Contacts of the helix formed by residues 3 - 34 (chain L) in PDB entry 2X17
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 3 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1L MET 3.7 1.8 + - - -
2L LEU* 1.3 75.0 - - - +
4L GLU* 1.3 65.2 + - - +
5L ARG* 3.6 5.5 - - - +
6L MET* 3.1 15.1 + - - +
7L LEU* 2.9 23.1 + - - +
111L GLU* 2.7 39.4 + - - -
113L ASP* 5.2 1.0 + - - -
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Residues in contact with GLU 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L LEU 3.9 1.0 + - - -
3L SER* 1.3 72.6 - - - +
5L ARG* 1.3 62.5 + - + +
7L LEU* 3.7 11.6 + - + +
8L LYS* 3.3 22.5 + - - +
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Residues in contact with ARG 5 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L SER* 3.6 5.6 - - - +
4L GLU* 1.3 75.0 - - + +
6L MET* 1.3 61.2 + - - +
8L LYS* 3.5 9.1 + - - +
9L ALA* 3.1 22.5 + - - +
107L LEU* 4.6 7.8 - - + +
111L GLU* 3.4 24.5 - - - +
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Residues in contact with MET 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L LEU* 4.0 12.6 - - + -
3L SER* 3.1 26.1 + - - +
5L ARG* 1.3 74.6 - - - +
7L LEU* 1.3 61.0 + - - +
9L ALA* 3.2 4.5 + - - +
10L LEU* 3.0 32.8 + - + +
104L LEU* 4.6 11.7 - - - +
107L LEU* 3.6 28.0 - - + +
108L ALA* 3.6 33.9 - - + +
111L GLU* 3.4 17.9 + - - +
113L ASP* 3.8 18.4 - - + +
116L THR* 3.9 21.1 - - - +
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Residues in contact with LEU 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L LEU* 4.1 25.0 - - + +
3L SER 2.9 15.7 + - - +
4L GLU* 3.9 10.1 - - + +
6L MET* 1.3 76.7 - - - +
8L LYS* 1.3 61.7 + - - +
10L LEU* 3.4 3.9 + - - +
11L ASN* 3.1 36.9 + - - +
61L ILE* 3.8 15.5 - - + -
66L GLY* 4.3 3.4 - - - -
67L ARG* 3.4 43.1 - - + +
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Residues in contact with LYS 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L GLU 3.3 14.3 + - - +
5L ARG* 3.6 9.0 - - - +
6L MET 3.3 0.2 - - - -
7L LEU* 1.3 78.8 - - - +
9L ALA* 1.3 57.4 + - - +
11L ASN* 3.5 8.8 + - + +
12L ASP* 3.1 53.3 + - - +
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Residues in contact with ALA 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L ARG 3.1 14.8 + - - +
6L MET* 3.2 8.5 + - - +
8L LYS* 1.3 76.1 - - - +
10L LEU* 1.3 63.0 + - - +
12L ASP* 3.4 10.8 + - - +
13L GLN* 3.3 18.0 + - - +
16L ARG* 4.5 2.1 + - - -
104L LEU* 3.7 25.7 - - + +
107L LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L LEU* 3.8 38.8 - - + -
6L MET* 3.0 23.8 + - + +
7L LEU 3.8 3.4 - - - +
9L ALA* 1.3 73.8 - - - +
11L ASN* 1.3 64.5 + - - +
13L GLN 3.4 0.9 + - - +
14L LEU* 3.1 22.2 + - - +
57L PHE* 3.7 36.3 - - + -
60L TYR* 3.9 15.9 - - + -
61L ILE* 4.1 16.7 - - + +
104L LEU* 4.2 12.3 - - + -
116L THR* 4.0 20.0 - - + -
119L PHE* 4.4 8.7 - - + -
120L LEU* 5.2 1.3 - - + -
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Residues in contact with ASN 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L LEU* 3.1 34.1 + - - +
8L LYS* 3.7 7.9 - - - +
9L ALA 3.4 0.2 - - - -
10L LEU* 1.3 76.0 - - - +
12L ASP* 1.3 64.1 + - - +
14L LEU* 3.4 8.8 - - - +
15L ASN* 3.2 21.8 + - - +
61L ILE* 4.1 7.9 - - - +
67L ARG 3.2 21.2 + - - -
68L VAL* 3.4 13.6 - - - +
69L GLU* 3.0 41.9 + - + +
71L ASP* 4.8 6.1 - - - +
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Residues in contact with ASP 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LYS* 3.1 42.8 + - - +
9L ALA* 3.5 13.1 - - - +
10L LEU 3.2 0.4 - - - -
11L ASN* 1.3 78.1 - - - +
13L GLN* 1.3 57.4 + - - +
15L ASN* 3.2 8.6 + - - +
16L ARG* 2.9 52.9 + - - +
71L ASP* 4.1 13.2 - - - +
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Residues in contact with GLN 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ALA 3.3 4.8 + - - +
10L LEU 3.9 6.5 - - - +
12L ASP* 1.3 76.2 - - - +
14L LEU* 1.3 56.7 + - - +
16L ARG* 3.1 27.7 + - - +
17L GLU* 2.8 62.1 + - - +
57L PHE* 3.4 30.1 - - + -
97L ILE* 3.8 18.4 - - - +
100L SER* 3.0 26.4 + - - +
101L ILE* 3.8 12.4 - - + +
104L LEU* 3.7 20.2 - - + -
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Residues in contact with LEU 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253 PHE* 4.4 7.2 - - + -
10L LEU 3.1 11.6 + - - +
11L ASN* 3.4 13.7 - - - +
13L GLN* 1.3 77.9 - - - +
15L ASN* 1.3 56.8 + - - +
17L GLU* 3.5 6.4 + - - +
18L LEU* 3.1 44.7 + - + +
54L ALA* 3.5 21.4 - - + +
57L PHE* 4.0 10.2 - - + -
58L TYR* 3.6 31.2 - - + +
61L ILE* 4.0 14.8 - - + -
68L VAL* 4.0 19.1 - - + -
70L LEU* 3.9 17.5 - - + -
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Residues in contact with ASN 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223 TYR* 3.4 11.3 + - - -
11L ASN 3.2 9.8 + - - +
12L ASP* 3.4 10.5 - - - +
13L GLN 3.2 0.2 - - - -
14L LEU* 1.3 79.5 - - - +
16L ARG* 1.3 59.3 + - + +
18L LEU* 3.4 6.3 + - - +
19L TYR* 2.9 28.8 + - - +
70L LEU* 5.4 0.4 - - - +
71L ASP* 2.9 46.7 + - + +
72L GLU 3.4 16.6 + - - +
73L ILE* 4.1 8.1 - - - +
74L PRO* 4.8 6.6 - - - +
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Residues in contact with ARG 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ALA 4.5 2.8 + - - -
12L ASP* 2.9 34.3 + - - +
13L GLN* 3.1 55.3 + - - +
15L ASN* 1.3 77.1 - - + +
17L GLU* 1.3 57.3 + - - +
19L TYR* 3.3 9.1 + - - +
20L SER* 2.9 31.6 + - - -
96L PHE* 4.0 26.6 - - + -
97L ILE* 4.1 9.2 - - + +
100L SER* 3.8 24.4 + - - -
103L GLU* 5.0 6.9 + - - -
104L LEU* 5.2 2.2 - - - +
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Residues in contact with GLU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L GLN* 2.8 45.5 + - - +
14L LEU 3.8 4.9 - - - +
16L ARG* 1.3 72.7 - - - +
18L LEU* 1.3 61.3 + - - +
20L SER* 3.5 4.1 + - - -
21L ALA* 3.3 16.1 + - - +
50L GLU* 2.9 53.2 - - - +
53L HIS* 3.4 24.5 + - + +
54L ALA* 4.0 8.3 - - + +
57L PHE* 4.3 12.7 - - + -
97L ILE* 3.7 15.2 - - - +
101L ILE* 4.5 1.2 - - - +
123L PHE* 4.3 14.0 - - - -
127L GLN* 4.4 4.0 + - - -
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Residues in contact with LEU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223 TYR* 3.6 37.7 - - + +
253 PHE* 4.3 10.3 - - + -
14L LEU* 3.1 38.3 + - + +
15L ASN* 3.7 8.1 - - - +
16L ARG 3.3 0.2 - - - -
17L GLU* 1.3 74.1 - - - +
19L TYR* 1.3 62.8 + - - +
21L ALA* 3.5 7.1 - - + +
22L TYR* 3.2 20.4 + - - +
50L GLU 5.3 0.2 - - - -
51L ILE* 4.9 21.3 - - + -
54L ALA* 3.8 16.6 - - + -
70L LEU* 4.0 3.8 - - + -
73L ILE* 4.4 17.6 - - + +
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Residues in contact with TYR 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L ASN* 2.9 18.3 + - - +
16L ARG* 3.3 8.5 + - - +
18L LEU* 1.3 75.4 - - - +
20L SER* 1.3 53.4 + - - +
22L TYR* 2.9 4.4 + - + +
23L LEU* 2.7 48.0 + - + +
73L ILE* 4.0 14.5 - - + +
74L PRO* 3.6 49.8 - - + -
75L LYS 4.5 1.9 + - - -
76L PRO* 3.9 13.4 - - + +
77L PRO* 3.7 23.9 - - - +
93L HIS* 3.8 31.4 - + - -
96L PHE* 6.2 0.2 - + - -
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Residues in contact with SER 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ARG 2.9 14.1 + - - -
17L GLU* 3.5 10.8 - - - -
18L LEU 3.4 0.2 - - - -
19L TYR* 1.3 75.8 - - - +
21L ALA* 1.3 55.6 + - - +
23L LEU* 3.2 5.4 + - - +
24L TYR* 2.9 44.6 + - - -
50L GLU* 3.8 22.1 + - - -
93L HIS* 3.2 27.1 + - - -
94L GLU* 5.7 0.4 - - - -
97L ILE* 3.4 14.4 - - - +
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Residues in contact with ALA 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L GLU 3.3 5.1 + - - +
18L LEU* 3.5 12.8 - - + +
19L TYR 3.2 0.6 - - - -
20L SER* 1.3 79.7 - - - +
22L TYR* 1.3 56.4 + - - +
25L PHE* 3.0 27.7 + - - +
47L ALA* 3.3 37.6 - - + +
50L GLU* 3.6 10.6 - - + +
51L ILE* 3.7 20.2 - - + -
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Residues in contact with TYR 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153 ASN* 3.9 6.4 + - - -
183 LEU* 3.6 30.3 - - + +
703 LEU* 3.4 33.5 - - + +
713 ASP 2.6 30.9 + - - -
733 ILE* 3.7 22.9 - - + +
18L LEU 3.2 9.5 + - - +
19L TYR* 2.9 9.9 + + + +
21L ALA* 1.3 76.5 - - - +
23L LEU* 1.3 61.2 + - - +
25L PHE* 3.6 10.4 + + - +
26L ALA* 3.0 25.5 + - - +
73L ILE* 3.7 23.8 - - + -
74L PRO 3.9 4.9 - - - -
76L PRO* 3.6 31.6 - - + +
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Residues in contact with LEU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L TYR* 2.7 32.3 + - + +
20L SER* 3.2 5.6 + - - +
22L TYR* 1.3 72.4 - - - +
24L TYR* 1.3 64.8 + - + +
26L ALA* 3.1 7.1 + - - +
27L MET* 2.9 54.9 + - + +
76L PRO* 4.3 5.4 - - + +
77L PRO* 3.8 28.9 - - + -
80L TRP* 4.2 8.5 - - + -
89L ALA 5.2 1.1 - - - +
93L HIS* 3.6 46.4 - - + +
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Residues in contact with TYR 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L SER* 2.9 33.3 + - - +
21L ALA 4.2 3.1 - - - +
23L LEU* 1.3 78.2 - - + +
25L PHE* 1.3 59.1 + - - +
27L MET* 3.8 13.2 - - + +
28L ALA* 3.0 21.5 + - - +
42L TRP* 5.9 1.1 - + - -
43L MET* 3.4 49.6 - - + +
46L GLN* 4.0 16.2 - - + -
47L ALA* 4.2 4.0 - - + -
50L GLU* 3.7 32.1 - - + -
90L ALA* 3.7 31.4 + - + +
93L HIS* 4.6 9.5 - + - -
94L GLU* 2.6 34.9 + - - +
134L VAL* 4.9 5.3 - - + +
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Residues in contact with PHE 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143 LEU* 4.3 6.1 - - + -
183 LEU* 4.2 19.3 - - + -
543 ALA* 5.1 3.1 - - + -
553 LEU* 3.8 27.8 - - + -
583 TYR* 3.6 40.3 - + + -
703 LEU* 3.6 37.8 - - + +
21L ALA 3.0 18.9 + - - +
22L TYR* 3.7 16.4 - + + +
24L TYR* 1.3 76.1 - - - +
26L ALA* 1.3 58.7 + - - +
28L ALA* 3.5 8.4 + - + -
29L ALA* 3.2 25.6 + - - +
44L LYS* 5.0 7.6 - - + -
47L ALA* 4.3 8.9 - - + +
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Residues in contact with ALA 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673 ARG* 5.2 0.2 + - - -
703 LEU* 3.6 11.6 - - + +
22L TYR 3.0 14.8 + - - +
23L LEU 3.1 9.6 + - - +
25L PHE* 1.3 75.4 - - - +
27L MET* 1.3 58.8 + - - +
29L ALA* 3.4 6.8 + - - +
30L TYR* 3.1 24.9 + - - +
76L PRO* 3.7 19.3 - - + -
77L PRO 3.6 22.0 - - - +
78L LYS* 4.6 4.3 - - - +
80L TRP* 4.0 6.3 - - + -
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Residues in contact with MET 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L LEU* 2.9 35.9 + - + +
24L TYR* 3.8 11.4 - - + +
25L PHE 3.4 0.2 - - - -
26L ALA* 1.3 72.3 - - - +
28L ALA* 1.3 60.6 + - - +
30L TYR* 3.2 2.2 + - - +
31L PHE* 2.9 41.6 + - + -
43L MET* 3.7 31.6 - - + -
80L TRP* 3.5 39.5 - - + -
86L ALA* 3.4 29.8 - - + +
89L ALA* 4.2 4.9 - - + -
90L ALA* 3.8 24.9 - - + +
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Residues in contact with ALA 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583 TYR* 3.0 14.1 + - - +
24L TYR 3.0 19.6 + - - +
25L PHE* 3.5 12.1 - - + +
27L MET* 1.3 77.4 - - - +
29L ALA* 1.3 55.6 + - - +
31L PHE 3.4 0.5 + - - -
32L GLU* 2.9 24.9 + - - +
40L ALA* 3.5 28.9 - - - +
43L MET* 3.8 8.7 - - + +
44L LYS* 3.9 17.7 - - + +
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Residues in contact with ALA 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583 TYR* 3.4 19.2 + - + -
623 TYR* 2.5 31.2 + - - +
673 ARG* 3.7 10.9 + - - +
683 VAL* 4.2 15.3 - - + +
703 LEU* 5.5 2.5 - - + -
25L PHE 3.2 11.1 + - - +
26L ALA* 3.5 11.0 - - - +
27L MET 3.3 0.2 - - - -
28L ALA* 1.3 79.3 - - - +
30L TYR* 1.3 62.7 + - - +
33L ASP* 3.2 14.4 + - - +
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Residues in contact with TYR 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673 ARG* 3.9 19.7 - - - +
26L ALA 3.1 13.0 + - - +
27L MET 3.2 10.3 + - - +
29L ALA* 1.3 77.6 - - - +
31L PHE* 1.3 74.0 + + - +
33L ASP* 3.4 14.1 + - + +
34L LEU* 3.4 42.5 + - + +
78L LYS 4.0 4.7 - - - +
79L GLU* 4.3 4.9 - - + -
80L TRP* 3.0 62.8 + + + -
81L GLU 3.7 1.9 + - - -
82L SER* 3.2 24.6 - - - -
83L PRO 3.6 1.0 - - - -
86L ALA* 3.8 24.7 - - + -
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Residues in contact with PHE 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L MET* 2.9 31.5 + - + +
28L ALA 3.9 2.2 - - - +
30L TYR* 1.3 83.4 - + - +
32L GLU* 1.3 60.7 + - - +
33L ASP 3.3 0.2 - - - -
34L LEU* 3.5 4.9 + - + +
35L GLY 3.4 2.6 + - - -
36L LEU* 2.9 42.8 + - + +
39L PHE* 3.5 27.8 - + + -
40L ALA* 3.8 17.7 - - - +
43L MET* 4.1 30.5 - - + -
83L PRO* 3.6 29.8 - - + -
86L ALA* 3.9 26.5 - - + -
87L PHE* 3.9 21.1 - + - -
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Residues in contact with GLU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583 TYR* 3.0 27.2 + - + +
593 ASN* 6.0 0.4 - - - -
623 TYR* 3.8 34.5 - - + -
28L ALA 2.9 14.4 + - - +
29L ALA 3.6 5.2 - - - +
30L TYR 3.3 0.2 - - - -
31L PHE* 1.3 77.2 - - - +
33L ASP* 1.3 58.4 + - - +
35L GLY* 3.1 18.8 + - - +
36L LEU 4.7 1.6 - - - +
37L GLU* 3.7 27.9 - - - +
40L ALA* 3.5 15.6 - - - +
41L ASN* 5.1 0.3 - - - +
44L LYS* 3.1 21.6 + - - -
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Residues in contact with ASP 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623 TYR* 3.7 8.1 - - + -
663 GLY 4.2 9.5 - - - +
673 ARG* 3.5 38.0 + - - +
29L ALA 3.2 13.1 + - - +
30L TYR* 3.5 11.5 - - + +
31L PHE 3.3 0.2 - - - -
32L GLU* 1.3 78.0 - - - +
34L LEU* 1.3 64.7 + - - +
35L GLY* 3.1 1.4 + - - -
79L GLU* 5.5 1.2 - - - +
139Y ASP* 5.6 1.2 - - - +
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.4 51.7 + - + +
31L PHE* 3.5 8.5 + - + +
32L GLU 3.3 0.8 - - - -
33L ASP* 1.3 81.6 - - - +
35L GLY* 1.3 59.0 - - - +
36L LEU* 3.3 19.6 + - + +
83L PRO* 4.2 19.7 - - + -
139Y ASP* 6.0 2.0 - - - +
143Y PHE* 5.9 3.1 - - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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