Contacts of the helix formed by residues 22 - 54 (chain I) in PDB entry 1F33
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 22 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ASP 3.6 3.4 + - - -
21I VAL* 1.3 74.9 - - - +
23I ASP* 1.3 61.8 + - - +
24I SER* 3.6 10.2 - - - -
25I GLU* 3.0 32.9 + - - +
26I LYS* 2.8 25.8 + - - +
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Residues in contact with ASP 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I THR* 4.5 17.0 + - + +
14I LEU* 3.6 27.9 - - + +
21I VAL 3.4 4.3 + - - +
22I SER* 1.3 72.7 - - - +
24I SER* 1.3 62.6 + - - +
26I LYS* 3.7 7.2 + - - +
27I LYS* 2.9 28.6 + - + +
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Residues in contact with SER 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I SER* 2.9 12.0 - - - -
23I ASP* 1.3 81.6 - - - +
25I GLU* 1.3 64.9 + - - +
27I LYS* 3.5 3.1 + - - +
28I ALA* 3.1 21.1 + - - +
140I LYS* 4.3 12.7 + - - -
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Residues in contact with GLU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I VAL* 3.7 17.6 - - + +
22I SER* 3.0 18.6 + - - +
24I SER* 1.3 78.5 - - - +
26I LYS* 1.3 57.1 + - - +
28I ALA* 4.1 6.3 - - - -
29I THR* 2.6 44.0 + - - +
140I LYS* 3.1 44.8 - - + +
141I ASP* 3.4 15.9 + - - +
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Residues in contact with LYS 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 4.0 20.0 - - + -
15I LEU 5.1 2.2 + - - -
17I THR* 3.3 23.7 + - - +
19I ASN* 2.8 31.6 + - - -
20I ASP* 4.9 0.2 - - - +
21I VAL* 2.9 38.2 + - + +
22I SER 2.8 20.9 + - - +
23I ASP* 3.7 9.3 + - - +
25I GLU* 1.3 72.6 - - - +
27I LYS* 1.3 58.9 + - - +
29I THR* 3.7 2.7 - - - -
30I VAL* 2.8 37.3 + - - +
87I LEU* 3.1 35.9 - - + +
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Residues in contact with LYS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ALA 5.3 0.6 + - - -
12I THR* 2.9 40.3 + - + +
13I ASN* 5.2 2.1 - - - +
14I LEU* 4.1 19.7 - - + -
23I ASP 2.9 19.0 + - - +
24I SER* 3.8 3.1 - - - +
26I LYS* 1.3 78.3 - - - +
28I ALA* 1.3 63.5 + - - +
30I VAL* 3.2 6.3 + - - +
31I GLU* 3.0 24.7 + - - +
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Residues in contact with ALA 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I SER 3.1 15.8 + - - +
25I GLU* 3.6 4.7 - - - +
27I LYS* 1.3 78.3 - - - +
29I THR* 1.3 57.7 + - - +
31I GLU* 3.3 9.6 + - - +
32I LEU* 3.0 27.3 + - - +
140I LYS* 3.9 29.2 - - + +
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Residues in contact with THR 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I VAL* 5.7 0.2 - - - +
25I GLU* 2.6 30.3 + - - +
26I LYS 3.7 0.2 - - - -
28I ALA* 1.3 69.4 - - - +
30I VAL* 1.3 67.1 + - - +
32I LEU* 3.0 8.3 + - - +
33I LEU* 2.8 32.5 + - + +
87I LEU* 3.3 25.9 - - + +
140I LYS* 5.3 4.2 + - - +
141I ASP* 3.8 17.7 + - - +
144I THR* 3.1 35.7 - - + +
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Residues in contact with VAL 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 4.9 2.9 - - + -
26I LYS 2.8 30.9 + - - +
27I LYS* 3.5 6.3 - - - +
29I THR* 1.3 72.1 - - - +
31I GLU* 1.3 59.4 + - - +
33I LEU* 3.5 1.9 + - - +
34I ASN* 3.0 47.0 + - - +
84I ALA* 3.6 33.2 - - + +
87I LEU* 4.2 10.1 - - + +
89I GLY* 3.7 28.3 - - - +
90I VAL 4.2 2.7 - - - +
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Residues in contact with GLU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LYS 3.0 12.9 + - - +
28I ALA* 3.4 12.3 - - - +
30I VAL* 1.3 76.6 - - - +
32I LEU* 1.3 65.6 + - - +
34I ASN* 3.5 4.8 + - - +
35I ARG* 3.1 27.7 + - - +
101I LYS* 6.4 0.2 - - - +
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Residues in contact with LEU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ALA 3.0 12.4 + - - +
29I THR* 3.0 11.8 + - - +
31I GLU* 1.3 76.6 - - - +
33I LEU* 1.3 63.6 + - + +
35I ARG* 3.2 49.5 - - - +
36I GLN* 3.2 10.7 + - + +
135I ALA* 3.9 32.8 - - + +
138I GLU* 3.6 20.0 - - + +
139I ALA* 4.0 23.8 - - + +
144I THR* 5.0 5.4 - - + -
148I LEU* 4.3 9.6 - - + -
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Residues in contact with LEU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I THR* 2.8 30.2 + - + +
30I VAL 3.8 2.9 - - - +
32I LEU* 1.3 71.8 - - - +
34I ASN* 1.3 61.6 + - - +
35I ARG 3.0 1.3 - - - -
36I GLN* 2.8 23.8 + - - +
37I VAL* 2.8 16.9 + - + +
80I MET* 3.6 33.4 - - + +
83I ARG* 3.5 20.6 - - + -
84I ALA* 3.4 37.0 - - + +
144I THR* 3.6 26.2 - - + -
147I ILE* 5.2 2.7 - - + -
148I LEU* 4.6 9.6 - - + -
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Residues in contact with ASN 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I VAL* 3.0 38.5 + - - +
31I GLU* 4.0 5.1 - - - +
33I LEU* 1.3 76.2 - - - +
35I ARG* 1.3 62.4 + - - +
37I VAL* 3.6 8.7 - - - +
38I ILE* 3.1 33.8 + - + +
84I ALA* 4.5 4.4 - - - +
90I VAL 2.9 21.5 + - - -
91I ALA* 3.3 5.8 - - - +
92I LEU* 2.6 50.5 + - + +
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Residues in contact with ARG 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLU* 3.1 18.0 + - - +
32I LEU* 3.2 37.8 - - - +
33I LEU 3.0 0.4 - - - -
34I ASN* 1.3 78.1 - - - +
36I GLN* 1.3 69.1 + - - +
38I ILE* 3.7 8.6 + - - +
39I GLN* 3.4 23.4 + - - +
101I LYS* 5.7 11.4 - - - +
103I PRO* 5.7 1.2 - - - +
131I ASP* 2.9 39.8 + - - -
135I ALA* 4.3 4.4 - - - +
138I GLU* 3.8 14.3 + - - -
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Residues in contact with GLN 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LEU* 3.5 15.9 - - + +
33I LEU* 2.8 8.7 + - - +
35I ARG* 1.3 84.6 + - - +
37I VAL* 1.3 58.9 + - - +
39I GLN* 2.9 26.6 + - - +
40I PHE* 2.8 54.5 + - - -
80I MET* 3.6 19.7 - - + -
131I ASP* 3.7 14.0 - - - +
132I VAL* 3.7 16.7 - - - +
135I ALA* 3.6 20.3 - - - +
148I LEU* 4.0 18.2 - - + -
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Residues in contact with VAL 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 2.8 19.9 + - + +
34I ASN* 3.3 14.8 + - - +
36I GLN* 1.3 76.9 - - - +
38I ILE* 1.3 57.3 + - - +
40I PHE* 3.3 2.4 + - - +
41I ILE* 2.8 53.0 + - + +
77I LEU* 4.0 14.1 - - + +
80I MET* 4.0 14.4 - - + -
81I ALA* 3.8 31.4 - - + +
84I ALA* 6.2 0.4 - - + -
91I ALA* 5.8 0.2 - - + -
92I LEU 3.6 21.3 - - - +
52J TRP* 4.5 7.4 - - + -
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Residues in contact with ILE 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ASN* 3.1 21.0 + - + +
35I ARG* 3.9 7.2 - - - +
37I VAL* 1.3 75.0 - - - +
39I GLN* 1.3 63.1 + - - +
41I ILE 3.5 0.2 + - - -
42I ASP* 3.1 23.7 + - - +
92I LEU* 4.0 16.8 - - + +
97I VAL* 3.6 23.8 - - + -
98I ILE* 3.5 42.5 - - + +
101I LYS* 3.8 28.5 - - + +
102I THR* 4.0 22.7 - - - +
103I PRO* 5.0 1.1 - - + -
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Residues in contact with GLN 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I ARG* 3.4 12.0 + - - +
36I GLN* 2.9 36.4 + - - +
38I ILE* 1.3 79.9 - - - +
40I PHE* 1.3 57.2 + - + +
42I ASP* 3.4 4.7 + - - +
43I LEU* 2.9 28.5 + - - +
102I THR* 5.3 0.2 - - - -
103I PRO* 3.4 39.4 - - + +
104I LEU* 4.0 3.6 - - + +
127I ILE* 4.3 6.5 + - - +
128I VAL* 3.4 37.7 - - + +
131I ASP* 3.0 35.2 + - - +
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Residues in contact with PHE 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I GLN* 2.8 54.2 + - - +
37I VAL 3.8 2.5 - - - +
39I GLN* 1.3 71.0 - - - +
41I ILE* 1.3 67.1 + - - +
43I LEU* 3.2 7.7 + - + +
44I SER* 2.9 24.4 + - - -
73I LEU* 3.9 31.4 - - + +
76I HIS* 4.0 15.9 - + + -
77I LEU* 4.1 16.1 - - + +
80I MET* 3.6 22.4 - - + -
128I VAL* 3.7 16.6 - - + -
132I VAL* 4.3 9.4 - - + -
151I ALA* 3.9 14.4 - - + -
155I LEU* 3.3 34.1 - - + -
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Residues in contact with ILE 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 2.8 41.8 + - + +
38I ILE 3.9 3.4 - - - +
40I PHE* 1.3 71.8 - - - +
42I ASP* 1.3 62.9 + - - +
44I SER* 2.7 22.7 + - - +
45I LEU* 3.1 16.5 + - + +
77I LEU* 3.3 25.4 - - + -
93I GLY* 3.7 28.0 - - - +
98I ILE* 4.0 15.7 - - + -
45J LEU* 3.5 29.8 - - + -
52J TRP* 4.3 11.2 - - + -
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Residues in contact with ASP 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ILE 3.1 18.1 + - - +
39I GLN 3.8 3.8 - - - +
41I ILE* 1.3 78.0 - - - +
43I LEU* 1.3 57.1 + - - +
45I LEU* 3.2 5.9 + - - +
46I ILE* 2.9 43.1 + - - +
98I ILE* 3.8 9.4 - - + +
102I THR* 2.7 30.7 + - - +
104I LEU* 3.4 19.8 - - + +
95J THR* 2.9 37.6 + - - +
96J GLN* 4.8 1.6 - - - +
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Residues in contact with LEU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I GLN 2.9 18.0 + - - +
40I PHE* 3.7 6.7 - - + +
42I ASP* 1.3 75.5 - - - +
44I SER* 1.3 54.7 + - - +
46I ILE* 3.3 8.0 + - + +
47I THR* 2.7 37.0 + - - -
73I LEU* 4.1 11.0 - - + -
104I LEU* 3.9 11.4 - - + +
124I ARG* 3.8 26.0 - - + +
125I TYR* 3.5 49.4 - - + +
128I VAL* 4.0 12.3 - - + -
155I LEU* 3.8 28.9 - - + -
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Residues in contact with SER 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I PHE 2.9 13.2 + - - -
41I ILE* 2.7 25.2 + - - +
43I LEU* 1.3 78.4 - - - +
45I LEU* 1.3 65.2 + - - +
47I THR* 3.2 5.3 + - - -
48I LYS* 3.2 24.1 + - - +
70I ARG* 4.1 16.5 - - - +
73I LEU* 3.9 26.6 - - - +
74I ILE* 4.6 13.5 - - - +
77I LEU* 4.7 2.3 - - - +
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Residues in contact with LEU 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ILE* 3.1 23.8 + - + +
42I ASP* 3.2 11.4 + - - +
44I SER* 1.3 84.1 + - - +
46I ILE* 1.3 63.4 + - + +
48I LYS* 3.2 8.8 + - + +
49I GLN* 3.1 22.2 + - - +
52I TRP* 5.3 0.5 - - - -
98I ILE* 5.2 2.2 - - + -
41J ILE* 3.6 31.4 - - + -
45J LEU* 4.6 19.3 - - + -
93J GLY 3.8 17.3 - - - +
94J THR* 5.0 0.7 - - - -
95J THR* 4.1 33.9 - - - +
98J ILE* 5.2 1.6 - - + -
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Residues in contact with ILE 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I ASP* 2.9 41.5 + - - +
43I LEU* 3.6 6.5 - - + +
45I LEU* 1.3 74.8 - - + +
47I THR* 1.3 66.2 + - - +
49I GLN* 3.0 18.5 + - - +
50I ALA* 3.1 12.6 + - - +
104I LEU* 3.7 23.8 - - + -
105I LYS 4.8 2.2 - - - +
107I TYR* 3.4 41.5 - - + +
121I LEU* 3.9 11.2 - - + -
124I ARG* 4.1 23.3 - - + +
94J THR* 5.2 6.3 - - + -
96J GLN* 5.8 2.5 - - - +
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Residues in contact with THR 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU 2.7 23.5 + - - -
44I SER* 3.2 11.4 + - - -
46I ILE* 1.3 76.7 - - - +
48I LYS* 1.3 59.3 + - + +
50I ALA* 3.5 2.6 + - - +
51I HIS* 2.9 28.9 + - + +
66I LEU* 3.3 44.9 - - + +
69I PHE* 4.5 1.3 - - + -
70I ARG* 4.5 8.3 - - + +
73I LEU* 3.8 3.5 - - - +
121I LEU* 4.2 9.9 - - - -
125I TYR* 2.6 32.2 + - - +
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Residues in contact with LYS 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I SER 3.2 10.0 + - - +
45I LEU* 3.6 9.9 - - + +
46I ILE 3.1 0.2 - - - -
47I THR* 1.3 78.6 - - + +
49I GLN* 1.3 59.1 + - - +
51I HIS* 3.1 34.8 + - + +
52I TRP* 2.8 63.5 + - + +
67I ASP* 2.8 22.2 + - - +
70I ARG* 2.9 49.1 - - + +
78J ASP* 2.7 26.0 + - - +
82J GLU* 5.4 0.8 + - - -
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Residues in contact with GLN 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I LEU 3.1 8.5 + - - +
46I ILE* 3.0 13.4 + - - +
48I LYS* 1.3 79.6 - - - +
50I ALA* 1.3 63.5 + - - +
52I TRP* 4.0 5.1 - - - -
53I ASN* 3.0 48.2 + - - +
107I TYR* 4.2 17.0 - - + -
108I PRO 4.4 3.4 + - - -
109I LEU* 4.0 19.5 - - - +
117I HIS* 4.6 1.4 - - - -
90J VAL* 5.2 0.6 - - - +
91J ALA 2.5 24.8 + - - +
92J LEU* 3.1 3.8 - - - -
93J GLY 2.9 19.9 + - - +
94J THR* 3.3 36.6 - - + +
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Residues in contact with ALA 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ILE 3.1 2.7 + - - +
47I THR 3.8 3.1 - - - +
49I GLN* 1.3 78.7 - - - +
51I HIS* 1.3 64.1 + - - +
53I ASN 3.4 1.9 + - - -
54I MET* 3.2 31.7 + - + +
107I TYR* 3.4 23.5 - - - +
117I HIS* 3.5 17.8 + - + +
121I LEU* 3.6 35.2 - - + -
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Residues in contact with HIS 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I THR* 2.9 21.4 + - + +
48I LYS* 3.1 42.4 + - + +
50I ALA* 1.3 77.6 - - - +
52I TRP* 1.3 82.1 + + - +
54I MET* 3.5 9.7 + - - +
59I PHE* 4.6 0.7 - - - -
63I HIS* 2.7 82.7 + + - -
64I GLU* 5.0 0.2 - - - -
66I LEU* 3.9 17.4 - - + +
67I ASP* 3.9 20.5 + - + +
82J GLU* 4.6 5.3 + - - -
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Residues in contact with TRP 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I LEU 5.3 0.4 - - - -
48I LYS* 2.8 49.8 + - + +
49I GLN* 4.0 8.5 - - - +
51I HIS* 1.3 94.4 - + - +
53I ASN* 1.3 61.7 + - - +
54I MET 3.5 2.1 + - - +
63I HIS* 4.7 2.9 - + - -
37J VAL* 4.5 3.4 - - + -
41J ILE* 4.3 10.8 - - + -
77J LEU* 3.4 21.5 - - + -
78J ASP* 3.2 35.1 + - - +
81J ALA* 3.3 26.3 - - + +
82J GLU* 4.2 16.1 - - + +
85J VAL* 3.4 25.6 - - + +
91J ALA* 3.8 27.8 - - + -
93J GLY* 4.2 23.6 - - - -
160L TRP* 3.8 10.5 - - - -
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Residues in contact with ASN 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I GLN* 3.0 36.2 + - - +
52I TRP* 1.3 79.1 - - - +
54I MET* 1.3 59.9 + - - +
55I ARG* 4.7 3.2 - - - +
111I ILE 4.6 1.1 - - - +
112I HIS* 3.0 34.8 + - + +
117I HIS* 3.4 17.8 + - + +
85J VAL* 3.3 15.7 - - - +
89J GLY 4.3 0.9 - - - +
90J VAL* 3.4 14.5 - - + +
91J ALA* 2.9 49.5 + - - +
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Residues in contact with MET 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I ALA* 3.2 16.9 + - + +
51I HIS 3.5 11.0 - - - +
52I TRP 3.5 2.9 - - - +
53I ASN* 1.3 77.9 - - - +
55I ARG* 1.3 69.5 + - - +
59I PHE* 3.3 33.9 - - + +
62I VAL* 3.5 28.7 - - + -
63I HIS* 4.1 14.8 - - - -
66I LEU* 3.4 28.3 - - + -
112I HIS 3.2 6.5 - - - +
114I VAL* 4.4 16.4 - - + +
117I HIS* 3.6 29.4 - - + -
118I LEU* 5.0 0.9 - - + -
121I LEU* 4.7 1.8 - - + -
85J VAL* 6.0 0.3 - - - +
160L TRP* 5.1 1.4 + - - -
164L SER* 4.4 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