Contacts of the helix formed by residues 11 - 42 (chain E) 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 ASP 11 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LYS* 1.3 93.8 + - - +
13E LYS* 3.3 10.4 - - - +
14E ALA* 3.5 16.5 + - - +
15E SER* 3.5 19.6 + - - -
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Residues in contact with LYS 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP* 1.3 88.6 + - - +
13E LYS* 1.3 95.5 + - + +
15E SER* 2.9 19.9 + - - -
16E ASP* 2.4 25.7 - - - +
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Residues in contact with LYS 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP 4.9 7.2 - - - +
12E LYS* 1.3 106.8 - - + +
14E ALA* 1.3 49.3 + - - +
16E ASP* 2.7 30.2 + - - +
17E VAL* 2.8 23.8 + - + +
129E ASP 5.3 5.4 + - - +
130E LEU* 4.0 27.8 - - + +
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Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP* 3.5 18.4 + - - +
12E LYS 3.3 0.4 - - - -
13E LYS* 1.3 77.5 - - - +
15E SER* 1.3 53.2 + - - +
17E VAL* 3.7 10.1 - - - +
18E ALA* 2.8 35.9 + - - +
75E LEU* 4.1 31.6 - - + +
77E LYS* 6.0 0.2 - - - -
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Residues in contact with SER 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP 3.5 10.6 + - - -
12E LYS* 2.9 15.7 + - - -
14E ALA* 1.3 77.8 - - - +
16E ASP* 1.3 53.0 + - - +
17E VAL 3.4 0.2 - - - -
18E ALA* 4.2 4.6 - - - +
19E ASP* 2.8 42.5 + - - +
77E LYS* 3.2 30.5 + - - +
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Residues in contact with ASP 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LYS* 2.4 35.2 - - - +
13E LYS* 2.7 12.9 + - - +
15E SER* 1.3 74.5 - - - +
17E VAL* 1.3 60.8 + - - +
19E ASP* 3.8 11.6 - - - +
20E LEU* 3.0 32.2 + - - +
130E LEU* 4.2 13.1 - - + +
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Residues in contact with VAL 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LYS* 2.8 26.4 + - + +
14E ALA* 3.7 9.0 - - - +
16E ASP* 1.3 76.4 - - - +
18E ALA* 1.3 55.0 + - - +
19E ASP 3.1 0.9 - - - -
20E LEU* 3.2 2.9 + - - +
21E LEU* 2.8 40.3 + - + +
75E LEU* 3.8 13.5 - - + -
127E LEU* 3.6 22.7 - - + -
130E LEU* 3.7 26.2 - - + -
131E ASP* 4.0 12.3 - - + -
134E SER* 3.6 26.5 - - - +
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Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ALA 2.8 19.1 + - - +
15E SER* 4.2 3.4 - - - +
17E VAL* 1.3 75.7 - - - +
19E ASP* 1.3 59.0 + - - +
21E LEU* 3.7 9.5 - - - +
22E GLN* 2.8 31.6 + - - +
72E ILE* 4.0 12.9 - - + +
75E LEU* 4.5 9.8 - - + +
77E LYS* 3.7 36.8 - - + -
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Residues in contact with ASP 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E SER* 2.8 26.7 + - - +
16E ASP* 4.0 13.2 - - - +
17E VAL 3.1 0.6 - - - -
18E ALA* 1.3 78.7 - - - +
20E LEU* 1.3 65.2 + - + +
22E GLN* 3.5 6.7 + - - +
23E LYS* 3.2 37.2 + - - +
77E LYS* 4.9 10.9 - - - +
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ASP 3.0 20.4 + - - +
17E VAL 3.2 4.8 + - - +
19E ASP* 1.3 77.3 - - + +
21E LEU* 1.3 60.1 + - + +
23E LYS* 3.0 27.3 + - + +
24E GLN* 2.8 29.1 + - - +
123E SER* 4.6 18.5 + - - +
126E LYS* 4.1 42.8 - - + +
127E LEU* 3.5 36.3 - - + -
130E LEU* 5.3 2.9 - - + -
138E LEU* 6.3 1.3 - - + -
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 2.8 21.2 + - + +
18E ALA 3.8 0.7 - - - +
20E LEU* 1.3 76.9 - - - +
22E GLN* 1.3 57.3 + - - +
24E GLN* 3.4 2.8 + - + +
25E LEU* 2.9 25.1 + - - +
68E VAL* 3.3 28.2 - - + +
71E ARG* 3.5 31.0 - - + -
72E ILE* 3.5 23.1 - - + +
75E LEU* 3.8 16.2 - - + -
127E LEU* 4.8 3.6 - - + -
134E SER* 3.7 22.7 - - - +
137E LEU* 5.2 2.7 - - + -
138E LEU* 4.2 28.0 - - + -
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Residues in contact with GLN 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ALA 2.8 18.4 + - - +
19E ASP* 3.7 7.9 - - - +
20E LEU 3.2 0.2 - - - -
21E LEU* 1.3 73.9 - - - +
23E LYS* 1.3 64.5 + - + +
25E LEU* 3.3 19.9 - - - +
26E SER* 3.3 12.4 + - - -
72E ILE* 3.6 9.6 - - + +
78E SER 4.1 1.0 - - - +
79E PRO* 3.3 12.5 - - - +
80E LYS* 3.2 67.0 + - + +
85E ALA 5.1 1.2 + - - -
89E ASP* 3.5 15.3 + - - +
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Residues in contact with LYS 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ASP* 3.2 23.6 + - - +
20E LEU* 3.0 27.0 + - + +
22E GLN* 1.3 77.5 - - + +
24E GLN* 1.3 60.3 + - - +
26E SER* 3.5 5.9 + - - -
27E THR* 2.8 23.9 + - - -
89E ASP* 3.7 28.2 - - + +
92E TRP* 5.7 0.3 - - - -
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Residues in contact with GLN 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU 2.8 12.8 + - - +
21E LEU* 3.5 13.9 - - + +
23E LYS* 1.3 76.0 - - - +
25E LEU* 1.3 65.7 + - - +
27E THR* 2.9 31.5 + - - +
28E TYR* 2.7 46.2 + - + -
68E VAL* 4.4 3.6 - - + -
116E VAL* 5.4 0.2 - - - +
119E ASP* 4.8 4.8 + - - +
120E THR* 3.6 26.6 + - - +
123E SER* 4.3 16.0 + - - +
138E LEU* 3.3 30.1 - - + +
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 4.0 15.5 - - + -
21E LEU 2.9 10.8 + - - +
22E GLN* 3.3 28.9 - - - +
24E GLN* 1.3 76.1 - - - +
26E SER* 1.3 50.7 + - - +
28E TYR* 2.8 9.3 + - - +
29E ASN* 2.8 58.1 + - - +
65E ALA* 3.8 24.0 - - - +
68E VAL* 3.9 17.9 - - + +
69E ALA* 4.0 5.4 - - + +
72E ILE* 3.8 19.1 - - + -
79E PRO* 3.9 19.5 - - + -
80E LYS 4.1 6.3 - - - +
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Residues in contact with SER 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 3.3 10.7 + - - -
23E LYS 3.7 9.2 - - - -
25E LEU* 1.3 77.3 - - - +
27E THR* 1.3 56.4 + - - +
29E ASN* 3.8 10.3 - - - +
30E ASP* 2.9 32.6 + - - +
80E LYS 4.8 1.6 + - - -
85E ALA 3.6 2.6 + - - -
86E ILE* 3.6 23.9 - - - +
89E ASP* 2.6 39.1 + - - -
90E ARG* 5.1 1.6 - - - -
92E TRP* 4.5 3.3 - - - -
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Residues in contact with THR 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LYS 2.8 17.2 + - - -
24E GLN* 2.9 26.5 + - - +
26E SER* 1.3 77.3 - - - +
28E TYR* 1.3 57.1 - - + +
30E ASP* 4.3 1.4 - - - +
31E LEU* 2.9 29.1 + - - +
92E TRP* 4.1 26.4 - - + -
115E GLY 5.5 0.4 - - - +
116E VAL* 4.1 38.7 - - + +
119E ASP* 5.4 9.6 - - + +
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Residues in contact with TYR 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLN* 2.7 49.2 + - + -
25E LEU* 2.8 6.9 + - - +
27E THR* 1.3 77.3 - - - +
29E ASN* 1.3 59.2 + - - +
31E LEU* 3.3 6.4 - - + +
32E HIS* 2.8 35.8 + - - -
61E VAL* 3.3 31.4 - - + +
64E TYR* 3.9 7.2 - + + -
65E ALA* 3.9 15.3 - - + -
68E VAL* 3.6 30.1 - - + -
116E VAL* 5.1 5.2 - - + -
120E THR* 4.8 0.3 - - - +
138E LEU* 3.6 6.8 - - - +
141E HIS* 2.6 38.2 + + - +
145E LEU* 4.2 19.2 - - + +
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Residues in contact with ASN 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.4 13.4 - - + +
40A TRP* 4.4 6.3 - - - -
25E LEU* 2.8 43.6 + - - +
26E SER* 4.1 7.6 - - - +
28E TYR* 1.3 72.4 - - - +
30E ASP* 1.3 62.4 + - - +
32E HIS* 3.4 20.3 + - - +
33E LEU* 3.2 29.6 + - - +
65E ALA* 4.0 12.1 - - - +
80E LYS 4.1 4.4 + - - -
81E GLY* 3.9 23.2 + - - -
86E ILE* 4.0 18.2 - - + +
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Residues in contact with ASP 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO* 3.1 19.4 - - - +
26E SER 2.9 20.7 + - - +
29E ASN* 1.3 75.2 - - - +
31E LEU* 1.3 52.9 + - - +
33E LEU* 3.7 1.8 - - - +
34E THR* 2.5 50.0 + - - -
86E ILE* 3.4 18.7 - - + +
90E ARG* 2.9 25.8 + - - +
92E TRP* 2.8 39.1 + - + -
94E ASP* 5.2 0.9 - - - -
95E TYR 5.6 0.3 + - - -
112E VAL* 5.6 4.2 - - - +
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E THR 2.9 21.5 + - - +
28E TYR* 3.3 8.7 - - + +
30E ASP* 1.3 77.9 + - - +
32E HIS* 1.3 53.6 + - - +
34E THR* 2.8 10.2 + - - -
35E LEU* 2.5 52.4 + - + +
61E VAL* 3.7 22.2 - - + -
109E LEU* 5.5 0.7 - - + -
112E VAL* 5.1 9.0 - - + -
113E TYR* 3.5 33.7 - - + +
116E VAL* 3.9 36.6 - - + -
145E LEU* 4.2 8.3 - - + -
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Residues in contact with HIS 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 4.6 10.3 - + - -
33A LEU* 4.3 16.2 - - + +
62A ARG* 5.0 4.8 + - - -
28E TYR 2.8 31.3 + - - +
29E ASN* 3.4 29.7 + - - +
31E LEU* 1.3 73.8 - - - +
33E LEU* 1.3 65.4 + - + +
35E LEU* 3.5 10.7 - - - +
36E LYS* 2.9 33.8 + - - +
58E VAL* 4.0 8.7 - - + +
61E VAL* 3.8 17.9 - - + -
62E ARG* 3.5 49.4 + - + +
65E ALA* 4.9 2.8 - - + +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 4.0 20.0 - - + +
32A HIS* 4.4 13.9 - - + +
33A LEU* 3.8 21.5 - - + -
81A GLY* 3.3 24.5 - - - +
83A PRO* 4.3 20.2 - - + -
86A ILE* 3.7 30.7 - - + -
29E ASN 3.2 19.8 + - - +
30E ASP* 3.7 3.6 - - - +
31E LEU 3.2 0.6 - - - -
32E HIS* 1.3 78.6 + - + +
34E THR* 1.3 54.7 + - - +
36E LYS* 3.8 4.6 - - + +
37E HIS* 2.8 34.8 + - - +
40E TRP* 5.2 2.1 - - + -
83E PRO* 6.2 0.4 - - + -
86E ILE* 4.5 5.2 - - + -
----------------------------------------------------------
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Residues in contact with THR 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY 4.3 0.2 + - - -
82A THR* 4.0 13.8 - - - +
30E ASP* 2.5 43.3 + - - -
31E LEU* 3.1 8.7 - - + -
33E LEU* 1.3 72.8 - - - +
35E LEU* 1.3 58.2 + - - +
37E HIS* 3.0 9.4 - - - +
38E VAL* 2.9 34.9 + - + +
95E TYR* 3.4 42.4 + - + +
109E LEU* 4.9 3.6 - - + -
112E VAL* 4.8 14.6 - - + -
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Residues in contact with LEU 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 2.5 41.1 + - + +
32E HIS* 3.5 9.2 - - - +
33E LEU 3.2 0.2 - - - -
34E THR* 1.3 71.5 - - - +
36E LYS* 1.3 63.6 + - - +
38E VAL* 3.0 18.4 + - - +
39E HIS* 3.0 11.1 + - - +
54E ILE* 4.1 10.1 - - + +
57E GLN* 3.5 25.1 - - + -
58E VAL* 3.6 27.8 - - + +
61E VAL* 3.7 12.1 - - + -
109E LEU* 3.9 29.4 - - + -
113E TYR* 3.8 8.7 - - + +
148E PHE* 4.4 7.4 - - + -
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Residues in contact with LYS 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 2.9 38.9 + - - +
32E HIS* 2.9 14.2 + - - +
33E LEU* 3.8 5.2 - - + +
35E LEU* 1.3 72.2 - - - +
37E HIS* 1.3 68.8 + - - +
39E HIS* 2.9 51.7 + - - +
40E TRP* 3.2 28.6 + - + +
55E ASP* 5.5 1.3 - - - +
58E VAL* 3.4 30.5 - - + +
62E ARG* 3.6 24.7 - - - +
----------------------------------------------------------
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Residues in contact with HIS 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO 3.5 19.5 + - - -
80A LYS* 3.5 16.5 - - + -
81A GLY* 2.8 27.6 + - - +
82A THR* 4.1 12.0 + - + +
33E LEU 2.8 19.1 + - - +
34E THR* 3.0 14.8 + - - +
36E LYS* 1.3 71.5 - - - +
38E VAL* 1.3 62.1 + - - +
40E TRP* 3.1 25.5 + - - +
41E ASN* 3.1 23.7 + - - +
95E TYR* 3.4 33.8 + + - -
96E SER 4.9 0.6 + - - -
97E VAL 3.1 22.1 + - - -
98E GLU* 5.3 5.4 - - + -
105E HIS* 5.4 0.2 - + - -
----------------------------------------------------------
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Residues in contact with VAL 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E THR 2.9 24.1 + - - +
35E LEU* 3.0 10.3 + - - +
37E HIS* 1.3 77.7 - - - +
39E HIS* 1.3 66.5 + - - +
40E TRP 2.8 2.1 + - - -
41E ASN* 2.8 13.2 + - - -
42E VAL* 3.0 36.9 + - + +
50E VAL* 4.8 0.7 - - + -
54E ILE* 3.8 13.7 - - + -
95E TYR* 3.5 31.6 - - + +
105E HIS* 3.7 22.4 - - + +
109E LEU* 4.2 17.3 - - + -
----------------------------------------------------------
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Residues in contact with HIS 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D TRP* 6.0 0.9 - - - -
35E LEU 3.0 6.5 + - - +
36E LYS* 2.9 48.8 + - - +
38E VAL* 1.3 76.4 - - - +
40E TRP* 1.3 65.3 + + + +
41E ASN 3.7 0.3 + - - -
42E VAL* 4.4 4.7 + - - +
51E HIS* 3.1 56.8 + + - +
54E ILE* 4.0 20.6 - - + +
55E ASP* 2.8 34.0 + - - -
----------------------------------------------------------
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Residues in contact with TRP 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.2 24.9 - - + -
29A ASN* 4.6 9.4 - - - -
65A ALA* 4.1 9.0 - - + -
66A ASP* 3.4 32.5 + - - +
69A ALA* 3.5 26.1 - - + +
70A GLU* 4.8 13.2 - - + -
73A ALA* 4.3 7.5 - - + +
79A PRO* 4.0 25.8 - - + -
81A GLY* 3.9 20.2 - - - -
150D TRP* 4.2 23.4 - - - -
33E LEU* 5.5 2.0 - - + -
36E LYS* 3.5 30.4 + - + +
37E HIS* 3.1 28.0 + - - +
38E VAL 2.8 5.9 + - - -
39E HIS* 1.3 84.5 - + - +
41E ASN* 1.3 62.0 + - - +
42E VAL 3.8 0.9 - - - -
99E ARG* 5.6 0.7 - - - +
----------------------------------------------------------
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Residues in contact with ASN 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 2.7 28.2 + - - +
79A PRO* 3.2 33.1 + - - +
37E HIS* 3.1 28.9 + - - +
38E VAL 2.8 2.8 + - - +
40E TRP* 1.3 85.5 + - - +
42E VAL* 1.3 65.3 + - - +
43E VAL* 3.2 12.2 + - - +
98E GLU* 3.2 22.0 - - - +
99E ARG* 3.5 9.0 - - - +
100E ASP 3.2 20.3 + - - +
105E HIS* 3.4 10.8 - - + +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D TRP* 5.6 0.5 - - - -
38E VAL* 3.0 43.0 + - + +
39E HIS* 4.4 4.8 + - - +
40E TRP 3.8 0.7 - - - -
41E ASN* 1.3 74.0 - - - +
43E VAL* 1.3 64.7 + - - +
47E PHE* 3.2 23.1 - - - +
50E VAL* 3.2 46.0 - - + -
51E HIS* 4.1 5.8 + - + -
54E ILE* 4.7 0.2 - - + -
102E VAL* 4.1 22.2 - - + -
105E HIS* 3.5 16.4 - - + -
----------------------------------------------------------
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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