Contacts of the helix formed by residues 10 - 41 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K GLY 4.3 0.6 + - - -
9K LEU* 1.3 71.2 - - - +
11K ASP* 1.3 54.5 + - - +
12K LYS* 2.6 22.2 + - - +
13K LYS* 2.8 53.3 + - - +
14K ALA* 2.9 10.6 + - - +
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Residues in contact with ASP 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K SER 4.8 8.8 - - - +
4K PHE 5.0 1.7 - - - +
5K THR* 4.0 24.7 - - - +
9K LEU 3.4 2.6 + - - +
10K SER* 1.3 69.0 - - - +
12K LYS* 1.3 56.3 + - - +
14K ALA* 4.2 9.4 - - - +
15K SER* 3.6 19.9 + - - -
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Residues in contact with LYS 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K SER* 2.6 12.2 + - - +
11K ASP* 1.3 73.9 - - - +
13K LYS* 1.3 73.9 + - + +
14K ALA 3.1 0.9 - - - -
15K SER* 3.2 5.7 + - - -
16K ASP* 2.6 54.9 + - - +
130K LEU* 6.5 0.2 - - + -
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Residues in contact with LYS 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K LEU* 4.5 12.1 - - + -
10K SER* 2.8 34.6 + - - +
12K LYS* 1.3 83.5 - - + +
14K ALA* 1.3 63.8 + - - +
16K ASP* 3.1 7.5 + - - +
17K VAL* 3.0 27.6 + - - +
129K ASP 4.1 16.7 + - - +
130K LEU* 4.4 32.2 + - + +
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Residues in contact with ALA 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K THR* 3.6 23.6 - - - +
9K LEU* 4.2 23.0 - - + +
10K SER 2.9 14.7 + - - +
11K ASP* 4.2 6.5 - - - +
13K LYS* 1.3 77.2 - - - +
15K SER* 1.3 62.5 + - - +
17K VAL* 3.2 7.4 + - - +
18K ALA* 3.1 19.6 + - - +
75K LEU* 3.8 19.6 - - + +
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Residues in contact with SER 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ASP 3.6 16.6 + - - -
12K LYS* 3.2 7.1 + - - -
14K ALA* 1.3 79.7 - - - +
16K ASP* 1.3 59.6 + - - +
18K ALA* 3.4 9.1 - - - +
19K ASP* 3.1 34.4 + - - +
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Residues in contact with ASP 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LYS* 2.6 47.0 + - - +
13K LYS* 3.1 11.9 + - - +
15K SER* 1.3 75.4 - - - +
17K VAL* 1.3 66.6 + - - +
19K ASP* 3.6 12.3 + - - +
20K LEU* 3.3 23.0 + - - +
130K LEU* 4.5 16.2 - - + +
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Residues in contact with VAL 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K LEU* 5.3 2.7 - - + -
13K LYS 3.0 16.6 + - - +
14K ALA* 3.5 7.6 - - - +
16K ASP* 1.3 73.6 - - - +
18K ALA* 1.3 71.1 + - - +
20K LEU* 2.8 17.8 + - - +
21K LEU* 3.0 18.1 + - + +
75K LEU* 3.8 17.9 - - + -
127K LEU* 3.9 16.6 - - + -
130K LEU* 3.7 33.4 - - + -
131K ASP* 4.3 10.8 - - + -
134K SER* 3.9 20.6 - - - +
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Residues in contact with ALA 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K ALA 3.1 10.1 + - - +
15K SER* 3.4 13.2 - - - +
17K VAL* 1.3 78.6 - - - +
19K ASP* 1.3 63.6 + - - +
20K LEU 2.9 0.7 + - - -
21K LEU* 3.0 7.4 + - - +
22K GLN* 2.9 27.0 + - - +
72K ILE* 4.4 10.3 - - + +
75K LEU* 3.9 14.3 - - + +
77K LYS* 3.8 28.9 - - + -
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Residues in contact with ASP 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K SER* 3.1 22.0 + - - +
16K ASP* 3.7 16.5 - - - +
18K ALA* 1.3 78.8 - - - +
20K LEU* 1.3 61.9 + - + +
22K GLN* 3.8 8.0 + - - +
23K LYS* 3.6 16.3 + - - +
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Residues in contact with LEU 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ASP 3.3 13.2 + - - +
17K VAL* 2.8 11.2 + - - +
19K ASP* 1.3 77.8 - - + +
21K LEU* 1.3 70.1 + - + +
23K LYS* 3.3 14.9 + - + +
24K GLN* 3.2 16.8 + - - +
123K SER* 3.3 38.4 + - - +
126K LYS* 4.5 25.6 - - + +
127K LEU* 4.1 29.6 - - + -
130K LEU* 4.2 11.4 - - + -
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Residues in contact with LEU 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K VAL* 3.0 30.3 + - + +
18K ALA 3.0 1.7 + - - +
20K LEU* 1.3 74.9 - - + +
22K GLN* 1.3 58.3 + - - +
23K LYS 2.8 4.7 - - - -
24K GLN* 2.6 29.2 + - + +
25K LEU* 2.7 13.5 + - - +
68K VAL* 3.6 18.6 - - + +
71K ARG* 3.8 28.9 - - + -
72K ILE* 3.6 21.3 - - + -
75K LEU* 4.5 5.2 - - + -
127K LEU* 5.0 8.5 - - + -
134K SER* 4.5 6.3 - - - +
137K LEU* 6.1 0.7 - - + -
138K LEU* 4.1 27.6 - - + -
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Residues in contact with GLN 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ALA 2.9 17.1 + - - +
19K ASP* 3.9 9.4 - - - +
21K LEU* 1.3 76.4 - - - +
23K LYS* 1.3 59.9 + - - +
25K LEU* 3.7 6.3 + - - +
26K SER* 3.4 17.7 + - - -
72K ILE* 3.4 13.6 - - + +
78K SER 4.3 2.1 - - - +
79K PRO* 3.6 9.9 - - - +
80K LYS* 3.0 53.3 + - + +
85K ALA* 4.9 0.4 - - - +
89K ASP* 3.2 26.1 + - - +
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Residues in contact with LYS 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ASP 3.6 8.9 + - - +
20K LEU* 3.3 17.4 + - + +
21K LEU 2.7 4.4 + - - -
22K GLN* 1.3 75.9 - - - +
24K GLN* 1.3 66.5 + - - +
26K SER* 3.1 5.7 + - - -
27K THR* 2.9 29.0 + - - +
89K ASP* 4.6 27.8 - - + +
91K THR* 5.2 14.0 + - - +
119K ASP* 3.4 27.4 + - + -
123K SER* 5.8 2.7 - - - +
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Residues in contact with GLN 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K LEU 3.2 4.3 + - - +
21K LEU* 2.6 23.7 + - + +
23K LYS* 1.3 75.5 - - - +
25K LEU* 1.3 57.7 + - - +
27K THR* 2.8 16.0 + - - +
28K TYR* 2.8 62.0 + - + +
68K VAL* 4.8 4.9 - - + -
116K VAL* 5.5 0.8 - - - +
119K ASP* 4.6 6.8 - - - +
120K THR* 2.6 35.8 + - - -
123K SER* 4.3 13.5 + - - -
138K LEU* 3.1 32.1 - - + +
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Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H TRP* 4.4 11.0 - - + -
21K LEU 2.7 17.2 + - - +
22K GLN* 3.8 10.8 - - - +
24K GLN* 1.3 73.0 - - - +
26K SER* 1.3 66.1 + - - +
28K TYR* 3.1 12.3 + - - +
29K ASN* 2.9 55.9 + - - +
65K ALA* 4.4 8.7 - - - +
68K VAL* 4.3 8.9 - - + +
69K ALA* 3.2 43.5 - - + +
72K ILE* 4.5 6.7 - - + -
79K PRO* 4.6 5.4 - - + -
80K LYS 3.4 24.7 - - - +
81K GLY* 4.3 3.4 - - - -
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Residues in contact with SER 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K GLN* 3.4 11.8 + - - -
23K LYS 3.1 8.1 + - - -
25K LEU* 1.3 80.1 - - - +
27K THR* 1.3 63.0 + - - +
29K ASN* 3.5 10.9 + - - +
30K ASP* 3.1 22.7 + - - +
80K LYS 4.5 0.7 + - - -
85K ALA 3.9 0.7 + - - -
86K ILE* 3.7 28.4 + - - +
89K ASP* 3.1 38.7 + - - +
90K ARG* 4.9 5.3 - - - +
92K TRP* 5.3 0.4 - - - -
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Residues in contact with THR 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LYS* 2.9 23.7 + - - +
24K GLN* 2.8 23.1 + - - +
26K SER* 1.3 78.7 - - - +
28K TYR* 1.3 62.6 + - + +
30K ASP* 3.3 2.8 + - - +
31K LEU* 3.0 20.4 + - - +
90K ARG* 6.2 0.4 - - - -
92K TRP* 3.4 36.5 - - + -
115K GLY 5.5 0.2 - - - +
116K VAL* 3.9 32.5 - - + +
119K ASP* 5.2 8.3 + - + +
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Residues in contact with TYR 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K GLN* 2.8 53.1 + - + +
25K LEU* 3.1 5.4 + - - +
27K THR* 1.3 75.0 - - + +
29K ASN* 1.3 58.5 + - - +
31K LEU* 2.9 13.1 + - + +
32K HIS* 2.7 36.7 + - - -
61K VAL* 3.7 23.4 - - + +
64K TYR* 3.5 36.6 - + + -
65K ALA* 4.2 7.9 - - + -
68K VAL* 3.6 18.6 - - + -
116K VAL* 4.7 10.1 - - + -
120K THR* 4.8 0.7 + - - +
138K LEU* 3.9 2.4 - - - +
141K HIS* 2.6 33.4 + - + +
145K LEU* 4.6 14.4 - - + +
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Residues in contact with ASN 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 3.7 22.4 - - + +
40H TRP* 5.0 5.3 - - - -
25K LEU* 2.9 49.7 + - - +
26K SER* 3.8 7.8 - - - +
28K TYR* 1.3 76.7 - - - +
30K ASP* 1.3 62.3 + - - +
32K HIS* 3.5 22.4 + - - +
33K LEU* 3.1 29.3 + - - +
65K ALA* 4.3 12.2 - - - +
81K GLY* 4.4 10.9 - - - -
86K ILE* 4.0 16.5 - - + +
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Residues in contact with ASP 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H PRO* 2.9 32.5 - - - +
26K SER 3.1 13.1 + - - +
27K THR 3.6 8.1 - - - +
28K TYR 3.1 0.6 - - - -
29K ASN* 1.3 74.4 - - - +
31K LEU* 1.3 57.7 + - - +
33K LEU* 3.0 3.8 + - - +
34K THR* 2.7 47.8 + - - -
86K ILE* 3.6 13.8 - - + +
90K ARG* 3.2 12.1 + - + -
92K TRP* 3.5 31.8 + - + +
94K ASP* 4.4 4.4 - - - +
95K TYR 5.6 0.5 + - - -
112K VAL* 5.0 9.4 - - - +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K THR 3.0 13.7 + - - +
28K TYR* 2.9 12.5 + - + +
30K ASP* 1.3 78.2 + - - +
32K HIS* 1.3 52.2 + - - +
34K THR* 2.9 9.5 + - - -
35K LEU* 2.7 59.8 + - + +
61K VAL* 3.6 29.2 - - + -
109K LEU* 5.6 0.9 - - + -
112K VAL* 4.6 12.1 - - + -
113K TYR* 3.4 29.2 - - + +
116K VAL* 4.6 25.1 - - + -
145K LEU* 4.0 15.5 - - + -
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Residues in contact with HIS 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H HIS* 4.4 19.3 - + - -
33H LEU* 4.5 5.9 - - + +
62H ARG* 3.3 25.5 + - - +
28K TYR 2.7 12.6 + - - -
29K ASN* 3.5 40.5 + - - +
31K LEU* 1.3 74.7 - - - +
33K LEU* 1.3 79.5 + - + +
35K LEU* 3.7 11.6 - - - +
36K LYS* 3.3 21.3 + - - +
58K VAL* 4.2 7.5 - - + +
61K VAL* 3.5 24.0 - - + -
62K ARG* 4.2 26.7 - - + +
65K ALA* 5.1 2.2 - - + -
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Residues in contact with LEU 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ASN* 3.7 30.7 - - + +
32H HIS* 4.5 6.1 - - - +
33H LEU* 3.7 28.7 - - + -
81H GLY 3.3 32.2 - - - +
82H THR 5.1 0.4 - - - -
83H PRO* 4.5 23.6 - - + -
86H ILE* 5.2 4.7 - - + -
29K ASN 3.1 18.0 + - - +
30K ASP* 3.0 5.6 + - - +
32K HIS* 1.3 98.0 + - + +
34K THR* 1.3 58.8 + - - +
36K LYS* 3.5 10.1 + - + +
37K HIS 3.1 19.1 + - - -
40K TRP* 4.9 2.8 - - + -
86K ILE* 5.2 1.3 - - + -
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Residues in contact with THR 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H THR* 4.7 3.6 - - - +
83H PRO* 4.3 5.7 - - - +
30K ASP* 2.7 40.9 + - - +
31K LEU* 3.3 7.4 - - - -
33K LEU* 1.3 75.5 - - - +
35K LEU* 1.3 66.5 + - - +
37K HIS* 2.8 23.6 + - - +
38K VAL* 3.1 14.4 + - + +
95K TYR* 3.5 46.7 + - + +
109K LEU* 4.7 7.6 - - + -
112K VAL* 5.2 8.3 - - + -
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Residues in contact with LEU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LEU* 2.7 66.0 + - + +
32K HIS* 3.7 7.2 - - - +
34K THR* 1.3 72.9 - - - +
36K LYS* 1.3 56.6 + - - +
38K VAL* 3.1 12.4 + - - +
39K HIS* 2.9 25.3 + - - +
54K ILE* 3.6 24.3 - - + +
57K GLN* 4.6 5.6 - - + +
58K VAL* 3.4 23.3 - - + -
61K VAL* 5.1 1.1 - - + -
109K LEU* 3.9 28.3 - - + -
113K TYR* 3.6 15.7 - - + +
148K PHE* 4.2 8.1 - - + -
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Residues in contact with LYS 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62H ARG* 4.6 20.0 - - + +
65H ALA* 6.1 1.1 - - + -
66H ASP* 3.0 39.9 + - - +
32K HIS 3.3 8.5 + - - +
33K LEU* 3.7 12.6 - - + +
34K THR 3.2 0.4 - - - -
35K LEU* 1.3 76.2 - - - +
37K HIS* 1.3 65.8 + - - +
39K HIS* 3.0 31.9 + - + +
40K TRP* 3.1 48.0 + - + -
55K ASP* 3.2 19.7 + - - +
58K VAL* 3.6 28.0 - - + -
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Residues in contact with HIS 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H PRO 3.4 11.4 + - - -
80H LYS* 3.5 11.4 - - + -
81H GLY 3.0 32.2 + - - +
82H THR* 3.9 19.1 - - + +
33K LEU 3.1 14.5 + - - +
34K THR* 2.8 19.6 + - - +
36K LYS* 1.3 79.3 - - - +
38K VAL* 1.3 58.0 + - - -
40K TRP* 3.2 17.0 + - - +
41K ASN* 2.8 47.3 + - - -
95K TYR* 3.5 28.8 + + - -
97K VAL 3.2 16.4 + - - -
98K GLU* 4.7 3.5 + - - -
105K HIS* 5.4 0.2 - + - -
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Residues in contact with VAL 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K THR 3.1 18.4 + - - +
35K LEU 3.6 4.3 - - - +
37K HIS* 1.3 69.5 - - - +
39K HIS* 1.3 64.0 + - - +
40K TRP 2.7 6.9 + - - -
41K ASN 4.2 1.6 - - - +
42K VAL* 2.7 39.3 + - + +
50K VAL* 5.4 1.1 - - + -
54K ILE* 3.1 27.1 - - + -
95K TYR* 3.8 26.5 - - + +
105K HIS* 4.0 26.7 - - + +
106K LEU* 6.4 1.1 - - + -
109K LEU* 4.2 21.1 - - + -
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Residues in contact with HIS 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G TRP* 5.0 0.3 - - - -
66H ASP* 3.0 8.0 + - - -
211H FE 2.4 26.6 - - - -
35K LEU 2.9 14.0 + - - +
36K LYS* 3.0 41.1 + - + +
38K VAL* 1.3 76.1 - - - +
40K TRP* 1.3 66.5 + + - +
42K VAL* 4.8 1.9 + - - +
47K PHE* 5.0 1.4 - - - -
51K HIS* 2.7 86.7 + + - +
52K GLU* 5.2 0.2 - - - -
54K ILE* 3.9 19.3 - - + +
55K ASP* 3.3 22.4 - - - -
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Residues in contact with TRP 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G TRP* 3.7 23.8 - - - -
25H LEU* 4.4 9.4 - - + -
29H ASN* 4.9 8.3 - - - -
65H ALA* 4.2 9.2 - - + -
66H ASP* 3.2 36.8 + - - +
69H ALA* 3.3 32.6 - - + +
70H GLU* 3.7 23.5 - - + +
73H ALA* 4.4 6.4 - - + +
79H PRO* 4.5 16.6 - - + +
81H GLY* 4.1 22.2 - - - -
33K LEU* 4.9 2.5 - - + -
36K LYS* 3.1 48.4 + - + -
37K HIS* 3.5 17.7 - - - +
38K VAL 2.7 1.8 + - - -
39K HIS* 1.3 86.7 - + - +
41K ASN* 1.3 65.0 + - - +
42K VAL 3.3 9.1 + - - +
43K VAL* 5.7 0.7 - - - +
47K PHE* 5.6 0.3 - - - -
51K HIS* 5.4 0.2 - + - -
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Residues in contact with ASN 41 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H SER* 3.0 19.4 + - - +
79H PRO* 3.0 26.4 + - - +
37K HIS* 2.8 57.7 + - - +
38K VAL* 3.2 3.2 + - - +
40K TRP* 1.3 76.5 - - - +
42K VAL* 1.3 60.6 + - - +
43K VAL* 4.7 1.8 - - - -
97K VAL 4.6 0.2 + - - -
98K GLU* 3.7 7.1 - - - +
99K ARG* 3.2 24.3 - - - +
100K ASP 3.1 23.0 + - - -
105K HIS* 3.2 9.6 + - + +
----------------------------------------------------------
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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