Contacts of the helix formed by residues 10 - 41 (chain L) in PDB entry 1VEQ
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 10 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L GLY 4.3 0.4 + - - -
9L LEU* 1.3 71.9 - - - +
11L ASP* 1.3 55.9 + - - +
12L LYS* 2.6 21.5 + - - +
13L LYS* 2.8 54.7 + - - +
14L ALA* 2.8 10.4 + - - +
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Residues in contact with ASP 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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3L SER 4.8 9.2 - - - +
4L PHE 5.0 1.4 - - - +
5L THR* 3.9 24.6 - - - +
9L LEU 3.3 3.4 + - - +
10L SER* 1.3 69.7 - - - +
12L LYS* 1.3 57.8 + - - +
14L ALA* 4.2 9.6 - - - +
15L SER* 3.6 20.1 + - - -
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Residues in contact with LYS 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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10L SER* 2.6 12.6 + - - +
11L ASP* 1.3 73.1 - - - +
13L LYS* 1.3 76.0 + - + +
14L ALA 3.1 1.1 - - - -
15L SER* 3.1 6.6 + - - -
16L ASP* 2.5 58.1 + - - +
130L LEU* 6.5 0.4 - - - -
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Residues in contact with LYS 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 LEU* 4.5 13.0 - - + -
10L SER* 2.8 34.3 + - - +
12L LYS* 1.3 84.8 - - + +
14L ALA* 1.3 63.3 + - - +
16L ASP* 3.1 6.4 + - - +
17L VAL* 3.1 28.0 + - - +
129L ASP 4.1 16.7 + - - +
130L LEU* 4.5 33.2 + - + +
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Residues in contact with ALA 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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5L THR* 3.6 24.0 - - - +
9L LEU* 4.2 21.9 - - + +
10L SER 2.8 15.0 + - - +
11L ASP* 4.2 6.5 - - - +
13L LYS* 1.3 79.3 - - - +
15L SER* 1.3 62.6 + - - +
17L VAL* 3.2 7.5 + - - +
18L ALA* 3.1 20.8 + - - +
75L LEU* 3.8 17.8 - - + +
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Residues in contact with SER 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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11L ASP 3.6 15.8 + - - -
12L LYS* 3.1 7.1 + - - -
14L ALA* 1.3 79.0 - - - +
16L ASP* 1.3 59.4 + - - +
18L ALA* 3.4 8.2 - - - +
19L ASP* 3.1 35.6 + - - +
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Residues in contact with ASP 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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12L LYS* 2.5 47.1 + - - +
13L LYS* 3.1 10.7 + - - +
15L SER* 1.3 75.6 - - - +
17L VAL* 1.3 64.4 + - - +
19L ASP* 3.6 11.5 + - - +
20L LEU* 3.3 24.3 + - - +
130L LEU* 4.6 16.1 - - + +
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Residues in contact with VAL 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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9L LEU* 5.4 1.8 - - + -
13L LYS 3.1 16.7 + - - +
14L ALA* 3.5 8.1 - - - +
16L ASP* 1.3 73.4 - - - +
18L ALA* 1.3 69.6 + - - +
20L LEU* 2.8 18.6 + - - +
21L LEU* 3.0 18.8 + - + +
75L LEU* 3.8 17.3 - - + -
127L LEU* 3.9 16.4 - - + -
130L LEU* 3.6 33.2 - - + -
131L ASP* 4.3 11.9 - - + -
134L SER* 4.0 19.3 - - - +
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Residues in contact with ALA 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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14L ALA 3.1 10.3 + - - +
15L SER* 3.4 13.5 - - - +
17L VAL* 1.3 78.0 - - - +
19L ASP* 1.3 65.6 + - - +
20L LEU 2.9 1.6 + - - -
21L LEU* 2.9 7.0 + - - +
22L GLN* 2.9 25.1 + - - +
72L ILE* 4.5 11.1 - - + +
75L LEU* 3.9 14.1 - - + +
77L LYS* 3.8 28.9 - - + -
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Residues in contact with ASP 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 SER* 3.1 22.2 + - - +
16L ASP* 3.7 16.4 - - - +
17L VAL 3.3 0.2 - - - -
18L ALA* 1.3 78.7 - - - +
20L LEU* 1.3 62.5 + - + +
22L GLN* 3.8 9.0 + - - +
23L LYS* 3.6 16.8 + - - +
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Residues in contact with LEU 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 ASP 3.3 12.8 + - - +
17L VAL* 2.8 13.6 + - - +
19L ASP* 1.3 77.2 - - + +
21L LEU* 1.3 66.8 + - + +
23L LYS* 3.2 15.6 + - + +
24L GLN* 3.2 17.3 + - - +
123L SER* 3.3 37.0 + - - +
126L LYS* 4.5 26.5 - - + +
127L LEU* 4.1 29.2 - - + -
130L LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 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 VAL* 3.4 30.3 - - + +
18L ALA 2.9 2.9 + - - +
20L LEU* 1.3 74.6 - - + +
22L GLN* 1.3 54.1 + - - +
23L LYS 2.8 4.9 - - - -
24L GLN* 2.6 28.6 + - + +
25L LEU* 2.6 18.5 + - - +
68L VAL* 3.6 17.2 - - + +
71L ARG* 3.8 30.3 - - + -
72L ILE* 3.6 20.6 - - + -
75L LEU* 4.5 6.1 - - + -
127L LEU* 5.0 5.4 - - + -
134L SER* 4.6 10.3 - - - +
137L LEU* 6.1 0.4 - - + -
138L LEU* 4.0 28.3 - - + -
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Residues in contact with GLN 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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18L ALA 2.9 15.3 + - - +
19L ASP* 3.9 10.1 - - - +
21L LEU* 1.3 76.4 - - - +
23L LYS* 1.3 59.7 + - - +
25L LEU* 3.8 5.5 + - - +
26L SER* 3.4 18.4 + - - -
72L ILE* 3.5 14.6 - - + +
78L SER 4.3 2.3 - - - +
79L PRO* 3.6 9.4 - - - +
80L LYS* 2.9 53.3 + - + +
85L ALA* 4.8 0.4 - - - +
89L ASP* 3.3 26.2 + - - +
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Residues in contact with LYS 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 ASP 3.6 8.9 + - - +
20L LEU* 3.2 18.8 + - + +
21L LEU 2.8 2.0 + - - -
22L GLN* 1.3 78.1 - - - +
24L GLN* 1.3 67.2 + - - +
26L SER* 3.2 5.0 + - - -
27L THR* 2.9 29.4 + - - +
89L ASP* 4.7 27.1 - - + +
91L THR* 5.2 14.6 + - - +
119L ASP* 3.3 27.9 + - + +
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Residues in contact with GLN 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 LEU 3.2 4.3 + - - +
21L LEU* 2.6 23.5 + - + +
23L LYS* 1.3 76.6 - - - +
25L LEU* 1.3 57.8 + - - +
27L THR* 2.9 14.7 + - - +
28L TYR* 2.8 66.4 + - + +
68L VAL* 4.7 4.9 - - + -
116L VAL* 4.8 1.2 + - - +
119L ASP* 4.6 6.5 - - - +
120L THR* 2.6 34.8 + - - -
123L SER* 4.2 14.5 + - - -
138L LEU* 3.2 30.9 - - + +
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Residues in contact with LEU 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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40F TRP* 4.5 9.6 - - + -
21L LEU 2.6 18.3 + - - +
22L GLN* 3.8 10.3 - - - +
24L GLN* 1.3 72.2 - - - +
26L SER* 1.3 67.1 + - - +
28L TYR* 3.0 14.0 + - - +
29L ASN* 2.9 54.2 + - - +
65L ALA* 4.3 8.1 - - - +
68L VAL* 4.2 8.2 - - + +
69L ALA* 3.2 43.7 - - + +
72L ILE* 4.5 7.2 - - + -
79L PRO* 4.6 5.2 - - + -
80L LYS 3.4 26.7 - - - +
81L GLY* 4.3 1.6 - - - -
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Residues in contact with SER 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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22L GLN* 3.4 11.6 + - - -
23L LYS 3.2 8.7 + - - -
25L LEU* 1.3 80.5 - - - +
27L THR* 1.3 62.7 + - - +
29L ASN* 3.3 11.3 + - - +
30L ASP* 3.0 23.7 + - - +
80L LYS 4.4 0.9 + - - -
85L ALA 3.9 0.5 + - - -
86L ILE* 3.7 26.9 + - - +
89L ASP* 3.1 38.0 + - - +
90L ARG* 5.0 4.8 - - - +
92L TRP* 5.3 0.4 - - - -
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Residues in contact with THR 27 (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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23L LYS* 2.9 25.6 + - - +
24L GLN* 2.9 22.8 + - - +
26L SER* 1.3 77.3 - - - +
28L TYR* 1.3 58.7 + - + +
30L ASP* 3.3 3.5 + - - +
31L LEU* 2.9 26.2 + - - +
90L ARG* 6.2 0.4 - - - -
92L TRP* 3.4 36.4 - - + -
115L GLY 5.5 0.2 - - - +
116L VAL* 3.9 32.7 - - + +
119L ASP* 5.2 9.0 + - + +
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Residues in contact with TYR 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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24L GLN* 2.8 49.6 + - + +
25L LEU* 3.5 7.2 - - - +
27L THR* 1.3 78.4 - - + +
29L ASN* 1.3 60.0 + - - +
31L LEU* 2.9 13.8 + - + +
32L HIS* 2.7 37.8 + - - +
61L VAL* 3.7 21.9 - - + +
64L TYR* 3.6 28.9 - + + -
65L ALA* 4.2 8.5 - - + -
68L VAL* 3.6 18.4 - - + -
116L VAL* 4.7 12.3 - - + -
120L THR* 4.8 0.7 + - - -
138L LEU* 4.0 2.4 - - - +
141L HIS* 2.7 41.2 + + + +
145L LEU* 4.6 12.5 - - + +
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Residues in contact with ASN 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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33F LEU* 3.8 22.1 - - + +
40F TRP* 4.9 6.2 - - - -
25L LEU* 2.9 48.3 + - - +
26L SER* 3.7 8.5 - - - +
28L TYR* 1.3 76.3 - - - +
30L ASP* 1.3 65.2 + - - +
32L HIS* 3.5 21.8 + - - +
33L LEU* 3.2 27.2 + - - +
65L ALA* 4.3 12.0 - - - +
81L GLY* 4.4 10.9 + - - -
86L ILE* 3.9 16.1 - - + +
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Residues in contact with ASP 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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83F PRO* 2.9 32.3 - - - +
26L SER 3.0 13.3 + - - +
27L THR 3.6 7.9 - - - +
29L ASN* 1.3 74.9 - - - +
31L LEU* 1.3 56.4 + - - +
33L LEU* 3.0 4.0 + - - +
34L THR* 2.7 46.7 + - - -
86L ILE* 3.5 14.1 - - + +
90L ARG* 3.2 11.4 + - + -
92L TRP* 3.4 32.6 + - + +
94L ASP* 4.4 4.0 - - - +
95L TYR 5.6 0.5 + - - -
112L VAL* 5.0 9.7 - - - +
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Residues in contact with LEU 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 THR 2.9 13.9 + - - +
28L TYR* 2.9 13.4 + - + +
30L ASP* 1.3 77.9 - - - +
32L HIS* 1.3 52.7 + - - +
34L THR* 2.9 8.0 + - - -
35L LEU* 2.7 60.8 + - + +
61L VAL* 3.6 29.6 - - + -
109L LEU* 5.6 1.1 - - + -
112L VAL* 4.7 12.3 - - + -
113L TYR* 3.4 29.6 - - + +
116L VAL* 4.5 24.9 - - + -
145L LEU* 4.0 16.2 - - + -
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Residues in contact with HIS 32 (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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32F HIS* 4.4 19.3 - + - -
33F LEU* 4.5 5.2 - - + +
62F ARG* 3.3 24.3 + - - +
28L TYR 2.7 13.5 + - - -
29L ASN* 3.5 39.2 + - - +
31L LEU* 1.3 76.5 - - - +
33L LEU* 1.3 80.7 + - + +
35L LEU* 3.6 9.8 - - - +
36L LYS* 3.3 21.7 + - - +
58L VAL* 4.2 7.1 - - + +
61L VAL* 3.4 25.6 - - + -
62L ARG* 4.2 27.3 + - + +
65L ALA* 5.1 2.5 - - + -
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Residues in contact with LEU 33 (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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29F ASN* 3.7 29.2 - - + +
32F HIS* 4.5 6.7 - - - +
33F LEU* 3.6 29.8 - - + -
81F GLY* 3.4 30.0 - - - +
82F THR 5.2 0.7 - - - -
83F PRO* 4.6 23.1 - - + -
86F ILE* 5.3 4.3 - - + -
29L ASN 3.2 17.8 + - - +
30L ASP* 3.0 5.4 + - - +
32L HIS* 1.3 95.2 + - + +
34L THR* 1.3 59.4 + - - +
36L LYS* 3.5 10.1 + - + +
37L HIS 3.1 19.9 + - - -
40L TRP* 5.0 2.8 - - + -
86L ILE* 5.2 1.6 - - + -
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Residues in contact with THR 34 (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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82F THR* 4.6 3.7 - - - +
83F PRO* 4.3 6.2 - - - +
30L ASP* 2.7 37.2 + - - +
31L LEU* 3.3 11.4 - - + -
33L LEU* 1.3 75.5 - - - +
35L LEU* 1.3 66.2 + - - +
37L HIS* 2.8 23.4 + - - +
38L VAL* 3.1 13.6 + - + +
95L TYR* 3.5 48.4 + - + +
109L LEU* 4.7 8.3 - - + -
112L VAL* 5.3 7.6 - - + -
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Residues in contact with LEU 35 (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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31L LEU* 2.7 65.3 + - + +
32L HIS* 3.6 6.7 - - - +
33L LEU 3.3 0.2 - - - -
34L THR* 1.3 74.4 - - - +
36L LYS* 1.3 56.8 + - - +
38L VAL* 3.2 10.3 + - - +
39L HIS* 2.9 25.3 + - - +
54L ILE* 3.5 24.0 - - + +
57L GLN* 4.6 5.8 - - + +
58L VAL* 3.3 22.9 - - + -
61L VAL* 5.1 1.3 - - + -
109L LEU* 3.9 28.0 - - + -
113L TYR* 3.5 15.9 - - + +
148L PHE* 4.2 8.5 - - + -
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Residues in contact with LYS 36 (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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62F ARG* 4.6 19.7 - - + +
65F ALA* 6.2 1.1 - - + -
66F ASP* 3.0 39.4 + - - +
32L HIS 3.3 8.0 + - - +
33L LEU* 3.7 13.0 - - + +
34L THR 3.2 0.6 - - - -
35L LEU* 1.3 79.2 - - - +
37L HIS* 1.3 64.0 + - - +
39L HIS* 3.0 33.7 + - + +
40L TRP* 3.1 45.1 - - + -
55L ASP* 3.2 20.5 + - - +
58L VAL* 3.6 28.5 - - + -
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Residues in contact with HIS 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F PRO 3.6 2.2 + - - -
80F LYS* 3.5 20.4 - - + -
81F GLY* 3.0 33.1 + - - +
82F THR* 3.8 20.4 - - + +
33L LEU 3.1 11.3 + - - +
34L THR* 2.8 22.4 + - - +
36L LYS* 1.3 76.3 - - - +
38L VAL* 1.3 59.5 + - - -
40L TRP* 3.1 19.6 + - - +
41L ASN* 2.8 44.9 + - - -
95L TYR* 3.5 29.9 + + - -
97L VAL 3.1 18.1 + - - -
98L GLU* 4.8 3.1 + - - -
105L HIS* 5.4 0.2 - + - -
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Residues in contact with VAL 38 (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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34L THR* 3.1 17.9 - - + +
35L LEU 3.7 4.0 - - - +
37L HIS* 1.3 69.6 - - - +
39L HIS* 1.3 67.3 + - - +
40L TRP 2.7 7.1 + - - -
41L ASN 3.2 7.6 + - - +
42L VAL* 2.8 30.2 - - + +
50L VAL* 5.4 0.7 - - + -
54L ILE* 3.1 27.1 - - + -
95L TYR* 3.8 26.2 - - + +
105L HIS* 3.9 28.0 - - + +
106L LEU* 6.5 0.9 - - + -
109L LEU* 4.2 20.4 - - + -
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Residues in contact with HIS 39 (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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150E TRP* 5.0 0.2 - - - -
66F ASP* 3.0 8.9 + - - -
212F FE 2.3 27.0 - - - -
35L LEU 2.9 14.0 + - - +
36L LYS* 3.0 39.8 + - + +
38L VAL* 1.3 76.7 - - - +
40L TRP* 1.3 63.2 + + - +
42L VAL* 4.8 2.2 + - - +
47L PHE* 4.9 2.1 - - - -
51L HIS* 2.7 86.0 + + - +
52L GLU* 5.1 0.2 - - - -
54L ILE* 3.9 19.8 - - + +
55L ASP* 3.3 20.6 - - - -
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Residues in contact with TRP 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E TRP* 3.8 24.5 - - - -
25F LEU* 4.4 9.6 - - + -
29F ASN* 4.9 8.3 - - - -
65F ALA* 4.0 9.6 - - + -
66F ASP* 3.2 36.3 + - - +
69F ALA* 3.2 31.9 - - + +
70F GLU* 3.7 23.7 - - + +
73F ALA* 4.3 7.2 - - + +
79F PRO* 4.5 16.4 - - + -
81F GLY* 4.2 22.0 - - - -
33L LEU* 5.8 2.2 - - + -
36L LYS* 3.1 47.5 + - + -
37L HIS* 3.4 18.6 - - - +
38L VAL 2.7 1.8 + - - -
39L HIS* 1.3 86.5 - + - +
41L ASN* 1.3 63.9 + - - +
42L VAL 3.3 9.3 + - - +
43L VAL* 5.7 0.5 - - - +
47L PHE* 5.6 0.2 - - - -
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Residues in contact with ASN 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F SER* 2.9 15.0 + - - +
79F PRO* 2.9 32.5 + - - +
37L HIS* 2.8 56.9 + - - +
38L VAL 3.2 3.0 + - - -
40L TRP* 1.3 75.3 - - - +
42L VAL* 1.3 61.0 + - - +
43L VAL* 4.7 2.7 - - - -
98L GLU 3.7 7.2 - - - +
99L ARG* 3.3 24.2 - - - +
100L ASP 3.1 22.9 + - - +
105L HIS* 3.2 9.3 + - + +
----------------------------------------------------------
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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