Contacts of the helix formed by residues 13 - 42 (chain B) in PDB entry 2YW7
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 LYS 13 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP 2.9 10.5 + - - +
12B LYS* 1.3 77.7 - - + +
14B ALA* 1.3 70.3 + - + +
15B SER 2.9 3.1 - - - -
16B ASP* 2.4 44.8 + - + +
17B VAL* 3.3 4.7 + - + -
129B ASP 4.3 11.3 + - - -
130B LEU* 3.7 45.8 + - + +
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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
----------------------------------------------------------
11B ASP* 3.4 27.5 - - - +
13B LYS* 1.3 85.9 - - + +
15B SER* 1.3 56.3 + - - +
17B VAL* 3.0 15.5 + - - +
18B ALA* 2.9 27.2 + - - +
75B LEU* 4.3 28.6 - - + +
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 3.9 18.7 + - - -
12B LYS 5.0 5.4 - - - -
13B LYS 2.6 5.4 + - - +
14B ALA* 1.3 75.0 - - - +
16B ASP* 1.3 65.6 + - - -
18B ALA* 3.1 11.7 + - - +
19B ASP* 3.0 32.7 + - - +
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS 3.9 10.3 - - - +
13B LYS* 2.4 33.6 + - - +
15B SER* 1.3 70.0 + - - +
17B VAL* 1.3 60.3 + - - +
19B ASP* 3.1 14.1 + - - +
20B LEU* 3.0 26.2 + - + +
130B LEU* 4.4 19.2 - - + +
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 4.1 3.8 - - + +
14B ALA* 3.0 22.6 + - - +
16B ASP* 1.3 73.1 - - - +
18B ALA* 1.3 65.8 + - - +
19B ASP 2.9 1.9 + - - -
20B LEU* 2.9 8.6 + - - +
21B LEU* 2.9 35.2 + - + +
75B LEU* 3.6 14.1 - - + -
127B LEU* 4.0 11.7 - - + -
130B LEU* 4.4 23.3 - - + +
131B ASP* 3.5 43.3 - - + +
134B SER* 3.8 2.7 - - - +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 2.9 15.4 + - - +
15B SER* 3.2 15.3 - - - +
17B VAL* 1.3 72.0 - - - +
19B ASP* 1.3 55.6 + - - +
21B LEU* 3.5 10.2 + - - +
22B GLN* 2.7 35.4 + - - +
72B ILE* 3.9 21.3 - - + +
75B LEU* 4.7 13.0 - - + +
77B LYS 5.3 4.5 - - - +
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Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 3.0 22.5 + - - +
16B ASP* 3.3 14.9 - - - +
17B VAL 2.9 1.8 + - - -
18B ALA* 1.3 75.4 - - - +
20B LEU* 1.3 68.0 + - + +
21B LEU 2.9 1.6 - - - -
22B GLN* 2.9 8.0 + - - +
23B LYS* 2.8 41.2 + - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 3.0 16.0 + - + +
17B VAL* 2.9 11.5 + - - +
19B ASP* 1.3 71.6 - - + +
21B LEU* 1.3 57.7 + - + +
23B LYS* 3.8 22.2 - - + +
24B GLN* 3.2 23.9 + - - +
123B SER* 4.1 22.4 + - - +
126B LYS* 3.3 60.8 - - + +
127B LEU* 3.8 33.7 - - + -
130B LEU* 4.8 6.3 - - + -
138B LEU* 5.4 0.8 - - - +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 2.9 30.1 + - + +
18B ALA* 3.6 4.5 - - - +
19B ASP 2.9 0.6 - - - -
20B LEU* 1.3 76.5 - - + +
22B GLN* 1.3 59.9 + - - +
24B GLN* 3.0 6.4 + - - +
25B LEU 2.8 25.1 + - - -
68B VAL* 3.4 20.2 - - + +
71B ARG* 3.6 31.6 - - + -
72B ILE* 3.7 17.7 - - + -
75B LEU* 3.9 7.4 - - + -
127B LEU* 4.9 2.9 - - + -
134B SER* 3.7 23.3 - - - +
137B LEU* 5.2 2.9 - - + -
138B LEU* 3.9 30.1 - - + -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA 2.7 21.8 + - - +
19B ASP* 2.9 9.4 + - - +
21B LEU* 1.3 72.9 - - - +
23B LYS* 1.3 63.3 + - + +
25B LEU* 3.0 18.7 + - - +
26B SER* 3.2 11.1 + - - -
72B ILE* 3.6 15.7 - - + +
78B SER 4.9 4.5 - - - +
79B PRO* 4.9 2.2 - - + -
80B LYS* 2.7 61.1 + - + +
85B ALA* 5.3 0.6 - - - +
89B ASP* 2.9 26.9 - - - +
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 2.8 31.0 + - + +
20B LEU* 3.8 24.1 - - + +
22B GLN* 1.3 74.8 + - + +
24B GLN* 1.3 61.3 + - - +
26B SER* 3.6 3.6 + - - -
27B THR* 3.2 21.7 + - - -
89B ASP* 4.3 34.7 - - + +
92B TRP* 5.1 0.9 - - - -
126B LYS* 5.0 5.3 - - - +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 3.2 10.7 + - - +
21B LEU* 3.0 13.6 + - - +
23B LYS* 1.3 77.7 - - - +
25B LEU* 1.3 66.8 + - - +
27B THR* 2.8 26.6 + - - +
28B TYR* 3.0 49.3 + - + -
68B VAL* 4.5 2.9 - - + -
119B ASP* 4.8 4.3 - - - +
120B THR* 2.8 43.6 + - - +
123B SER* 4.2 12.1 + - - -
138B LEU* 3.7 23.8 - - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 2.8 11.5 + - - +
22B GLN* 3.0 18.6 + - - +
24B GLN* 1.3 70.9 - - - +
26B SER* 1.3 59.1 + - - +
28B TYR* 3.0 10.6 + - - +
29B ASN* 2.8 49.2 + - - +
65B ALA* 3.5 23.6 - - + +
68B VAL* 3.7 23.9 - - + +
69B ALA* 4.2 1.3 - - + +
72B ILE* 4.2 3.8 - - + -
79B PRO* 3.9 22.9 - - + -
80B LYS 3.6 25.8 - - - +
40G TRP* 3.8 14.4 - - + -
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN* 3.2 12.9 + - - -
23B LYS 3.9 4.0 - - - -
24B GLN 3.2 1.0 - - - -
25B LEU* 1.3 73.2 - - - +
27B THR* 1.3 68.9 + - - +
29B ASN* 3.9 8.0 + - - +
30B ASP* 2.9 26.8 + - - +
80B LYS 4.5 5.0 + - - -
85B ALA 3.5 9.2 + - - -
86B ILE* 4.0 23.2 - - - +
89B ASP* 2.6 32.6 + - - -
92B TRP* 4.7 4.0 - - - -
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS 3.2 14.4 + - - -
24B GLN* 2.8 27.4 + - - +
26B SER* 1.3 71.5 - - - +
28B TYR* 1.3 60.7 + - + +
30B ASP* 3.5 2.8 - - - +
31B LEU* 2.7 37.9 + - + +
92B TRP* 3.5 29.3 - - + -
116B VAL* 3.7 43.3 - - + +
119B ASP* 5.0 8.2 + - + +
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Residues in contact with TYR 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.0 44.4 + - + -
25B LEU* 3.0 7.9 + - - +
27B THR* 1.3 84.7 - - + +
29B ASN* 1.3 63.0 + - - +
31B LEU* 2.9 8.3 + - + +
32B HIS* 2.9 22.9 + - - -
61B VAL* 3.4 18.3 - - + +
64B TYR* 3.4 15.0 - + + -
65B ALA* 3.5 33.2 - - + -
68B VAL* 3.5 22.4 - - + -
116B VAL* 5.3 1.3 - - + -
120B THR* 4.8 0.6 - - - +
138B LEU* 3.4 5.5 - - - +
141B HIS* 2.5 42.2 + + - +
145B LEU* 4.4 19.1 - - + +
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Residues in contact with ASN 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 2.8 37.9 + - - +
26B SER* 3.9 2.8 - - - +
28B TYR* 1.3 70.3 - - - +
30B ASP* 1.3 58.6 + - - +
31B LEU 2.9 2.4 + - - -
32B HIS* 2.9 21.7 + - - -
33B LEU* 2.8 33.9 + - - +
65B ALA* 3.6 14.9 - - - +
80B LYS 4.7 0.6 + - - -
81B GLY* 3.6 30.9 + - - -
86B ILE* 3.8 20.3 - - + +
33G LEU* 4.0 11.7 - - + +
40G TRP* 4.1 7.4 - - - -
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 2.9 20.2 + - - +
27B THR 3.9 0.8 - - - +
29B ASN* 1.3 72.2 - - - +
31B LEU* 1.3 55.4 + - - +
33B LEU* 4.1 3.3 - - - +
34B THR* 2.6 37.6 + - - -
86B ILE* 3.5 18.7 - - + +
90B ARG* 3.4 12.3 + - - -
92B TRP* 2.5 38.2 + - + -
94B ASP* 4.8 1.0 - - - +
95B TYR 5.9 0.3 + - - -
82G THR* 5.3 0.5 - - - +
83G PRO* 3.0 37.7 - - - +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 2.7 23.9 + - + +
28B TYR* 3.1 13.2 - - + +
29B ASN 2.9 0.2 - - - -
30B ASP* 1.3 77.7 - - - +
32B HIS* 1.3 56.1 + - - +
34B THR* 3.5 5.0 - - + -
35B LEU* 2.8 52.0 + - + +
61B VAL* 3.2 39.0 - - + -
109B LEU* 5.7 0.2 - - + -
112B VAL* 3.7 30.3 - - + -
113B TYR* 3.4 18.2 - - + +
116B VAL* 4.4 19.1 - - + -
145B LEU* 4.8 4.0 - - + -
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR 2.9 23.8 + - - +
29B ASN* 3.4 22.1 + - - -
31B LEU* 1.3 72.8 - - - +
33B LEU* 1.3 90.0 + - + +
34B THR 3.0 1.3 - - - -
35B LEU* 3.8 9.1 - - + +
36B LYS* 3.1 24.6 + - - +
58B VAL* 4.3 13.2 - - + +
61B VAL* 4.0 11.7 - - + -
62B ARG* 3.4 54.8 + - + +
65B ALA* 4.6 1.9 - - + +
32G HIS* 4.4 16.5 - + - -
33G LEU* 4.5 4.2 - - + +
62G ARG* 5.1 4.4 + - - -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 2.8 32.8 + - + +
30B ASP* 4.1 5.4 - - - +
32B HIS* 1.3 97.6 + - + +
34B THR* 1.3 57.4 + - - +
36B LYS* 3.9 4.5 + - - +
37B HIS* 3.1 20.1 + - - +
40B TRP* 5.1 1.3 - - + -
86B ILE* 4.5 1.6 - - + -
29G ASN* 4.4 14.1 - - + +
32G HIS* 4.7 6.7 - - + +
33G LEU* 3.6 30.5 - - + -
81G GLY* 3.4 33.4 - - - +
82G THR* 5.0 0.2 - - - -
83G PRO* 4.1 16.8 - - + -
86G ILE* 3.7 20.9 - - + -
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 2.6 30.0 + - - -
31B LEU* 3.5 7.0 - - + +
32B HIS 3.0 0.2 - - - -
33B LEU* 1.3 77.9 - - - +
35B LEU* 1.3 66.8 + - - +
36B LYS 3.2 0.2 - - - -
37B HIS* 2.9 22.9 + - - +
38B VAL* 3.2 11.8 + - + +
95B TYR* 3.7 39.5 + - + +
109B LEU* 4.7 9.6 - - + -
112B VAL* 5.1 9.6 - - + -
82G THR* 3.7 15.3 - - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 2.8 57.2 + - + +
32B HIS* 3.3 7.6 + - - +
34B THR* 1.3 78.0 - - - +
36B LYS* 1.3 63.1 + - - +
38B VAL* 3.3 12.4 + - - +
39B HIS 3.5 7.1 + - - -
54B ILE* 3.8 29.2 - - + +
57B GLN* 4.5 9.4 - - + -
58B VAL* 3.4 24.2 - - + +
61B VAL* 4.6 2.5 - - + -
109B LEU* 4.0 30.1 - - + -
113B TYR* 3.6 13.2 - - + +
148B PHE* 4.8 7.9 - - + -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS 3.1 16.0 + - - +
33B LEU* 3.9 4.5 - - - +
35B LEU* 1.3 73.9 - - - +
37B HIS* 1.3 66.8 + - - +
39B HIS* 2.9 33.0 + - + +
40B TRP* 3.2 40.1 + - + +
55B ASP* 5.2 7.9 - - - +
58B VAL* 4.0 18.6 - - + -
59B GLU* 5.9 0.4 + - - -
62B ARG* 3.6 32.0 - - - +
62G ARG* 5.1 6.9 + - - +
66G ASP* 3.0 30.7 + - - +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 3.1 14.3 + - - +
34B THR* 2.9 17.2 + - - +
36B LYS* 1.3 78.9 - - - +
38B VAL* 1.3 58.7 + - - +
40B TRP* 3.5 12.9 - - - +
41B ASN* 3.0 38.7 + - + +
95B TYR* 3.4 33.9 + + - -
97B VAL 3.1 20.4 + - - -
98B GLU* 5.5 0.2 - - - -
78G SER* 5.0 1.1 - - - -
79G PRO 3.1 23.6 + - - -
80G LYS* 3.7 10.1 - - + -
81G GLY 2.9 26.2 + - - +
82G THR* 4.2 15.2 + - + -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.2 17.7 - - + +
35B LEU* 3.7 2.9 - - - +
36B LYS 3.1 0.6 - - - -
37B HIS* 1.3 75.3 - - - +
39B HIS* 1.3 66.7 + - - +
40B TRP 3.0 1.6 - - - -
41B ASN* 2.8 15.1 + - - +
42B VAL* 2.9 29.7 + - + +
50B VAL* 4.5 1.3 - - + -
54B ILE* 3.1 33.7 - - + -
95B TYR* 3.9 26.0 - - + +
105B HIS* 4.0 20.9 - - + +
109B LEU* 4.3 18.2 - - + -
----------------------------------------------------------
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Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU 3.5 4.5 + - - +
36B LYS* 2.9 28.7 + - + +
38B VAL* 1.3 83.6 - - - +
40B TRP* 1.3 69.8 + - + +
42B VAL* 3.7 8.0 + - - +
50B VAL* 5.4 0.9 - - + -
51B HIS* 2.6 70.3 + + + +
54B ILE* 3.9 20.9 - - + -
55B ASP* 2.8 37.6 + - - -
66G ASP* 5.6 1.6 + - - -
----------------------------------------------------------
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Residues in contact with TRP 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 5.1 0.9 - - - -
36B LYS* 3.6 32.2 - - + +
37B HIS* 3.5 21.8 - - - +
38B VAL 3.0 0.2 - - - -
39B HIS* 1.3 86.0 - - + +
41B ASN* 1.3 61.4 + - - +
42B VAL 3.6 5.4 + - - +
25G LEU* 3.8 22.7 - - + -
29G ASN* 3.9 13.9 - - - -
62G ARG 5.6 0.2 - - - -
65G ALA* 4.4 2.9 - - + -
66G ASP* 3.2 40.6 + - - +
69G ALA* 3.5 24.7 - - + +
70G GLU* 5.3 3.4 - - + -
73G ALA* 4.5 11.8 - - - +
79G PRO* 3.8 34.0 - - + +
81G GLY* 3.6 28.9 - - - -
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.0 27.7 + - - +
38B VAL* 2.8 11.5 + - - +
40B TRP* 1.3 73.4 - - - +
42B VAL* 1.3 56.1 + - - -
43B VAL* 4.9 0.9 - - - -
98B GLU* 3.1 17.5 - - - +
99B ARG* 2.9 43.7 - - - +
100B ASP 3.0 2.3 + - - -
105B HIS* 2.9 14.1 + - + -
78G SER* 2.7 33.9 + - - +
79G PRO* 2.6 31.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 2.9 37.8 + - + +
39B HIS* 3.7 8.6 + - - +
40B TRP 3.4 6.0 - - - +
41B ASN* 1.3 77.2 - - - +
43B VAL* 1.3 71.1 + - - +
47B PHE* 3.5 35.8 - - + +
50B VAL* 4.2 14.4 - - + -
51B HIS* 4.7 8.0 + - - +
100B ASP 4.0 2.2 - - - +
102B VAL* 3.8 19.1 - - + -
105B HIS* 3.5 22.2 - - + -
----------------------------------------------------------
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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