Contacts of the helix formed by residues 11 - 43 (chain B) in PDB entry 1O9R
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 PRO 11 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASP 3.2 7.6 - - - +
10B LEU* 1.4 98.1 - - + +
12B SER* 1.3 64.9 + - - +
13B ASN* 4.6 4.3 - - + +
14B ALA* 3.0 14.6 + - + +
15B LYS* 2.9 19.2 + - - +
132B GLY 5.6 0.7 - - - +
122D ARG* 5.9 0.7 - - - -
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Residues in contact with SER 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU 3.4 2.9 + - - -
11B PRO* 1.3 68.6 - - - +
13B ASN* 1.3 65.6 + - - +
15B LYS* 3.2 17.2 + - - +
16B SER* 3.1 22.7 + - - -
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Residues in contact with ASN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.3 4.2 - - + +
12B SER* 1.3 81.1 - - - +
14B ALA* 1.3 58.6 + - - +
16B SER* 3.4 6.4 + - - -
17B THR* 3.0 33.1 + - - -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.8 22.7 - - + -
11B PRO* 3.0 20.7 + - + +
13B ASN* 1.3 74.9 - - - +
15B LYS* 1.3 62.2 + - - +
17B THR* 3.3 5.5 + - - -
18B VAL* 2.8 35.1 + - + +
131B ALA* 3.3 29.6 - - + +
132B GLY 5.3 0.2 - - - -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B THR* 3.9 17.8 + - + +
8B ASN* 2.8 35.9 + - - +
9B ASP* 4.2 1.0 - - - +
10B LEU* 2.8 40.4 + - + +
11B PRO 2.9 16.0 + - - +
12B SER* 3.2 17.5 + - - +
14B ALA* 1.3 77.6 - - - +
16B SER* 1.3 58.0 + - - +
18B VAL* 4.0 0.2 - - - -
19B ILE* 2.9 40.3 + - + +
76B LEU* 3.3 37.5 - - + +
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER 3.1 13.9 + - - -
13B ASN* 3.6 11.0 - - - -
14B ALA 3.2 0.2 - - - -
15B LYS* 1.3 79.6 - - - +
17B THR* 1.3 62.5 + - - +
19B ILE* 3.9 7.9 - - - +
20B GLY* 3.2 17.5 + - - -
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASN 3.0 18.8 + - - -
14B ALA* 3.7 3.8 - - - -
16B SER* 1.3 76.0 - - - +
18B VAL* 1.3 63.7 + - - +
20B GLY* 3.3 4.0 + - - -
21B ILE* 3.2 36.9 + - + +
127B ASP* 5.1 1.8 - - + +
131B ALA* 4.2 18.6 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 2.8 19.4 + - - +
15B LYS 4.2 1.1 - - - +
17B THR* 1.3 74.7 - - - +
19B ILE* 1.3 62.3 + - - +
21B ILE* 3.1 7.8 + - + +
22B LEU* 2.8 38.5 + - + +
76B LEU* 4.2 6.3 - - + -
128B SER* 4.4 12.8 - - - +
131B ALA* 3.8 23.8 - - + -
133B ASP* 3.7 21.3 - - + +
136B THR* 3.3 38.1 - - + +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 2.9 26.5 + - + +
16B SER* 3.9 7.9 - - - +
18B VAL* 1.3 76.3 - - - +
20B GLY* 1.4 56.9 + - - +
22B LEU* 3.7 6.7 - - - +
23B ASN* 2.9 38.5 + - - +
73B VAL* 4.0 32.3 - - + +
76B LEU* 3.7 34.3 - - + +
77B GLY 4.5 0.4 - - - -
78B GLY* 3.8 21.1 - - - +
79B THR 5.2 1.1 - - - +
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Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER 3.2 13.1 + - - -
17B THR 3.3 4.0 + - - -
18B VAL 3.2 0.8 - - - -
19B ILE* 1.4 77.5 - - - +
21B ILE* 1.3 55.6 + - - +
23B ASN* 4.0 2.8 - - - +
24B GLU* 2.9 32.2 + - - +
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 3.2 32.0 + - + +
18B VAL* 3.1 12.7 + - + +
20B GLY* 1.3 75.5 - - - +
22B LEU* 1.3 59.0 + - - +
24B GLU* 3.7 11.2 - - - +
25B SER* 3.0 29.1 + - - +
124B ALA* 3.7 19.7 - - + -
127B ASP* 3.7 37.2 - - + +
128B SER* 4.2 5.6 - - - +
140B PHE* 3.7 25.6 - - + -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 2.8 41.2 + - + +
19B ILE* 3.7 2.0 - - - +
21B ILE* 1.3 77.8 - - - +
23B ASN* 1.4 58.5 + - - +
25B SER* 3.2 1.6 + - - -
26B LEU* 2.8 24.8 + - - +
69B ILE* 3.3 38.9 - - + +
72B ARG* 3.6 26.5 - - + +
73B VAL* 3.4 29.4 - - + +
76B LEU* 4.4 3.1 - - + -
136B THR* 4.0 7.0 - - + -
139B ILE* 5.1 3.1 - - + -
140B PHE* 3.6 27.4 - - + -
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Residues in contact with ASN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 2.9 27.9 + - - +
20B GLY* 4.3 2.7 - - - +
22B LEU* 1.4 72.9 - - - +
24B GLU* 1.4 63.5 + - - +
26B LEU* 3.4 10.2 + - - +
27B ALA* 3.2 21.8 + - - +
73B VAL* 3.7 16.5 - - - +
79B THR 3.0 22.4 + - - -
80B ALA* 3.6 5.7 - - - -
81B LEU* 2.9 49.5 + - + +
90B THR* 4.2 4.5 - - + +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY 2.9 20.1 + - - +
21B ILE* 3.7 11.4 - - - +
23B ASN* 1.4 79.7 - - - +
25B SER* 1.4 64.8 + - - +
27B ALA* 3.3 10.7 + - - +
28B SER* 3.5 11.8 + - - -
90B THR* 3.9 23.4 - - + +
92B LYS* 3.6 27.7 + - + +
120B MET* 4.5 14.9 - - - +
123B LYS* 5.8 4.3 - - - -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.0 18.3 + - - +
22B LEU 3.7 3.1 - - - -
24B GLU* 1.4 78.0 + - - +
26B LEU* 1.3 64.2 + - - +
28B SER* 3.2 4.0 + - - -
29B VAL* 2.9 28.6 + - - +
69B ILE* 4.5 4.3 - - - -
120B MET* 4.0 20.9 - - - +
121B ILE* 3.6 18.6 - - - +
124B ALA* 4.1 5.5 - - - +
140B PHE* 3.5 27.2 - - - -
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TRP* 4.5 4.9 - - + -
22B LEU 2.8 17.5 + - - +
23B ASN* 3.6 19.3 - - - +
24B GLU 3.3 0.2 - - - -
25B SER* 1.3 76.1 - - - +
27B ALA* 1.3 62.6 + - - +
29B VAL* 3.3 4.9 + - - +
30B ILE* 2.9 44.2 + - + +
66B GLY* 3.3 37.2 - - - +
69B ILE* 4.0 8.0 - - + +
70B ALA* 3.9 26.2 - - + +
73B VAL* 5.6 0.2 - - + -
81B LEU 3.6 27.1 - - - +
82B GLY* 4.3 4.7 - - - +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN 3.2 6.4 + - - +
24B GLU 3.7 2.0 - - - +
25B SER 3.2 0.4 - - - -
26B LEU* 1.3 79.6 - - - +
28B SER* 1.4 59.0 + - - +
30B ILE 3.5 0.3 + - - -
31B ASP* 3.1 24.3 + - - +
81B LEU 5.0 4.0 + - - +
86B ALA 4.2 0.9 - - - +
87B VAL* 3.4 30.8 - - - +
90B THR* 3.5 39.3 - - + -
91B THR* 3.8 11.6 - - - +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU 3.5 4.1 + - - -
25B SER 3.2 2.6 + - - -
27B ALA* 1.4 75.1 - - - +
29B VAL* 1.3 61.4 + - - +
31B ASP* 3.8 1.6 - - - +
32B LEU* 2.9 28.4 + - - +
91B THR* 3.8 9.3 - - - -
92B LYS* 2.9 30.9 + - - +
93B LEU* 3.8 6.6 - - - +
117B VAL* 3.9 11.7 - - - +
120B MET* 3.6 38.3 - - - +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 2.9 23.1 + - - +
26B LEU* 3.7 6.3 - - - +
28B SER* 1.3 74.6 - - - +
30B ILE* 1.3 60.9 + - + +
32B LEU* 3.3 7.7 + - - +
33B ALA* 2.9 26.7 + - - +
62B LEU* 3.7 38.9 - - + +
65B HIS* 4.9 3.4 - - + -
66B GLY* 3.9 16.8 - - - +
69B ILE* 4.4 14.4 - - + -
117B VAL* 4.1 20.6 - - + -
121B ILE* 4.5 7.9 - - + -
147B LEU* 5.5 2.5 - - + -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.8 26.7 - - + -
41A TRP* 4.5 9.0 - - + -
26B LEU* 2.9 38.9 + - + +
27B ALA 3.9 0.2 - - - +
29B VAL* 1.3 74.7 - - + +
31B ASP* 1.3 65.2 + - - +
33B ALA* 3.0 10.3 + - + +
34B LEU* 3.0 27.1 + - + +
66B GLY* 5.7 1.3 - - - -
82B GLY* 3.6 36.1 - - - +
87B VAL* 3.8 22.9 - - + -
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.7 24.6 + - - +
85A GLN* 5.1 3.5 + - - +
27B ALA 3.1 18.6 + - - +
28B SER 3.8 3.4 - - - +
30B ILE* 1.3 74.6 - - - +
32B LEU* 1.3 57.7 + - - +
34B LEU* 3.0 11.2 + - - +
35B VAL* 2.9 37.1 + - - +
87B VAL* 4.0 10.0 - - + +
91B THR* 2.7 33.0 + - - +
93B LEU* 3.4 20.6 - - + +
94B LYS 5.3 0.9 - - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER 2.9 18.9 + - - +
29B VAL* 3.3 6.3 + - - +
31B ASP* 1.3 75.7 - - - +
33B ALA* 1.3 53.7 - - - +
35B VAL* 3.5 10.3 - - + +
36B THR* 2.7 37.9 + - - -
62B LEU* 3.8 22.4 - - + -
93B LEU* 3.9 5.8 - - + +
113B ARG* 3.7 31.4 - - + +
114B TYR* 3.5 48.5 - - + -
117B VAL* 3.9 24.7 - - + -
147B LEU* 4.1 2.7 - - + -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 6.2 0.2 - - - +
29B VAL 2.9 14.8 + - - +
30B ILE* 3.0 13.4 + - + +
32B LEU* 1.3 77.8 - - - +
34B LEU* 1.4 62.4 + - + +
36B THR* 3.4 2.5 + - - -
37B LYS 3.3 13.0 + - - -
59B ARG* 2.9 48.3 + - - +
62B LEU* 3.7 18.7 - - + +
63B ASP* 4.3 4.9 - - - +
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.7 29.2 - - + -
34A LEU* 4.7 22.2 - - + -
82A GLY 4.0 17.0 - - - +
83A SER* 4.6 2.0 - - - -
84A LEU* 3.9 45.5 - - + +
87A VAL* 5.4 1.3 - - + -
30B ILE* 3.0 23.2 + - + +
31B ASP* 3.4 9.9 - - - +
33B ALA* 1.4 74.4 - - + +
35B VAL* 1.3 58.9 + - - +
37B LYS* 3.3 4.2 + - - +
38B GLN* 2.9 28.3 + - - +
41B TRP* 5.3 0.3 - - - -
59B ARG* 4.1 16.8 - - - +
84B LEU* 5.5 0.7 - - + -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER* 5.5 3.6 - - - +
84A LEU 6.1 0.4 - - - +
31B ASP* 2.9 28.5 + - - +
32B LEU* 3.5 18.8 - - + +
34B LEU* 1.3 75.9 - - + +
36B THR* 1.3 59.5 + - - +
38B GLN* 3.2 8.6 + - - +
39B ALA* 2.9 29.3 + - - +
93B LEU* 5.0 1.3 - - + -
94B LYS 5.7 0.7 - - - +
96B TYR* 3.5 48.0 - - + +
110B LEU* 3.6 15.3 - - + -
113B ARG* 4.2 16.8 - - - +
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU 2.7 20.8 + - - -
33B ALA* 3.6 8.5 - - - -
34B LEU 3.2 0.2 - - - -
35B VAL* 1.3 77.4 - - - +
37B LYS* 1.3 57.5 + - - +
39B ALA* 3.5 2.9 + - - +
40B HIS* 3.0 27.2 + - - +
55B LEU* 3.2 41.3 - - + +
59B ARG* 4.0 11.9 - - + +
62B LEU* 3.7 2.9 - - - +
110B LEU* 4.3 8.1 - - - -
114B TYR* 2.7 34.9 + - - +
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Residues in contact with LYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP* 2.7 41.7 + - - +
1163A FE 4.3 1.8 - - - -
33B ALA 3.3 1.4 + - - -
34B LEU 3.3 4.7 + - - +
35B VAL 3.3 0.2 - - - -
36B THR* 1.3 78.9 - - + +
38B GLN* 1.3 65.1 + - - +
40B HIS* 3.1 21.6 + - + +
41B TRP* 2.9 49.7 + - + -
55B LEU 6.0 0.4 - - - +
56B ASP* 2.6 35.4 + - - +
59B ARG* 3.4 47.8 - - + +
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 4.7 0.9 - - - +
80A ALA 3.0 21.0 + - - +
81A LEU* 3.8 0.8 - - - +
82A GLY* 2.8 35.0 - - - +
83A SER* 3.3 20.5 - - - +
34B LEU 2.9 17.0 + - - +
35B VAL* 3.2 9.6 + - - +
37B LYS* 1.3 77.1 - - - +
39B ALA* 1.4 62.5 + - - +
41B TRP* 3.8 7.7 - - - -
42B ASN* 3.0 36.8 + - - +
96B TYR* 3.8 24.5 - - + -
97B PRO 5.0 0.6 - - - +
98B THR* 4.1 21.6 - - + +
106B HIS* 4.5 1.1 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL 2.9 15.8 + - - +
36B THR 3.7 4.0 - - - +
38B GLN* 1.4 75.8 - - - +
40B HIS* 1.3 64.9 + - - +
42B ASN 3.0 12.3 + - - -
43B LEU* 3.0 20.0 + - - +
55B LEU* 4.0 3.4 - - + -
96B TYR* 3.5 22.2 - - - +
106B HIS* 3.6 18.2 - - + +
110B LEU* 3.8 22.7 - - + -
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Residues in contact with HIS 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1163A FE 3.4 15.5 - - - -
36B THR 3.0 19.3 + - - +
37B LYS* 3.1 17.4 + - + +
39B ALA* 1.3 77.2 - - - +
41B TRP* 1.4 85.6 + + - +
42B ASN 3.5 0.2 + - - -
43B LEU* 3.8 11.2 + - - +
48B PHE* 4.5 1.0 - - - -
52B HIS* 2.7 76.3 + + - -
55B LEU* 3.8 18.6 - - + +
56B ASP* 3.0 36.6 + - - -
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Residues in contact with TRP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.4 4.3 - - + -
30A ILE* 4.5 16.6 - - + -
66A GLY 4.4 1.8 - - - -
67A ASP* 3.4 34.5 + - - +
70A ALA* 3.2 30.7 - - + +
71A GLU* 4.2 16.7 - - + +
74A VAL* 3.6 18.2 - - + +
80A ALA* 3.8 26.9 - - + -
82A GLY* 4.0 24.5 - - - -
34B LEU 5.3 0.2 - - - -
37B LYS* 2.9 48.6 + - + +
38B GLN* 3.8 11.7 - - - -
40B HIS* 1.4 99.1 + + - +
42B ASN* 1.3 62.3 + - - +
43B LEU 3.5 2.4 + - - +
44B LYS* 5.0 1.2 + - - -
52B HIS* 4.7 3.4 - + - -
152C TRP* 3.7 17.1 + + - -
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.6 8.5 - - - +
78A GLY 4.3 0.5 - - - +
79A THR* 3.5 16.7 - - + +
80A ALA 3.0 45.2 + - - +
38B GLN* 3.0 33.4 + - - +
39B ALA 3.0 3.8 + - - -
41B TRP* 1.3 81.6 - - - +
43B LEU* 1.3 65.0 + - - +
44B LYS* 3.6 10.4 + - - +
100B ILE 4.5 5.4 - - - +
101B TYR* 3.6 23.1 - - + +
106B HIS* 3.6 19.5 + - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA 3.0 27.9 + - - +
40B HIS 3.8 4.7 - - - +
41B TRP 3.5 2.1 - - - +
42B ASN* 1.3 78.9 - - - +
44B LYS* 1.3 66.4 + - - +
48B PHE* 3.3 30.2 - - + +
51B VAL* 3.7 22.7 - - + -
52B HIS* 3.3 42.6 - - + +
55B LEU* 4.2 8.5 - - + -
101B TYR 3.6 4.0 - - - -
103B ILE* 4.0 17.3 - - + -
106B HIS* 3.8 28.3 - - + -
110B LEU* 5.6 0.4 - - + -
152C TRP* 5.3 0.3 + - - -
156C ALA* 4.2 0.9 - - - +
----------------------------------------------------------
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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