE* 3.8 19.5 - - + -
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Residues in contact with TRP 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 4.0 13.5 - - + -
6C ASP 5.9 0.7 - - - +
7C LEU* 3.5 27.6 - - + -
8C MLY 5.7 2.0 - - - +
9C TRP* 3.5 30.5 + + + -
23C ASN* 4.2 16.2 - - + -
26C HIS* 3.4 40.2 - + + -
27C TYR* 3.8 32.7 - + + -
31C HIS* 2.9 29.6 + + - -
81C HIS* 3.0 30.5 + + + -
82C CYS* 4.3 2.5 - - - +
84C PHE* 1.3 97.4 - + - +
86C GLU* 1.3 65.2 + - + +
88C LEU* 3.2 22.3 + - + +
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 5.8 3.6 - - + +
6C ASP 4.3 4.0 - - - +
8C MLY 3.1 62.3 - - - +
82C CYS* 3.3 14.7 + - + +
83C LEU* 3.2 1.4 + - - -
84C PHE 3.2 0.6 - - - -
85C TRP* 1.3 81.2 - - + +
87C ASN* 1.3 58.9 + - - +
88C LEU 3.3 2.2 + - - +
194C ASN* 3.7 9.7 + - - -
197C GLU* 3.4 31.1 - - + +
201C ARG* 3.5 20.2 - - - +
----------------------------------------------------------
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Residues in contact with ASN 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU 3.0 21.8 + - - -
84C PHE 3.1 6.4 + - - +
86C GLU* 1.3 77.0 - - - +
88C LEU* 1.3 63.1 + - - +
164C LEU 4.3 5.2 - - - +
165C VAL* 3.6 11.8 - - + +
166C ALA* 2.9 46.1 + - - +
167C ILE* 4.8 0.7 - - - +
193C VAL* 3.5 8.1 - - - +
194C ASN* 2.8 35.7 + - - +
197C GLU* 4.5 1.8 - - + -
201C ARG* 2.9 27.8 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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