Contacts of the helix formed by residues 41 - 65 (chain B) in PDB entry 5DYE
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 THR 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 4.6 5.8 - - - +
40B PRO* 1.3 77.3 - - - +
42B ILE* 1.3 66.0 + - - +
43B LEU* 4.1 4.2 + - - +
44B GLN* 3.2 30.0 + - - +
45B ILE* 3.2 23.0 + - - +
41C THR* 6.2 4.3 - - - -
41D THR* 6.0 7.9 - - + -
43D LEU* 5.2 4.7 - - - +
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO 5.3 1.8 - - - +
41B THR* 1.3 75.3 - - - +
43B LEU* 1.3 65.8 + - - +
45B ILE* 3.2 12.7 + - + +
46B ALA* 3.1 22.0 + - - +
173B HIS 5.1 0.4 - - - +
174B LEU* 4.8 10.1 - - + +
177B ILE* 4.0 38.7 - - + +
178B TYR* 4.1 20.9 - - + +
37C SER* 6.4 0.4 - - - -
38C ALA* 4.6 17.0 - - + -
44C GLN* 3.2 33.8 + - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 4.1 4.6 + - - +
42B ILE* 1.3 77.3 - - - +
44B GLN* 1.3 62.1 + - - +
46B ALA* 3.6 1.6 + - + +
47B LEU* 3.1 40.4 + - + +
170B THR* 5.4 1.3 - - + -
174B LEU* 4.1 25.1 - - + -
41C THR* 4.9 3.1 - - + +
43C LEU* 3.4 41.7 - - + -
44C GLN* 3.9 26.6 + - + +
47C LEU* 3.5 26.0 - - + -
43D LEU* 3.7 19.1 - - + -
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 3.7 10.0 + - - +
39B LEU 4.7 0.5 - - - +
40B PRO* 3.6 20.4 - - - +
41B THR* 3.2 35.1 + - - +
42B ILE 3.2 0.2 - - - -
43B LEU* 1.3 79.3 - - - +
45B ILE* 1.3 57.3 + - - +
47B LEU* 3.5 0.7 + - - +
48B ALA* 2.9 29.8 + - + +
42D ILE* 3.4 29.7 - - + +
43D LEU* 4.2 19.0 + - + +
174D LEU* 3.8 29.4 + - + +
178D TYR* 3.0 26.0 + - - -
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 4.1 4.0 - - - +
32B ALA* 3.6 36.6 - - + -
40B PRO* 3.8 26.2 - - + +
41B THR 3.2 18.8 + - - +
42B ILE* 3.2 17.5 + - + +
44B GLN* 1.3 72.8 - - - +
46B ALA* 1.3 66.3 + - - +
48B ALA* 3.7 5.1 - - - +
49B PHE* 3.1 42.4 + - + +
173B HIS* 4.7 0.4 - - - +
177B ILE* 4.0 20.4 - - + -
181B GLY 6.0 0.4 - - - +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE 3.1 15.5 + - - +
43B LEU* 3.8 4.9 - - + +
44B GLN 3.4 0.2 - - - -
45B ILE* 1.3 77.5 - - - +
47B LEU* 1.3 57.5 + - - +
49B PHE* 4.1 1.2 - - - +
50B GLY* 2.9 24.8 + - - -
170B THR* 3.5 40.1 + - + +
173B HIS* 3.7 19.2 - - + +
174B LEU* 4.0 17.7 - - + +
177B ILE* 4.3 1.7 - - + +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.1 36.3 + - + +
44B GLN 3.8 3.8 - - - +
46B ALA* 1.3 73.0 - - - +
48B ALA* 1.3 61.5 + - - +
51B LEU* 3.1 47.8 + - + +
167B LEU* 4.8 11.2 - - + -
170B THR* 3.7 22.9 - - + +
47C LEU* 5.0 8.3 - - + -
51C LEU* 5.6 1.1 - - + -
43D LEU* 3.5 37.2 - - + -
47D LEU* 5.3 7.0 - - + -
174D LEU* 4.2 5.2 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE 4.5 5.5 - - - +
31B SER* 3.1 38.1 - - - +
44B GLN 2.9 17.9 + - - +
45B ILE 3.7 2.5 - - - +
46B ALA 3.3 0.2 - - - -
47B LEU* 1.3 74.2 - - - +
49B PHE* 1.3 65.9 + - - +
52B ALA* 3.3 12.0 + - - +
171D LEU* 3.3 26.1 - - + +
174D LEU* 3.8 18.3 - - + +
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.5 39.0 - + - -
25B VAL* 6.1 0.4 - - - -
28B GLY* 3.0 48.0 - - - -
29B LEU* 3.9 7.4 - - + -
31B SER* 4.7 0.2 - - - -
32B ALA* 4.8 4.7 - - + -
45B ILE* 3.1 32.9 + - + +
48B ALA* 1.3 78.2 - - - +
50B GLY* 1.3 63.2 + - - +
52B ALA* 3.6 5.8 + - - +
53B ILE 3.7 1.2 + - - -
169B VAL* 3.8 5.7 - - + +
173B HIS* 3.3 41.5 - + + +
181B GLY 5.3 1.1 - - - -
188B ARG* 3.6 50.0 - - + -
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Residues in contact with GLY 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 2.9 12.1 + - - -
49B PHE* 1.3 77.8 - - - +
51B LEU* 1.3 57.2 + - - +
53B ILE* 3.2 6.1 + - - +
54B GLY 3.1 19.6 + - - -
166B GLY* 3.1 33.3 - - - -
169B VAL* 3.8 10.7 - - - +
170B THR* 3.5 11.7 - - - -
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.1 39.8 + - + +
48B ALA 4.3 1.3 - - - +
50B GLY* 1.3 73.0 - - - +
52B ALA* 1.3 59.2 - - - +
53B ILE 3.3 0.2 - - - -
54B GLY* 3.5 6.5 - - - +
55B THR* 2.8 37.2 + - - +
163B LEU* 4.8 10.5 - - + -
166B GLY* 5.9 1.6 - - - -
167B LEU* 4.7 18.2 - - + -
170B THR* 5.4 0.7 - - - +
47D LEU* 6.2 0.9 - - + -
167D LEU* 3.9 47.6 - - + +
170D THR* 4.6 16.2 - - + -
171D LEU* 3.7 18.6 - - + +
174D LEU* 5.1 2.0 - - + -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 5.2 0.4 - - + +
24B PHE* 3.6 28.0 - - + +
27B PHE* 4.2 16.8 - - + -
28B GLY 5.0 0.4 - - - +
48B ALA 3.3 14.1 + - - +
49B PHE* 3.7 7.6 - - - +
50B GLY 3.2 0.8 - - - -
51B LEU* 1.3 77.0 - - - +
53B ILE* 1.3 56.8 + - - +
55B THR* 4.2 0.6 - - - -
56B LEU* 3.1 38.6 + - + +
171D LEU* 3.6 15.6 - - + +
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.6 36.8 - - + -
49B PHE 3.7 4.4 + - - +
50B GLY 3.2 8.8 + - - +
52B ALA* 1.3 74.9 - - - +
54B GLY* 1.3 58.0 + - - +
55B THR 3.2 1.3 - - - -
56B LEU* 4.6 1.5 - - - +
57B ALA* 3.1 32.9 + - + +
67B HIS 4.8 5.4 - - - +
68B ILE* 3.8 32.0 - - + +
69B ASN* 5.9 2.7 - - + +
142B LEU* 5.8 0.2 - - + -
146B ILE* 6.3 0.7 - - + -
165B ILE* 4.0 26.5 - - + -
166B GLY* 4.3 1.8 - - - -
169B VAL* 4.0 24.2 - - + -
185B ASN* 5.3 1.3 - - - +
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLY 3.1 11.0 + - - -
51B LEU* 3.4 9.1 + - - -
53B ILE* 1.3 76.4 - - - +
55B THR* 1.3 58.0 + - - +
57B ALA 4.4 1.3 - - - -
58B GLN* 4.2 3.8 - - - +
162B ALA* 3.3 42.7 - - - +
163B LEU* 4.5 14.3 + - - +
166B GLY* 3.7 7.3 - - - -
164D SER* 5.3 3.8 - - - +
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 2.8 22.9 + - - +
52B ALA 4.2 1.8 - - - -
54B GLY* 1.3 78.9 + - - +
56B LEU* 1.3 64.6 - - + +
57B ALA 3.1 1.6 - - - -
58B GLN* 3.0 21.4 + - - +
59B ALA* 3.0 14.0 + - + +
141D GLN* 3.4 29.4 - - + +
145D CYS* 3.9 17.2 - - + +
164D SER 4.6 3.2 + - - -
167D LEU 4.5 2.3 + - - -
168D SER* 3.7 25.8 + - - +
171D LEU* 4.0 9.4 - - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 3.0 50.7 - - + +
23B ILE* 4.0 24.7 - - + -
24B PHE* 3.5 23.8 - - + +
52B ALA* 3.1 23.6 + - + +
53B ILE* 4.6 2.0 - - - +
55B THR* 1.3 75.5 - - + +
57B ALA* 1.3 59.2 + - - +
59B ALA* 4.0 7.4 - - + +
60B LEU* 3.1 37.4 + - + +
61B GLY* 3.3 5.5 + - - -
68B ILE* 4.4 14.7 - - + +
141D GLN* 5.7 5.2 - - + -
144D LEU* 5.4 2.2 - - + -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 3.1 22.9 + - + +
54B GLY* 4.6 0.2 - - - -
55B THR 3.1 0.2 - - - -
56B LEU* 1.3 75.4 - - - +
58B GLN* 1.3 65.9 + - - +
61B GLY* 3.0 27.7 + - - +
62B PRO* 3.5 3.8 - - - +
66B GLY* 5.0 10.3 - - - +
68B ILE* 5.2 1.5 - - - +
162B ALA* 3.8 25.8 - - + +
165B ILE* 5.8 6.7 - - + -
154D ARG* 5.1 1.6 + - - -
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY 4.2 9.0 - - - +
55B THR 3.0 10.7 + - - +
57B ALA* 1.3 80.1 - - - +
59B ALA* 1.3 60.8 + - - +
62B PRO* 3.8 0.5 - - - +
160B SER* 4.1 0.7 + - - -
162B ALA* 3.2 22.1 - - - +
145D CYS* 4.3 14.6 - - - +
148D ALA* 3.4 15.6 - - - +
149D SER* 3.7 19.8 + - - -
154D ARG* 3.5 30.6 + - - +
157D PRO 5.2 0.3 - - - +
158D VAL* 3.2 40.8 + - - +
160D SER 4.5 0.4 + - - -
164D SER* 3.2 31.5 + - - +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 3.0 14.0 + - + +
56B LEU* 4.6 6.1 - - + +
58B GLN* 1.3 81.2 - - - +
60B LEU* 1.3 65.5 + - + +
61B GLY 3.4 0.2 - - - -
62B PRO* 3.6 10.9 - - - +
63B VAL* 4.6 5.7 - - - +
141D GLN 5.3 1.1 - - - +
144D LEU* 3.5 46.7 - - + +
145D CYS* 4.1 3.6 - - + +
148D ALA* 3.8 17.3 - - - +
221D TYR* 5.3 2.1 - - - -
225D LEU* 6.0 0.2 - - - +
226D PHE* 5.2 2.9 - - - -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 6.1 0.2 - - + -
16B ALA* 3.6 42.0 - - + +
19B LEU* 4.0 22.2 - - + -
20B ALA* 3.7 24.5 - - + +
23B ILE* 5.0 0.2 - - + -
56B LEU* 3.1 18.8 + - + +
59B ALA* 1.3 77.8 - - + +
61B GLY* 1.3 61.9 + - - +
62B PRO 3.5 0.7 - - - -
63B VAL* 3.3 7.2 + - + +
64B SER* 3.0 28.2 + - - +
66B GLY* 4.8 1.1 - - - -
68B ILE* 5.8 0.4 - - + -
144D LEU* 3.8 21.8 - - + -
225D LEU* 4.0 28.5 - - + -
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 3.3 3.0 + - - -
57B ALA* 3.0 17.6 + - - -
60B LEU* 1.3 74.9 - - - +
62B PRO* 1.4 67.2 - - - +
65B GLY* 2.6 33.7 + - - -
66B GLY* 3.7 20.0 - - - -
156D GLU* 4.8 1.5 - - - +
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Residues in contact with PRO 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA 3.5 10.1 - - - +
58B GLN 3.8 3.8 - - - +
59B ALA 3.6 13.5 - - - +
61B GLY* 1.4 87.3 - - - +
63B VAL* 1.3 60.7 + - - +
65B GLY 4.7 0.5 + - - -
148D ALA* 5.3 3.4 - - + -
154D ARG* 3.3 31.2 - - + +
156D GLU* 3.7 28.9 - - + +
226D PHE* 4.0 23.6 - - + -
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 4.8 1.9 - - - +
12B LYS* 3.2 43.5 - - + +
13B ALA* 3.6 12.9 + - - +
16B ALA* 3.4 11.4 - - + -
59B ALA 4.6 2.2 - - - +
60B LEU* 3.3 17.9 + - + +
61B GLY 3.2 1.0 - - - -
62B PRO* 1.3 78.7 - - - +
64B SER* 1.3 58.4 + - - +
86B ARG* 5.5 0.3 + - - -
225D LEU* 4.1 21.5 - - + -
226D PHE* 3.4 32.8 - - + -
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 3.3 24.7 - - - -
16B ALA* 4.0 9.1 + - - +
17B GLU* 2.8 28.9 + - - +
20B ALA* 5.8 0.2 - - - +
60B LEU* 3.0 17.1 + - - +
63B VAL* 1.3 76.3 - - - +
65B GLY* 1.3 57.6 + - - +
66B GLY* 3.2 8.3 + - - -
67B HIS* 4.4 1.7 + - - -
68B ILE* 5.3 0.9 - - - +
86B ARG* 3.8 6.0 + - - -
90B TYR* 2.6 33.6 + - - -
----------------------------------------------------------
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY* 2.6 24.4 + - - -
62B PRO 4.6 0.8 + - - -
63B VAL 3.8 0.6 - - - -
64B SER* 1.3 71.7 - - - +
66B GLY* 1.3 62.1 + - - +
67B HIS* 3.7 13.6 - - - -
150B THR* 5.4 7.8 - - - +
----------------------------------------------------------
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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