Contacts of the helix formed by residues 22 - 54 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ASP 3.6 2.8 + - - -
21G VAL* 1.3 76.3 - - - +
23G ASP* 1.3 61.1 + - - +
24G SER* 3.6 11.0 - - - -
25G GLU* 3.0 32.8 + - - +
26G LYS* 2.8 25.8 + - - +
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Residues in contact with ASP 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 3.6 29.2 - - + +
21G VAL 4.2 3.4 - - - +
22G SER* 1.3 73.0 - - - +
24G SER* 1.3 63.4 + - - +
26G LYS* 4.0 5.0 + - - +
27G LYS* 3.0 32.0 + - + +
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Residues in contact with SER 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G SER* 2.9 12.0 - - - -
23G ASP* 1.3 80.0 - - - +
25G GLU* 1.3 64.6 + - - +
27G LYS* 3.5 2.5 + - - +
28G ALA* 3.1 21.9 + - - +
140G LYS* 4.2 12.3 + - - -
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Residues in contact with GLU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G VAL* 3.7 18.4 - - + +
22G SER* 3.0 19.0 + - - +
24G SER* 1.3 79.0 - - - +
26G LYS* 1.3 57.5 + - - +
28G ALA* 4.1 6.1 - - - -
29G THR* 2.6 43.8 + - - +
140G LYS* 3.2 44.6 - - + +
141G ASP* 3.5 15.8 + - + +
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Residues in contact with LYS 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 3.5 27.7 - - + +
15G LEU 5.2 2.4 + - - -
17G THR* 3.3 24.2 + - - +
19G ASN* 2.8 31.0 + - - -
20G ASP* 4.9 0.2 - - - +
21G VAL* 2.9 36.0 + - + +
22G SER 2.8 20.2 + - - +
23G ASP* 4.3 5.2 + - - -
25G GLU* 1.3 72.3 - - - +
27G LYS* 1.3 58.9 + - - +
29G THR* 3.7 2.3 - - - -
30G VAL* 2.8 36.8 + - - +
87G LEU* 3.1 34.8 - - + +
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Residues in contact with LYS 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G THR* 2.6 51.5 + - + +
13G ASN* 3.6 12.7 + - - +
14G LEU* 3.4 41.1 - - + +
23G ASP* 3.0 19.1 + - + +
24G SER 4.1 2.0 - - - +
26G LYS* 1.3 76.3 - - - +
28G ALA* 1.3 61.2 + - - +
30G VAL* 4.0 6.9 - - - +
31G GLU* 3.2 24.8 + - - +
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Residues in contact with ALA 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G SER 3.1 18.1 + - - +
25G GLU* 3.6 4.3 - - - +
27G LYS* 1.3 76.2 - - - +
29G THR* 1.3 59.1 + - - +
31G GLU* 3.3 9.5 + - - +
32G LEU* 3.0 27.1 + - - +
140G LYS* 3.8 30.1 - - + +
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Residues in contact with THR 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G VAL* 5.7 0.2 - - - +
25G GLU* 2.6 30.0 + - - +
28G ALA* 1.3 71.6 - - - +
30G VAL* 1.3 59.6 + - - +
32G LEU* 3.1 8.6 + - + +
33G LEU* 2.8 38.9 + - + +
87G LEU* 3.3 25.5 - - + +
140G LYS* 5.3 4.7 + - - +
141G ASP* 3.8 18.1 + - - +
144G THR* 3.2 35.4 - - + +
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Residues in contact with VAL 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 4.6 2.9 - - + -
26G LYS 2.8 31.6 + - - +
27G LYS* 4.0 7.6 - - - +
29G THR* 1.3 73.6 - - - +
31G GLU* 1.3 57.2 + - - +
33G LEU* 3.9 0.7 - - - +
34G ASN* 3.0 46.5 + - - +
84G ALA* 3.6 32.5 - - + +
87G LEU* 4.1 10.8 - - + +
89G GLY* 3.7 28.3 - - - +
90G VAL 4.2 2.9 - - - +
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Residues in contact with GLU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LYS 3.2 16.9 + - - +
28G ALA* 3.4 7.6 - - - +
29G THR 3.1 0.4 - - - -
30G VAL* 1.3 79.4 - - - +
32G LEU* 1.3 64.2 + - - +
34G ASN* 4.0 4.7 - - - +
35G ARG* 3.1 28.3 + - - +
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Residues in contact with LEU 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ALA 3.0 12.8 + - - +
29G THR* 3.5 10.8 - - - +
31G GLU* 1.3 76.9 - - - +
33G LEU* 1.3 63.0 + - + +
35G ARG* 3.3 40.3 + - - +
36G GLN* 3.2 20.0 + - + +
135G ALA* 3.9 33.0 - - + +
138G GLU* 3.6 19.5 - - + +
139G ALA* 4.0 23.3 - - + +
144G THR* 5.1 4.9 - - + -
148G LEU* 4.3 10.8 - - + -
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Residues in contact with LEU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G THR* 2.8 32.3 + - + +
30G VAL 3.9 3.4 - - - +
32G LEU* 1.3 73.7 - - - +
34G ASN* 1.3 61.0 + - - +
35G ARG 3.0 1.3 - - - -
36G GLN* 2.8 10.2 + - - +
37G VAL* 2.8 30.6 + - - +
80G MET* 3.6 34.5 - - + +
83G ARG* 3.5 20.2 - - + -
84G ALA* 3.4 37.0 - - + +
144G THR* 3.5 22.7 - - + -
147G ILE* 5.2 2.7 - - + -
148G LEU* 4.6 10.8 - - + -
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Residues in contact with ASN 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G VAL* 3.0 37.7 + - - +
31G GLU* 4.0 4.9 - - - +
33G LEU* 1.3 76.7 - - - +
35G ARG* 1.3 62.1 + - - +
37G VAL* 3.7 9.0 - - - +
38G ILE* 3.1 33.9 + - + +
84G ALA* 4.5 4.8 - - - +
90G VAL 3.0 21.9 + - - -
91G ALA* 3.3 5.8 - - - +
92G LEU* 2.6 50.3 + - + +
101G LYS* 6.2 0.7 - - - +
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Residues in contact with ARG 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G GLU* 3.1 17.6 + - - +
32G LEU* 3.3 38.0 - - - +
33G LEU 3.0 0.6 - - - -
34G ASN* 1.3 79.6 - - - +
36G GLN* 1.3 68.1 + - - +
38G ILE* 3.7 9.0 + - - +
39G GLN* 3.4 23.9 + - - +
103G PRO* 5.7 1.2 - - - +
131G ASP* 2.8 41.0 + - - -
135G ALA* 4.3 4.0 - - - +
138G GLU* 3.9 14.1 + - - -
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Residues in contact with GLN 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 3.5 16.8 - - + +
33G LEU* 2.8 8.5 + - - +
35G ARG* 1.3 83.8 + - - +
37G VAL* 1.3 64.9 + - - +
39G GLN* 2.8 28.0 + - - +
40G PHE* 2.8 46.6 + - - -
80G MET* 3.7 19.5 - - + -
131G ASP* 3.7 9.2 - - - +
132G VAL* 3.6 20.2 - - - +
135G ALA* 3.5 22.0 - - - +
148G LEU* 3.9 17.7 - - + -
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Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU* 2.8 23.0 + - + +
34G ASN* 3.7 15.0 - - - +
36G GLN* 1.3 73.0 - - - +
38G ILE* 1.3 57.9 + - - +
40G PHE* 3.3 1.8 + - - +
41G ILE* 2.8 53.6 + - + +
77G LEU* 4.0 17.5 - - + +
80G MET* 4.0 11.9 - - + -
81G ALA* 3.8 31.9 - - + +
92G LEU 3.6 20.6 - - - +
52H TRP* 4.6 7.2 - - + -
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Residues in contact with ILE 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ASN* 3.1 19.7 + - + +
35G ARG* 3.9 8.5 - - - +
37G VAL* 1.3 75.4 - - - +
39G GLN* 1.3 63.7 + - - +
42G ASP* 3.1 23.4 + - - +
92G LEU* 4.0 14.8 - - + +
97G VAL* 3.6 12.1 - - + -
98G ILE* 3.4 40.8 - - + +
101G LYS* 3.4 39.0 - - + +
102G THR* 4.0 23.3 - - - +
103G PRO* 5.0 1.3 - - + -
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Residues in contact with GLN 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ARG* 3.4 10.3 + - - +
36G GLN* 2.8 37.5 + - - +
38G ILE* 1.3 80.3 - - - +
40G PHE* 1.3 56.1 + - + +
42G ASP* 3.4 5.2 + - - +
43G LEU* 2.9 29.5 + - - +
103G PRO* 3.4 37.7 - - + +
104G LEU* 4.0 3.8 - - + +
127G ILE* 4.3 6.5 - - - +
128G VAL* 3.4 37.7 - - + +
131G ASP* 3.0 34.7 + - - +
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Residues in contact with PHE 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G GLN* 2.8 46.6 + - - +
37G VAL 3.8 2.7 - - - +
39G GLN* 1.3 69.4 - - - +
41G ILE* 1.3 67.3 + - - +
43G LEU* 3.1 6.8 + - + +
44G SER* 2.8 25.5 + - - -
73G LEU* 3.8 29.7 - - + +
76G HIS* 4.0 14.8 - - + -
77G LEU* 4.0 15.5 - - + -
80G MET* 3.7 21.3 - - + -
128G VAL* 3.6 19.1 - - + -
132G VAL* 4.3 8.3 - - + -
151G ALA* 4.0 13.9 - - + -
155G LEU* 3.2 35.2 - - + -
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Residues in contact with ILE 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G VAL* 2.8 35.5 + - + +
38G ILE 3.9 3.8 - - - +
40G PHE* 1.3 75.1 - - - +
42G ASP* 1.3 62.3 + - - +
44G SER* 2.6 21.6 + - - +
45G LEU* 3.0 17.9 + - + +
77G LEU* 3.3 26.0 - - + -
93G GLY* 3.6 33.2 - - - +
98G ILE* 3.9 17.7 - - + -
45H LEU* 3.6 29.2 - - + -
52H TRP* 4.3 11.7 - - + -
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Residues in contact with ASP 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ILE 3.1 18.1 + - - +
39G GLN 3.8 3.8 - - - +
41G ILE* 1.3 80.0 - - - +
43G LEU* 1.3 56.7 + - - +
45G LEU* 3.2 6.3 + - - +
46G ILE* 2.9 43.3 + - - +
98G ILE* 3.8 9.6 - - + +
102G THR* 2.6 31.1 + - - +
104G LEU* 3.4 20.1 - - + +
95H THR* 3.1 36.0 + - - +
96H GLN* 4.8 1.6 - - - +
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G GLN 2.9 17.6 + - - +
40G PHE* 3.1 5.6 + - - +
42G ASP* 1.3 77.5 - - - +
44G SER* 1.3 52.5 + - - +
46G ILE* 3.3 7.4 + - + +
47G THR* 2.7 37.3 + - - -
73G LEU* 4.0 11.0 - - + -
104G LEU* 3.9 10.9 - - + +
124G ARG* 3.8 28.7 - - + +
125G TYR* 3.5 46.0 - - + -
128G VAL* 4.0 12.1 - - + -
155G LEU* 3.8 28.7 - - + -
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Residues in contact with SER 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G PHE 2.8 13.3 + - - -
41G ILE* 2.6 26.0 + - - +
43G LEU* 1.3 74.7 - - - +
45G LEU* 1.3 68.9 + - - +
47G THR* 3.2 6.2 + - - -
48G LYS* 3.2 24.1 + - - +
70G ARG* 4.1 16.3 - - - +
73G LEU* 3.9 25.7 - - - +
74G ILE* 4.6 11.7 - - - +
77G LEU* 4.7 3.8 - - - +
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ILE* 3.0 25.7 + - + +
42G ASP* 3.5 11.7 - - - +
44G SER* 1.3 84.8 + - - +
46G ILE* 1.3 63.1 + - + +
48G LYS* 3.2 9.1 + - - +
49G GLN* 3.1 21.6 + - - +
52G TRP* 5.3 0.9 - - - -
98G ILE* 5.2 2.2 - - + -
41H ILE* 3.7 30.5 - - + -
45H LEU* 4.7 18.6 - - + -
93H GLY 3.9 17.5 - - - +
94H THR* 5.0 1.1 - - - -
95H THR* 4.1 33.2 - - - +
98H ILE* 5.3 1.3 - - + -
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Residues in contact with ILE 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ASP* 2.9 34.1 + - - +
43G LEU* 3.5 7.4 - - + +
45G LEU* 1.3 74.5 - - + +
47G THR* 1.3 66.2 + - - +
49G GLN* 3.0 9.8 + - - +
50G ALA* 3.0 21.8 + - - +
104G LEU* 3.8 29.2 - - + -
105G LYS 4.8 2.5 - - - +
107G TYR* 3.4 42.4 - - + +
121G LEU* 3.8 11.2 - - + -
124G ARG* 4.1 25.1 - - + +
94H THR* 5.2 5.6 - - + -
96H GLN* 5.9 2.7 - - - +
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Residues in contact with THR 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU 2.7 23.2 + - - -
44G SER* 3.4 11.4 - - - -
46G ILE* 1.3 76.0 - - - +
48G LYS* 1.3 58.6 + - + +
50G ALA* 3.5 2.6 + - - +
51G HIS* 2.9 28.8 + - + +
66G LEU* 3.3 44.2 - - + +
70G ARG* 4.5 9.9 - - + +
73G LEU* 3.8 3.0 - - - +
121G LEU* 4.3 9.6 - - - -
125G TYR* 2.6 32.7 + - + +
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Residues in contact with LYS 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G SER 3.2 9.0 + - - +
45G LEU* 3.2 10.8 + - + +
46G ILE 3.2 0.4 - - - -
47G THR* 1.3 79.3 - - + +
49G GLN* 1.3 56.3 + - - +
51G HIS* 3.1 34.4 + - + +
52G TRP* 2.8 69.3 + - + +
67G ASP* 2.8 23.8 + - - +
70G ARG* 2.9 47.8 - - + +
78H ASP* 2.8 23.4 + - - +
82H GLU* 5.4 1.4 + - - -
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Residues in contact with GLN 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LEU 3.1 9.6 + - - +
46G ILE* 3.0 12.7 + - - +
48G LYS* 1.3 78.3 - - - +
50G ALA* 1.3 62.3 + - - +
52G TRP* 4.0 6.0 - - - -
53G ASN* 2.9 49.3 + - - +
107G TYR* 4.2 16.4 - - + -
108G PRO 4.4 3.4 + - - -
109G LEU* 4.0 19.9 - - - +
117G HIS* 5.4 1.0 - - - -
90H VAL* 5.2 0.6 - - - +
91H ALA 2.6 24.6 + - - +
92H LEU* 3.2 3.3 - - - -
93H GLY* 3.0 19.8 + - - +
94H THR* 3.3 36.1 - - + +
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Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ILE 3.0 4.2 + - - +
47G THR 3.8 1.3 - - - +
49G GLN* 1.3 76.3 - - - +
51G HIS* 1.3 65.8 + - - +
53G ASN 3.3 1.6 + - - -
54G MET* 3.2 32.6 + - + +
107G TYR* 3.3 23.7 - - - +
117G HIS* 3.4 17.8 - - + +
121G LEU* 3.6 35.7 - - + -
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Residues in contact with HIS 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G THR* 2.9 20.8 + - + +
48G LYS* 3.1 37.8 + - + +
50G ALA* 1.3 78.0 - - - +
52G TRP* 1.3 80.3 + + - +
54G MET* 3.5 10.4 - - - +
59G PHE* 4.6 0.9 - - - -
63G HIS* 2.7 82.7 + + - -
64G GLU* 5.0 0.2 - - - -
66G LEU* 4.0 17.0 - - + +
67G ASP* 3.9 20.7 + - + -
82H GLU* 4.6 5.5 + - - -
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Residues in contact with TRP 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LEU 5.3 0.4 - - - -
48G LYS* 2.8 53.4 + - + +
49G GLN* 4.0 7.6 - - - -
51G HIS* 1.3 94.3 - + - +
53G ASN* 1.3 61.3 + - - +
54G MET 3.6 3.2 + - - +
59G PHE* 5.5 1.9 - - - -
63G HIS* 4.7 4.5 - + - -
37H VAL* 4.6 1.8 - - + -
41H ILE* 4.4 10.3 - - + -
77H LEU* 3.5 21.1 - - + -
78H ASP* 3.2 32.8 + - - +
81H ALA* 3.4 25.7 - - + +
82H GLU* 4.2 16.8 - - + +
85H VAL* 3.5 25.1 - - + +
91H ALA* 3.8 28.9 - - + -
92H LEU 4.9 0.9 - - - -
93H GLY* 4.2 23.8 - - - -
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Residues in contact with ASN 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLN* 2.9 34.3 + - - +
50G ALA 3.3 2.6 + - - -
52G TRP* 1.3 81.5 - - - +
54G MET* 1.3 61.7 + - - +
55G ARG* 4.7 3.1 - - - +
111G ILE 4.6 1.3 - - - +
112G HIS* 3.0 32.8 + - + +
117G HIS* 3.4 17.9 + - + +
85H VAL* 3.4 15.2 - - - +
89H GLY 4.3 0.7 - - - +
90H VAL* 3.5 15.8 - - + +
91H ALA 3.0 44.9 + - - +
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Residues in contact with MET 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ALA* 3.2 17.2 + - + +
51G HIS 3.5 11.2 - - - +
52G TRP 3.6 2.9 - - - +
53G ASN* 1.3 79.1 - - - +
55G ARG* 1.3 68.2 + - - +
59G PHE* 3.2 34.0 - - + +
62G VAL* 3.4 28.5 - - + -
63G HIS* 4.1 13.9 - - - -
66G LEU* 3.3 28.9 - - + -
112G HIS 3.2 5.8 - - - +
114G VAL* 4.4 15.9 - - + +
117G HIS* 3.7 30.1 - - + -
118G LEU* 5.0 0.7 - - + -
121G LEU* 4.7 2.0 - - + -
----------------------------------------------------------
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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